EP1268758A2 - Molecules for diagnostics and therapeutics - Google Patents

Molecules for diagnostics and therapeutics

Info

Publication number
EP1268758A2
EP1268758A2 EP00938123A EP00938123A EP1268758A2 EP 1268758 A2 EP1268758 A2 EP 1268758A2 EP 00938123 A EP00938123 A EP 00938123A EP 00938123 A EP00938123 A EP 00938123A EP 1268758 A2 EP1268758 A2 EP 1268758A2
Authority
EP
European Patent Office
Prior art keywords
cell
proteins
polynucleotide
protein
cells
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP00938123A
Other languages
German (de)
French (fr)
Inventor
David M Hodgson
Stephen E. Lincoln
Frank D. Russo
Peter A. Spiro
Steven C. Banville
Shawn R. Bratcher
Gerard E. Dufour
Howard J. Cohen
Bruce H. Rosen
Michael S. Chalup
Jennifer L. Hillman
Anissa L. Jones
Jimmy Y. Yu
Lila B. Greenawalt
Scott R. Panzer
Ann M. Roseberry
Rachel J. Wright
Susan E. Daniels
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Incyte Corp
Original Assignee
Incyte Genomics Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Incyte Genomics Inc filed Critical Incyte Genomics Inc
Publication of EP1268758A2 publication Critical patent/EP1268758A2/en
Withdrawn legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • DNA-based array technology is especially relevant for the rapid screening of expression of a large number of genes.
  • a genetic predisposition, disease or therapeutic treatment may affect, directly or indirectly, the expression of a large number of genes.
  • the interactions may be expected, such as when 0 the genes are part of the same signaling pathway.
  • the interactions may be totally unexpected. Therefore, DNA-based arrays can be used to investigate how genetic predisposition, disease, or therapeutic treatment affects the expression of a large number of genes.
  • NADJNADH-dependent oxidoreductase activity include those of L-DOPA (precursor of dopamine, a neuronal excitatory compound), glycine (an inhibitory neurotransmitter in the brain and spinal cord), histamine (liberated from mast cells during the inflammatory response), and taurine (an inhibitory neurotransmitter of the brain stem, spinal cord and retina) (Newsholme, supra, pp. 790, 792).
  • L-DOPA precursor of dopamine, a neuronal excitatory compound
  • glycine an inhibitory neurotransmitter in the brain and spinal cord
  • histamine liberated from mast cells during the inflammatory response
  • taurine an inhibitory neurotransmitter of the brain stem, spinal cord and retina
  • Epigenetic or genetic defects in neurotransmitter o metabolic pathways can result in a spectrum of disease states in different tissues including Parkinson disease and inherited myoclonus (McCance, K.L. and S.E. Huether (1994) Pathophvsi
  • 2,4-dienoyl-CoA reductase is located in both mitochondria and peroxisomes. Inherited deficiencies in mitochondrial and peroxisomal beta-oxidation enzymes are 5 associated with severe diseases, some of which manifest themselves soon after birth and lead to death within a few years. Defects in beta-oxidation are associated with Reye's syndrome, Zellweger syndrome, neonatal adrenoleukodystrophy, infantile Refsum's disease, acyl-CoA oxidase deficiency, and bifunctional protein deficiency (Suzuki, Y. et al. (1994) Am. J. Hum.
  • Prenyl transferases are heterodimers, consisting of an alpha and a beta subunit, that catalyze the transfer of an isoprenyl group.
  • An example of a prenyl transferase is the mammalian protein farnesyl transferase.
  • the alpha subunit of farnesyl transferase consists of 5 repeats of 34 amino acids each, with each repeat containing an invariant tryptophan (PROSITE: PDOC00703).
  • Hydrolysis is the breaking of a covalent bond in a substrate by introduction of a molecule of water.
  • the reaction involves a nucleophilic attack by the water molecule's oxygen atom on a target bond in the substrate.
  • the water molecule is split across the target bond, breaking the bond and generating two product molecules.
  • Hydrolases participate in reactions essential to such functions as synthesis and degradation of cell components, and for regulation of cell functions including cell signaling, cell proliferation, inflamation, apoptosis, secretion and excretion. Hydrolases are involved in key steps in disease processes involving these functions.
  • Glyoxylases are involved in hyperglycemia, non-insulin-dependent diabetes mellitus, the detoxification of bacterial toxins, and in the control of cell proliferation and microtubule assembly. Lyases
  • Isomerases are a class of enzymes that catalyze geometric or structural changes within a molecule to form a single product. This class includes racemases and epimerases, cis-trans- isomerases, intramolecular oxidoreductases, intramolecular transferases (mutases) and intramolecular lyases. Isomerases are critical components of cellular biochemistry with roles in metabolic energy production including glycolysis, as well as other diverse enzymatic processes (Stryer, L. (1995) Biochemistry. W.H. Freeman and Co., New York NY, pp.483-507).
  • Oxidoreductases can be isomerases as well. Oxidoreductases catalyze the reversible transfer of electrons from a substrate that becomes oxidized to a substrate that becomes reduced. This class of enzymes includes dehydrogenases, hydroxylases, oxidases, oxygenases, peroxidases, and reductases. 5 Proper maintenance of oxidoreductase levels is physiologically important. For example, genetically- linked deficiencies in lipoamide dehydrogenase can result in lactic acidosis (Robinson, B.H. et al. (1977) Pediat. Res. 11:1198-1202).
  • Transferases transfera chemical group from one compound (the donor) to another compound (the acceptor).
  • the types of groups transferred by these enzymes include acyl groups, amino groups, phosphate groups
  • the 20 aminoacyl-tRNA synthetase enzymes can be divided into two structural classes, and each class is characterized by a distinctive topology of the catalytic domain.
  • Class I enzymes contain a catalytic domain based on the nucleotide-binding Rossman fold.
  • Class II enzymes contain a central catalytic domain, which consists of a seven-stranded antiparallel ⁇ -sheet motif, as well as N- and C- terminal regulatory domains.
  • Class II enzymes are separated into two groups based on the heterodimeric or homodimeric structure of the enzyme; the latter group is further subdivided by the structure of the N- and C-terminal regulatory domains (Hartlein, M. and S. Cusack (1995) J. Mol. Evol.
  • Examples of such reactions include the tricarboxylic acid cycle, synthesis of fatty acids and long-chain phospholipids, synthesis of alcohols and aldehydes, synthesis of intermediary metabolites, and reactions involved in the amino acid degradation pathways. Some of these reactions require input of energy, usually in the form of conversion of ATP to either ADP or AMP and pyrophosphate.
  • acyl-CoA synthetase activity i) acetyl-CoA synthetase, which activates acetate and several other low molecular weight carboxylic acids and is found in muscle mitochondria and the cytosol of other tissues; ii) medium-chain acyl-CoA synthetase, which activates fatty acids containing between four and eleven carbon atoms (predominantly from dietary sources), and is present only in liver mitochondria; and iii) acyl CoA synthetase, which is specific for long chain fatty acids with between six and twenty carbon atoms, and 5 is found in microsomes and the mitochondria.
  • Adenylosuccinate synthetase catalyzes a later step in purine biosynthesis that converts inosinic acid to o adenylosuccinate, a key step on the path to ATP synthesis.
  • This enzyme is also similar to another carbon-nitrogen ligase, argininosuccinate synthetase, that catalyzes a similar reaction in the urea cycle (Powell, S.M. et al. (1992) FEBS Lett. 303:4-10).
  • de novo synthesis of the pyrimidine nucleotides uridylate and cytidylate also arises from a common precursor, in this instance the nucleotide 5 orotidylate derived from orotate and phosphoribosyl pyrophosphate (PPRP).
  • PPRP phosphoribosyl pyrophosphate
  • ATCase aspartate transcarbamylase
  • carbamyl phosphate synthetase II carbamyl phosphate synthetase II
  • DHOase dihydroorotase
  • Ligases forming phosphoric ester bonds include the DNA ligases involved in both DNA replication and repair.
  • DNA ligases seal phosphodiester bonds between two adjacent nucleotides in a DNA chain using the energy from ATP hydrolysis to first activate the free 5 ' -phosphate of one nucleotide and then react it with the 3' -OH group of the adjacent nucleotide. This reseating reaction is used in both DNA replication to join small DNA fragments called Okazaki fragments that are transiently formed in the process of replicating new DNA, and in DNA repair.
  • DNA repair is the process by which accidental base changes, such as those produced by oxidative damage, hydrolytic attack, or uncontrolled methylation of DNA, are corrected before replication or transcription of the DNA can occur.
  • Regulated progression of the cell cycle depends on the integration of growth control pathways with the basic cell cycle machinery.
  • Cell cycle regulators have been identified by selecting for human and yeast cDNAs that block or activate cell cycle arrest signals in the yeast mating pheromone pathway when they are overexpressed.
  • Known regulators include human CPR (cell cycle progression restoration) genes, such as CPR8 and CPR2, and yeast CDC (cell division control) genes, including CDC91, that block the arrest signals.
  • the CPR genes express a variety of proteins including cyclins, tumor suppressor binding proteins, chaperones, transcription factors, translation factors, and RNA-binding proteins (Edwards, M.C. et al.(1997) Genetics 147:1063-1076).
  • FSH follicle-stimulating hormone
  • LH luteinizing hormone
  • Cell Differentiation and Proliferation Tissue growth involves complex and ordered patterns of cell proliferation, cell differentiation, and apoptosis.
  • Cell proliferation must be regulated to maintain both the number of cells and their spatial organization. This regulation depends upon the appropriate expression of proteins which control cell cycle progression in response to extracellular signals, such as growth factors and other mitogens, and intracellular cues, such as DNA damage or nutrient starvation. Molecules which directly or indirectly modulate cell cycle progression fall into several categories, including growth factors and their receptors, second messenger and signal transduction proteins, oncogene products, tumor-suppressor proteins, and mitosis-promoting factors.
  • ECM molecules such as laminin or fibronectin
  • laminin or fibronectin may act as growth factors.
  • Tenascin-C and -R expressed in developing and lesioned neural tissue, provide stimulatory/anti-adhesive or inhibitory properties, respectively, for axonal growth (Faissner, A. (1997) Cell Tissue Res. 290:331-341).
  • Cancers are associated with the activation of oncogenes which are derived from normal cellular genes. These oncogenes encode oncoproteins which convert normal cells into malignant cells. Some oncoproteins are mutant isoforms of the normal protein, and other oncoproteins are abnormally expressed with respect to location or amount of expression. The latter category of oncoprotein causes cancer by altering transcriptional control of cell proliferation.
  • Five classes of oncoproteins are known to affect cell cycle controls. These classes include growth factors, growth factor receptors, intracellular signal transducers, nuclear transcription factors, and cell-cycle control proteins.
  • Viral oncogenes are integrated into the human genome after infection of human cells by certain viruses. Examples of viral oncogenes include v-src, v-abl, and v-fps.
  • the Philadelphia chromosome characteristic of chronic myeloid leukemia and a subset of acute lymphoblastic leukemias, results from a reciprocal translocation between chromosomes 9 and 22 that moves a truncated portion of the proto-oncogene c-abl to the breakpoint cluster region (bcr) on chromosome 22.
  • Tumor-suppressor genes are involved in regulating cell proliferation. Mutations which cause reduced or loss of function in tumor-suppressor genes result in uncontrolled cell proUferation.
  • the retinoblastoma gene product (RB) in a non-phosphorylated state, binds several early- response genes and suppresses their transcription, thus blocking cell division. Phosphorylation of RB causes it to dissociate from the genes, releasing the suppression, and allowing cell division to proceed. Apoptosis
  • Apoptosis is the genetically controlled process by which unneeded or defective cells undergo programmed cell death. Selective elimination of cells is as important for morphogenesis and tissue remodeling as is cell proliferation and differentiation. Lack of apoptosis may result in hyperplasia and other disorders associated with increased cell proliferation. Apoptosis is also a critical component of the immune response. Immune cells such as cytotoxic T-cells and natural killer cells prevent the spread of disease by inducing apoptosis in tumor cells and virus-infected cells. In addition, immune cells that fail to distinguish self molecules from foreign molecules must be eliminated by apoptosis to avoid an autoimmune response.
  • DNA Deoxyribonucleic acid
  • DNA the genetic material, is found in both the nucleus and mitochondria of human cells.
  • the bulk of human DNA is nuclear, in the form of linear chromosomes, while mitochondrial DNA is circular.
  • DNA replication begins at specific sites called origins of replication. Bidirectional synthesis occurs from the origin via two growing forks that move in opposite directions. Rephcation is semi-conservative, with each daughter duplex containing one old strand and its newly synthesized complementary partner.
  • Proteins involved in DNA replication include DNA polymerases, DNA primase, telomerase, DNA helicase, topoisomerases, DNA Ugases, replication factors, and DNA-binding proteins.
  • hnRNPs Heterogeneous nuclear ribonucleoproteins
  • RNA helicases alter and regulate RNA conformation and secondary structure by using energy derived from ATP hydrolysis to destabihze and unwind RNA duplexes.
  • the most well-characterized and ubiquitous family of RNA heUcases is the DEAD-box family, so named for the conserved B-type ATP-binding motif which is diagnostic of proteins in this family.
  • DEAD-box heUcases Over 40 DEAD-box heUcases have been identified in organisms as diverse as bacteria, insects, yeast, amphibians, mammals, and plants. DEAD-box helicases function in diverse processes such as translation initiation, splicing, ribosome assembly, and RNA editing, transport, and stability. Some DEAD-box helicases play tissue- and stage- specific roles in spermatogenesis and embryogenesis. (Reviewed in Linder, P. et al. (1989) Nature 337:121-122.)
  • DEAD-box 1 protein may play a role in the progression of neuroblasto a (Nb) and retinoblastoma (Rb) tumors.
  • DEAD-box helicases have been implicated either directly or indirectly in ultraviolet light-induced tumors, B cell lymphoma, and myeloid malignancies. (Reviewed in Godbout, R. et al. (1998) J. Biol. Chem. 273:21161-21168.)
  • Initiation of ttanslation can be divided into three stages.
  • the first stage brings an initiator transfer RNA (Met-tRNA f ) together with the 40S ribosomal subunit to form the 43S preinitiation complex.
  • the second stage binds the 43S preinitiation complex to the mRNA, followed by migration of the complex to the correct AUG initiation codon.
  • the third stage brings the 60S ribosomal subunit to the 40S subunit to generate an 80S ribosome at the initiation codon.
  • Regulation of translation primarily involves the first and second stage in the initiation process (Pain, V.M. (1996) Eur. J. Biochem. 236:747-771).
  • Cholesterol composed of four fused hydrocarbon rings with an alcohol at one end, moderates the fluidity of membranes in which it is inco ⁇ orated.
  • cholesterol is used in the synthesis of steroid hormones such as cortisol, progesterone, estrogen, and testosterone.
  • Cholesterol in the skin forms a barrier that prevents excess water evaporation from the body.
  • Farnesyl and geranylgeranyl groups which are derived from cholesterol biosynthesis intermediates, are post-franslationally added to signal transduction proteins such as ras and protein-targeting proteins such as rab. These modifications are important for the activities of these proteins (Guyton, supra; Stryer, supra, pp.
  • OSBP oxysterol- binding protein
  • NH 4 + is assimilated into amino acids by the actions of two enzymes, glutamate dehydrogenase and glutamine synthetase.
  • the carbon skeletons of amino acids come from the intermediates of glycolysis, the pentose phosphate pathway, or the citric acid cycle.
  • humans can synthesize only thirteen (nonessential amino acids). The remaining nine must come from the diet (essential amino acids).
  • Acetyl CoA is oxidized to C0 2 with concomitant formation of NADH, FADH 2 , and GTP.
  • oxidative phosphorylation the transport of electrons from NADH and FADH 2 to oxygen by dehydrogenases is coupled to the synthesis of ATP from ADP and P. by the F Q F, ATPase complex in 5 the mitochondrial inner membrane.
  • Po ⁇ hyrin groups contain four substituted pyrroles covalentiy joined in a ring, often with a bound metal atom.
  • Enzymes involved in po ⁇ hyrin synthesis include ⁇ - aminolevulinate synthase, ⁇ -aminolevulinate dehydrase, po ⁇ hobilinogen deaminase, and cosynthase. Deficiencies in heme formation cause po ⁇ hyrias. Heme is broken down as a part of erythrocyte turnover.
  • Enzymes involved in heme degradation include heme oxygenase and biliverdin reductase. o Iron is a required cofactor for many enzymes.
  • iron is found in iron-sulfur clusters in proteins including aconitase, succinate dehydrogenase, and NADH-Q reductase. Iron is transported in the blood by the protein transferrin. Binding of transferrin to the fransferrin receptor on cell surfaces allows uptake by receptor mediated endocytosis. Cytosolic iron is bound to ferritin protein. 5 A molybdenum-containing cofactor (molybdopterin) is found in enzymes including sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase.
  • molybdenum-containing cofactor molybdenum-containing cofactor
  • Molybdopterin biosynthesis is performed by two molybdenum cofactor synthesizing enzymes. Deficiencies in these enzymes cause mental retardation and lens dislocation. Other diseases caused by defects in cofactor metabolism include pernicious anemia and methylmalonic aciduria. 0 Secretion and Trafficking
  • the final Golgi compartment is the Trans-Golgi Network (TGN), where both membrane and lumenal proteins are sorted for their final destination.
  • TGN Trans-Golgi Network
  • secretory vesicle which contains proteins destined for the plasma membrane, such as receptors, adhesion molecules, and ion channels, and secretory proteins, such as hormones, neurofransmitters, and digestive enzymes. Secretory vesicles eventually fuse with the plasma membrane (GUck, B.S. and V. Malhofra (1998) Cell 95:883-889).
  • Activation of the Fc receptors initiates a signal cascade involving src-family cytosolic kinases and the monomeric GTP-binding (G) protein Rho.
  • G GTP-binding
  • the resulting actin reorganization leads to phagocytosis of the particle.
  • This process is an important component of the humoral immune response, allowing the processing and presentation of bacterial-derived peptides to antigen-specific T-lymphocytes.
  • the second form of endocytosis, pinocytosis is a more generalized uptake of material from the external miUeu. Like phagocytosis, pinocytosis is activated by Ugand binding to cell surface receptors.
  • Activation of individual receptors stimulates an internal response that includes coalescence of the receptor-ligand complexes and formation of clathrin-coated pits.
  • Imagination of the plasma membrane at clathrin-coated pits produces an endocytic vesicle within the cell cytoplasm.
  • These vesicles undergo homotypic fusion to form an early endosomal (EE) compartment.
  • the tubulovesicular EE serves as a sorting site for incoming material.
  • ATP-driven proton pumps in the EE membrane lowers the pH of the EE lumen (pH 6.3-6.8).
  • the acidic environment causes many hgands to dissociate from their receptors.
  • RecycUng vesicles may return directly to the plasma membrane. Receptors internalized and returned directly to the plasma membrane have a turnover rate of 2-3 minutes. Some RVs undergo microtubule-directed relocation to a perinuclear site, from which they then return to the plasma membrane. Receptors following this route have a turnover rate of 5-10 minutes. Still other RVs are retained within the cell until an appropriate signal is received (Mellman, supra; and James, D.E. et al. (1994) Trends Cell Biol. 4:120-126). Vesicle Formation
  • the initial budding and coating processes are controlled by a cytosolic ras-like GTP-binding protein, ADP- ribosylating factor (Arf), and adapter proteins (AP). Different isoforms of both Arf and AP are involved at different sites of budding.
  • Another small G-protein, dynamin forms a ring complex around the neck of the forming vesicle and may provide the mechanochemical force to accomplish the final step of the budding process.
  • the coated vesicle complex is then transported through the cytosol. During the transport process, Arf -bound GTP is hydrolyzed to GDP and the coat dissociates from the transport vesicle (West, M.A. et al. (1997) J. Cell Biol.
  • coat protein Two different classes have also been identified. Clathrin coats form on the TGN and PM surfaces, whereas coatomer or COP coats form on the ER and Golgi. COP coats can further be distinguished as COPI, involved in retrograde traffic through the Golgi and from the Golgi to the ER, and COPII, involved in anterograde traffic from the ER to the Golgi (Mellman, supra).
  • the COP coat consists of two major components, a 5 G-protein (Arf or Sar) and coat protomer (coatomer).
  • Coatomer is an equimolar complex of seven proteins, termed alpha-, beta-, beta'-, gamma-, delta-, epsilon- and zeta-COP. (Harter, C. and F.T. Wieland (1998) Proc. Nati. Acad. Sci. USA 95:11649-11654.) Membrane Fusion
  • Transport vesicles undergo homotypic or heterotypic fusion in the secretory and endocytotic 0 pathways.
  • Molecules required for appropriate targeting and fusion of vesicles with their target membrane include proteins inco ⁇ orated in the vesicle membrane, the target membrane, and proteins recruited from the cytosol.
  • VAMP vesicle-associated membrane protein
  • a cytosolic prenylated GTP-binding protein, Rab a member of the Ras 5 superfamily
  • GTP-bound Rab proteins are directed into nascent fransport vesicles where they interact with VAMP. Following vesicle fransport, GTPase activating proteins (GAPs) in the target membrane convert Rab proteins to the GDP-bound form. A cytosolic protein, guanine-nucleotide dissociation inhibitor (GDI) helps return GDP-bound Rab proteins to their membrane of origin.
  • GAPs GTPase activating proteins
  • GDI guanine-nucleotide dissociation inhibitor
  • Rab proteins appear to play a role in mediating the function of a viral gene, Rev, which is essential for replication of HIV-1, the virus responsible for AIDS (Flavell, R.A. et al. (1996) Proc. Nati. Acad. Sci. USA 93:4421-4424).
  • N-ethylmaleimide sensitive factor (NSF) and soluble NSF-attachment protein ( ⁇ -SNAP and ⁇ -SNAP) are two such proteins that are conserved from yeast to man and function in most intracellular membrane fusion o reactions.
  • Seel represents a family of yeast proteins that function at many different stages in the secretory pathway including membrane fusion. Recently, mammalian homologs of Seel , called Munc-18 proteins, have been identified (Katagiri, H. et al. (1995) J. Biol. Chem. 270:4963-4966; Hata et al. supra).
  • the SNARE complex involves three SNARE molecules, one in the vesicular membrane and 5 two in the target membrane.
  • Synaptotagmin is an integral membrane protein in the synaptic vesicle which associates with the t-SNARE syntaxin in the docking complex.
  • Synaptotagmin binds calcium in a complex with negatively charged phospholipids, which allows the cytosolic SNAP protein to displace synaptotagmin from syntaxin and fusion to occur.
  • synaptotagmin is a negative regulator of fusion in the neuron (Littleton, J.T. et al. (1993) Cell 74:1125-1134).
  • the most abundant membrane 5 protein of synaptic vesicles appears to be the glycoprotein synaptophysin, a 38 kDa protein with four transmembrane domains.
  • NPCs nuclear 5 pore complexes
  • All nuclear proteins are imported from the cytoplasm, their site of synthesis.
  • tRNA and mRNA are exported from the nucleus, their site of synthesis, to the cytoplasm, their site of function.
  • Processing of small nuclear RNAs involves export into the cytoplasm, assembly with proteins and modifications such as hypermethylation to produce small nuclear ribonuclear proteins (snRNPs), and o subsequent import of the snRNPs back into the nucleus.
  • snRNPs small nuclear ribonuclear proteins
  • ribosomes require the initial import of ribosomal proteins from the cytoplasm, their incorporation with RNA into ribosomal subunits, and export back to the cytoplasm. (Gorlich, D. and l.W. Mattaj (1996) Science 271 :1513- 1518.)
  • abnormal hormonal secretion is Unked to disorders such as diabetes insipidus (vasopressin), hyper- and hypoglycemia (insutin, glucagon), Grave's disease 5 and goiter (thyroid hormone), and Cushing's and Addison's diseases (adrenocorticotropic hormone, ACTH).
  • cancer cells secrete excessive amounts of hormones or other biologically active peptides.
  • Biologically active peptides that are ectopically synthesized in and secreted from tumor cells include ACTH and vasopressin (lung and pancreatic cancers); parathyroid hormone (lung 5 and bladder cancers); calcitonin (lung and breast cancers); and thyroid-stimulating hormone (medullary thyroid carcinoma).
  • ACTH and vasopressin lung and pancreatic cancers
  • parathyroid hormone lung 5 and bladder cancers
  • calcitonin lung and breast cancers
  • thyroid-stimulating hormone medullary thyroid carcinoma.
  • Such peptides may be useful as diagnostic markers for tumorigenesis (Schwartz, M.Z. (1997) Semin. Pediatr. Surg. 3:141-146; and Said, S.I. and GR. Faloona (1975) N. Engl. J. Med. 293:155-160).
  • Aquaporins are channels that fransport water and, in some cases, nonionic small solutes such as urea and glycerol. Water movement is important for a number of physiological processes 5 including renal fluid filtration, aqueous humor generation in the eye, cerebrospinal fluid production in the brain, and appropriate hydration of the lung. Aquaporins are members of the major intrinsic protein (MIP) family of membrane transporters (King, L.S. and P. Agre (1996) Annu. Rev. Physiol. 58:619- 648; Ishibasbi, K. et al. (1997) J. Biol. Chem. 272:20782-20786).
  • MIP major intrinsic protein
  • MTs The metallothioneins
  • cysteine-rich proteins that bind heavy metals such as cadmium, zinc, mercury, lead, and copper and are thought to play a role in metal detoxification or the metabolism and homeostasis of metals.
  • Arsenite-resistance proteins have been identified in hamsters that are resistant to toxic levels of arsenite (Rossman, T.G. et al. (1997) Mutat. Res. 386:307-314). 5 Humans respond to light and odors by specific protein pathways. Proteins involved in light perception include rhodopsin, fransducin, and cGMP phosphodiesterase.
  • the cellular components of the humoral immune system include six different types of 5 leukocytes: monocytes, lymphocytes, polymo ⁇ honuclear granulocytes (consisting of monrophils, eosinophils, and basopbils) and plasma cells. Additionally, fragments of megakaryocytes, a seventh type of white blood cell in the bone marrow, occur in large numbers in the blood as platelets.
  • Leukocytes are formed from two stem cell lineages in bone marrow.
  • the myeloid stem cell line produces granulocytes and monocytes and, the lymphoid stem cell produces lymphocytes.
  • o Lymphoid cells fravel to the thymus, spleen and lymph nodes, where they mature and differentiate into lymphocytes.
  • Leukocytes are responsible for defending the body against invading pathogens. Neufrophils and monocytes attack invading bacteria, viruses, and other pathogens and destroy them by phagocytosis.
  • Monocytes enter tissues and differentiate into macrophages which are extremely phagocytic. Lymphocytes and plasma cells are a part of the immune system which recognizes 5 specific foreign molecules and organisms and inactivates them, as well as signals other cells to attack the invaders.
  • Tissue inflammation in response to pathogen invasion results in production of chemo-attractants for leukocytes, such as endotoxins or other bacterial products, prostaglandins, and products of leukocytes 0 or platelets.
  • Helper T cells constitute up to 75% of the total T cell population. They regulate the immune functions by producing a variety of lymphokines that act on other cells in the immune system and on bone marrow. Among these lymphokines are: interleukins-2,3,4,5,6; granulocyte-monocyte colony stimulating factor, and ⁇ -interferon.
  • B-lymphocytes produce antibodies which react with specific antigenic proteins presented by pathogens. Once activated, B cells become filled with extensive rough endoplasmic reticulum and are known as plasma cells. As with T cells, interaction of B cells with antigen stimulates proliferation of only those B cells which produce antibody specific to that antigen.
  • AIDS l o Abnormal Immunodeficiency Syndrome
  • helper T cells are depleted, leaving the patient susceptible to infection by microorganisms and parasites.
  • Another widespread medical condition attributable to the immune system is that of allergic reactions to certain antigens. Allergic reactions include: hay fever, asthma, anaphylaxis, and urticaria (hives).
  • Leukemias are an excess production of white blood cells, to the point where a major portion of the body' s metabolic resources
  • Intercellular communication is essential for the growth and survival of multicellular organisms, and in particular, for the function of the endocrine, nervous, and immune systems.
  • intercellular communication is critical for developmental processes such as tissue construction and organogenesis, in which cell proliferation, cell differentiation, and mo ⁇ hogenesis must be spatially and temporally regulated in a precise and coordinated manner.
  • Cells communicate with one another through the secretion and uptake of diverse types of signaling molecules such as hormones, growth factors, neuropeptides, and cytokines.
  • Hormones include hormones, growth factors, neuropeptides, and cytokines.
  • disorders of the hypothalamus and pituitary often result from lesions such as primary brain tumors, adenomas, infarction associated with pregnancy, hypophysectomy, aneurysms, vascular o malformations, thrombosis, infections, immunological disorders, and complications due to head frauma. Such disorders have profound effects on the function of other endocrine glands.
  • Disorders associated with hypopituitarism include hypogonadism, Sheehan syndrome, diabetes insipidus, Kallman's disease, Hand-SchuUer-Christian disease, Letterer-Siwe disease, sarcoidosis, empty sella syndrome, and dwarfism.
  • Disorders associated with hype ⁇ ituitarism include acromegaly, giantism, and syndrome of 5 inappropriate ADH secretion (SIADH), often caused by benign adenomas.
  • Thyroid hormones secreted by the thyroid and parathyroid primarily control metabolic rates and the regulation of serum calcium levels, respectively.
  • Thyroid hormones include calcitonin, somatostatin, and thyroid hormone.
  • the parathyroid secretes parathyroid hormone.
  • Disorders associated with hypothyroidism include goiter, myxedema, acute thyroiditis associated with bacterial infection, o subacute thyroiditis associated with viral infection, autoimmune thyroiditis (Hashimoto's disease), and cretinism.
  • Disorders associated with hyperthyroidism include thyrotoxicosis and its various forms, Grave's disease, pretibial myxedema, toxic multinodular goiter, thyroid carcinoma, and Plummer's disease.
  • Diabetes melUtus is generally classified as either Type I (insulin-dependent, juvenile diabetes) or Type II (non- 5 insuUn-dependent, adult diabetes).
  • Cytokine structure and function have been extensively characterized in vitro. Most cytokines are small polypeptides of about 30 kilodaltons or less. Over 50 cytokines have been identified from human and rodent sources. Examples of cytokine subfamiUes include the interferons (IFN- ⁇ , - ⁇ , and - ⁇ ), the interleukins (IL1-IL13), the tumor necrosis factors (TNF- ⁇ and - ⁇ ), and the chemokines. Many cytokines have been produced using recombinant DNA techniques, and the activities of individual cytokines have been determined in vitro. These activities include regulation of leukocyte proliferation, differentiation, and motiUty.
  • cytokine activity in vitro may not reflect the full scope of that cytokine' s activity in vivo.
  • Cytokines are not expressed individually in vivo but are instead expressed in combination with a multitude of other cytokines when the organism is challenged with a stimulus. Together, these cytokines collectively modulate the immune response in a manner appropriate for that particular stimulus. Therefore, the physiological activity of a cytokine is determined by the stimulus itself and by complex interactive networks among co-expressed cytokines which may demonstrate both synergistic and antagonistic relationships.
  • the CC chemokines for example, each contain a conserved motif consisting of two consecutive cysteines followed by two additional cysteines which occur downstream at 24- and 16- residue intervals, respectively (ExPASy PROSITE database, documents PS00472 and PDOC00434).
  • the presence and spacing of these four cysteine residues are highly conserved, whereas the intervening residues diverge significantly.
  • a conserved tyrosine located about 15 residues downstream of the cysteine doublet seems to be important for chemotactic activity.
  • Most of the human genes encoding CC chemokines are clustered on chromosome 17, although there are a few examples of CC chemokine genes that map elsewhere.
  • Receptor Molecules 0 SEQ ID NO:6 and SEQ ID NO:7 encode, for example, receptor molecules.
  • receptor describes proteins that specifically recognize other molecules.
  • the category is broad and includes proteins with a variety of functions.
  • the bulk of receptors are cell surface proteins which bind exfracellular ligands and produce cellular responses in the areas of growth, differentiation, endocytosis, and immune response.
  • Other receptors facilitate the selective fransport of 5 proteins out of the endoplasmic reticulum and localize enzymes to particular locations in the cell.
  • the term may also be applied to proteins which act as receptors for ligands with known or unknown chemical composition and which interact with other cellular components. For example, the steroid hormone receptors bind to and regulate transcription of DNA.
  • Exfracellular loops of the GPCR alternate with intracellular loops and link the transmembrane domains.
  • the most conserved domains of GPCRs are the transmembrane domains and the first two cytoplasmic loops.
  • the transmembrane domains account for structural and functional features of the receptor. In most cases, the bundle of ⁇ helices forms a binding pocket.
  • the extracellular N-terminal segment or one or more of the three exfracellular loops may also participate in ligand binding. Ligand binding activates the receptor by inducing a conformational change in intracellular portions of the receptor.
  • GPCRs include those for acetylchoUne, adenosine, epinephrine and norepinephrine, bombesin, bradykinin, chemokines, dopamine, endothelin, ⁇ -aminobutyric acid (GABA), follicle-stimulating hormone (FSH), glutamate, gonadotropin-releasing hormone (GnRH), hepatocyte growth factor, histamine, leukotrienes, melanocortins, neuropeptide Y, opioid peptides, opsins, prostanoids, serotonin, 5 somatostatin, tachykinins, thrombin, thyrottopin-releasing hormone (TRH), vasoactive intestinal polypeptide family, vasopressin and oxytocin, and o ⁇ han receptors.
  • GABA ⁇ -aminobutyric acid
  • FSH follicle-stimulating hormone
  • GPCR mutations which may cause loss of function or constitutive activation, have been associated with numerous human diseases (Coughlin, supra). For instance, retinitis pigmentosa may arise from mutations in the rhodopsin gene. Rhodopsin is the retinal photoreceptor which is located 0 within the discs of the eye rod cell. Parma, J. et al. (1993, Nature 365:649-651) report that somatic activating mutations in the thyrofropin receptor cause hyperfunctioning thyroid adenomas and suggest that certain GPCRs susceptible to constitutive activation may behave as protooncogenes. Nuclear Receptors
  • Macrophage scavenger receptors with broad ligand specificity may participate in the binding of low density lipoproteins (LDL) and foreign antigens.
  • Scavenger receptors types I and II are trimeric 5 membrane proteins with each subunit containing a small N-terminal intracellular domain, a transmembrane domain, a large extracellular domain, and a C-terminal cysteine-rich domain.
  • the extracellular domain contains a short spacer domain, an ⁇ -helical coiled-coil domain, and a friple helical collagenous domain.
  • Enterokinase the initiator of intestinal digestion, is a serine protease found in the intestinal brush border, where it cleaves the acidic propeptide from trypsinogen to yield active trypsin (Kitamoto, Y. et al. (1994) Proc. Nati. Acad. Sci. USA 91:7588-7592).
  • o Prolylcarboxypeptidase a lysosomal serine peptidase that cleaves peptides such as angiotensin II and III and [des-Arg9] bradykinin, shares sequence homology with members of both the serine carboxypeptidase and prolylendopeptidase families (Tan, F. et al. (1993) J. Biol. Chem. 268:16631- 16638).
  • Cysteine proteases have a cysteine as the major catalytic residue at an active site where 5 catalysis proceeds via an intermediate thiol ester and is facilitated by adjacent histidine and aspartic acid residues.
  • CPs are involved in diverse cellular processes ranging from the processing of precursor proteins to intracellular degradation. Mammalian CPs include lysosomal cathepsins and cytosolic calcium activated proteases, calpains. CPs are produced by monocytes, macrophages and other cells of the immune system which migrate to sites of inflammation and secrete molecules involved in o tissue repair. Overabundance of these repair molecules plays a role in certain disorders.
  • RNases also serve a variety of functions.
  • RNase P is a ribonucleoprotein enzyme which cleaves the 5' end of pre-tRNAs as part of their maturation process.
  • RNase H digests the RNA strand of an RNA/DNA hybrid. Such hybrids occur in cells invaded by refroviruses, and RNase H is an important enzyme in the retroviral replication cycle.
  • Pancreatic RNase secreted by the pancreas into 5 the intestine hydrolyzes RNA present in ingested foods.
  • RNase activity in serum and cell extracts is elevated in a variety of cancers and infectious diseases (Schein, CH. (1997) Nat. Biotechnol. 15:529- 536).
  • RNA helicases utilize energy derived from ATP hydrolysis to destabilize and unwind RNA duplexes.
  • the most well-characterized and ubiquitous family of RNA helicases is the DEAD-box family, so named for the conserved B-type ATP-binding motif which is diagnostic of proteins in this family.
  • DEAD-box helicases Over 40 DEAD-box helicases have been identified in organisms as diverse as bacteria, insects, o yeast, amphibians, mammals, and plants. DEAD-box helicases function in diverse processes such as translation initiation, splicing, ribosome assembly, and RNA editing, fransport, and stability. Some DEAD-box helicases play tissue- and stage-specific roles in spermatogenesis and embryogenesis.
  • murine p68 is mutated in ultraviolet Ught-induced tumors
  • human DDX6 is located at a chromosomal breakpoint associated with B-cell lymphoma.
  • a chimeric protein comprised of DDX10 and NUP98, a nucleoporin protein, may be involved in the pathogenesis of certain myeloid maUgnancies. Topoisomerases
  • the spUceosomal complex is composed of five small nuclear ribonucleoprotein particles 0 (snRNPs) designated Ul, U2, U4, U5, and U6, and a number of additional proteins.
  • snRNP small nuclear ribonucleoprotein particles 0
  • Ul small nuclear ribonucleoprotein particles 0
  • U2, U4, U5, and U6 small nuclear ribonucleoprotein particles 0
  • snRNP contains a single species of snRNA and about ten proteins.
  • the RNA components of some snRNPs recognize and base pair with intron consensus sequences.
  • the protein components mediate spliceosome assembly and the splicing reaction.
  • Autoantibodies to snRNP proteins are found in the blood of patients with systemic lupus erythematosus (Stryer, L. (1995) Biochemistry, W.H. Freeman and 5 Company, New York NY, p. 863).
  • N-cadherin is present on nerve, muscle, and lens cells and is also critical for embryonic development.
  • P-cadherin is present on cells of the placenta and epidermis. Recent studies report that protocadherins are involved in 5 a variety of cell-cell interactions (Suzuki, S.T. (1996) J. Cell Sci. 109:2609-2611).
  • the infracellular anchorage of cadherins is regulated by their dynamic association with catenins, a family of cytoplasmic signal transduction proteins associated with the actin cytoskeleton.
  • o Galectins contain a characteristic carbohydrate recognition domain (CRD). The CRD is about
  • Galectins play a number of roles in diseases and conditions associated with cell-cell and cell- matrix interactions. For example, certain galectins associate with sites of inflammation and bind to cell surface immunoglobulin E molecules. In addition, galectins may play an important role in cancer metastasis.
  • Selectins comprise a specialized lectin subfamily involved primarily in o inflammation and leukocyte adhesion (Reviewed in Lasky, supra). Selectins mediate the recruitment of leukocytes from the circulation to sites of acute inflammation and are expressed on the surface of vascular endothelial cells in response to cytokine signaling. Selectins bind to specific ligands on the leukocyte cell membrane and enable the leukocyte to adhere to and migrate along the endothehal surface. Binding of selectin to its ligand leads to polarized rearrangement of the actin cytoskeleton and 5 stimulates signal transduction within the leukocyte (Brenner, B. et al. (1997) Biochem. Biophys. Res.
  • MHC proteins are cell surface markers that bind to and present foreign antigens to T cells. MHC molecules are classified as either class I or class II. Class I MHC molecules (MHC I) are expressed on the surface of almost all cells and are involved in the presentation of antigen to cytotoxic T cells. For example, a cell infected with virus will degrade intracellular viral proteins and express the protein fragments bound to MHC I molecules on the cell surface. The MHC I/antigen 5 complex is recognized by cytotoxic T-cells which destroy the infected cell and the virus within.
  • MHC I major histocompatibility
  • the five antibody classes, IgA, IgD, o IgE, IgG and IgM, are defined by the ⁇ , ⁇ , e, ⁇ , and ⁇ H-chain types.
  • IgG the most common class of antibody found in the circulation, is tettameric, while the other classes of antibodies are generally variants or multimers of this basic structure.
  • Both H-chains and L-chains contain repeated Ig domains.
  • a typical H-chain contains four Ig domains, three of which occur within the constant region and one of which occurs 5 within the variable region and contributes to the formation of the antigen recognition site.
  • a typical L-chain contains two Ig domains, one of which occurs within the constant region and one of which occurs within the variable region.
  • the immune system is capable of recognizing and responding to any foreign molecule that enters the body. Therefore, the immune system must be armed with a full repertoire of antibodies 5 against all potential antigens.
  • antibody diversity is generated by somatic rearrangement of gene segments encoding variable and constant regions. These gene segments are joined together by site- specific recombination which occurs between highly conserved DNA sequences that flank each gene segment. Because there are hundreds of different gene segments, millions of unique genes can be generated combinatorially. In addition, imprecise joining of these segments and an unusually high 0 rate of somatic mutation within these segments further contribute to the generation of a diverse antibody population.
  • T-cell receptors are both structurally and functionally related to antibodies. (Reviewed in Alberts, supra, pp. 1228-1229.) T-cell receptors are cell surface proteins that bind foreign antigens and mediate diverse aspects of the immune response.
  • a typical T-cell receptor is a heterodimer comprised 5 of two disulfide-linked polypeptide chains called ⁇ and ⁇ . Each chain is about 280 amino acids in length and contains one variable region and one constant region. Each variable or constant region folds into an Ig domain. The variable regions from the ⁇ and ⁇ chains come together in the heterodimer to form the antigen recognition site.
  • T-cell receptor diversity is generated by somatic rearrangement of gene segments encoding the ⁇ and ⁇ chains.
  • Protein secretion is essential for cellular function. Protein secretion is mediated by a signal peptide located at the amino terminus of the protein to be secreted.
  • the signal peptide is comprised of about ten to twenty hydrophobic amino acids which target the nascent protein from the ribosome to the endoplasmic reticulum (ER). Proteins targeted to the ER may either proceed through the secretory o pathway or remain in any of the secretory organelles such as the ER, Golgi apparatus, or lysosomes.
  • Proteins that transit through the secretory pathway are either secreted into the exfracellular space or retained in the plasma membrane.
  • Secreted proteins are often synthesized as inactive precursors that are activated by post-franslational processing events during transit through the secretory pathway. Such events include glycosylation, proteolysis, and removal of the signal peptide by a signal peptidase. 5
  • Other events that may occur during protein fransport include chaperone-dependent unfolding and folding of the nascent protein and interaction of the protein with a receptor or pore complex.
  • the collagens comprise a family of ECM proteins that provide structure to bone, teeth, skin, Ugaments, tendons, cartilage, blood vessels, and basement membranes. Multiple collagen proteins have been identified. Three collagen molecules fold together in a friple helix stabilized by interchain disulfide bonds. Bundles of these friple helices then associate to form fibrils. Collagen primary structure o consists of hundreds of (Gly-X-Y) repeats where about a third of the X and Y residues are Pro.
  • Glycines are crucial to helix formation as the bulkier amino acid sidechains cannot fold into the friple helical conformation. Because of these strict sequence requirements, mutations in collagen genes have severe consequences. Osteogenesis imperfecta patients have brittle bones that fracture easily; in severe cases patients die in utero or at birth. Ehlers-Danlos syndrome patients have hyperelastic skin, 5 hypermobile joints, and susceptibility to aortic and intestinal rupture. Chondrodysplasia patients have short stature and ocular disorders. Alport syndrome patients have hematuria, sensorineural deafness, and eye lens deformation. (Isselbacher, K.J. et al.
  • Elastin is a highly hydrophobic protein of about 750 amino acids that is rich in proline and glycine residues. Elastin molecules are highly cross-linked, forming an extensive extracellular network of fibers and sheets. Elastin fibers are surrounded by a sheath of microfibrils which are composed of a number of glycoproteins, including fibrillin. Mutations in the gene encoding fibrillin are responsible for 5 Marfan's syndrome, a genetic disorder characterized by defects in connective tissue. In severe cases, the aortas of afflicted individuals are prone to rupture. (Reviewed in Alberts, supra, pp. 984-986.)
  • proteoglycans are composed of unbranched polysaccharide chains (glycosaminoglycans) attached to protein cores. Common proteoglycans include aggrecan, betaglycan, decorin, perlecan, serglycin, and syndecan-1. Some of these molecules not only provide mechanical support, but also bind to extracellular signaling molecules, such as fibroblast growth factor and transforming growth factor ⁇ , suggesting a role for proteoglycans in cell-cell communication and cell growth. (Reviewed in Alberts, supra, pp.
  • glycoproteins tenascin-C and tenascin-R are expressed in developing and lesioned neural tissue and provide stimulatory and anti- adhesive (inhibitory) properties, respectively, for axonal growth. (Faissner, A. (1997) Cell Tissue Res. 290:331-341.)
  • Microtubules cytoskeletal fibers with a diameter of about 24 nm, have multiple roles in the cell. Bundles of microtubules form cilia and flagella, which are whip-like extensions of the cell membrane that are necessary for sweeping materials across an epithelium and for swimming of sperm, respectively. Marginal bands of microtubules in red blood cells and platelets are important for these cells' pliability. Organelles, membrane vesicles, and proteins are transported in the cell along tracks of microtubules. For example, microtubules run through nerve cell axons, allowing bidirectional transport of materials and membrane vesicles between the cell body and the nerve terminal. Failure to supply the nerve terminal with these vesicles blocks the transmission of neural signals. Microtubules are also critical to chromosomal movement during cell division. Both stable and short-lived populations of microtubules exist in the cell.
  • G-actin the monomeric form of actin, polymerizes into polarized, helical F- actin filaments, accompanied by the hydrolysis of ATP to ADP.
  • Actin filaments associate to form o bundles and networks, providing a framework to support the plasma membrane and determine cell shape. These bundles and networks are connected to the cell membrane.
  • thin filaments containing actin slide past thick filaments containing the motor protein myosin during contraction.
  • a family of actin-related proteins exist that are not part of the actin cytoskeleton, but rather associate with microtubules and dynein.
  • Severing proteins regulate the length of actin filaments by breaking them into short pieces or by blocking their ends.
  • Severing proteins include gCAP39, severin (fragmin), gelsolin, and villin.
  • Capping proteins can cap the ends of actin filaments, but cannot break filaments.
  • Capping proteins 5 include CapZ and fropomodulin.
  • the proteins thymosin and profilin sequester actin monomers in the cytosol, allowing a pool of unpolymerized actin to exist.
  • the actin-associated proteins tropomyosin, froponin, and caldesmon regulate muscle confraction in response to calcium.
  • Intermediate filaments are cytoskeletal fibers with a diameter of about 10 nm, o intermediate between that of microfilaments and microtubules. IFs serve structural roles in the cell, reinforcing cells and organizing cells into tissues. IFs are particularly abundant in epidermal cells and in neurons. IFs are extremely stable, and, in contrast to microfilaments and microtubules, do not function in cell motility.
  • Type III IF proteins include desmin, glial fibrillary acidic protein, vimentin, and peripherin.
  • Desmin filaments in muscle cells link myofibrils into bundles and stabilize sarcomeres in contracting 5 muscle.
  • GUal fibrillary acidic protein filaments are found in the glial cells that surround neurons and astrocytes.
  • Vimentin filaments are found in blood vessel endothelial cells, some epitheUal cells, and mesenchymal cells such as fibroblasts, and are commonly associated with microtubules. Vimentin filaments may have roles in keeping the nucleus and other organelles in place in the cell.
  • Type IV IFs include the neurofilaments and nestin.
  • Neurofilaments composed of three polypeptides NF-L, NF-M, and NF-H, are frequently associated with microtubules in axons. Neurofilaments are responsible for the radial growth and diameter of an axon, and ultimately for the speed of nerve impulse transmission. Changes in phosphorylation and metabolism of neurofilaments are observed in neurodegenerative diseases including amyofrophic lateral sclerosis, Parkinson's disease, and Alzheimer's disease (Julien, J.P. and W.E. Mushynski (1998) Prog. Nucleic Acid Res. Mol. Biol. 61:1-23). Type V IFs, the lamins, are found in the nucleus where they support the nuclear membrane.
  • IFs have a central ⁇ -helical rod region interrupted by short nonhelical linker segments.
  • the rod region is bracketed, in most cases, by non-hehcal head and tail domains.
  • the rod regions of intermediate filament proteins associate to form a coiled-coil dimer.
  • a highly ordered assembly process leads from the dimers to the IFs. Neither ATP nor GTP is needed for IF assembly, unlike that of microfilaments and microtubules.
  • Cytoskeletal fibers are attached to the plasma membrane by specific proteins. These attachments are important for maintaining cell shape and for muscle confraction.
  • the spectrin- actin cytoskeleton is attached to cell membrane by three proteins, band 4J, ankyrin, and adducin. Defects in this attachment result in abnormally shaped cells which are more rapidly degraded by the spleen, leading to anemia.
  • the spectrin-actin cytoskeleton is also linked to the membrane by ankyrin; a second actin network is anchored to the membrane by filamin.
  • the protein dysfrophin links actin filaments to the plasma membrane; mutations in the dysfrophin gene lead to Duchenne muscular dystrophy.
  • adherens junctions and adhesion plaques the peripheral membrane proteins ⁇ -actinin and vinculin attach actin filaments to the cell membrane.
  • IFs are also attached to membranes by cytoskeletal-membrane anchors.
  • the nuclear lamina is attached to the inner surface of the nuclear membrane by the lamin B receptor.
  • Vimentin IFs are attached to the plasma membrane by ankyrin and plectin.
  • Desmosome and hemidesmosome membrane junctions hold together epithelial cells of organs and skin. These membrane junctions allow shear forces to be distributed across the entire epithelial cell layer, thus providing strength and rigidity to the epithelium.
  • IFs in epithelial cells are attached to the desmosome by plakoglobin and desmoplakins. The proteins that link IFs to hemidesmosomes are not known.
  • Myosin provides the motor function for muscle confraction and intracellular movements such as phagocytosis and rearrangement of cell contents during mitotic cell division (cytokinesis).
  • the contractile unit of skeletal muscle termed the sarcomere, consists of highly ordered arrays of thin actin-containing filaments and thick myosin-containing filaments. Crossbridges form o between the thick and thin filaments, and the ATP-dependent movement of myosin heads within the thick filaments pulls the thin filaments, shortening the sarcomere and thus the muscle fiber.
  • Myosins are composed of one or two heavy chains and associated light chains.
  • Myosin heavy chains contain an amino-terminal motor or head domain, a neck that is the site of light-chain binding, and a carboxy-terminal tail domain.
  • the tail domains may associate to form an ⁇ -helical 5 coiled coil.
  • Conventional myosins such as those found in muscle tissue, are composed of two myosin heavy-chain subunits, each associated with two light-chain subunits that bind at the neck region and play a regulatory role.
  • Unconventional myosins believed to function in infracellular motion, may contain either one or two heavy chains and associated light chains. There is evidence for about 25 myosin heavy chain genes in vertebrates, more than half of them unconventional. 0 Dynein-related Motor Proteins
  • Kinesins are (+) end-directed motor proteins which act on microtubules.
  • the prototypical kinesin molecule is involved in the transport of membrane-bound vesicles and organelles. This function is particularly important for axonal fransport in neurons.
  • Kinesin is also important in all cell types for 5 the fransport of vesicles from the Golgi complex to the endoplasmic reticulum. This role is critical for maintaining the identity and functionality of these secretory organelles.
  • dynamin disassembly. Following disassembly the dynamin may either dissociate from the membrane or remain associated to the vesicle and be fransported to another region of the cell.
  • Three homologous dynamin genes have been discovered, in addition to several dynamin-related proteins. conserveed dynamin regions are the N-terminal GTP-binding domain, a central pleckstrin homology domain that binds membranes, a central coiled-coil region that may activate dynamin' s GTPase activity, and a C-terminal proline-rich domain that contains several motifs that bind SH3 domains on other proteins.
  • the cytoskeleton is reviewed in Lodish, H. et al. (1995) Molecular Cell Biology, Scientific 5 American Books, New York NY.
  • Chromatin is associated with disorders of protein expression such as thalassemia, a genetic anemia resulting from the removal of the locus confrol region (LCR) required for decondensation of the 15 globin gene locus .
  • LCR locus confrol region
  • Glucose is initially converted 0 to pyruvate in the cytoplasm.
  • Fatty acids and pyruvate are fransported to the mitochondria for complete oxidation to C0 2 coupled by enzymes to the fransport of electrons from NADH and FADH 2 to oxygen and to the synthesis of ATP (oxidative phosphorylation) from ADP and P..
  • Pyruvate is transported into the mitochondria and converted to acetyl-CoA for oxidation via the citric acid cycle, involving pyruvate dehydrogenase components, dihydrolipoyl fransacetylase, and 5 dihydrolipoyl dehydrogenase.
  • Enzymes involved in the cifric acid cycle include: citrate synthetase, aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including transsuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate dehydrogenase.
  • Mitochondria are oval-shaped organelles comprising an outer membrane, a tightly folded 5 inner membrane, an intermembrane space between the outer and inner membranes, and a matrix inside the inner membrane.
  • the outer membrane contains many porin molecules that allow ions and charged molecules to enter the intermembrane space, while the inner membrane contains a variety of fransport proteins that transfer only selected molecules.
  • Mitochondria are the primary sites of energy production in cells. o Mitochondria contain a small amount of DNA.
  • Human mitochondrial DNA encodes 13 proteins, 22 tRNAs, and 2 rRNAs.
  • Mitochondrial-DNA encoded proteins include NADH-Q reductase, a cytochrome reductase subunit, cytochrome oxidase subunits, and ATP synthase subunits.
  • mitochondrial proteins The majority of mitochondrial proteins are encoded by nuclear genes, are synthesized on cytosolic ribosomes, and are imported into the mitochondria. Nuclear-encoded proteins which are destined for the mitochondrial matrix typically contain positively-charged amino terminal signal sequences. Import of these preproteins from the cytoplasm requires a multisubunit protein complex in the outer membrane known as the translocase of outer mitochondrial membrane (TOM; previously designated MOM; Pfanner, N. et al. (1996) Trends Biochem. Sci. 21 :51-52) and at least three inner membrane proteins which comprise the translocase of inner mitochondrial membrane (TIM; previously designated MIM; Pfanner, supra). An inside-negative membrane potential across the inner mitochondrial membrane is also required for preprotein import.
  • TOM translocase of outer mitochondrial membrane
  • TIM inner membrane proteins which comprise the translocase of inner mitochondrial membrane
  • Mitochondria are implicated in disorders of cell proliferation, since they play an important role in a cell's decision to proliferate or self-destruct through apoptosis.
  • the oncoprotein Bcl-2 for example, promotes cell proliferation by stabilizing mitochondrial membranes so that apoptosis signals are not released (Susin, S.A. (1998) Biochim.
  • SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, and SEQ ID NO:43 encode, for example, franscription factor molecules.
  • the double helix structure and repeated sequences of DNA create topological and chemical features which can be recognized by franscription factors. These features are hydrogen bond donor 15 and acceptor groups, hydrophobic patches, major and minor grooves, and regular, repeated stretches of sequence which induce distinct bends in the helix.
  • franscription factors recognize specific DNA sequence motifs of about 20 nucleotides in length. Multiple, adjacent franscription factor-binding motifs may be required for gene regulation.
  • the helix-turn-helix motif consists of two ⁇ helices connected at a fixed angle by a short chain of amino acids. One of the helices binds to the major groove. Helix-turn-helix motifs are 5 exemplified by the homeobox motif which is present in homeodomain proteins. These proteins are critical for specifying the anterior-posterior body axis during development and are conserved throughout the animal kingdom.
  • the Antennapedia and Ultrabithorax proteins of Drosophila melanogaster are prototypical homeodomain proteins (Pabo, CO. and R.T. Sauer (1992) Annu. Rev. Biochem. 61 :1053-1095).
  • the zinc finger motif which binds zinc ions, generally contains tandem repeats of about 30 amino acids consisting of periodically spaced cysteine and histidine residues. Examples of this sequence pattern, designated C2H2 and C3HC4 ("RING" finger), have been described (Lewin, supra). Zinc finger proteins each contain an ⁇ helix and an antiparallel ⁇ sheet whose proximity and conformation are maintained by the zinc ion. Contact with DNA is made by the arginine prece ding 5 the ⁇ helix and by the second, third, and sixth residues of the ⁇ hehx. Variants of the zinc finger motif include poorly defined cysteine-rich motifs which bind zinc or other metal ions. These motifs may not contain histidine residues and are generally nonrepetitive.
  • the helix-loop-helix motif (HLH) consists of a short ⁇ hehx connected by a loop to a longer ⁇ hetix.
  • the loop is flexible and allows the two helices to fold back against each other and to bind to DNA.
  • the transcription factor Myc contains a prototypical HLH motif.
  • neoplastic disorders in humans can be attributed to inappropriate gene expression. Malignant cell growth may result from either excessive expression of tumor promoting genes or insufficient expression of tumor suppressor genes (Cleary, M.L. (1992) Cancer Surv. 15:89-104).
  • Chromosomal franslocations may also produce chimeric loci which fuse the coding sequence of one gene with the regulatory regions of a second unrelated gene. Such an arrangement likely results in inappropriate gene franscription, potentially contributing to malignancy.
  • the immune system responds to infection or frauma by activating a cascade of events that coordinate the progressive selection, amplification, and mobilization of cellular defense mechanisms. A complex and balanced program of gene activation and repression is involved in this process.
  • hyperactivity of the immune system as a result of improper or insufficient regulation of gene expression may result in considerable tissue or organ damage. This damage is well documented in immunological responses associated with arthritis, allergens, heart attack, sfroke, and infections (Isselbacher, K.J. et al. (1996) Harrison's Principles of Internal Medicine, 13/e, McGraw
  • CeU Membrane Molecules SEQ ID NO:28 and SEQ ID NO:29 encode, for example, cell membrane molecules.
  • Eukaryotic cells are surrounded by plasma membranes which enclose the cell and maintain an environment inside the cell that is distinct from its surroundings.
  • eukaryotic organisms are distinct from prokaryotes in possessing many intracellular organelle and vesicle structures. Many of the metabolic reactions which distinguish eukaryotic biochemistry from prokaryotic biochemistry take place within these structures.
  • the plasma membrane and the membranes surrounding organelles and vesicles are composed of phosphoglycerides, fatty acids, cholesterol, phosphoUpids, glycolipids, proteoglycans, and proteins. These components confer identity and functionality to the membranes with which they associate.
  • Integral Membrane Proteins The majority of known integral membrane proteins are fransmembrane proteins (TM) which are characterized by an exfracellular, a transmembrane, and an infracellular domain. TM domains are typically comprised of 15 to 25 hydrophobic amino acids which are predicted to adopt an ⁇ -helical conformation. TM proteins are classified as bitopic (Types I and II) and polytopic (Types III and IV) (Singer, S.J. (1990) Annu. Rev. Cell Biol. 6:247-296). Bitopic proteins span the membrane once while polytopic proteins contain multiple membrane-spanning segments. TM proteins function as cell-surface receptors, receptor-interacting proteins, fransporters of ions or metabolites, ion channels, cell anchoring proteins, and cell type- specific surface antigens.
  • TM proteins function as cell-surface receptors, receptor-interacting proteins, fransporters of ions or metabolites, ion channels, cell anchoring proteins, and cell type- specific surface antigens.
  • NGR NGR
  • GSL motif-containing peptides have been used as drug delivery agents in targeted cancer treatment of tumor vasculature (Arap, W. et al. (1998) Science 279:377-380).
  • MPs may also contain amino acid sequence motifs, such as the carbohydrate recognition domain (CRD), that mediate interactions with exfracellular or infracellular molecules.
  • CCD carbohydrate recognition domain
  • GPCR G-protein coupled receptors
  • GPCRs include receptors for biogenic amines, lipid mediators of inflammation, peptide hormones, and sensory signal mediators.
  • the structure of these highly-conserved receptors consists of seven hydrophobic fransmembrane regions, an extracellular N-terminus, and a cytoplasmic C-terminus. Three extracellular loops alternate with three infracellular loops to link the seven transmembrane regions. Cysteine disulfide bridges connect the second and third extracellular loops.
  • the most conserved regions of GPCRs are the transmembrane regions and the first two cytoplasmic loops.
  • a conserved, acidic-Arg-aromatic residue triplet present in the second cytoplasmic loop may interact with G proteins.
  • a GPCR consensus pattern is characteristic of 5 most proteins belonging to this superfamily (ExPASy PROSITE document PS00237; and Watson, S. and S. Arkinstall (1994) The G-protein Linked Receptor Facts Book, Academic Press, San Diego CA, pp. 2-6). Mutations and changes in franscriptional activation of GPCR-encoding genes have been associated with neurological disorders such as schizophrenia, Parkinson's disease, Alzheimer's disease, drug addiction, and feeding disorders. 0 Scavenger Receptors
  • Macrophage scavenger receptors with broad ligand specificity may participate in the binding of low density lipoproteins (LDL) and foreign antigens.
  • Scavenger receptors types I and II are trimeric membrane proteins with each subunit containing a small N-terminal infracellular domain, a fransmembrane domain, a large exfracellular domain, and a C-terminal cysteine-rich domain.
  • the 5 exfracellular domain contains a short spacer region, an ⁇ -helical coiled-coil region, and a triple helical collagen-like region.
  • the fransmembrane 4 superfamily (TM4SF) or tetraspan family is a multigene family encoding type III integral membrane proteins (Wright, M.D. and M.G. Tomlinson (1994) Immunol. 5 Today 15 :588-594).
  • the TM4SF is comprised of membrane proteins which traverse the cell membrane four times.
  • Members of the TM4SF include platelet and endothelial cell membrane proteins, melanoma-associated antigens, leukocyte surface glycoproteins, colonal carcinoma antigens, tumor-associated antigens, and surface proteins of the schistosome parasites (Jankowski, S.A. (1994) Oncogene 9:1205-1211).
  • Members of the TM4SF share about 25-30% amino acid sequence identity o with one another.
  • Tumor antigens are cell surface molecules that are differentially expressed in tumor cells relative to normal cells. Tumor antigens distinguish tumor cells immunologically from normal cells and provide diagnostic and therapeutic targets for human cancers (Takagi, S. et al. (1995) Int. J. Cancer 61:706-715; Liu, E. et al. (1992) Oncogene 7:1027-1032). 5 Leukocyte Antigens
  • cell surface antigens include those identified on leukocytic cells of the immune system. These antigens have been identified using systematic, monoclonal antibody (mAb)-based "shot gun” techniques. These techniques have resulted in the production of hundreds of mAbs directed against unknown cell surface leukocytic antigens. These antigens have been grouped into o "clusters of differentiation” based on common immunocytochemical localization patterns in various differentiated and undifferentiated leukocytic cell types. Antigens in a given cluster are presumed to identify a single cell surface protein and are assigned a "cluster of differentiation" or "CD" designation.
  • mAb monoclonal antibody
  • CD antigens Some of the genes encoding proteins identified by CD antigens have been cloned and verified by standard molecular biology techniques. CD antigens have been characterized as both 5 fransmembrane proteins and cell surface proteins anchored to the plasma membrane via covalent attachment to fatty acid-containing glycolipids such as glycosylphosphatidylinositol (GPI). (Reviewed in Barclay, A.N. et al. (1995) The Leucocyte Antigen Facts Book, Academic Press, San Diego CA, pp. 17-20.) Ion Channels o Ion channels are found in the plasma membranes of virtually every cell in the body.
  • GPI glycosylphosphatidylinositol
  • chloride channels mediate a variety of cellular functions including regulation of membrane potentials and abso ⁇ tion and secretion of ions across epithelial membranes.
  • Chloride channels also regulate the pH of organelles such as the Golgi apparatus and endosomes (see, e.g., Greger, R. (1988) Annu. Rev. Physiol. 50:111-122).
  • Elecfrophysiological and pharmacological properties of chloride 5 channels including ion conductance, current-voltage relationships, and sensitivity to modulators, suggest that different chloride channels exist in muscles, neurons, fibroblasts, epithelial cells, and lymphocytes.
  • the resultant gradient may be used to transport other ions across the membrane (Na + , K + , or Cl " ) or to maintain organelle pH.
  • Proton ATPases are further subdivided into the mitochondrial F- ATPases, the plasma membrane ATPases, and the vacuolar ATPases.
  • the vacuolar ATPases establish and maintain an acidic pH 5 within various organelles involved in the processes of endocytosis and exocytosis (Mellman, I. et al. (1986) Annu. Rev. Biochem. 55:663-700).
  • ABC ATP-binding cassette
  • fransporters also called the "traffic ATPases”
  • ATP-binding cassettes comprise a o superfamily of membrane proteins that mediate fransport and channel functions in prokaryotes and eukaryotes (Higgins, C.F. (1992) Annu. Rev. Cell Biol. 8:67-113).
  • ABC proteins share a similar overall structure and significant sequence homology. All ABC proteins contain a conserved domain of approximately two hundred amino acid residues which includes one or more nucleotide binding domains.
  • Membrane o anchors are covalentiy joined to a protein post-franslationally and include such moieties as prenyl, myristyl, and glycosylphosphatidyl inositol groups.
  • Membrane localization of peripheral and anchored proteins is important for their function in processes such as receptor-mediated signal transduction. For example, prenylation of Ras is required for its localization to the plasma membrane and for its normal and oncogenic functions in signal transduction. 5 Vesicle Coat Proteins Intercellular communication is essential for the development and survival of multicellular organisms. Cells communicate with one another through the secretion and uptake of protein signaling molecules.
  • the uptake of proteins into the cell is achieved by the endocytic pathway, in which the interaction of exfracellular signaling molecules with plasma membrane receptors results in 5 the formation of plasma membrane-derived vesicles that enclose and transport the molecules into the cytosol. These transport vesicles fuse with and mature into endosomal and lysosomal (digestive) compartments.
  • the secretion of proteins from the cell is achieved by exocytosis, in which molecules inside of the cell proceed through the secretory pathway. In this pathway, molecules transit from the ER to the Golgi apparatus and finally to the plasma membrane, where they are secreted from the cell.
  • Clathrin coats form on vesicles derived from the TGN and PM, whereas coatomer (COP) coats form on vesicles derived from the ER and Golgi.
  • COP coats can be further classified as COPI, involved in retrograde traffic through the Golgi and from the Golgi to the ER, and COPII, involved in anterograde traffic from the 0 ER to the Golgi (Mellman, supra).
  • adapter proteins bring vesicle cargo and coat proteins together at the surface of the budding membrane.
  • Adapter protein- 1 and -2 select cargo from the TGN and plasma membrane, respectively, based on molecular information encoded on the cytoplasmic tail of integral membrane cargo proteins.
  • Adapter proteins also recruit clathrin to the bud 5 site.
  • Clathrin is a protein complex consisting of three large and three small polypeptide chains arranged in a three-legged structure called a friskelion. Multiple triskelions and other coat proteins appear to self-assemble on the membrane to form a coated pit. This assembly process may serve to deform the membrane into a budding vesicle.
  • GTP-bound ADP-ribosylation factor (Arf) is also inco ⁇ orated into the coated assembly.
  • Another small G-protein, dynamin forms a ring complex o around the neck of the forming vesicle and may provide the mechanochemical force to seal the bud, thereby releasing the vesicle.
  • the coated vesicle complex is then transported through the cytosol.
  • Arf-bound GTP is hydrolyzed to GDP, and the coat dissociates from the fransport vesicle (West, M.A. et al. (1997) J. Cell Biol. 138:1239-1254).
  • the coat protein is assembled from cytosolic precursor molecules at specific budding regions on the organelle.
  • the COP coat consists of two major components, a G-protein (Arf or Sar) and coat protomer (coatomer).
  • Coatomer is an equimolar complex of seven proteins, termed alpha-, beta-, beta'-, gamma-, delta-, epsilon- and zeta-COP.
  • the coatomer complex binds to dilysine motifs contained on the cytoplasmic tails of integral membrane 5 proteins.
  • the p24 family of type I membrane proteins represent the major membrane proteins of COPI vesicles (Harter, C and F.T. Wieland (1998) Proc. Nati. Acad. Sci. USA 95:11649-11654).
  • SEQ ID NO:44, SEQ ID NO:45, and SEQ ID NO:46 encode, for example, organelle associated molecules.
  • DNA-binding structural motifs which comprise either ⁇ helices or ⁇ sheets that bind to the major groove of DNA.
  • Four well-characterized structural motifs are helix-turn-heUx, zinc finger, leucine zipper, and helix-loop-helix. Proteins containing these motifs may act alone as monomers, or they may form homo- or heterodimers that interact with DNA. 5 Many neoplastic disorders in humans can be attributed to inappropriate gene expression.
  • Chromosomal franslocations may also produce chimeric loci which fuse the coding sequence of one gene with the regulatory regions of a second unrelated gene. Such an arrangement likely results in o inappropriate gene franscription, potentially contributing to malignancy.
  • the immune system responds to infection or frauma by activating a cascade of events that coordinate the progressive selection, amplification, and mobilization of cellular defense mechanisms.
  • a complex and balanced program of gene activation and repression is involved in this process.
  • hyperactivity of the immune system as a result of improper or insufficient 5 regulation of gene expression may result in considerable tissue or organ damage. This damage is well documented in immunological responses associated with arthritis, allergens, heart attack, sfroke, and infections (Isselbacher, KJ. et al. (1996) Harrison's Principles of Internal Medicine, 13/e, McGraw Hill, Inc. and Teton Data Systems Software).
  • RNA polymerase I makes large ribosomal RNA
  • the nucleolus is a highly organized subcompartment in the nucleus that contains high o concenfrations of RNA and proteins and functions mainly in ribosomal RNA synthesis and assembly
  • Ribosomal RNA is a structural RNA that is complexed with proteins to form ribonucleoprotein structures called ribosomes. Ribosomes provide the platform on which protein synthesis takes place.
  • proteins are synthesized within the endoplasmic reticulum (ER), delivered from 5 the ER to the Golgi apparatus for post-franslational processing and sorting, and transported from the Golgi to specific infracellular and exfracellular destinations. Synthesis of integral membrane proteins, secreted proteins, and proteins destined for the lumen of a particular organelle occurs on the rough endoplasmic reticulum (ER).
  • the rough ER is so named because of the rough appearance in electron micrographs imparted by the attached ribosomes on which protein synthesis proceeds.
  • Synthesis of l o proteins destined for the ER actually begins in the cytosol with the synthesis of a specific signal peptide which directs the growing polypeptide and its attached ribosome to the ER membrane where the signal peptide is removed and protein synthesis is completed.
  • Soluble proteins destined for the ER lumen, for secretion, or for transport to the lumen of other organelles pass completely into the ER lumen.
  • Transmembrane proteins destined for the ER or for other cell membranes are translocated
  • Translocated polypeptide chains destined for other organelles or for secretion also fold and assemble in the ER lumen with the aid of certain "resident" ER proteins. Protein folding in the ER is aided by two principal types of protein isomerases, protein disulfide isomerase (PDI), and peptidyl-
  • prolyl isomerase catalyzes the oxidation of free sulfhydryl groups in cysteine residues to form inframolecular disulfide bonds in proteins.
  • PPI an enzyme that catalyzes the isomerization of certain proline imide bonds in oligopeptides and proteins, is considered to govern one of the rate limiting steps in the folding of many proteins to their final functional conformation.
  • the cyclophilins represent a major class of PPI that was originally identified as the major receptor for the 5 immunosuppressive drug cyclosporin A (Handschumacher, R.E. et al. (1984) Science 226:544-547).
  • Molecular "chaperones" such as BiP (binding protein) in the ER recognize incorrectly folded proteins as well as proteins not yet folded into their final form and bind to them, both to prevent improper aggregation between them, and to promote proper folding.
  • the Golgi apparatus is a complex structure that lies adjacent to the ER in eukaryotic cells and serves primarily as a sorting and dispatching station for products of the ER (Alberts, et al. supra, pp. 5 600-610). Additional postfranslational processing, principally additional glycosylation, also occurs in the Golgi. Indeed, the Golgi is a major site of carbohydrate synthesis, including most of the glycosaminoglycans of the extracellular matrix. N-linked oligosaccharides, added to proteins in the ER, are also further modified in the Golgi by the addition of more sugar residues to form complex N- linked oligosaccharides.
  • the terminal compartment of the Golgi is the Trans-Golgi Network (TGN), where both membrane and lumenal proteins are sorted for their final destination.
  • Other fransport vesicles bud off containing proteins destined for the plasma membrane, such as receptors, adhesion 5 molecules, and ion channels, and secretory proteins, such as hormones, neurofransmitters, and digestive enzymes.
  • Lysosomes 5 Lysosomes are membranous vesicles containing various hydrolytic enzymes used for the controlled intracellular digestion of macromolecules.
  • Lysosomes contain some 40 types of enzymes including proteases, nucleases, glycosidases, Upases, phospholipases, phosphatases, and sulfatases, all of which are acid hydrolases that function at a pH of about 5. Lysosomes are surrounded by a unique membrane containing fransport proteins that allow the final products of macromolecule degradation, 5 such as sugars, amino acids, and nucleotides, to be fransported to the cytosol where they may be either excreted or reutilized by the cell. A vp-ATPase, such as that described above, maintains the acidic environment necessary for hydrolytic activity (Alberts, supra, pp. 610-611). Endosomes
  • Late endosomes 5 appear later in the endocytic process close to the Golgi apparatus and the nucleus, and appear to be associated with delivery of endocytosed material to lysosomes or to the TGN where they may be recycled.
  • Specific proteins are associated with particular transport vesicles and their target compartments that may provide selectivity in targeting vesicles to their proper compartments.
  • a cytosolic prenylated GTP-binding protein, Rab is one such protein.
  • Rabs 4, 5, and 11 are associated o with the early endosome, whereas Rabs 7 and 9 associate with the late endosome.
  • Glucose is initially converted to pyruvate in the cytoplasm.
  • Fatty acids and pyruvate are fransported to the mitochondria for o complete oxidation to C0 2 coupled by enzymes to the transport of elecfrons from NADH and FADH 2 to oxygen and to the synthesis of ATP (oxidative phosphorylation) from ADP and P..
  • Pyruvate is fransported into the mitochondria and converted to acetyl-CoA for oxidation via the citric acid cycle, involving pyruvate dehydrogenase components, dihydrolipoyl fransacetylase, and dihydrolipoyl dehydrogenase.
  • Enzymes involved in the cifric acid cycle include: citrate synthetase, 5 aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including ttanssuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate dehydrogenase.
  • ⁇ oxidation results in shortening of the alkyl chain of fatty acids by blocks of two carbon atoms that are converted to acetyl CoA and exported to the cytosol for reuse in biosynthetic reactions.
  • peroxisomes import their proteins from the cytosol using a specific signal sequence located near the C-terminus of the protein.
  • the importance of this import process is o evident in the inherited human disease Zellweger syndrome, in which a defect in importing proteins into perixosomes leads to a perixosomal deficiency resulting in severe abnormalities in the brain, liver, and kidneys, and death soon after birth.
  • One form of this disease has been shown to be due to a mutation in the gene encoding a perixosomal integral membrane protein called peroxisome assembly factor- 1. 5
  • the discovery of new human molecules for diagnostics and therapeutics satisfies a need in the art by providing new compositions which are useful in the diagnosis, study, prevention, and treatment of diseases associated with human molecules.
  • the present invention relates to nucleic acid sequences comprising human diagnostic and therapeutic polynucleotides (dithp) as presented in the Sequence Listing. Some of the dithp uniquely identify genes encoding human structural, functional, and regulatory molecules.
  • the invention provides an isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of 5 SEQ ID NOJ-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d).
  • the polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52.
  • the polynucleotide comprises at least 60 contiguous nucleotides of a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d).
  • the method comprises a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof.
  • the probe comprises at least 30 contiguous nucleotides.
  • the probe comprises at least 60 contiguous nucleotides.
  • the invention provides a cell transformed with the recombinant polynucleotide.
  • the invention provides a transgenic organism comprising the recombinant polynucleotide.
  • the invention provides a method 5 for producing a human diagnostic and therapeutic polypeptide, the method comprising a) culturing a cell under conditions suitable for expression of the human diagnostic and therapeutic polypeptide, wherein said cell is transformed with the recombinant polynucleotide, and b) recovering the human diagnostic and therapeutic polypeptide so expressed.
  • the invention also provides a purified human diagnostic and therapeutic polypeptide (DITHP) o encoded by at least one polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52. Additionally, the invention provides an isolated antibody which specifically binds to the human diagnostic and therapeutic polypeptide.
  • DITHP human diagnostic and therapeutic polypeptide
  • the invention further provides a method of identifying a test compound which specifically binds to the human diagnostic and therapeutic polypeptide, the method comprising the steps of a) providing a test compound; b) combining 5 the human diagnostic and therapeutic polypeptide with the test compound for a sufficient time and under suitable conditions for binding; and c) detecting binding of the human diagnostic and therapeutic polypeptide to the test compound, thereby identifying the test compound which specifically binds the human diagnostic and therapeutic polypeptide.
  • the invention further provides a microarray wherein at least one element of the microarray is 0 an isolated polynucleotide comprising at least 60 contiguous nucleotides of a polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence 5 complementary to b); and e) an RNA equivalent of a) through d).
  • the invention also provides a method for generating a transcript image of a sample which contains polynucleotides.
  • the method comprises a) labeling the polynucleotides of the sample, b) contacting the elements of the microarray with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample.
  • the invention provides a method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ 5 ID NOJ-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d).
  • the method comprises a) exposing a sample comprising the target polynucleotide to a compound, and b) detecting altered expression of the target polynucleotide.
  • the invention further provides a method for detecting a target polynucleotide in a sample for toxicity testing of a compound, said target polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d).
  • Table 2 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with polynucleotide segments of each template sequence as defined by the indicated “start” and “stop” nucleotide positions.
  • SEQ ID NO:s sequence identification numbers
  • template IDs template identification numbers
  • Table 3 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with polynucleotide segments of each template sequence as defined by the indicated “start” and “stop” nucleotide positions.
  • the reading frames of the polynucleotide segments are shown, and the polypeptides encoded by the polynucleotide segments constitute either signal peptide (SP) or fransmembrane (TM) domains, as indicated.
  • SP signal peptide
  • TM fransmembrane
  • Table 5 summarizes the bioinformatics tools which are useful for analysis of the polynucleotides of the present invention.
  • the first column of Table 5 lists analytical tools, programs, o and algorithms, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are inco ⁇ orated by reference herein in their entirety, and the fourth column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score, the greater the homology between two sequences). 5
  • dithp refers to a nucleic acid sequence
  • DITHP amino acid sequence encoded by dithp
  • a “full-length” dithp refers to a nucleic acid sequence containing the entire coding region of a gene endogenously expressed in human tissue.
  • Adjuvants are materials such as Freund's adjuvant, mineral gels (aluminum hydroxide), and 5 surface active substances (lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole Umpet hemocyanin, and dinifrophenol) which may be administered to increase a host's immunological response.
  • Alleles refers to an alternative form of a nucleic acid sequence. Alleles result from a “mutation,” a change or an alternative reading of the genetic code. Any given gene may have none, one, or many allelic forms. Mutations which give rise to alleles include deletions, additions, or substitutions of nucleotides. Each of these changes may occur alone, or in combination with the others, one or more times in a given nucleic acid sequence.
  • the present invention encompasses allelic dithp.
  • Amplification refers to the production of additional copies of a sequence and is carried out using polymerase chain reaction (PCR) technologies well known in the art.
  • PCR polymerase chain reaction
  • Antibody refers to intact molecules as well as to fragments thereof, such as Fab, F(ab') 2 , and Fv fragments, which are capable of binding the epitopic determinant.
  • Antibodies that bind DITHP polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen.
  • the polypeptide or peptide used to immunize an animal e.g., a mouse, a rat, or a rabbit
  • an animal e.g., a mouse, a rat, or a rabbit
  • RNA e.g., a mouse, a rat, or a rabbit
  • Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobuUn, and keyhole limpet hemocyanin (KLH). The coupled peptide is then used to immunize the animal.
  • Antisense sequence refers to a sequence capable of specifically hybridizing to a target sequence.
  • the antisense sequence may include DNA, RNA, or any nucleic acid mimic or analog such as peptide nucleic acid (PNA); oligonucleotides having modified backbone linkages such as phosphorothioates, methylphosphonates, or benzylphosphonates; oligonucleotides having modified sugar groups such as 2'-methoxyethyl sugars or 2'-methoxyethoxy sugars; or oligonucleotides having modified bases such as 5-methyl cytosine, 2'-deoxyuracil, or 7-deaza-2'-deoxyguanosine.
  • PNA peptide nucleic acid
  • Antisense sequence refers to a sequence capable of specifically hybridizing to a target sequence.
  • the antisense sequence can be DNA, RNA, or any nucleic acid mimic or analog.
  • Antisense technology refers to any technology which relies on the specific hybridization of an antisense sequence to a target sequence.
  • a "bin” is a portion of computer memory space used by a computer program for storage of data, and bounded in such a manner that data stored in a bin may be retrieved by the program.
  • Bioly active refers to an amino acid sequence having a structural, regulatory, or biochemical function of a naturally occurring amino acid sequence.
  • “Clone joining” is a process for combining gene bins based upon the bins' containing sequence information from the same clone. The sequences may assemble into a primary gene transcript as well as one or more splice variants.
  • a "consensus sequence” or “template sequence” is a nucleic acid sequence which has been assembled from overlapping sequences, using a computer program for fragment assembly such as the GEL VIEW fragment assembly system (Genetics Computer Group (GCG), Madison WI) or using a relational database management system (RDMS).
  • GCG Genetics Computer Group
  • RDMS relational database management system
  • Constant amino acid substitutions are those substitutions that, when made, least interfere with the properties of the original protein, i.e., the structure and especially the function of the protein is conserved and not significantly changed by such substitutions.
  • the table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative substitutions.
  • Lys Arg Gin, Glu Met Leu, He Phe His, Met, Leu, Trp, Tyr Ser Cys, Thr Thr Ser, Val T ⁇ Phe, Tyr Tyr His, Phe, T ⁇ Val He, Leu, Thr
  • Conservative substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.
  • “Deletion” refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or amino acid residue, respectively, is absent.
  • “Derivative” refers to the chemical modification of a nucleic acid sequence, such as by replacement of hydrogen by an alkyl, acyl, amino, hydroxyl, or other group.
  • E-value refers to the statistical probability that a match between two sequences occurred by chance.
  • a “fragment” is a unique portion of dithp or DITHP which is identical in sequence to but o shorter in length than the parent sequence.
  • a fragment may comprise up to the entire length of the defined sequence, minus one nucleotide/amino acid residue.
  • a fragment may comprise from 10 to 1000 contiguous amino acid residues or nucleotides.
  • a fragment used as a probe, primer, antigen, therapeutic molecule, or for other pu ⁇ oses may be at least 5, 10, 15, 16, 20, 25, 30, 40, 50, 60, 75, 100, 150, 250 or at least 500 contiguous amino acid residues or nucleotides in length. 5 Fragments may be preferentially selected from certain regions of a molecule.
  • a polypeptide fragment may comprise a certain length of contiguous amino acids selected from the first 250 or 500 amino acids (or first 25% or 50%) of a polypeptide as shown in a certain defined sequence.
  • a fragment of dithp comprises a region of unique polynucleotide sequence that specifically identifies dithp, for example, as distinct from any other sequence in the same genome.
  • a fragment of dithp is useful, for example, in hybridization and amplification technologies and in analogous methods that distinguish dithp from related polynucleotide sequences.
  • the precise length of a fragment of dithp and the region of dithp to which the fragment corresponds are routinely determinable by one of ordinary 5 skill in the art based on the intended pu ⁇ ose for the fragment.
  • a fragment of DITHP is encoded by a fragment of dithp.
  • a fragment of DITHP comprises a region of unique amino acid sequence that specifically identifies DITHP.
  • a fragment of DITHP is useful as an immunogenic peptide for the development of antibodies that specifically recognize DITHP.
  • the precise length of a fragment of DITHP and the region of DITHP to which the o fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended pu ⁇ ose for the fragment.
  • a “full length” nucleotide sequence is one containing at least a start site for translation to a protein sequence, followed by an open reading frame and a stop site, and encoding a "full length” polypeptide.
  • 5 "Hit” refers to a sequence whose annotation will be used to describe a given template. Criteria for selecting the top hit are as follows: if the template has one or more exact nucleic acid matches, the top hit is the exact match with highest percent identity. If the template has no exact matches but has significant protein hits, the top hit is the protein hit with the lowest E-value. If the template has no significant protein hits, but does have significant non-exact nucleotide hits, the top hit is the nucleotide hit with the lowest E-value.
  • Homology refers to sequence similarity either between a reference nucleic acid sequence and at least a fragment of a dithp or between a reference amino acid sequence and a fragment of a DITHP.
  • Hybridization refers to the process by which a strand of nucleotides anneals with a complementary strand through base pairing. Specific hybridization is an indication that two nucleic acid sequences share a high degree of identity. Specific hybridization complexes form under defined annealing conditions, and remain hybridized after the "washing" step.
  • the defined hybridization conditions include the annealing conditions and the washing step(s), the latter of which is particularly important in determining the stringency of the hybridization process, with more stringent conditions allowing less non-specific binding, i.e., binding between pairs of nucleic acid probes that are not perfectly matched.
  • Permissive conditions for annealing of nucleic acid sequences are routinely determinable and may be consistent among hybridization experiments, whereas wash conditions may be varied among experiments to achieve the desired stringency.
  • stringency of hybridization is expressed with reference to the temperature under which the wash step is carried out.
  • wash temperatures are selected to be about 5°C to 20°C lower than the thermal melting point (T Rule) for the specific sequence at a defined ionic strength and pH.
  • T m is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe.
  • High stringency conditions for hybridization between polynucleotides of the present invention include wash conditions of 68°C in the presence of about 0.2 x SSC and about 0J % SDS, for 1 hour. Alternatively, temperatures of about 65°C, 60°C, or 55°C may be used. SSC concentration may be varied from about 0.2 to 2 x SSC, with SDS being present at about 0.1%.
  • blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, denatured salmon sperm DNA at about 100-200 ⁇ g/ml. Useful variations on these conditions will be readily apparent to those skilled in the art.
  • Hybridization particularly under high stringency conditions, may be suggestive of evolutionary similarity between the nucleotides. Such similarity is strongly indicative of a similar role for the nucleotides and their resultant proteins. Other parameters, such as temperature, salt concentration, and detergent concentration may be varied to achieve the desired stringency. Denaturants, such as formamide at a concentration of about 35-50% v/v, may also be used under particular circumstances, such as RNA:DNA hybridizations. Appropriate hybridization conditions are routinely determinable by one of ordinary skill in the art.
  • Immunogenic describes the potential for a natural, recombinant, or synthetic peptide, epitope, 5 polypeptide, or protein to induce antibody production in appropriate animals, cells, or cell Unes.
  • “Insertion” or “addition” refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or residue, respectively, is added to the sequence.
  • LabeleUng refers to the covalent or noncovalent joining of a polynucleotide, polypeptide, or antibody with a reporter molecule capable of producing a detectable or measurable signal.
  • a reporter molecule capable of producing a detectable or measurable signal.
  • 0 "Microarray” is any arrangement of nucleic acids, amino acids, antibodies, etc., on a substrate.
  • the substrate may be a solid support such as beads, glass, paper, nitrocellulose, nylon, or an appropriate membrane.
  • BLAST 2 Sequences can be accessed and used interactively at http://www.ncbi.nlm.nih.gov/gorf/bl2/.
  • the "BLAST 2 Sequences” tool can be used for both blastn and blastp (discussed below).
  • BLAST programs are commonly used with gap and other parameters set to default settings. For example, to compare two nucleotide sequences, one may use blastn with the "BLAST 2 Sequences" tool Version o 2.0.9 (May-07-1999) set at default parameters.
  • Such default parameters may be, for example:
  • Transformation may occur under natural or artificial conditions using various methods well known in the art. Transformation may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method is selected based on the host cell being transformed. 5 "Transformants" include stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as cells which transiently express inserted DNA or RNA.
  • the 5 corresponding polypeptide may possess additional functional domains or lack domains that are present in the reference molecule.
  • Species variants are polynucleotide sequences that vary from one species to another. The resulting polypeptides generally will have significant amino acid identity relative to each other.
  • SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.
  • variants of the polynucleotides of the present invention may be generated through recombinant methods.
  • One possible method is a DNA shuffling technique such as 5 MOLECULARBREEDING (Maxygen Inc. , Santa Clara C A; described in U. S . Patent Number 5,837,458; Chang, C-C. et al. (1999) Nat. Biotechnol. 17:793-797; Christians, F.C et al. (1999) Nat. Biotechnol. 17:259-264; and Crameri, A. et al. (1996) Nat. Biotechnol.
  • 5 MOLECULARBREEDING Maxygen Inc. , Santa Clara C A; described in U. S . Patent Number 5,837,458; Chang, C-C. et al. (1999) Nat. Biotechnol. 17:793-797; Christians, F.C et al. (1999) Nat. Biotechnol. 17:259-264
  • sequences of the present invention are used to develop a transcript image for a particular cell or tissue.
  • Chain termination reaction products may be elecfrophoresed on urea-poly acrylamide gels and detected either by autoradiography (for radioisotope-labeled nucleotides) or by fluorescence (for fluorophore-labeled nucleotides).
  • Automated methods for mechanized reaction preparation, sequencing, and analysis using fluorescence detection methods have been developed.
  • Machines used to prepare cDNAs for sequencing can include the MICROLAB 2200 liquid transfer system (Hamilton Company (Hamilton), Reno NV), Peltier thermal cycler (PTC200; MJ Research, Inc.
  • Sequencing can be carried out using, for example, the ABI 373 or 377 (PE Biosystems) or MEGABACE 1000 (Molecular Dynamics, Inc. (Molecular Dynamics), Sunnyvale CA) DNA sequencing systems, or other automated and manual sequencing systems well known in the art.
  • cDNA sequences are used as "component" sequences that are assembled into “template” or “consensus” sequences as follows. Sequence chromatograms are processed, verified, and quatity scores are obtained using PHRED. Raw sequences are edited using an editing pathway known as Block 1 (See, e.g., the LIFESEQ Assembled User Guide, Incyte Genomics, Palo Alto, CA). A series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucleotide repeats, Alu repeats, etc.) are replaced by "n's", or masked, to prevent spurious matches. Mitochondrial and ribosomal RNA sequences are also removed.
  • Block 1 See, e.g., the LIFESEQ Assembled User Guide, Incyte Genomics, Palo Alto, CA).
  • a series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucleo
  • Template sequences may be extended to include additional contiguous sequences derived from the parent RNA transcript using a variety of methods known to those of skill in the art. Extension may thus be used to achieve the full length coding sequence of a gene.
  • the cDNA sequences are analyzed using a variety of programs and algorithms which are well known in the art. (See, e.g., Ausubel, 1997, supra. Chapter 7.7; Meyers, R.A. (Ed.) (1995) Molecular Biology and Biotechnology, Wiley VCH, New York NY, pp. 856-853; and Table 5.) These analyses comprise both reading frame determinations, e.g., based on triplet codon periodicity for particular organisms (Fickett, J.W. (1982) Nucleic Acids Res. 10:5303-5318); analyses of potential start and stop codons; and homology searches.
  • BLAST Basic Local Ahgnment Search Tool
  • BLAST is especially useful in determining exact matches and comparing two sequence fragments of arbitrary but equal lengths, whose alignment is locally maximal and for which the alignment score meets or exceeds a threshold or cutoff score set by the user (Karlin, S. et al. (1988) Proc. Nati. Acad. Sci. USA 85:841-845).
  • GenBank e.g., GenBank
  • SwissProt e.g., GenBank
  • BLOCKS e.g., GenBank
  • PFAM e.g., PFAM
  • other databases may be searched for sequences containing regions of homology to a query dithp or DITHP of the present invention.
  • search tool e.g., BLAST or HMM
  • GenBank e.g., GenBank
  • SwissProt e.g., BLOCKS
  • PFAM e.g., PFAM
  • Other approaches to the identification, assembly, storage, and display of nucleotide and polypeptide sequences are provided in "Relational Database for Storing Biomolecule Information," U.S.S.N. 08/947,845, filed October 9, 1997; "Project-Based Full-Length Biomolecular Sequence Database," U.S.S.N.
  • SEQ ID NO:30 and SEQ ID NO:31 encode, for example, ribosomal molecules.
  • SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, and SEQ ID NO:43 encode, for example, transcription factor molecules.
  • SEQ ID NO:44, SEQ ID NO:45, and SEQ ID NO:46 encode, for example, organelle associated molecules.
  • SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, and SEQ ID NO:50 encode, for example, biochemical pathway molecules.
  • SEQ ID NO:51 and SEQ ID NO:52 encode, for example, molecules associated with growth and development.
  • This type 5 of analysis is useful, for example, to assess the relative levels of dithp expression in fully or partially differentiated cells or tissues, to determine if changes in dithp expression levels are correlated with the development or progression of specific disease states, and to assess the response of a cell or tissue to a specific therapy, for example, in pharmacological or toxicological studies.
  • Methods for the analysis of dithp expression are based on hybridization and amplification technologies and include membrane- 0 based procedures such as northern blot analysis, high-throughput procedures that utilize, for example, microarrays, and PCR-based procedures.
  • the dithp, their fragments, or complementary sequences may be used to identify the presence 5 of and/or to determine the degree of similarity between two (or more) nucleic acid sequences.
  • the dithp may be hybridized to naturally occurring or recombinant nucleic acid sequences under appropriately selected temperatures and salt concenfrations. Hybridization with a probe based on the nucleic acid sequence of at least one of the dithp allows for the detection of nucleic acid sequences, including genomic sequences, which are identical or related to the dithp of the Sequence Listing. Probes may be o selected from non-conserved or unique regions of at least one of the polynucleotides of SEQ ID NO: 1 -
  • Polynucleotide sequences that are capable of hybridizing, in particular, to those shown in SEQ ID NOJ-52 and fragments thereof, can be identified using various conditions of stringency. (See, e.g., 5 Wahl, G.M. and S.L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A.R. (1987) Methods Enzymol. 152:507-511.) Hybridization conditions are discussed in "Definitions.”
  • a probe for use in Southern or northern hybridization may be derived from a fragment of a dithp sequence, or its complement, that is up to several hundred nucleotides in length and is either single-stranded or double-stranded. Such probes may be hybridized in solution to biological materials o such as plasmids, bacterial, yeast, or human artificial chromosomes, cleared or sectioned tissues, or to artificial substrates containing dithp. Microarrays are particularly suitable for identifying the presence of and detecting the level of expression for multiple genes of interest by examining gene expression correlated with, e.g., various stages of development, treatment with a drug or compound, or disease progression.
  • An array analogous to a dot or slot blot may be used to arrange and link polynucleotides 5 to the surface of a subsfrate using one or more of the following: mechanical (vacuum), chemical, thermal, or UV bonding procedures.
  • Such an array may contain any number of dithp and may be produced by hand or by using available devices, materials, and machines.
  • dithp may be cloned into commercially available vectors for the production of RNA probes.
  • Such probes may be transcribed in the presence of at least one labeled nucleotide (e.g., 32 P-ATP, Amersham Pharmacia Biotech).
  • Alzheimer's disease has been linked to a gene on chromosome 21 ; other studies predict a different gene and location. Mapping of disease genes is a complex and reiterative process and generally proceeds from genetic linkage analysis to physical mapping.
  • dithp sequences may be used to generate hybridization probes useful in chromosomal mapping of naturally occurring genomic sequences. Either coding or noncoding sequences of dithp may be used, and in some instances, noncoding sequences may be preferable over coding sequences. For example, conservation of a dithp coding sequence among members of a multi-gene family may potentially cause undesired cross hybridization during chromosomal mapping.
  • sequences may be mapped to a particular chromosome, to a specific region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial PI constructions, or single chromosome cDN A libraries.
  • HACs human artificial chromosomes
  • YACs yeast artificial chromosomes
  • BACs bacterial artificial chromosomes
  • PI constructions or single chromosome cDN A libraries.
  • Fluorescent in situ hybridization may be correlated with other physical chromosome mapping techniques and genetic map data. (See, e.g., Meyers, supra, pp. 965-968.) Correlation between the location of dithp on a physical chromosomal map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA associated with that disorder.
  • the dithp sequences may also be used to detect polymo ⁇ hisms that are genetically linked to the inheritance of a particular condition, disease, or disorder.
  • any sequences mapping to that area may represent associated or regulatory genes for further investigation.
  • the nucleotide sequences of the subject invention may also be used to detect differences in chromosomal architecture due to translocation, inversion, etc., among normal, carrier, or affected individuals.
  • a disease-associated gene is mapped to a chromosomal region, the gene must be cloned in order to identify mutations or other alterations (e.g., franslocations or inversions) that may be correlated with disease.
  • This process requires a physical map of the chromosomal region containing the disease- gene of interest along with associated markers.
  • a physical map is necessary for determining the nucleotide sequence of and order of marker genes on a particular chromosomal region. Physical mapping techniques are well known in the art and require the generation of overlapping sets of cloned DNA fragments from a particular organelle, chromosome, or genome. These clones are analyzed to reconstruct and catalog their order. Once the position of a marker is determined, the DNA from that region is obtained by consulting the catalog and selecting clones from that region. The gene of interest is located through positional cloning techniques using hybridization or similar methods.
  • the dithp of the present invention may be used to design probes useful in diagnostic assays. Such assays, well known to those skilled in the art, may be used to detect or confirm conditions, disorders, or diseases associated with abnormal levels of dithp expression. Labeled probes developed from dithp sequences are added to a sample under hybridizing conditions of desired stringency. In some instances, dithp, or fragments or oligonucleotides derived from dithp, may be used as primers in amplification steps prior to hybridization. The amount of hybridization complex formed is quantified and compared with standards for that cell or tissue. If dithp expression varies significantly from the standard, the assay indicates the presence of the condition, disorder, or disease.
  • Qualitative or quantitative diagnostic methods may include northern, dot blot, or other membrane or dip-stick based technologies or multiple-sample format technologies such as PCR, enzyme-linked immunosorbent assay (ELISA)-like, pin, or chip-based assays.
  • PCR enzyme-linked immunosorbent assay
  • the probes described above may also be used to monitor the progress of conditions, disorders, or diseases associated with abnormal levels of dithp expression, or to evaluate the efficacy of a particular therapeutic treatment.
  • the candidate probe may be identified from the dithp that are specific to a given human tissue and have not been observed in GenBank or other genome databases. Such a probe may be used in animal studies, preclinical tests, clinical trials, or in monitoring the treatment of an individual patient.
  • standard expression is established by methods well known in the art for use as a basis of comparison, samples from patients affected by the disorder or disease are combined with the probe to evaluate any deviation from the standard profile, and a therapeutic agent is administered and effects are monitored to generate a treatment profile. Efficacy is evaluated by determining whether the expression progresses toward or returns to the standard normal pattern. Treatment profiles may be generated over a period of several days or several months. Statistical methods well known to those skilled in the art may be use to determine the significance of such therapeutic agents.
  • oligonucleotide primers derived from the dithp of the invention may be used to detect single nucleotide polymo ⁇ hisms (SNPs).
  • SNPs are substitutions, insertions and deletions that are a frequent cause of inherited or acquired genetic disease in humans.
  • Methods of SNP detection include, but are not limited to, single-stranded conformation polymo ⁇ hism (SSCP) and fluorescent SSCP (fSSCP) methods.
  • SSCP single-stranded conformation polymo ⁇ hism
  • fSSCP fluorescent SSCP
  • oligonucleotide primers derived from the polynucleotide sequences encoding DITHP are used to amplify DNA using the polymerase chain reaction (PCR).
  • the DNA may be derived, for example, from diseased or normal tissue, biopsy samples, bodily fluids, and the like.
  • SNPs in the DNA cause differences in the secondary and tertiary structures of PCR products in single-stranded form, and these differences are detectable using gel elecfrophoresis in non-denaturing gels.
  • the oUgonucleotide primers are fluorescently labeled, which allows detection of the amplimers in high-throughput equipment such as DNA sequencing machines.
  • sequence database analysis methods termed in silico SNP (isSNP) are capable of identifying polymo ⁇ hisms by comparing the sequences of individual overlapping DNA fragments which assemble into a common consensus sequence.
  • SNPs may be detected and characterized by mass spectromefry using, for example, the high throughput MASSARRAY system (Sequenom, Inc., San Diego CA).
  • DNA-based identification techniques are critical in forensic technology. DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saliva, semen, etc., can be amplified using, e.g., PCR, to identify individuals. (See, e.g., Erlich, H. (1992) PCR Technology. Freeman and Co., New York, NY). Similarly, polynucleotides of the present invention can be used as polymo ⁇ hic markers.
  • reagents capable of identifying the source of a particular tissue.
  • Appropriate reagents can comprise, for example, DNA probes or primers prepared from the sequences of the present invention that are specific for particular tissues. Panels of such reagents can identify tissue by species and/or by organ type. In a similar fashion, these reagents can be used to screen tissue cultures for contamination.
  • polynucleotides of the present invention can also be used as molecular weight markers on nucleic acid gels or Southern blots, as diagnostic probes for the presence of a specific mRNA in a 5 particular cell type, in the creation of subfracted cDNA libraries which aid in the discovery of novel polynucleotides, in selection and synthesis of oligomers for attachment to an array or other support, and as an antigen to eUcit an immune response.
  • the dithp of the invention or their mammalian homologs may be "knocked out" in an animal model system using homologous recombination in embryonic stem (ES) cells.
  • ES embryonic stem
  • Such techniques are well known in the art and are useful for the generation of animal models of human disease. (See, e.g., U.S. Patent Number 5,175,383 and U.S. Patent Number 5,161,331.)
  • mouse ES cells such as the mouse 129/SvJ cell line, are derived from the early mouse embryo and grown in culture.
  • the ES 5 cells are fransformed with a vector containing the gene of interest disrupted by a marker gene, e.g., the neomycin phosphofransferase gene (neo; Capecchi, M.R. (1989) Science 244:1288-1292).
  • the vector integrates into the corresponding region of the host genome by homologous recombination.
  • homologous recombination takes place using the Cre-loxP system to knockout a gene of interest in a tissue- or developmental stage-specific manner (Marth, J.D. (1996) Clin. Invest. 97:1999- 0 2002; Wagner, K.U. et al. (1997) Nucleic Acids Res. 25:4323-4330).
  • the dithp of the invention can also be used to create "knockin" humanized animals (pigs) or transgenic animals (mice or rats) to model human disease.
  • pigs humanized animals
  • mice or rats transgenic animals
  • a region of dithp is injected into animal ES cells, and the injected sequence integrates into the animal cell genome.
  • Transformed cells are injected into blastulae, and the blastulae are implanted as described above.
  • Transgenic progeny or inbred lines are studied and treated with potential pharmaceutical agents to 5 obtain information on treatment of a human disease.
  • a mammal inbred to overexpress dithp may also serve as a convenient source of that protein (Janne, J. et al. (1998) Biotechnol. Annu. Rev. 4:55-74).
  • DITHP encoded by polynucleotides of the present invention may be used to screen for molecules that bind to or are bound by the encoded polypeptides.
  • the binding of the polypeptide and the molecule may activate (agonist), increase, inhibit (antagonist), or decrease activity of the polypeptide or the bound molecule.
  • Examples of such molecules include antibodies, oligonucleotides, proteins (e.g., receptors), or small molecules.
  • the molecule is closely related to the natural ligand of the polypeptide, e.g., a ligand or fragment thereof, a natural subsfrate, or a structural or functional mimetic.
  • the molecule can be closely related to the natural receptor to which the polypeptide binds, or to at least a fragment of the receptor, e.g., the active site. In either case, the molecule can be rationally designed using known techniques. 5
  • the screening for these molecules involves producing appropriate cells which express the polypeptide, either as a secreted protein or on the cell membrane. Preferred cells include cells from mammals, yeast, Drosophila, or E. coli.
  • the assay can be carried out using cell-free preparations, polypeptide/molecule affixed to a soUd support, chemical libraries, or natural product mixtures.
  • the assay may also simply 5 comprise the steps of mixing a candidate compound with a solution containing a polypeptide, measuring polypeptide/molecule activity or binding, and comparing the polypeptide/molecule activity or binding to a standard.
  • an ELISA assay using, e.g., a monoclonal or polyclonal antibody can measure polypeptide level in a sample.
  • the antibody can measure polypeptide level by either binding, directly or o indirectly, to the polypeptide or by competing with the polypeptide for a subsfrate.
  • Transcript images which profile dithp expression may be generated using transcripts isolated from tissues, cell lines, biopsies, or other biological samples.
  • the transcript image may thus reflect dithp expression in vivo, as in the case of a tissue or biopsy sample, or in vitro, as in the case of a cell line.
  • Transcript images may be used to profile dithp expression in distinct tissue types. This process can be used to determine the activity of human diagnostic and therapeutic molecules in a particular 5 tissue type relative to this activity in a different tissue type.
  • Transcript images may be used to generate a profile of dithp expression characteristic of diseased tissue.
  • Transcript images of tissues before and after treatment may be used for diagnostic pu ⁇ oses, to monitor the progression of disease, and to monitor the efficacy of drug treatments for diseases which affect the activity of human diagnostic and therapeutic molecules.
  • Transcript images which profile dithp expression may also be used in conjunction with in vitro model systems and preclinical evaluation of pharmaceuticals.
  • Transcript images of cell lines can be used to assess the activity of human diagnostic and therapeutic molecules and/or to identify cell lines that lack or misregulate this activity. Such cell lines may then be treated with pharmaceutical agents, and a transcript image following treatment may indicate the efficacy of these agents in restoring desired 5 levels of this activity.
  • a similar approach may be used to assess the toxicity of pharmaceutical agents as reflected by undesirable changes in the activity of human diagnostic and therapeutic molecules.
  • Candidate pharmaceutical agents may be evaluated by comparing their associated transcript images with those of pharmaceutical agents of known effectiveness.
  • the polynucleotides of the present invention are useful in antisense technology.
  • Antisense technology or therapy relies on the modulation of expression of a target protein through the specific binding of an antisense sequence to a target sequence encoding the target protein or directing its expression.
  • Agrawal, S., ed. 1996 Antisense Therapeutics, Humana Press Inc., Totawa NJ; Alama, A. et al. (1997) Pharmacol. Res. 36(3):171-178; Crooke, S.T. (1997) Adv. Pharmacol. 40:1-49; Sharma, H.W. and R. Narayanan (1995) Bioessays 17(12):1055-1063; and Lavrosky, Y.
  • An antisense sequence is a polynucleotide sequence capable of specifically hybridizing to at least a portion of the target sequence. Antisense sequences bind to cellular mRNA and/or genomic DNA, affecting translation and/or franscription. Antisense 5 sequences can be DNA, RNA, or nucleic acid mimics and analogs.
  • the polynucleotides of the present invention and fragments thereof can be used as antisense sequences to modify the expression of the polypeptide encoded by dithp.
  • the antisense sequences can be produced ex vivo, such as by using any of the ABI nucleic acid synthesizer series (PE Biosystems) or other automated systems known in the art. Antisense sequences can also be produced biologically,
  • Antisense sequences can be delivered infracellularly in the form of an expression plasmid which, upon franscription, produces a sequence complementary to at
  • Antisense sequences can also be introduced infracellularly through the use of viral vectors, such as refrovirus and adeno-associated virus vectors.
  • viral vectors such as refrovirus and adeno-associated virus vectors.
  • nucleotide sequences encoding DITHP or fragments thereof may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for ttanscriptional and franslational control of the inserted coding sequence in a suitable host.
  • an appropriate expression vector i.e., a vector which contains the necessary elements for ttanscriptional and franslational control of the inserted coding sequence in a suitable host.
  • 35 expression vectors containing sequences encoding DITHP and appropriate ttanscriptional and franslational control elements are 35 expression vectors containing sequences encoding DITHP and appropriate ttanscriptional and franslational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. (See, e.g., Sambrook, supra. Chapters 4, 8, 16, and 17; and Ausubel, supra. Chapters 9, 10, 13, and 16.)
  • a variety of expression vector/host systems may be utilized to contain and express sequences encoding DITHP. These include, but are not Umited to, microorganisms such as bacteria fransformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast fransformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems fransformed with viral expression vectors (e.g., cauUflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal (mammaUan) cell systems.
  • microorganisms such as bacteria fransformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast fransformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculo
  • Expression vectors derived from refroviruses, adenoviruses, or he ⁇ es or vaccinia viruses, or from various bacterial plasmids, may be used for delivery of nucleotide sequences to the targeted organ, tissue, or cell population.
  • DITHP in cell Unes is preferred.
  • sequences encoding DITHP can be transformed into cell Unes using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Any number of selection systems may be used to recover fransformed cell lines.
  • the dithp of the invention may be used for somatic or germhne gene therapy.
  • Gene therapy may be performed to (i) correct a genetic deficiency (e.g., in the cases of severe combined immunodeficiency (SCID)-Xl disease characterized by X-linked inheritance (Cavazzana-Calvo, M. et al. (2000) Science 288:669-672), severe combined immunodeficiency syndrome associated with an 5 inherited adenosine deaminase (ADA) deficiency (Blaese, R.M. et al. (1995) Science 270:475-480; Bordignon, C et al.
  • SCID severe combined immunodeficiency
  • ADA 5 inherited adenosine deaminase
  • diseases or disorders caused by deficiencies in dithp 0 are treated by constructing mammalian expression vectors comprising dithp and introducing these vectors by mechanical means into dithp-deficient cells.
  • Mechanical fransfer technologies for use with cells in vivo or ex vitro include (i) direct DNA microinjection into individual cells, (ii) ballistic gold particle delivery, (iii) liposome-mediated transfection, (iv) receptor-mediated gene fransfer, and (v) the use of DNA fransposons (Morgan, R.A. and Anderson, W.F. (1993) Annu. Rev. Biochem. 62:191-217; 5 Ivies, Z. (1997) Cell 91:501-510; Boulay, J-L. and Recipon, H. (1998) Curr. Opin. Biotechnol. 9:445- 450).
  • Expression vectors that may be effective for the expression of dithp include, but are not limited to, the PCDNA 3.1, EPITAG, PRCCMV2, PREP, PVAX vectors (Invitrogen, Carlsbad CA), PCMV-SCRIPT, PCMV-TAG, PEGSH/PERV (Stratagene, La Jolla CA), and PTET-OFF, o PTET-ON, PTRE2, PTRE2-LUC, PTK-HYG (Clontech, Palo Alto CA).
  • the dithp of the invention may be expressed using (i) a constitutively active promoter, (e.g., from cytomegalovirus (CMV), Rous sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or ⁇ -actin genes), (ii) an inducible promoter (e.g., the tetracycUne-regulated promoter (Gossen, M. and Bujard, H. (1992) Proc. Nati. Acad. Sci. U.S.A. 89:5547-5551 ; Gossen, M. et al., (1995) Science 268:1766-1769; Rossi, F.M.V. and Blau, 5 H.M.
  • a constitutively active promoter e.g., from cytomegalovirus (CMV), Rous sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or ⁇ -act
  • Sequences complementary to the dithp are used to detect, decrease, or inhibit expression of the naturally occurring nucleotide.
  • oUgonucleotides comprising from about 15 to 30 base pairs is typical in the art. However, smaller or larger sequence fragments can also be used.
  • Appropriate oligonucleotides are designed from the dithp using OLIGO 4.06 software (National Biosciences) or other appropriate programs and are synthesized using methods standard in the art or ordered from a commercial suppUer.
  • a complementary oligonucleotide is designed from the most unique 5 ' sequence and used to prevent franscription factor binding to the promoter sequence.
  • a complementary oligonucleotide is designed to prevent ribosomal binding and processing of the transcript.
  • DITHP is synthesized as a fusion protein with, e.g., glutathione S- fransferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crude cell lysates.
  • GST a 26-kilodalton enzyme from Schistosoma iaponicum, enables the purification of fusion proteins on immobilized glutathione under conditions that maintain protein activity and antigenicity (Amersham Pharmacia Biotech).
  • Oxidoreductase activity of DITHP is measured by the increase in extinction coefficient of NAD(P)H coenzyme at 340 nmfor the measurement of oxidation activity, or the decrease in extinction coefficient of NAD(P)H coenzyme at 340 nmfor the measurement of reduction activity (Dalziel, K. (1963) J. Biol. Chem. 238:2850-2858).
  • One of three substrates may be used: Asn- ⁇ Gal, biocytidine, or ubiquinone- 10.
  • the respective subunits of the enzyme reaction for example, cytochtome c_ -b oxidoreductase and cytochrome c, are reconstituted.
  • the reaction mixture contains a) 1-2 mg/ml DITHP; and b) 15 mM subsfrate, 2.4 mM NAD(P) + in 0.1 M phosphate buffer, pH 7.1 (oxidation reaction), or 2.0 mM NAD(P)H, in 0.1 M Na 2 HP0 4 buffer, pH 1.4 ( reduction reaction); in a total volume of 0.1 ml.
  • Changes in absorbance at 340 nm (A 340 ) are measured at 23.5 ° C using a recording specfrophotometer (Shimadzu Scientific Insfruments, Inc., Pleasanton CA).
  • Transferase activity of DITHP is measured through assays such as a methyl transferase assay in which the transfer of radiolabeled methyl groups between a donor substrate and an acceptor substrate is measured (Bokar, J.A. et al. (1994) J. Biol. Chem. 269: 17697-17704).
  • Reaction mixtures (50 ⁇ l final volume) contain 15 mM HEPES, pH 7.9, 1.5 mM MgCl 2 , 10 mM dithiothreitol, 3% polyvinylalcohol, 1.5 ⁇ Ci [met ⁇ y/- 3 H]AdoMet (0.375 ⁇ M AdoMet) (DuPont-NEN), 0.6 ⁇ g DITHP, and acceptor substrate (0.4 ⁇ g [ 35 S]RNA or 6-mercaptopurine (6-MP) to 1 mM final concentration). Reaction mixtures are incubated at 30°C for 30 minutes, then 65 °C for 5 minutes. The products are separated by chromatography or elecfrophoresis and the level of methyl fransferase activity is determined by quantification of methyl- 3 recovery.
  • Growth factor activity of DITHP is measured by the stimulation of DNA synthesis in Swiss mouse 3T3 cells (McKay, I. and I. Leigh, eds. (1993) Growth Factors: A Practical Approach, Oxford 5 University Press, New York NY). Initiation of DNA synthesis indicates the cells' entry into the mitotic cycle and their commitment to undergo later division. 3T3 cells are competent to respond to most growth factors, not only those that are mitogenic, but also those that are involved in embryonic induction. This competence is possible because the in vivo specificity demonstrated by some growth factors is not necessarily inherent but is determined by the responding tissue.
  • An alternative assay for DITHP cytokine activity utilizes a Boyden micro chamber o (Neuroprobe, Cabin John MD) to measure leukocyte chemotaxis (Vicari, supra). In this assay, about
  • DITHP activity by immunoblotting Cells are denatured in SDS in the presence of ⁇ -mercaptoethanol, nucleic acids removed by ethanol precipitation, and proteins purified by acetone precipitation. Pellets are resuspended in 20 mM tris buffer at pH 7.5 and incubated with Protein G-Sepharose pre-coated with an antibody specific for DITHP. After washing, the Sepharose beads are boiled in elecfrophoresis i o sample buffer, and the eluted proteins subjected to SDS-PAGE.
  • DITHP kinase activity is measured by phosphorylation of a protein subsfrate using ⁇ -labeled
  • DITHP activity is measured by the increase in cell proliferation resulting from transformation of a mammalian cell line such as COS7, HeLa or CHO with an eukaryotic expression vector encoding DITHP.
  • Eukaryotic expression vectors are commercially available, and the techniques to introduce them into cells are well known to those skilled in the art.
  • the cells are 5 incubated for 48-72 hours after transformation under conditions appropriate for the cell line to allow expression of DITHP. Phase microscopy is then used to compare the mitotic index of transformed versus control cells. An increase in the mitotic index indicates DITHP activity.
  • an assay for DITHP signaling activity is based upon the ability of GPCR family proteins to modulate G protein-activated second messenger signal transduction 0 pathways (e.g., cAMP; Gaudin, P. et al. (1998) J. Biol. Chem. 273:4990-4996).
  • a plasmid encoding full length DITHP is fransfected into a mammalian cell line (e.g., Chinese hamster ovary (CHO) or human embryonic kidney (HEK-293) cell lines) using methods well-known in the art. Transfected cells are grown in 12-well trays in culture medium for 48 hours, then the culture medium is discarded, and the attached cells are gently washed with PBS.
  • a mammalian cell line e.g., Chinese hamster ovary (CHO) or human embryonic kidney (HEK-293) cell lines

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Enzymes And Modification Thereof (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The present invention provides purified human polynucleotides for diagnostics and therapeutics (dithp). Also encompassed are the polypeptides (DITHP) encoded by dithp. The invention also provides for the use of dithp, or complements, oligonucleotides, or fragments thereof in diagnostic assays. The invention further provides for vectors and host cells containing dithp for the expression of DITHP. The invention additionally provides for the use of isolated and purified DITHP to induce antibodies and to screen libraries of compounds and the use of anti-DITHP antibodies in diagnostic assays. Also provided are microarrays containing dithp and methods of use.

Description

MOLECULES FOR DIAGNOSTICS AND THERAPEUTICS
TECHNICAL HELD
The present invention relates to human molecules for diagnostics and therapeutics and to the 5 use of these sequences in the diagnosis, study, prevention, and treatment of diseases associated with human molecules.
BACKGROUND OF THE INVENTION
The human genome is comprised of thousands of genes, many encoding gene products that o function in the maintenance and growth of the various cells and tissues in the body. Aberrant expression or mutations in these genes and their products is the cause of, or is associated with, a variety of human diseases such as cancer and other cell prohferative disorders, autoimmune/inflammatory disorders, infections, developmental disorders, endocrine disorders, metabolic disorders, neurological disorders, gastrointestinal disorders, transport disorders, and connective tissue disorders. The 5 identification of these genes and their products is the basis of an ever-expanding effort to find markers for early detection of diseases, and targets for their prevention and treatment. Therefore, these genes and their products are useful as diagnostics and therapeutics. These genes may encode, for example, enzyme molecules, molecules associated with growth and development, biochemical pathway molecules, extracellular information transmission molecules, receptor molecules, intracellular signaling molecules, o membrane transport molecules, protein modification and maintenance molecules, nucleic acid synthesis and modification molecules, adhesion molecules, antigen recognition molecules, secreted and extracellular matrix molecules, cytoskeletal molecules, ribosomal molecules, electron transfer associated molecules, transcription factor molecules, chromatin molecules, cell membrane molecules, and organelle associated molecules. 5 For example, cancer represents a type of cell proliferative disorder that affects nearly every tissue in the body. A wide variety of molecules, either aberrantly expressed or mutated, can be the cause of, or involved with, various cancers because tissue growth involves complex and ordered patterns of cell proliferation, cell differentiation, and apoptosis. Cell proliferation must be regulated to maintain both the number of cells and their spatial organization. This regulation depends upon the o appropriate expression of proteins which control cell cycle progression in response to extracellular signals such as growth factors and other mitogens, and intracellular cues such as DNA damage or nutrient starvation. Molecules which directly or indirectly modulate cell cycle progression fall into several categories, including growth factors and their receptors, second messenger and signal transduction proteins, oncogene products, tumor-suppressor proteins, and mitosis-promoting factors. 5 Aberrant expression or mutations in any of these gene products can result in cell proliferative disorders such as cancer. Oncogenes are genes generally derived from normal genes that, through abnormal expression or mutation, can effect the transformation of a normal cell to a malignant one (oncogenesis). Oncoproteins, encoded by oncogenes, can affect cell proliferation in a variety of ways and include growth factors, growth factor receptors, intracellular signal transducers, nuclear transcription factors, 5 and cell-cycle control proteins. In contrast, tumor-suppressor genes are involved in inhibiting cell proliferation. Mutations which cause reduced function or loss of function in tumor-suppressor genes result in aberrant cell proliferation and cancer. Although many different genes and their products have been found to be associated with cell proliferative disorders such as cancer, many more may exist that are yet to be discovered. o DNA-based arrays can provide a simple way to explore the expression of a single polymorphic gene or a large number of genes. When the expression of a single gene is explored, DNA-based arrays are employed to detect the expression of specific gene variants. For example, a p53 tumor suppressor gene array is used to determine whether individuals are carrying mutations that predispose them to cancer. A cytochrome p450 gene array is useful to determine whether individuals have one of a number 5 of specific mutations that could result in increased drug metaboUsm, drug resistance or drug toxicity. DNA-based array technology is especially relevant for the rapid screening of expression of a large number of genes. There is a growing awareness that gene expression is affected in a global fashion. A genetic predisposition, disease or therapeutic treatment may affect, directly or indirectly, the expression of a large number of genes. In some cases the interactions may be expected, such as when 0 the genes are part of the same signaling pathway. In other cases, such as when the genes participate in separate signaUng pathways, the interactions may be totally unexpected. Therefore, DNA-based arrays can be used to investigate how genetic predisposition, disease, or therapeutic treatment affects the expression of a large number of genes.
5 Enzyme Molecules
SEQ ID NO:l, SEQ ID NO:2, SEQ ID NOJ, SEQ ID NO:4, and SEQ ID NO:5 encode, for example, human enzyme molecules.
The cellular processes of biogenesis and biodegradation involve a number of key enzyme classes including oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases. These o enzyme classes are each comprised of numerous substrate-specific enzymes having precise and well regulated functions. These enzymes function by facilitating metabolic processes such as glycolysis, the tricarboxylic cycle, and fatty acid metabolism; synthesis or degradation of amino acids, steroids, phospholipids, alcohols, etc.; regulation of cell signalling, proliferation, inflamation, apoptosis, etc., and through catalyzing critical steps in DNA replication and repair, and the process of translation. 5 Oxidoreductases Many pathways of biogenesis and biodegradation require oxidoreductase (dehydrogenase or reductase) activity, coupled to the reduction or oxidation of a donor or acceptor cofactor. Potential cofactors include cytochromes, oxygen, disulfide, iron-sulfur proteins, flavin adenine dinucleotide (FAD), and the nicotinamide adenine dinucleotides NAD and NADP (Newsholme, E.A. and A.R. 5 Leech (1983) Biochemistry for the Medical Sciences, John Wiley and Sons, Chichester, U.K., pp. 779-793). Reductase activity catalyzes the transfer of electrons between substrate(s) and cofactor(s) with concurrent oxidation of the cofactor. The reverse dehydrogenase reaction catalyzes the reduction of a cofactor and consequent oxidation of the substrate. Oxidoreductase enzymes are a broad superfamily of proteins that catalyze numerous reactions in all cells of organisms ranging from l o bacteria to plants to humans. These reactions include metabolism of sugar, certain detoxification reactions in the liver, and the synthesis or degradation of fatty acids, amino acids, glucocorticoids, estrogens, androgens, and prostaglandins. Different family members are named according to the direction in which their reactions are typically catalyzed; thus they may be referred to as oxidoreductases, oxidases, reductases, or dehydrogenases. In addition, family members often have
15 distinct cellular localizations, including the cytosol, the plasma membrane, mitochondrial inner or outer membrane, and peroxisomes.
Short-chain alcohol dehydrogenases (SCADs) are a family of dehydrogenases that only share 15% to 30% sequence identity, with similarity predominantly in the coenzyme binding domain and the substrate binding domain. In addition to the well-known role in detoxification of ethanol, SCADs
20 are also involved in synthesis and degradation of fatty acids, steroids, and some prostaglandins, and are therefore implicated in a variety of disorders such as lipid storage disease, myopathy, SCAD deficiency, and certain genetic disorders. For example, retinol dehydrogenase is a SCAD-family member (Simon, A. et al. (1995) J. Biol. Chem. 270:1107-1112) that converts retinol to retinal, the precursor of retinoic acid. Retinoic acid, a regulator of differentiation and apoptosis, has been shown 5 to down-regulate genes involved in cell proliferation and inflammation (Chai, X. et al. (1995) J. Biol. Chem. 270:3900-3904). In addition, retinol dehydrogenase has been linked to hereditary eye diseases such as autosomal recessive childhood-onset severe retinal dystrophy (Simon, A. et al. (1996) Genomics 36:424-430).
Propagation of nerve impulses, modulation of cell proliferation and differentiation, induction 0 of the immune response, and tissue homeostasis involve neurotransmitter metabolism (Weiss, B . (1991) Neurotoxicology 12:379-386; Collins, S.M. et al. (1992) Ann. N.Y. Acad. Sci. 664:415-424; Brown, J.K. and H. Imam (1991) J. Inherit. Metab. Dis. 14:436-458). Many pathways of neurotransmitter metabolism require oxidoreductase activity, coupled to reduction or oxidation of a cofactor, such as NAD7NADH (Newsholme, E.A. and A.R. Leech (1983) Biochemistry for the 5 Medical Sciences. John Wiley and Sons, Chichester, U.K. pp. 779-793). Degradation of catecholamines (epinephrine or norepinephrine) requires alcohol dehydrogenase (in the brain) or aldehyde dehydrogenase (in peripheral tissue). NAD+ -dependent aldehyde dehydrogenase oxidizes 5- hydroxyindole-3-acetate (the product of 5-hydroxytryptamine (serotonin) metabolism) in the brain, blood platelets, liver and pulmonary endothehum (Newsholme, supra, p. 786). Other 5 neurotransmitter degradation pathways that utilize NADJNADH-dependent oxidoreductase activity include those of L-DOPA (precursor of dopamine, a neuronal excitatory compound), glycine (an inhibitory neurotransmitter in the brain and spinal cord), histamine (liberated from mast cells during the inflammatory response), and taurine (an inhibitory neurotransmitter of the brain stem, spinal cord and retina) (Newsholme, supra, pp. 790, 792). Epigenetic or genetic defects in neurotransmitter o metabolic pathways can result in a spectrum of disease states in different tissues including Parkinson disease and inherited myoclonus (McCance, K.L. and S.E. Huether (1994) Pathophvsiology. Mosby- Year Book, Inc., St. Louis MO, pp. 402-404; Gundlach, A.L. (1990) FASEB J. 4:2761-2766).
Tetrahydrofolate is a derivatized glutamate molecule that acts as a carrier, providing activated one-carbon units to a wide variety of biosynthetic reactions, including synthesis of purines, 5 pyrimidines, and the amino acid methionine. Tetrahydrofolate is generated by the activity of a holoenzyme complex called tetrahydrofolate synthase, which includes three enzyme activities: tetrahydrofolate dehydrogenase, tetrahydrofolate cyclohydrolase, and tetrahydrofolate synthetase. Thus, tetrahydrofolate dehydrogenase plays an important role in generating building blocks for nucleic and amino acids, crucial to proliferating cells. o 3-Hydroxyacyl-CoA dehydrogenase (3HACD) is involved in fatty acid metabolism. It catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA, with concomitant oxidation of NAD to NADH, in the mitochondria and peroxisomes of eukaryotic cells. In peroxisomes, 3HACD and enoyl-CoA hydratase form an enzyme complex called bifunctional enzyme, defects in which are associated with peroxisomal bifunctional enzyme deficiency. This interruption in fatty acid 5 metabolism produces accumulation of very-long chain fatty acids, disrupting development of the brain, bone, and adrenal glands. Infants born with this deficiency typically die within 6 months (Watkins, P. et al. (1989) J. Clin. Invest. 83:771-777; Online Mendelian Inheritance in Man (OMIM), #261515). The neurodegeneration that is characteristic of Alzheimer's disease involves development of extracellular plaques in certain brain regions. A major protein component of these plaques is the o peptide amyloid- β (Aβ), which is one of several cleavage products of amyloid precursor protein
(APP). 3HACD has been shown to bind the Aβ peptide, and is overexpressed in neurons affected in / zheimer's disease. In addition, an antibody against 3HACD can block the toxic effects of Aβ in a cell culture model of Alzheimer's disease (Yan, S. et al. (1997) Nature 389:689-695; OMIM, #602057). 5 Steroids, such as estrogen, testosterone, corticosterone, and others, are generated from a common precursor, cholesterol, and are interconverted into one another. A wide variety of enzymes act upon cholesterol, including a number of dehydrogenases. Steroid dehydrogenases, such as the hydroxysteroid dehydrogenases, are involved in hypertension, fertility, and cancer (Duax, W.L. and D. Ghosh (1997) Steroids 62:95-100). One such dehydrogenase is 3-oxo-5-oc-steroid dehydrogenase 5 (OASD), a microsomal membrane protein highly expressed in prostate and other androgen-responsive tissues. OASD catalyzes the conversion of testosterone into dihydrotestosterone, which is the most potent androgen. Dihydrotestosterone is essential for the formation of the male phenotype during embryogenesis, as well as for proper androgen-mediated growth of tissues such as the prostate and male genitalia. A defect in OASD that prevents the conversion of testosterone into o dihydrotestosterone leads to a rare form of male pseudohermaphroditis, characterized by defective formation of the external genitalia (Andersson, S. et al. (1991) Nature 354:159-161; Labrie, F. et al. (1992) Endocrinology 131:1571-1573; OMIM #264600). Thus, OASD plays a central role in sexual differentiation and androgen physiology.
17β-hydroxysteroid dehydrogenase (17βHSD6) plays an important role in the regulation of s the male reproductive hormone, dihydrotestosterone (DHTT). 17βHSD6 acts to reduce levels of DHTT by oxidizing a precursor of DHTT, 3α-diol, to androsterone which is readily glucuronidated and removed from tissues. 17βHSD6 is active with both androgen and estrogen substrates when expressed in embryonic kidney 293 cells. At least five other isozymes of 17βHSD have been identified that catalyze oxidation and/or reduction reactions in various tissues with preferences for 0 different steroid substrates (Biswas, M.G. and D.W. Russell (1997) J. Biol. Chem. 272:15959- 15966). For example, 17βHSDl preferentially reduces estradiol and is abundant in the ovary and placenta. 17βHSD2 catalyzes oxidation of androgens and is present in the endometrium and placenta. 17βHSD3 is exclusively a reductive enzyme in the testis (Geissler, W.M. et al. (1994) Nat. Genet. 7:34-39). An excess of androgens such as DHTT can contribute to certain disease states such as 5 benign prostatic hyperplasia and prostate cancer.
Oxidoreductases are components of the fatty acid metabolism pathways in mitochondria and peroxisomes. The main beta-oxidation pathway degrades both saturated and unsaturated fatty acids, while the auxiliary pathway performs additional steps required for the degradation of unsaturated fatty acids. The auxiliary beta-oxidation enzyme 2,4-dienoyl-CoA reductase catalyzes the removal of o even-numbered double bonds from unsaturated fatty acids prior to their entry into the main beta- oxidation pathway. The enzyme may also remove odd-numbered double bonds from unsaturated fatty acids (Koivuranta, K.T. et al. (1994) Biochem. J. 304:787-792; Smeland, T.E. et al. (1992) Proc. Nati. Acad. Sci. USA 89:6673-6677). 2,4-dienoyl-CoA reductase is located in both mitochondria and peroxisomes. Inherited deficiencies in mitochondrial and peroxisomal beta-oxidation enzymes are 5 associated with severe diseases, some of which manifest themselves soon after birth and lead to death within a few years. Defects in beta-oxidation are associated with Reye's syndrome, Zellweger syndrome, neonatal adrenoleukodystrophy, infantile Refsum's disease, acyl-CoA oxidase deficiency, and bifunctional protein deficiency (Suzuki, Y. et al. (1994) Am. J. Hum. Genet. 54:36-43; Hoefler, supra; Cotran, R.S. et al. (1994) Robbins Pathologic Basis of Disease. W.B. Saunders Co., 5 Philadelphia PA, p.866). Peroxisomal beta-oxidation is impaired in cancerous tissue. Although neoplastic human breast epithelial cells have the same number of peroxisomes as do normal cells, fatty acyl-CoA oxidase activity is lower than in control tissue (el Bouhtoury, F. et al. (1992) J. Pathol. 166:27-35). Human colon carcinomas have fewer peroxisomes than normal colon tissue and have lower fatty-acyl-CoA oxidase and bifunctional enzyme (including enoyl-CoA hydratase) activities 0 than normal tissue (Cable, S. et al. (1992) Virchows Arch. B Cell Pathol. Incl. Mol. Pathol. 62:221- 226). Another important oxidoreductase is isocitrate dehydrogenase, which catalyzes the conversion of isocitrate to a-ketoglutarate, a substrate of the citric acid cycle. Isocitrate dehydrogenase can be either NAD or NADP dependent, and is found in the cytosol, mitochondria, and peroxisomes. Activity of isocitrate dehydrogenase is regulated developmentally, and by hormones, 5 neurotransmitters, and growth factors.
Hydroxypyruvate reductase (HPR), a peroxisomal 2-hydroxyacid dehydrogenase in the glycolate pathway, catalyzes the conversion of hydroxypyruvate to glycerate with the oxidation of both NADH and NADPH. The reverse dehydrogenase reaction reduces NAD+ and NADP+. HPR recycles nucleotides and bases back into pathways leading to the synthesis of ATP and GTP. ATP o and GTP are used to produce DNA and RNA and to control various aspects of signal transduction and energy metabolism. Inhibitors of purine nucleotide biosynthesis have long been employed as antiproliferative agents to treat cancer and viral diseases. HPR also regulates biochemical synthesis of serine and cellular serine levels available for protein synthesis.
The mitochondrial electron transport (or respiratory) chain is a series of oxidoreductase-type 5 enzyme complexes in the mitochondrial membrane that is responsible for the transport of electrons from NADH through a series of redox centers within these complexes to oxygen, and the coupling of this oxidation to the synthesis of ATP (oxidative phosphorylation). ATP then provides the primary source of energy for driving a cell's many energy-requiring reactions. The key complexes in the respiratory chain are NADH:ubiquinone oxidoreductase (complex I), succinate:ubiquinone 0 oxidoreductase (complex II), cytochrome c,-b oxidoreductase (complex III), cytochrome c oxidase (complex IV), and ATP synthase (complex V) (Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing, Inc., New York NY, pp. 677-678). All of these complexes are located on the inner matrix side of the mitochondrial membrane except complex II, which is on the cytosolic side. Complex II transports electrons generated in the citric acid cycle to the respiratory chain. The electrons generated by oxidation of succinate to fumarate in the citric acid cycle are transferred through electron carriers in complex II to membrane bound ubiquinone (Q). Transcriptional regulation of these nuclear-encoded genes appears to be the predominant means for controlling the biogenesis of respiratory enzymes. Defects and altered expression of enzymes in the respiratory chain are associated with a variety of disease conditions. 5 Other dehydrogenase activities using NAD as a cofactor are also important in mitochondrial function. 3-hydroxyisobutyrate dehydrogenase (3HBD), important in vatine catabolism, catalyzes the NAD-dependent oxidation of 3-hydroxyisobutyrate to methylmalonate semialdehyde within mitochondria. Elevated levels of 3-hydroxyisobutyrate have been reported in a number of disease states, including ketoacidosis, methylmalonic acidemia, and other disorders associated with 0 deficiencies in methylmalonate semialdehyde dehydrogenase (Rougraff, P.M. et al. (1989) J. Biol. Chem. 264:5899-5903).
Another mitochondrial dehydrogenase important in amino acid metabolism is the enzyme isovaleryl-CoA-dehydrogenase (IVD). IVD is involved in leucine metabolism and catalyzes the oxidation of isovaleryl-CoA to 3-methylcrotonyl-CoA. Human IVD is a tetrameric flavoprotein that 5 is encoded in the nucleus and synthesized in the cytosol as a 45 kDa precursor with a mitochondrial import signal sequence. A genetic deficiency, caused by a mutation in the gene encoding IVD, results in the condition known as isovaleric acidemia. This mutation results in inefficient mitochondrial import and processing of the IVD precursor (Vockley, J. et al. (1992) J. Biol. Chem. 267:2494-2501). Transferases o Transferases are enzymes that catalyze the transfer of molecular groups. The reaction may involve an oxidation, reduction, or cleavage of covalent bonds, and is often specific to a substrate or to particular sites on a type of substrate. Transferases participate in reactions essential to such functions as synthesis and degradation of cell components, regulation of cell functions including cell signaling, cell proliferation, inflamation, apoptosis, secretion and excretion. Transferases are 5 involved in key steps in disease processes involving these functions. Transferases are frequently classified according to the type of group transferred. For example, methyl transferases transfer one- carbon methyl groups, amino transferases transfer nitrogenous amino groups, and similarly denominated enzymes transfer aldehyde or ketone, acyl, glycosyl, alkyl or aryl, isoprenyl, saccharyl, phosphorous-containing, sulfur-containing, or selenium-containing groups, as well as small o enzymatic groups such as Coenzyme A.
Acyl transferases include peroxisomal carnitine octanoyl transferase, which is involved in the fatty acid beta-oxidation pathway, and mitochondrial carnitine palmitoyl transferases, involved in fatty acid metabolism and transport. Choline O-acetyl transferase catalyzes the biosynthesis of the neurotransmitter acetylchoUne. 5 Amino transferases play key roles in protein synthesis and degradation, and they contribute to other processes as well. For example, the amino transferase 5-aminolevulinic acid synthase catalyzes the addition of succinyl-CoA to glycine, the first step in heme biosynthesis. Other amino transferases participate in pathways important for neurological function and metabolism. For example, glutamine- phenylpyruvate amino transferase, also known as glutamine transaminase K (GTK), catalyzes several reactions with a pyridoxal phosphate cofactor. GTK catalyzes the reversible conversion of L- glutamine and phenylpyruvate to 2-oxoglutaramate and L-phenylalanine. Other amino acid substrates for GTK include L-methionine, L-histidine, and L-tyrosine. GTK also catalyzes the conversion of kynurenine to kynurenic acid, a tryptophan metabolite that is an antagonist of the N-methyl-D- aspartate (NMD A) receptor in the brain and may exert a neuromodulatory function. Alteration of the kynurenine metabolic pathway may be associated with several neurological disorders. GTK also plays a role in the metabolism of halogenated xenobiotics conjugated to glutathione, leading to nephrotoxicity in rats and neurotoxicity in humans. GTK is expressed in kidney, liver, and brain. Both human and rat GTKs contain a putative pyridoxal phosphate binding site (ExPASy ENZYME: EC 2.6.1.64; Perry, S.J. et al. (1993) Mol. Pharmacol. 43:660-665; Perry, S. et al. (1995) FEBS Lett. 360:277-280; and Alberati-Giani, D. et al. (1995) J. Neurochem. 64: 1448-1455). A second amino transferase associated with this pathway is kynurenine/α-aminoadipate amino transferase (AadAT). AadAT catalyzes the reversible conversion of α-aminoadipate and -ketoglutarate to α-ketoadipate and L-glutamate during lysine metabolism. AadAT also catalyzes the transamination of kynurenine to kynurenic acid. A cytosolic AadAT is expressed in rat kidney, liver, and brain (Nakatani, Y. et al. (1970) Biochim. Biophys. Acta 198:219-228; Buchli, R. et al. (1995) J. Biol. Chem. 270:29330- 29335).
Glycosyl transferases include the mammalian UDP-glucouronosyl transferases, a family of membrane-bound microsomal enzymes catalyzing the transfer of glucouronic acid to lipophilic substrates in reactions that play important roles in detoxification and excretion of drugs, carcinogens, and other foreign substances. Another mammalian glycosyl transferase, mammalian UDP-galactose- ceramide galactosyl transferase, catalyzes the transfer of galactose to ceramide in the synthesis of galactocerebrosides in myelin membranes of the nervous system. The UDP-glycosyl transferases share a conserved signature domain of about 50 amino acid residues (PROSITE: PDOC00359, http://expasy.hcuge.ch/sprot/prosite.html). Methyl transferases are involved in a variety of pharmacologically important processes.
Nicotinamide N-methyl transferase catalyzes the N-methylation of nicotinamides and other pyridines, an important step in the cellular handling of drugs and other foreign compounds. Phenylethanolamine N-methyl transferase catalyzes the conversion of noradrenalin to adrenalin. 6-0- methylguanine-DNA methyl transferase reverses DNA methylation, an important step in carcinogenesis. Uroporphyrin-III C-methyl transferase, which catalyzes the transfer of two methyl groups from S-adenosyl-L-methionine to uroporphyrinogen III, is the first specific enzyme in the biosynthesis of cobalamin, a dietary enzyme whose uptake is deficient in pernicious anemia. Protein- arginine methyl transferases catalyze the posttranslational methylation of arginine residues in proteins, resulting in the mono- and dimethylation of arginine on the guanidino group. Substrates include histones, myelin basic protein, and heterogeneous nuclear ribonucleoproteins involved in mRNA processing, splicing, and transport. Protein-arginine methyl transferase interacts with proteins upregulated by mitogens, with proteins involved in chronic lymphocytic leukemia, and with interferon, suggesting an important role for methylation in cytokine receptor signaling (Lin, W.-J. et al. (1996) J. Biol. Chem. 271 :15034-15044; Abramovich, C. et al. (1997) EMBO J. 16:260-266; and Scott, H.S. et al. (1998) Genomics 48:330-340).
Phosphotransferases catalyze the transfer of high-energy phosphate groups and are important in energy-requiring and -releasing reactions. The metabolic enzyme creatine kinase catalyzes the reversible phosphate transfer between creatine/creatine phosphate and ATP/ADP. Glycocyamine kinase catalyzes phosphate transfer from ATP to guanidoacetate, and arginine kinase catalyzes phosphate transfer from ATP to argenine. A cysteine-containing active site is conserved in this family (PROSITE: PDOC00103).
Prenyl transferases are heterodimers, consisting of an alpha and a beta subunit, that catalyze the transfer of an isoprenyl group. An example of a prenyl transferase is the mammalian protein farnesyl transferase. The alpha subunit of farnesyl transferase consists of 5 repeats of 34 amino acids each, with each repeat containing an invariant tryptophan (PROSITE: PDOC00703).
Saccharyl transferases are glycating enzymes involved in a variety of metabolic processes. Oligosacchryl transferase-48, for example, is a receptor for advanced glycation endproducts. Accumulation of these endproducts is observed in vascular complications of diabetes, macrovascular disease, renal insufficiency, and Alzheimer's disease (Thornalley, P.J. (1998) Cell Mol. Biol. (Noisy- Le-Grand) 44:1013-1023).
Coenzyme A (CoA) transferase catalyzes the transfer of CoA between two carboxylic acids. Succinyl CoA:3-oxoacid CoA transferase, for example, transfers CoA from succinyl-CoA to a recipient such as acetoacetate. Acetoacetate is essential to the metabolism of ketone bodies, which accumulate in tissues affected by metabolic disorders such as diabetes (PROSITE: PDOC00980). Hydrolases
Hydrolysis is the breaking of a covalent bond in a substrate by introduction of a molecule of water. The reaction involves a nucleophilic attack by the water molecule's oxygen atom on a target bond in the substrate. The water molecule is split across the target bond, breaking the bond and generating two product molecules. Hydrolases participate in reactions essential to such functions as synthesis and degradation of cell components, and for regulation of cell functions including cell signaling, cell proliferation, inflamation, apoptosis, secretion and excretion. Hydrolases are involved in key steps in disease processes involving these functions. Hydrolytic enzymes, or hydrolases, may be grouped by substrate specificity into classes including phosphatases, peptidases, lysophospholipases, phosphodiesterases, glycosidases, and glyoxalases. Phosphatases hydrolytically remove phosphate groups from proteins, an energy-providing step that regulates many cellular processes, including intracellular signaling pathways that in turn control cell growth and differentiation, cell -cell contact, the cell cycle, and oncogenesis.
LysophosphoUpases (LPLs) regulate intracellular lipids by catalyzing the hydrolysis of ester bonds to remove an acyl group, a key step in lipid degradation. Small LPL isoforms, approximately 15-30 kD, function as hydrolases; larger isoforms function both as hydrolases and transacylases. A particular substrate for LPLs, lysophosphatidylcholine, causes lysis of cell membranes. LPL activity is regulated by signaling molecules important in numerous pathways, including the inflammatory response.
Peptidases, also called proteases, cleave peptide bonds that form the backbone of peptide or protein chains. Proteolytic processing is essential to cell growth, differentiation, remodeling, and homeostasis as well as inflammation and immune response. Since typical protein half-lives range from hours to a few days, peptidases are continually cleaving precursor proteins to their active form, removing signal sequences from targeted proteins, and degrading aged or defective proteins. Peptidases function in bacterial, parasitic, and viral invasion and replication within a host. Examples of peptidases include trypsin and chymotrypsin (components of the complement cascade and the blood-clotting cascade) lysosomal cathepsins, calpains, pepsin, renin, and chymosin (Beynon, R.J. and J.S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University Press, New York NY, pp. 1-5).
The phosphodiesterases catalyze the hydrolysis of one of the two ester bonds in a phosphodiester compound. Phosphodiesterases are therefore crucial to a variety of cellular processes.
Phosphodiesterases include DNA and RNA endo- and exo-nucleases, which are essential to cell growth and replication as well as protein synthesis. Another phosphodiesterase is acid sphingomyelinase, which hydrolyzes the membrane phospholipid sphingomyelin to ceramide and phosphorylcholine. Phosphorylcholine is used in the synthesis of phosphatidylcholine, which is involved in numerous intracellular signaling pathways. Ceramide is an essential precursor for the generation of gangliosides, membrane lipids found in high concentration in neural tissue. Defective acid sphingomyelinase phosphodiesterase leads to a build-up of sphingomyelin molecules in lysosomes, resulting in Niemann-Pick disease.
Glycosidases catalyze the cleavage of hemiacetyl bonds of glycosides, which are compounds that contain one or more sugar. Mammalian lactase-phlorizin hydrolase, for example, is an intestinal enzyme that splits lactose. Mammalian beta-galactosidase removes the terminal galactose from gangliosides, glycoproteins, and glycosaminoglycans, and deficiency of this enzyme is associated with a gangliosidosis known as Morquio disease type B. Vertebrate lysosomal alpha-glucosidase, which hydrolyzes glycogen, maltose, and isomaltose, and vertebrate intestinal sucrase-isomaltase, 5 which hydrolyzes sucrose, maltose, and isomaltose, are widely distributed members of this family with highly conserved sequences at their active sites.
The glyoxylase system is involved in gluconeogenesis, the production of glucose from storage compounds in the body. It consists of glyoxylase I, which catalyzes the formation of S-D- lactoylglutathione from methyglyoxal, a side product of triose-phosphate energy metaboUsm, and o glyoxylase II, which hydrolyzes S-D-lactoylglutathione to D-lactic acid and reduced glutathione.
Glyoxylases are involved in hyperglycemia, non-insulin-dependent diabetes mellitus, the detoxification of bacterial toxins, and in the control of cell proliferation and microtubule assembly. Lyases
Lyases are a class of enzymes that catalyze the cleavage of C-C, C-O, C-N, C-S, C-(halide), 5 P-O or other bonds without hydrolysis or oxidation to form two molecules, at least one of which contains a double bond (Stryer, L. (1995) Biochemistry W.H. Freeman and Co. New York, NY p.620). Lyases are critical components of cellular biochemistry with roles in metabolic energy production including fatty acid metabolism, as well as other diverse enzymatic processes. Further classification of lyases reflects the type of bond cleaved as well as the nature of the cleaved group. The group of C-C lyases include carboxyl-lyases (decarboxylases), aldehyde-lyases
(aldolases), oxo-acid-lyases and others. The C-0 lyase group includes hydro-lyases, lyases acting on polysaccharides and other lyases. The C-N lyase group includes ammonia-lyases, amidine-lyases, amine-lyases (deaminases) and other lyases.
Proper regulation of lyases is critical to normal physiology. For example, mutation induced deficiencies in the uroporphyrinogen decarboxylase can lead to photosensitive cutaneous lesions in the genetically-linked disorder familial porphyria cutanea tarda (Mendez, M. et al. (1998) Am. J. Genet. 63:1363-1375). It has also been shown that adenosine deaminase (ADA) deficiency stems from genetic mutations in the ADA gene, resulting in the disorder severe combined immunodeficiency disease (SCID) (Hershfield, M.S. (1998) Semin. Hematol. 35:291-298). Isomerases
Isomerases are a class of enzymes that catalyze geometric or structural changes within a molecule to form a single product. This class includes racemases and epimerases, cis-trans- isomerases, intramolecular oxidoreductases, intramolecular transferases (mutases) and intramolecular lyases. Isomerases are critical components of cellular biochemistry with roles in metabolic energy production including glycolysis, as well as other diverse enzymatic processes (Stryer, L. (1995) Biochemistry. W.H. Freeman and Co., New York NY, pp.483-507).
Racemases are a subset of isomerases that catalyze inversion of a molecules configuration around the asymmetric carbon atom in a substrate having a single center of asymmetry, thereby interconverting two racemers. Epimerases are another subset of isomerases that catalyze inversion of 5 configuration around an asymmetric carbon atom in a substrate with more than one center of symmetry, thereby interconverting two epimers. Racemases and epimerases can act on amino acids and derivatives, hydroxy acids and derivatives, as well as carbohydrates and derivatives. The interconversion of UDP-galactose and UDP-glucose is catalyzed by UDP-galactose-4' -epimerase. Proper regulation and function of this epimerase is essential to the synthesis of glycoproteins and o glycolipids. Elevated blood galactose levels have been correlated with UDP-galactose-4' -epimerase deficiency in screening programs of infants (Gitzelmann, R. (1972) Helv. Paediat. Acta 27:125-130).
Oxidoreductases can be isomerases as well. Oxidoreductases catalyze the reversible transfer of electrons from a substrate that becomes oxidized to a substrate that becomes reduced. This class of enzymes includes dehydrogenases, hydroxylases, oxidases, oxygenases, peroxidases, and reductases. 5 Proper maintenance of oxidoreductase levels is physiologically important. For example, genetically- linked deficiencies in lipoamide dehydrogenase can result in lactic acidosis (Robinson, B.H. et al. (1977) Pediat. Res. 11:1198-1202).
Another subgroup of isomerases are the transferases (or mutases). Transferases transfer a chemical group from one compound (the donor) to another compound (the acceptor). The types of groups transferred by these enzymes include acyl groups, amino groups, phosphate groups
(phosphotransf erases or phosphomutases), and others. The transferase carnitine palmitoyltransferase is an important component of fatty acid metabolism. Genetically-linked deficiencies in this transferase can lead to myopathy (Scriver, C.R. et al. (1995) The Metabolic and Molecular Basis of Inherited Disease. McGraw-Hill, New York NY, pp.1501-1533). Yet another subgroup of isomerases are the topoisomersases. Topoisomerases are enzymes that affect the topological state of DNA. For example, defects in topoisomerases or their regulation can affect normal physiology. Reduced levels of topoisomerase II have been correlated with some of the DNA processing defects associated with the disorder ataxia-telangiectasia (Singh, S.P. et al. (1988) Nucleic Acids Res. 16:3919-3929). Li gases
Ligases catalyze the formation of a bond between two substrate molecules. The process involves the hydrolysis of a pyrophosphate bond in ATP or a similar energy donor. Ligases are classified based on the nature of the type of bond they form, which can include carbon-oxygen, carbon-sulfur, carbon-nitrogen, carbon-carbon and phosphoric ester bonds. Ligases forming carbon-oxygen bonds include the aminoacyl-transfer RNA (tRNA) synthetases which are important RNA-associated enzymes with roles in translation. Protein biosynthesis depends on each amino acid forming a linkage with the appropriate tRNA. The aminoacyl-tRNA synthetases are responsible for the activation and correct attachment of an amino acid with its cognate tRNA. The 20 aminoacyl-tRNA synthetase enzymes can be divided into two structural classes, and each class is characterized by a distinctive topology of the catalytic domain. Class I enzymes contain a catalytic domain based on the nucleotide-binding Rossman fold. Class II enzymes contain a central catalytic domain, which consists of a seven-stranded antiparallel β-sheet motif, as well as N- and C- terminal regulatory domains. Class II enzymes are separated into two groups based on the heterodimeric or homodimeric structure of the enzyme; the latter group is further subdivided by the structure of the N- and C-terminal regulatory domains (Hartlein, M. and S. Cusack (1995) J. Mol. Evol. 40:519-530). Autoantibodies against aminoacyl-tRNAs are generated by patients with dermatomyositis and polymyositis, and correlate strongly with complicating interstitial lung disease (ILD). These antibodies appear to be generated in response to viral infection, and coxsackie virus has been used to induce experimental viral myositis in animals. Ligases forming carbon-sulfur bonds (Acid-thiol ligases) mediate a large number of cellular biosynthetic intermediary metabolism processes involve intermolecular transfer of carbon atom-containing substrates (carbon substrates). Examples of such reactions include the tricarboxylic acid cycle, synthesis of fatty acids and long-chain phospholipids, synthesis of alcohols and aldehydes, synthesis of intermediary metabolites, and reactions involved in the amino acid degradation pathways. Some of these reactions require input of energy, usually in the form of conversion of ATP to either ADP or AMP and pyrophosphate.
In many cases, a carbon substrate is derived from a small molecule containing at least two carbon atoms. The carbon substrate is often covalently bound to a larger molecule which acts as a carbon substrate carrier molecule within the cell. In the biosynthetic mechanisms described above, the carrier molecule is coenzyme A. Coenzyme A (CoA) is structurally related to derivatives of the nucleotide ADP and consists of 4'-phosphopantetheine linked via a phosphodiester bond to the alpha phosphate group of adenosine 3',5'-bisphosphate. The terminal thiol group of 4'-phosphopantetheine acts as the site for carbon substrate bond formation. The predominant carbon substrates which utilize CoA as a carrier molecule during biosynthesis and intermediary metabolism in the cell are acetyl, succinyl, and propionyl moieties, collectively referred to as acyl groups. Other carbon substrates include enoyl lipid. which acts as a fatty acid oxidation intermediate, and carnitine, which acts as an acetyl-CoA flux regulator/ mitochondrial acyl group transfer protein. Acyl-CoA and acetyl-CoA are synthesized in the cell by acyl-CoA synthetase and acetyl-CoA synthetase, respectively.
Activation of fatty acids is mediated by at least three forms of acyl-CoA synthetase activity: i) acetyl-CoA synthetase, which activates acetate and several other low molecular weight carboxylic acids and is found in muscle mitochondria and the cytosol of other tissues; ii) medium-chain acyl-CoA synthetase, which activates fatty acids containing between four and eleven carbon atoms (predominantly from dietary sources), and is present only in liver mitochondria; and iii) acyl CoA synthetase, which is specific for long chain fatty acids with between six and twenty carbon atoms, and 5 is found in microsomes and the mitochondria. Proteins associated with acyl-CoA synthetase activity have been identified from many sources including bacteria, yeast, plants, mouse, and man. The activity of acyl-CoA synthetase may be modulated by phosphorylation of the enzyme by cAMP-dependent protein kinase.
Ligases forming carbon-nitrogen bonds include amide synthases such as glutamine synthetase o (glutamate-ammonia Ugase) that catalyzes the amination of glutamic acid to glutamine by ammonia using the energy of ATP hydrolysis. Glutamine is the primary source for the amino group in various amide transfer reactions involved in de novo pyrimidine nucleotide synthesis and in purine and pyrimidine ribonucleotide interconversions. Overexpression of glutamine synthetase has been observed in primary liver cancer (Christa, L. et al. (1994) Gastroent. 106:1312-1320). 5 Acid-amino-acid ligases (peptide synthases) are represented by the ubiquitin proteases which are associated with the ubiquitin conjugation system (UCS), a major pathway for the degradation of cellular proteins in eukaryotic cells and some bacteria. The UCS mediates the eUmination of abnormal proteins and regulates the half-lives of important regulatory proteins that control cellular processes such as gene transcription and cell cycle progression. In the UCS pathway, proteins o targeted for degradation are conjugated to a ubiquitin (Ub), a small heat stable protein. Ub is first activated by a ubiquitin-activating enzyme (El), and then transferred to one of several Ub- conjugating enzymes (E2). E2 then links the Ub molecule through its C-terminal glycine to an internal lysine (acceptor lysine) of a target protein. The ubiquitinated protein is then recognized and degraded by proteasome, a large, multisubunit proteolytic enzyme complex, and ubiquitin is released 5 for reutilization by ubiquitin protease. The UCS is implicated in the degradation of mitotic cyclic kinases, oncoproteins, tumor suppressor genes such as p53, viral proteins, cell surface receptors associated with signal transduction, transcriptional regulators, and mutated or damaged proteins (Ciechanover, A. (1994) Cell 79:13-21). A murine proto-oncogene, Unp, encodes a nuclear ubiquitin protease whose overexpression leads to oncogenic transformation of NIH3T3 cells, and the human o homolog of this gene is consistently elevated in small cell tumors and adenocarcinomas of the lung
(Gray, D.A. (1995) Oncogene 10:2179-2183).
Cyclo-ligases and other carbon-nitrogen ligases comprise various enzymes and enzyme complexes that participate in the de novo pathways to purine and pyrimidine biosynthesis. Because these pathways are critical to the synthesis of nucleotides for replication of both RNA and DNA, 5 many of these enzymes have been the targets of clinical agents for the treatment of cell proliferative disorders such as cancer and infectious diseases.
Purine biosynthesis occurs de novo from the amino acids glycine and glutamine, and other small molecules. Three of the key reactions in this process are catalyzed by a trifunctional enzyme composed of glycinamide-ribonucleotide synthetase (GARS), aminoimidazole ribonucleotide 5 synthetase (AIRS), and glycinamide ribonucleotide transformylase (GART). Together these three enzymes combine ribosylamine phosphate with glycine to yield phosphoribosyl aminoimidazole, a precursor to both adenylate and guanylate nucleotides. This trifunctional protein has been implicated in the pathology of Downs syndrome (Aimi, J. et al. (1990) Nucleic Acid Res. 18:6665-6672). Adenylosuccinate synthetase catalyzes a later step in purine biosynthesis that converts inosinic acid to o adenylosuccinate, a key step on the path to ATP synthesis. This enzyme is also similar to another carbon-nitrogen ligase, argininosuccinate synthetase, that catalyzes a similar reaction in the urea cycle (Powell, S.M. et al. (1992) FEBS Lett. 303:4-10).
Like the de novo biosynthesis of purines, de novo synthesis of the pyrimidine nucleotides uridylate and cytidylate also arises from a common precursor, in this instance the nucleotide 5 orotidylate derived from orotate and phosphoribosyl pyrophosphate (PPRP). Again a trifunctional enzyme comprising three carbon-nitrogen ligases plays a key role in the process. In this case the enzymes aspartate transcarbamylase (ATCase), carbamyl phosphate synthetase II, and dihydroorotase (DHOase) are encoded by a single gene called CAD. Together these three enzymes combine the initial reactants in pyrimidine biosynthesis, glutamine, C02 and ATP to form dihydroorotate, the 0 precursor to orotate and orotidylate (Iwahana, H. et al. (1996) Biochem. Biophys. Res. Commun. 219:249-255). Further steps then lead to the synthesis of uridine nucleotides from orotidylate. Cytidine nucleotides are derived from uridine-5'-triphosphate (UTP) by the amidation of UTP using glutamine as the amino donor and the enzyme CTP synthetase. Regulatory mutations in the human CTP synthetase are believed to confer multi-drug resistance to agents widely used in cancer therapy 5 (Yamauchi, M. et al. (1990) EMBO J. 9:2095-2099).
Ligases forming carbon-carbon bonds include the carboxylases acetyl-CoA carboxylase and pyruvate carboxylase. Acetyl-CoA carboxylase catalyzes the carboxylation of acetyl-CoA from C02 and H20 using the energy of ATP hydrolysis. Acetyl-CoA carboxylase is the rate-limiting step in the biogenesis of long-chain fatty acids. Two isoforms of acetyl-CoA carboxylase, types I and types II, are expressed in human in a tissue-specific manner (Ha, J. et al. (1994) Eur. J. Biochem. 219:297-
306). Pyruvate carboxylase is a nuclear-encoded mitochondrial enzyme that catalyzes the conversion of pyruvate to oxaloacetate, a key intermediate in the citric acid cycle.
Ligases forming phosphoric ester bonds include the DNA ligases involved in both DNA replication and repair. DNA ligases seal phosphodiester bonds between two adjacent nucleotides in a DNA chain using the energy from ATP hydrolysis to first activate the free 5 ' -phosphate of one nucleotide and then react it with the 3' -OH group of the adjacent nucleotide. This reseating reaction is used in both DNA replication to join small DNA fragments called Okazaki fragments that are transiently formed in the process of replicating new DNA, and in DNA repair. DNA repair is the process by which accidental base changes, such as those produced by oxidative damage, hydrolytic attack, or uncontrolled methylation of DNA, are corrected before replication or transcription of the DNA can occur. Bloom's syndrome is an inherited human disease in which individuals are partially deficient in DNA ligation and consequently have an increased incidence of cancer (Alberts, B. et al. (1994) The Molecular Biology of the Cell, Garland Publishing Inc., New York NY, p. 247).
Molecules Associated with Growth and Development
SEQ ID NO:51 and SEQ ID NO:52 encode, for example, molecules associated with growth and development.
Human growth and development requires the spatial and temporal regulation of cell differentiation, cell proliferation, and apoptosis. These processes coordinately control reproduction, aging, embryogenesis, morphogenesis, organogenesis, and tissue repair and maintenance. At the cellular level, growth and development is governed by the cell's decision to enter into or exit from the cell division cycle and by the cell's commitment to a terminally differentiated state. These decisions are made by the cell in response to extracellular signals and other environmental cues it receives. The following discussion focuses on the molecular mechanisms of cell division, reproduction, cell differentiation and proliferation, apoptosis, and aging. Cell Division
Cell division is the fundamental process by which all living things grow and reproduce. In unicellular organisms such as yeast and bacteria, each cell division doubles the number of organisms, while in multicellular species many rounds of cell division are required to replace cells lost by wear or by programmed cell death, and for cell differentiation to produce a new tissue or organ. Details of the cell division cycle may vary, but the basic process consists of three principle events. The first event, interphase, involves preparations for cell division, replication of the DNA, and production of essential proteins. In the second event, mitosis, the nuclear material is divided and separates to opposite sides of the cell. The final event, cytokinesis, is division and fission of the cell cytoplasm. The sequence and timing of cell cycle transitions is under the control of the cell cycle regulation system which controls the process by positive or negative regulatory circuits at various check points.
Regulated progression of the cell cycle depends on the integration of growth control pathways with the basic cell cycle machinery. Cell cycle regulators have been identified by selecting for human and yeast cDNAs that block or activate cell cycle arrest signals in the yeast mating pheromone pathway when they are overexpressed. Known regulators include human CPR (cell cycle progression restoration) genes, such as CPR8 and CPR2, and yeast CDC (cell division control) genes, including CDC91, that block the arrest signals. The CPR genes express a variety of proteins including cyclins, tumor suppressor binding proteins, chaperones, transcription factors, translation factors, and RNA-binding proteins (Edwards, M.C. et al.(1997) Genetics 147:1063-1076). 5 Several cell cycle transitions, including the entry and exit of a cell from mitosis, are dependent upon the activation and inhibition of cyclin-dependent kinases (Cdks). The Cdks are composed of a kinase subunit, Cdk, and an activating subunit, cyclin, in a complex that is subject to many levels of regulation. There appears to be a single Cdk in Saccharomyces cerevisiae and Saccharomyces pombe whereas mammals have a variety of specialized Cdks. Cyctins act by binding to and activating o cycUn-dependent protein kinases which then phosphorylate and activate selected proteins involved in the mitotic process. The Cdk-cyclin complex is both positively and negatively regulated by phosphorylation, and by targeted degradation involving molecules such as CDC4 and CDC53. In addition, Cdks are further regulated by binding to inhibitors and other proteins such as Sucl that modify their specificity or accessibility to regulators (Patra, D. and W.G. Dunphy (1996) Genes Dev. 5 10:1503-1515; and Mathias, N. et al. (1996) Mol. Cell Biol. 16:6634-6643). Reproduction
The male and female reproductive systems are complex and involve many aspects of growth and development. The anatomy and physiology of the male and female reproductive systems are reviewed in (Guyton, A.C. (1991) Textbook of Medical Physiology, W.B. Saunders Co., Philadelphia 0 PA, pp. 899-928).
The male reproductive system includes the process of spermatogenesis, in which the sperm are formed, and male reproductive functions are regulated by various hormones and their effects on accessory sexual organs, cellular metabolism, growth, and other bodily functions.
Spermatogenesis begins at puberty as a result of stimulation by gonadotropic hormones 5 released from the anterior pituitary. Immature sperm (spermatogonia) undergo several mitotic cell divisions before undergoing meiosis and full maturation. The testes secrete several male sex hormones, the most abundant being testosterone, that is essential for growth and division of the immature sperm, and for the mascuUne characteristics of the male body. Three other male sex hormones, gonadotropin- releasing hormone (GnRH), luteinizing hormone (LH), and follicle-stimulating hormone (FSH) control o sexual function.
The uterus, ovaries, fallopian tubes, vagina, and breasts comprise the female reproductive system. The ovaries and uterus are the source of ova and the location of fetal development, respectively. The fallopian tubes and vagina are accessory organs attached to the top and bottom of the uterus, respectively. Both the uterus and ovaries have additional roles in the development and loss of 5 reproductive capability during a female's lifetime. The primary role of the breasts is lactation. Multiple endocrine signals from the ovaries, uterus, pituitary, hypothalamus, adrenal glands, and other tissues coordinate reproduction and lactation. These signals vary during the monthly menstruation cycle and during the female's lifetime. Similarly, the sensitivity of reproductive organs to these endocrine signals varies during the female's Ufetime. 5 A combination of positive and negative feedback to the ovaries, pituitary and hypothalamus glands controls physiologic changes during the monthly ovulation and endometrial cycles. The anterior pituitary secretes two major gonadofropin hormones, follicle-stimulating hormone (FSH) and luteinizing hormone (LH), regulated by negative feedback of steroids, most notably by ovarian estradiol. If fertilization does not occur, estrogen and progesterone levels decrease. This sudden reduction of the o ovarian hormones leads to menstruation, the desquamation of the endometrium.
Hormones further govern all the steps of pregnancy, parturition, lactation, and menopause. During pregnancy large quantities of human chorionic gonadofropin (hCG), estrogens, progesterone, and human chorionic somatomammotropin (hCS) are formed by the placenta. hCG, a glycoprotein similar to luteinizing hormone, stimulates the corpus luteum to continue producing more progesterone 5 and estrogens, rather than to involute as occurs if the ovum is not fertilized. hCS is similar to growth hormone and is crucial for fetal nutrition.
The female breast also matures during pregnancy. Large amounts of estrogen secreted by the placenta trigger growth and branching of the breast milk ductal system while lactation is initiated by the secretion of prolactin by the pituitary gland. o Parturition involves several hormonal changes that increase uterine contractility toward the end of pregnancy, as follows. The levels of estrogens increase more than those of progesterone. Oxytocin is secreted by the neurohypophysis. Concomitantly, uterine sensitivity to oxytocin increases. The fetus itself secretes oxytocin, cortisol (from adrenal glands), and prostaglandins.
Menopause occurs when most of the ovarian follicles have degenerated. The ovary then 5 produces less estradiol, reducing the negative feedback on the pituitary and hypothalamus glands.
Mean levels of circulating FSH and LH increase, even as ovulatory cycles continue. Therefore, the ovary is less responsive to gonadotropins, and there is an increase in the time between menstrual cycles. Consequently, menstrual bleeding ceases and reproductive capability ends. Cell Differentiation and Proliferation Tissue growth involves complex and ordered patterns of cell proliferation, cell differentiation, and apoptosis. Cell proliferation must be regulated to maintain both the number of cells and their spatial organization. This regulation depends upon the appropriate expression of proteins which control cell cycle progression in response to extracellular signals, such as growth factors and other mitogens, and intracellular cues, such as DNA damage or nutrient starvation. Molecules which directly or indirectly modulate cell cycle progression fall into several categories, including growth factors and their receptors, second messenger and signal transduction proteins, oncogene products, tumor-suppressor proteins, and mitosis-promoting factors.
Growth factors were originally described as serum factors required to promote cell proliferation. Most growth factors are large, secreted polypeptides that act on cells in their local 5 environment. Growth factors bind to and activate specific cell surface receptors and initiate intracellular signal transduction cascades. Many growth factor receptors are classified as receptor tyrosine kinases which undergo autophosphorylation upon ligand binding. Autophosphorylation enables the receptor to interact with signal transduction proteins characterized by the presence of SH2 or SH3 domains (Src homology regions 2 or 3). These proteins then modulate the activity state of 0 small G-proteins, such as Ras, Rab, and Rho, along with GTPase activating proteins (GAPs), guanine nucleotide releasing proteins (GNRPs), and other guanine nucleotide exchange factors. Small G proteins act as molecular switches that activate other downstream events, such as mitogen-activated protein kinase (MAP kinase) cascades. MAP kinases ultimately activate transcription of mitosis- promoting genes. 5 In addition to growth factors, small signaling peptides and hormones also influence cell proliferation. These molecules bind primarily to another class of receptor, the trimeric G-protein coupled receptor (GPCR), found predominantly on the surface of immune, neuronal and neuroendocrine cells. Upon ligand binding, the GPCR activates a trimeric G protein which in turn triggers increased levels of intracellular second messengers such as phospholipase C, Ca2+, and cyclic AMP. Most o GPCR-mediated signaling pathways indirectly promote cell proliferation by causing the secretion or breakdown of other signaling molecules that have direct mitogenic effects. These signaling cascades often involve activation of kinases and phosphatases. Some growth factors, such as some members of the transforming growth factor beta (TGF-β) family, act on some cells to stimulate cell proliferation and on other cells to inhibit it. Growth factors may also stimulate a cell at one concentration and inhibit 5 the same cell at another concentration. Most growth factors also have a multitude of other actions besides the regulation of cell growth and division: they can control the proliferation, survival, differentiation, migration, or function of cells depending on the circumstance. For example, the tumor necrosis factor/nerve growth factor (TNF/NGF) family can activate or inhibit cell death, as well as regulate proliferation and differentiation. The cell response depends on the type of cell, its stage of o differentiation and transformation status, which surface receptors are stimulated, and the types of stimuli acting on the cell (Smith, A. et al. (1994) Cell 76:959-962; and Nocentini, G. et al. (1997) Proc. Nati. Acad. Sci. USA 94:6216-6221).
Neighboring cells in a tissue compete for growth factors, and when provided with "unlimited" quantities in a perfused system will grow to even higher cell densities before reaching density-dependent 5 inhibition of cell division. Cells often demonstrate an anchorage dependence of cell division as well. This anchorage dependence may be associated with the formation of focal contacts linking the cytoskeleton with the extracellular matrix (ECM). The expression of ECM components can be stimulated by growth factors. For example, TGF-β stimulates fibroblasts to produce a variety of ECM proteins, including fibronectin, collagen, and tenascin (Pearson, CA. et al. (1988) EMBO J. 7:2677- 2981). In fact, for some cell types specific ECM molecules, such as laminin or fibronectin, may act as growth factors. Tenascin-C and -R, expressed in developing and lesioned neural tissue, provide stimulatory/anti-adhesive or inhibitory properties, respectively, for axonal growth (Faissner, A. (1997) Cell Tissue Res. 290:331-341).
Cancers are associated with the activation of oncogenes which are derived from normal cellular genes. These oncogenes encode oncoproteins which convert normal cells into malignant cells. Some oncoproteins are mutant isoforms of the normal protein, and other oncoproteins are abnormally expressed with respect to location or amount of expression. The latter category of oncoprotein causes cancer by altering transcriptional control of cell proliferation. Five classes of oncoproteins are known to affect cell cycle controls. These classes include growth factors, growth factor receptors, intracellular signal transducers, nuclear transcription factors, and cell-cycle control proteins. Viral oncogenes are integrated into the human genome after infection of human cells by certain viruses. Examples of viral oncogenes include v-src, v-abl, and v-fps.
Many oncogenes have been identified and characterized. These include sis, erbA, erbB, her-2, mutated Gs, src, abl, ras, crk, jun, fos, myc, and mutated tumor-suppressor genes such as RB, p53, mdm2, Cipl , pi 6, and cyclin D. Transformation of normal genes to oncogenes may also occur by chromosomal translocation. The Philadelphia chromosome, characteristic of chronic myeloid leukemia and a subset of acute lymphoblastic leukemias, results from a reciprocal translocation between chromosomes 9 and 22 that moves a truncated portion of the proto-oncogene c-abl to the breakpoint cluster region (bcr) on chromosome 22. Tumor-suppressor genes are involved in regulating cell proliferation. Mutations which cause reduced or loss of function in tumor-suppressor genes result in uncontrolled cell proUferation. For example, the retinoblastoma gene product (RB), in a non-phosphorylated state, binds several early- response genes and suppresses their transcription, thus blocking cell division. Phosphorylation of RB causes it to dissociate from the genes, releasing the suppression, and allowing cell division to proceed. Apoptosis
Apoptosis is the genetically controlled process by which unneeded or defective cells undergo programmed cell death. Selective elimination of cells is as important for morphogenesis and tissue remodeling as is cell proliferation and differentiation. Lack of apoptosis may result in hyperplasia and other disorders associated with increased cell proliferation. Apoptosis is also a critical component of the immune response. Immune cells such as cytotoxic T-cells and natural killer cells prevent the spread of disease by inducing apoptosis in tumor cells and virus-infected cells. In addition, immune cells that fail to distinguish self molecules from foreign molecules must be eliminated by apoptosis to avoid an autoimmune response.
Apoptotic cells undergo distinct morphological changes. Hallmarks of apoptosis include cell shrinkage, nuclear and cytoplasmic condensation, and alterations in plasma membrane topology. Biochemically, apoptotic cells are characterized by increased intracellular calcium concentration, fragmentation of chromosomal DNA, and expression of novel cell surface components.
The molecular mechanisms of apoptosis are highly conserved, and many of the key protein regulators and effectors of apoptosis have been identified. Apoptosis generally proceeds in response to a signal which is transduced infracellularly and results in altered patterns of gene expression and protein activity. SignaUng molecules such as hormones and cytokines are known both to stimulate and to inhibit apoptosis through interactions with cell surface receptors. Transcription factors also play an important role in the onset of apoptosis. A number of downstream effector molecules, particularly proteases such as the cysteine proteases called caspases, have been implicated in the degradation of cellular components and the proteolytic activation of other apoptotic effectors. Aging and Senescence
Studies of the aging process or senescence have shown a number of characteristic cellular and molecular changes (Fauci et al. (1998) Harrison's Principles of Internal Medicine, McGraw-Hill, New York NY, p.37). These characteristics include increases in chromosome structural abnormalities, DNA cross-Unking, incidence of single-stranded breaks in DNA, losses in DNA methylation, and degradation of telomere regions. In addition to these DNA changes, post-translational alterations of proteins increase including, deamidation, oxidation, cross-linking, and nonenzymatic glycation. Still further molecular changes occur in the mitochondria of aging cells through deterioration of structure. These changes eventually contribute to decreased function in every organ of the body.
Biochemical Pathway Molecules
SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, and SEQ ID NO:50 encode, for example, biochemical pathway molecules.
Biochemical pathways are responsible for regulating metabolism, growth and development, protein secretion and trafficking, environmental responses, and ecological interactions including immune response and response to parasites. DNA replication
Deoxyribonucleic acid (DNA), the genetic material, is found in both the nucleus and mitochondria of human cells. The bulk of human DNA is nuclear, in the form of linear chromosomes, while mitochondrial DNA is circular. DNA replication begins at specific sites called origins of replication. Bidirectional synthesis occurs from the origin via two growing forks that move in opposite directions. Rephcation is semi-conservative, with each daughter duplex containing one old strand and its newly synthesized complementary partner. Proteins involved in DNA replication include DNA polymerases, DNA primase, telomerase, DNA helicase, topoisomerases, DNA Ugases, replication factors, and DNA-binding proteins. DNA Recombination and Repair
Cells are constantly faced with replication errors and environmental assault (such as ultraviolet irradiation) that can produce DNA damage. Damage to DNA consists of any change that modifies the structure of the molecule. Changes to DNA can be divided into two general classes, single base changes and structural distortions. Any damage to DNA can produce a mutation, and the mutation may produce a disorder, such as cancer.
Changes in DNA are recognized by repair systems within the cell. These repair systems act to correct the damage and thus prevent any deleterious affects of a mutational event. Repair systems can be divided into three general types, direct repair, excision repair, and retrieval systems. Proteins involved in DNA repair include DNA polymerase, excision repair proteins, excision and cross link repair proteins, recombination and repair proteins, RAD51 proteins, and BLN and WRN proteins that are homologs of RecQ helicase. When the repair systems are eliminated, cells become exceedingly sensitive to environmental mutagens, such as ultraviolet irradiation. Patients with disorders associated with a loss in DNA repair systems often exhibit a high sensitivity to environmental mutagens. Examples of such disorders include xeroderma pigmentosum (XP), Bloom's syndrome (BS), and Werner's syndrome (WS) (Yamagata, K. et al. (1998) Proc. Nati. Acad. Sci. USA 95:8733-8738), ataxia telangiectasia, Cockayne's syndrome, and Fanconi's anemia.
Recombination is the process whereby new DNA sequences are generated by the movements of large pieces of DNA. In homologous recombination, which occurs during meiosis and DNA repair, parent DNA duplexes align at regions of sequence similarity, and new DNA molecules form by the breakage and joining of homologous segments. Proteins involved include RAD51 recombinase. In site- specific recombination, two specific but not necessarily homologous DNA sequences are exchanged. In the immune system this process generates a diverse collection of antibody and T cell receptor genes. Proteins involved in site-specific recombination in the immune system include recombination activating genes 1 and 2 (RAG1 and RAG2). A defect in immune system site-specific recombination causes severe combined immunodeficiency disease in mice. RNA Metabolism
Ribonucleic acid (RNA) is a linear single-stranded polymer of four nucleotides, ATP, CTP, UTP, and GTP. In most organisms, RNA is transcribed as a copy of DNA, the genetic material of the organism. In refroviruses RNA rather than DNA serves as the genetic material. RNA copies of the genetic material encode proteins or serve various structural, catalytic, or regulatory roles in organisms. RNA is classified according to its cellular localization and function. Messenger RNAs ( RNAs) encode polypeptides. Ribosomal RNAs (rRNAs) are assembled, along with ribosomal proteins, into ribosomes, which are cytoplasmic particles that translate mRNA into polypeptides. Transfer RNAs (tRNAs) are cytosoUc adaptor molecules that function in mRNA translation by recognizing both an mRNA codon and the amino acid that matches that codon. Heterogeneous nuclear RNAs (hnRNAs) include mRNA precursors and other nuclear RNAs of various sizes. Small nuclear RNAs (snRNAs) are a part of the nuclear spUceosome complex that removes intervening, non-coding sequences (introns) and rejoins exons in pre-mRNAs. RNA Transcription
The transcription process synthesizes an RNA copy of DNA. Proteins involved include multi- subunit RNA polymerases, transcription factors IIA, UB, IID, HE, IIF, IIH, and IIJ. Many transcription factors incorporate DNA-binding structural motifs which comprise either -helices or β- sheets that bind to the major groove of DNA. Four well-characterized structural motifs are helix-turn- helix, zinc finger, leucine zipper, and helix-loop-helix. RNA Processing
Various proteins are necessary for processing of transcribed RNAs in the nucleus. Pre-mRNA processing steps include capping at the 5' end with methylguanosine, polyadenylating the 3' end, and spUcing to remove introns. The spUceosomal complex is comprised of five small nuclear ribonucleoprotein particles (snRNPs) designated Ul, U2, U4, U5, and U6. Each snRNP contains a single species of snRNA and about ten proteins. The RNA components of some snRNPs recognize and base-pair with intron consensus sequences. The protein components mediate spUceosome assembly and the spUcing reaction. Autoantibodies to snRNP proteins are found in the blood of patients with systemic lupus erythematosus (Stryer, L. (1995) Biochemistry W.H. Freeman and Company, New York NY, p. 863).
Heterogeneous nuclear ribonucleoproteins (hnRNPs) have been identified that have roles in spUcing, exporting of the mature RNAs to the cytoplasm, and mRNA translation (Biamonti, G. et al. (1998) Clin. Exp. Rheumatol. 16:317-326). Some examples of hnRNPs include the yeast proteins Hrplp, involved in cleavage and polyadenylation at the 3' end of the RNA; Cbp80p, involved in capping the 5 ' end of the RNA; and Npl3p, a homolog of mammalian hnRNP Al , involved in export of mRNA from the nucleus (Shen, E.C. et al. (1998) Genes Dev. 12:679-691). HnRNPs have been shown to be important targets of the autoimmune response in rheumatic diseases (Biamonti, supra).
Many snRNP proteins, hnRNP proteins, and alternative splicing factors are characterized by an RNA recognition motif (RRM). (Reviewed in Birney, E. et al. (1993) Nucleic Acids Res. 21 :5803- 5816.) The RRM is about 80 amino acids in length and forms four β-strands and two α-heUces arranged in an α/β sandwich. The RRM contains a core RNP-1 octapeptide motif along with surrounding conserved sequences. RNA Stability and Degradation
RNA helicases alter and regulate RNA conformation and secondary structure by using energy derived from ATP hydrolysis to destabihze and unwind RNA duplexes. The most well-characterized and ubiquitous family of RNA heUcases is the DEAD-box family, so named for the conserved B-type ATP-binding motif which is diagnostic of proteins in this family. Over 40 DEAD-box heUcases have been identified in organisms as diverse as bacteria, insects, yeast, amphibians, mammals, and plants. DEAD-box helicases function in diverse processes such as translation initiation, splicing, ribosome assembly, and RNA editing, transport, and stability. Some DEAD-box helicases play tissue- and stage- specific roles in spermatogenesis and embryogenesis. (Reviewed in Linder, P. et al. (1989) Nature 337:121-122.)
Overexpression of the DEAD-box 1 protein (DDX1) may play a role in the progression of neuroblasto a (Nb) and retinoblastoma (Rb) tumors. Other DEAD-box helicases have been implicated either directly or indirectly in ultraviolet light-induced tumors, B cell lymphoma, and myeloid malignancies. (Reviewed in Godbout, R. et al. (1998) J. Biol. Chem. 273:21161-21168.)
Ribonucleases (RNases) catalyze the hydrolysis of phosphodiester bonds in RNA chains, thus cleaving the RNA. For example, RNase P is a ribonucleoprotein enzyme which cleaves the 5' end of pre-tRNAs as part of their maturation process. RNase H digests the RNA strand of an RNA/DNA hybrid. Such hybrids occur in cells invaded by refroviruses, and RNase H is an important enzyme in the retroviral replication cycle. RNase H domains are often found as a domain associated with reverse transcriptases. RNase activity in serum and cell extracts is elevated in a variety of cancers and infectious diseases (Schein, CH. (1997) Nat. Biotechnol. 15:529-536). Regulation of RNase activity is being investigated as a means to control tumor angiogenesis, allergic reactions, viral infection and replication, and fungal infections. Protein Translation
The eukaryotic ribosome is composed of a 60S (large) subunit and a 40S (small) subunit, which together form the 80S ribosome. In addition to the 18S, 28S, 5S, and 5.8S rRNAs, the ribosome also contains more than fifty proteins. The ribosomal proteins have a prefix which denotes the subunit to which they belong, either L (large) or S (small). Three important sites are identified on the ribosome.
The aminoacyl-tRNA site (A site) is where charged tRNAs (with the exception of the initiator-tRNA) bind on arrival at the ribosome. The peptidyl-tRNA site (P site) is where new peptide bonds are formed, as well as where the initiator tRNA binds. The exit site (E site) is where deacylated tRNAs bind prior to their release from the ribosome. (Translation is reviewed in Stryer, L. (1995) Biochemistry, W.H. Freeman and Company, New York NY, pp. 875-908; and Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York NY, pp. 119-138.) tRNA Charging
Protein biosynthesis depends on each amino acid forming a linkage with the appropriate tRNA. The aminoacyl-tRNA synthetases are responsible for the activation and correct attachment of an amino acid with its cognate tRNA. The 20 aminoacyl-tRNA synthetase enzymes can be divided into two structural classes, Class I and Class II. Autoantibodies against aminoacyl-tRNAs are generated by patients with dermatomyositis and polymyositis, and correlate strongly with compUcating interstitial lung disease (ILD). These antibodies appear to be generated in response to viral infection, and coxsackie virus has been used to induce experimental viral myositis in animals. Translation Initiation
Initiation of ttanslation can be divided into three stages. The first stage brings an initiator transfer RNA (Met-tRNAf) together with the 40S ribosomal subunit to form the 43S preinitiation complex. The second stage binds the 43S preinitiation complex to the mRNA, followed by migration of the complex to the correct AUG initiation codon. The third stage brings the 60S ribosomal subunit to the 40S subunit to generate an 80S ribosome at the initiation codon. Regulation of translation primarily involves the first and second stage in the initiation process (Pain, V.M. (1996) Eur. J. Biochem. 236:747-771).
Several initiation factors, many of which contain multiple subunits, are involved in bringing an initiator tRNA and 40S ribosomal subunit together. eIF2, a guanine nucleotide binding protein, recruits the initiator tRNA to the 40S ribosomal subunit. Only when eIF2 is bound to GTP does it associate with the initiator tRNA. eIF2B, a guanine nucleotide exchange protein, is responsible for converting eIF2 from the GDP-bound inactive form to the GTP-bound active form. Two other factors, elFl A and eIF3 bind and stabilize the 40S subunit by interacting with 18S ribosomal RNA and specific ribosomal structural proteins. eIF3 is also involved in association of the 40S ribosomal subunit with mRNA. The Met-tRNAf, elFl A, eIF3, and 40S ribosomal subunit together make up the 43S preinitiation complex
(Pain, supra).
Additional factors are required for binding of the 43S preinitiation complex to an mRNA molecule, and the process is regulated at several levels. eIF4F is a complex consisting of three proteins: eIF4E, eIF4A, and eIF4G. eIF4E recognizes and binds to the mRNA 5 '-terminal m7GTP cap, eIF4A is a bidirectional RNA-dependent helicase, and eIF4G is a scaffolding polypeptide. eIF4G has three binding domains. The N-terminal third of eIF4G interacts with eIF4E, the central third interacts with eIF4A, and the C-terminal third interacts with eIF3 bound to the 43S preinitiation complex. Thus, eIF4G acts as a bridge between the 40S ribosomal subunit and the mRNA (Hentze, M.W. (1997) Science 275:500-501). The ability of eIF4F to initiate binding of the 43S preinitiation complex is regulated by structural features of the mRNA. The mRNA molecule has an untranslated region (UTR) between the 5' cap and the AUG start codon. In some mRNAs this region forms secondary structures that impede binding of the 43S preinitiation complex. The helicase activity of eIF4A is thought to function in removing this secondary structure to facihtate binding of the 43S preinitiation complex (Pain, supra). 5 Translation Elongation
Elongation is the process whereby additional amino acids are joined to the initiator methionine to form the complete polypeptide chain. The elongation factors EFlα, EFlβ γ, and EF2 are involved in elongating the polypeptide chain following initiation. EF1 α is a GTP-binding protein. In EF1 α's GTP-bound form, it brings an aminoacyl-tRNA to the ribosome' s A site. The amino acid attached to 0 the newly arrived aminoacyl-tRNA forms a peptide bond with the initiator methionine. The GTP on EF1 α is hydrolyzed to GDP, and EF1 α-GDP dissociates from the ribosome. EF1 β γ binds EF1 α -GDP and induces the dissociation of GDP from EFlα, allowing EFlα to bind GTP and a new cycle to begin.
As subsequent aminoacyl-tRNAs are brought to the ribosome, EF-G, another GTP-binding protein, catalyzes the translocation of tRNAs from the A site to the P site and finally to the E site of the 5 ribosome. This allows the processivity of ttanslation. Translation Termination
The release factor eRF carries out termination of translation. eRF recognizes stop codons in the mRNA, leading to the release of the polypeptide chain from the ribosome. Post-Translational Pathways o Proteins may be modified after translation by the addition of phosphate, sugar, prenyl, fatty acid, and other chemical groups. These modifications are often required for proper protein activity. Enzymes involved in post-translational modification include kinases, phosphatases, glycosyltransferases, and prenyltransferases. The conformation of proteins may also be modified after translation by the introduction and rearrangement of disulfide bonds (rearrangement catalyzed by 5 protein disulfide isomerase), the isomerization of proline sidechains by prolyl isomerase, and by interactions with molecular chaperone proteins.
Proteins may also be cleaved by proteases. Such cleavage may result in activation, inactivation, or complete degradation of the protein. Proteases include serine proteases, cysteine proteases, aspartic proteases, and metalloproteases. Signal peptidase in the endoplasmic reticulum o (ER) lumen cleaves the signal peptide from membrane or secretory proteins that are imported into the
ER. Ubiquitin proteases are associated with the ubiquitin conjugation system (UCS), a major pathway for the degradation of cellular proteins in eukaryotic cells and some bacteria. The UCS mediates the elimination of abnormal proteins and regulates the half-lives of important regulatory proteins that control cellular processes such as gene transcription and cell cycle progression. In the 5 UCS pathway, proteins targeted for degradation are conjugated to a ubiquitin, a small heat stable protein. Proteins involved in the UCS include ubiquitin-activating enzyme, ubiquitin-conjugating enzymes, ubiquitin-ligases, and ubiquitin C-terminal hydrolases. The ubiquitinated protein is then recognized and degraded by the proteasome, a large, multisubunit proteolytic enzyme complex, and ubiquitin is released for reutilization by ubiquitin protease. 5 Lipid MetaboUsm
Lipids are water-insoluble, oily or greasy substances that are soluble in nonpolar solvents such as chloroform or ether. Neutral fats (friacylglycerols) serve as major fuels and energy stores. Polar Upids, such as phosphoUpids, sphingolipids, glycolipids, and cholesterol, are key structural components of cell membranes. o Lipid metaboUsm is involved in human diseases and disorders. In the arterial disease atherosclerosis, fatty lesions form on the inside of the arterial wall. These lesions promote the loss of arterial flexibility and the formation of blood clots (Guyton, A.C. Textbook of Medical Physiology (1991) W.B. Saunders Company, Philadelphia PA, pp.760-763). In Tay-Sachs disease, the GM2 ganglioside (a sphingolipid) accumulates in lysosomes of the central nervous system due to a lack of the 5 enzyme N-acetylhexosaminidase. Patients suffer nervous system degeneration leading to early death (Fauci, AS. et al. (1998) Harrison's Principles of Internal Medicine McGraw-Hill, New York NY, p. 2171). The Niemann-Pick diseases are caused by defects in lipid metabolism. Niemann-Pick diseases types A and B are caused by accumulation of sphingomyelin (a sphingolipid) and other Upids in the central nervous system due to a defect in the enzyme sphingomyelinase, leading to neurodegeneration o and lung disease. Niemann-Pick disease type C results from a defect in cholesterol transport, leading to the accumulation of sphingomyelin and cholesterol in lysosomes and a secondary reduction in sphingomyeUnase activity. Neurological symptoms such as grand mal seizures, ataxia, and loss of previously learned speech, manifest 1-2 years after birth. A mutation in the NPC protein, which contains a putative cholesterol-sensing domain, was found in a mouse model of Niemann-Pick disease 5 type C (Fauci, supra, p. 2175; Loftus, S.K. et al. (1997) Science 277:232-235). (Lipid metabolism is reviewed in Stryer, L. (1995) Biochemistry, W.H. Freeman and Company, New York NY; Lehninger, A. (1982) Principles of Biochemistry Worth Publishers, Inc., New York NY; and ExPASy "Biochemical Pathways" index of Boehringer Mannheim World Wide Web site.) Fatty Acid Synthesis o Fatty acids are long-chain organic acids with a single carboxyl group and a long non-polar hydrocarbon tail. Long-chain fatty acids are essential components of glycolipids, phosphoUpids, and cholesterol, which are building blocks for biological membranes, and of triglycerides, which are biological fuel molecules. Long-chain fatty acids are also substrates for eicosanoid production, and are important in the functional modification of certain complex carbohydrates and proteins. 16-carbon and 5 18-carbon fatty acids are the most common. Fatty acid synthesis occurs in the cytoplasm. In the first step, acetyl-Coenzyme A (CoA) carboxylase (ACC) synthesizes malonyl-CoA from acetyl-CoA and bicarbonate. The enzymes which catalyze the remaining reactions are covalently linked into a single polypeptide chain, referred to as the multifunctional enzyme fatty acid synthase (FAS). FAS catalyzes the synthesis of palmitate from 5 acetyl-CoA and malonyl-CoA. FAS contains acetyl transferase, malonyl transferase, β-ketoacetyl synthase, acyl carrier protein, β-ketoacyl reductase, dehydratase, enoyl reductase, and thioesterase activities. The final product of the FAS reaction is the 16-carbon fatty acid palmitate. Further elongation, as well as unsaturation, of palmitate by accessory enzymes of the ER produces the variety of long chain fatty acids required by the individual cell. These enzymes include a NADH-cytochrome 0 b5 reductase, cytochrome b5, and a desaturase. Phospholipid and Triacylglycerol Synthesis
Triacylglycerols, also known as triglycerides and neutral fats, are major energy stores in animals. Triacylglycerols are esters of glycerol with three fatty acid chains. Glycerol-3-phosphate is produced from dihydroxyacetone phosphate by the enzyme glycerol phosphate dehydrogenase or from 5 glycerol by glycerol kinase. Fatty acid-CoA's are produced from fatty acids by fatty acyl-CoA synthetases. Glyercol-3-phosphate is acylated with two fatty acyl-CoA's by the enzyme glycerol phosphate acylfransferase to give phosphatidate. Phosphatidate phosphatase converts phosphatidate to diacylglycerol, which is subsequently acylated to a triacylglyercol by the enzyme diglyceride acylfransferase. Phosphatidate phosphatase and diglyceride acylfransferase form a triacylglyerol o synthetase complex bound to the ER membrane.
A major class of phosphoUpids are the phosphoglycerides, which are composed of a glycerol backbone, two fatty acid chains, and a phosphorylated alcohol. Phosphoglycerides are components of cell membranes. Principal phosphoglycerides are phosphatidyl choline, phosphatidyl ethanolamine, phosphatidyl serine, phosphatidyl inositol, and diphosphatidyl glycerol. Many enzymes involved in 5 phosphoglyceride synthesis are associated with membranes (Meyers, R.A. (1995) Molecular Biology and Biotechnology, VCH Publishers Inc., New York NY, pp. 494-501). Phosphatidate is converted to CDP-diacylglycerol by the enzyme phosphatidate cytidylylfransferase (ExPASy ENZYME EC 2.7.7.41). Transfer of the diacylglycerol group from CDP-diacylglycerol to serine to yield phosphatidyl serine, or to inositol to yield phosphatidyl inositol, is catalyzed by the enzymes CDP-diacylglycerol- o serine O-phosphatidyltransferase and CDP-diacylglycerol-inositol 3-phosphatidyltransferase, respectively (ExPASy ENZYME EC 2.7.8.8; ExPASy ENZYME EC 2.7.8.11). The enzyme phosphatidyl serine decarboxylase catalyzes the conversion of phosphatidyl serine to phosphatidyl ethanolamine, using a pyruvate cofactor (Voelker, D.R. (1997) Biochim. Biophys. Acta 1348:236-244). Phosphatidyl choline is formed using diet-derived choline by the reaction of CDP-choline with 1,2- 5 diacylglycerol, catalyzed by diacylglycerol choUnephosphofransferase (ExPASy ENZYME 2.7.8.2). Sterol, Steroid, and Isoprenoid Metabolism
Cholesterol, composed of four fused hydrocarbon rings with an alcohol at one end, moderates the fluidity of membranes in which it is incoφorated. In addition, cholesterol is used in the synthesis of steroid hormones such as cortisol, progesterone, estrogen, and testosterone. Bile salts derived from cholesterol faciUtate the digestion of lipids. Cholesterol in the skin forms a barrier that prevents excess water evaporation from the body. Farnesyl and geranylgeranyl groups, which are derived from cholesterol biosynthesis intermediates, are post-franslationally added to signal transduction proteins such as ras and protein-targeting proteins such as rab. These modifications are important for the activities of these proteins (Guyton, supra; Stryer, supra, pp. 279-280, 691-702, 934). Mammals obtain cholesterol derived from both de novo biosynthesis and the diet. The liver is the major site of cholesterol biosynthesis in mammals. Two acetyl-CoA molecules initially condense to form acetoacetyl-CoA, catalyzed by a thiolase. Acetoacetyl-CoA condenses with a third acetyl-CoA to form hydroxymethylglutaryl-CoA (HMG-CoA), catalyzed by HMG-CoA synthase. Conversion of HMG-CoA to cholesterol is accomplished via a series of enzymatic steps known as the mevalonate pathway. The rate-limiting step is the conversion of HMG-CoA to mevalonate by HMG-CoA reductase. The drug lovastatin, a potent inhibitor of HMG-CoA reductase, is given to patients to reduce their serum cholesterol levels. Other mevalonate pathway enzymes include mevalonate kinase, phosphomevalonate kinase, diphosphomevalonate decarboxylase, isopentenyldiphosphate isomerase, dimethylallyl transferase, geranyl transferase, farnesyl-diphosphate farnesyltransferase, squalene monooxygenase, lanosterol synthase, lathosterol oxidase, and 7-dehydrocholesterol reductase. Cholesterol is used in the synthesis of steroid hormones such as cortisol, progesterone, aldosterone, estrogen, and testosterone. First, cholesterol is converted to pregnenolone by cholesterol monooxygenases. The other steroid hormones are synthesized from pregnenolone by a series of enzyme-catalyzed reactions including oxidations, isomerizations, hydroxylations, reductions, and demethylations. Examples of these enzymes include steroid Δ-isomerase, 3β-hydroxy-Δ5-steroid dehydrogenase, steroid 21 -monooxygenase, steroid 19-hydroxylase, and 3β-hydroxysteroid dehydrogenase. Cholesterol is also the precursor to vitamin D.
Numerous compounds contain 5 -carbon isoprene units derived from the mevalonate pathway intermediate isopentenyl pyrophosphate. Isoprenoid groups are found in vitamin K, ubiquinone, retinal, dolichol phosphate (a carrier of oligosaccharides needed for N-linked glycosylation), and farnesyl and geranylgeranyl groups that modify proteins. Enzymes involved include farnesyl transferase, polyprenyl transferases, dolichyl phosphatase, and dolichyl kinase. Sphingolipid Metabolism
Sphingolipids are an important class of membrane Upids that contain sphingosine, a long chain amino alcohol. They are composed of one long-chain fatty acid, one polar head alcohol, and sphingosine or sphingosine derivative. The three classes of sphingolipids are sphingomyeUns, cerebrosides, and gangliosides. SphingomyeUns, which contain phosphochoUne or phosphoethanolamine as their head group, are abundant in the myelin sheath surrounding nerve cells.
Galactocerebrosides, which contain a glucose or galactose head group, are characteristic of the brain. 5 Other cerebrosides are found in nonneural tissues. Gangliosides, whose head groups contain multiple sugar units, are abundant in the brain, but are also found in nonneural tissues.
SphingoUpids are built on a sphingosine backbone. Sphingosine is acylated to ceramide by the enzyme sphingosine acetyltransferase. Ceramide and phosphatidyl choline are converted to sphingomyelin by the enzyme ceramide choline phosphotransferase. Cerebrosides are synthesized by 0 the linkage of glucose or galactose to ceramide by a fransferase. Sequential addition of sugar residues to ceramide by transferase enzymes yields gangliosides.
Eicosanoid Metabolism
Eicosanoids, including prostaglandins, prostacyclin, thromboxanes, and leukotrienes, are 20- carbon molecules derived from fatty acids. Eicosanoids are signaling molecules which have roles in 5 pain, fever, and inflammation. The precursor of all eicosanoids is arachidonate, which is generated from phosphoUpids by phospholipase A2 and from diacylglycerols by diacylglycerol lipase.
Leukotrienes are produced from arachidonate by the action of lipoxygenases. Prostaglandin synthase, reductases, and isomerases are responsible for the synthesis of the prostaglandins. Prostaglandins have roles in inflammation, blood flow, ion fransport, synaptic transmission, and sleep. Prostacyclin and the o thromboxanes are derived from a precursor prostaglandin by the action of prostacyclin synthase and thromboxane synthases, respectively.
Ketone Body Metabolism
Pairs of acetyl-CoA molecules derived from fatty acid oxidation in the liver can condense to form acetoacetyl-CoA, which subsequently forms acetoacetate, D-3-hydroxybutyrate, and acetone. 5 These three products are known as ketone bodies. Enzymes involved in ketone body metabolism include HMG-CoA synthetase, HMG-CoA cleavage enzyme, D-3-hydroxybutyrate dehydrogenase, acetoacetate decarboxylase, and 3-ketoacyl-CoA transferase. Ketone bodies are a normal fuel supply of the heart and renal cortex. Acetoacetate produced by the liver is transported to cells where the acetoacetate is converted back to acetyl-CoA and enters the citric acid cycle. In times of starvation, o ketone bodies produced from stored friacylglyerols become an important fuel source, especially for the brain. Abnormally high levels of ketone bodies are observed in diabetics. Diabetic coma can result if ketone body levels become too great. Lipid Mobilization
Within cells, fatty acids are transported by cytoplasmic fatty acid binding proteins (Online 5 MendeUan Inheritance in Man (OMIM) *134650 Fatty Acid-Binding Protein 1 , Liver; FABP1 ). Diazepam binding inhibitor (DBI), also known as endozepine and acyl CoA-binding protein, is an endogenous γ-aminobutyric acid (GABA) receptor ligand which is thought to down-regulate the effects of GABA. DBI binds medium- and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters (OMIM *125950 Diazepam Binding Inhibitor; 5 DBI; PROSITE PDOC00686 Acyl-CoA-binding protein signature).
Fat stored in liver and adipose triglycerides may be released by hydrolysis and transported in the blood. Free fatty acids are transported in the blood by albumin. Triacylglycerols and cholesterol esters in the blood are transported in lipoprotein particles. The particles consist of a core of hydrophobic Upids surrounded by a shell of polar lipids and apoUpoproteins. The protein components 0 serve in the solubiUzation of hydrophobic Upids and also contain cell-targeting signals. Lipoproteins include chylomicrons, chylomicron remnants, very-low-density lipoproteins (VLDL), intermediate- density lipoproteins (IDL), low-density lipoproteins (LDL), and high-density lipoproteins (HDL). There is a strong inverse correlation between the levels of plasma HDL and risk of premature coronary heart disease. 5 Triacylglycerols in chylomicrons and VLDL are hydrolyzed by lipoprotein Upases that line blood vessels in muscle and other tissues that use fatty acids. Cell surface LDL receptors bind LDL particles which are then internalized by endocytosis. Absence of the LDL receptor, the cause of the disease familial hypercholesterolemia, leads to increased plasma cholesterol levels and ultimately to atherosclerosis. Plasma cholesteryl ester transfer protein mediates the fransfer of cholesteryl esters o from HDL to apolipoprotein B-containing lipoproteins. Cholesteryl ester transfer protein is important in the reverse cholesterol transport system and may play a role in atherosclerosis (Yamashita, S. et al. (1997) Curr. Opin. Lipidol. 8:101-110). Macrophage scavenger receptors, which bind and internalize modified lipoproteins, play a role in Upid transport and may contribute to atherosclerosis (Greaves, D.R. et al. (1998) Curr. Opin. Lipidol. 9:425-432). 5 Proteins involved in cholesterol uptake and biosynthesis are tightly regulated in response to cellular cholesterol levels. The sterol regulatory element binding protein (SREBP) is a sterol-responsive transcription factor. Under normal cholesterol conditions, SREBP resides in the ER membrane. When cholesterol levels are low, a regulated cleavage of SREBP occurs which releases the extracellular domain of the protein. This cleaved domain is then transported to the nucleus where it activates the o transcription of the LDL receptor gene, and genes encoding enzymes of cholesterol synthesis, by binding the sterol regulatory element (SRE) upstream of the genes (Yang, J. et al. (1995) J. Biol. Chem. 270:12152-12161). Regulation of cholesterol uptake and biosynthesis also occurs via the oxysterol- binding protein (OSBP). OSBP is a high-affinity intracellular receptor for a variety of oxysterols that down-regulate cholesterol synthesis and stimulate cholesterol esterification (Lagace, T.A. et al. (1997) 5 Biochem. J. 326:205-213). Beta-oxidation
Mitochondrial and peroxisomal beta-oxidation enzymes degrade saturated and unsaturated fatty acids by sequential removal of two-carbon units from CoA-activated fatty acids. The main beta- oxidation pathway degrades both saturated and unsaturated fatty acids while the auxiliary pathway performs additional steps required for the degradation of unsaturated fatty acids.
The pathways of mitochondrial and peroxisomal beta-oxidation use similar enzymes, but have different substrate specificities and functions. Mitochondria oxidize short-, medium-, and long-chain fatty acids to produce energy for cells. Mitochondrial beta-oxidation is a major energy source for cardiac and skeletal muscle. In Uver, it provides ketone bodies to the peripheral circulation when glucose levels are low as in starvation, endurance exercise, and diabetes (Eaton, S. et al. (1996) Biochem. J. 320:345-357). Peroxisomes oxidize medium-, long-, and very-long-chain fatty acids, dicarboxylic fatty acids, branched fatty acids, prostaglandins, xenobiotics, and bile acid intermediates. The chief roles of peroxisomal beta-oxidation are to shorten toxic lipophilic carboxylic acids to facilitate their excretion and to shorten very-long-chain fatty acids prior to mitochondrial beta-oxidation (Mannaerts, G.P. and P.P. van Veldhoven (1993) Biochimie 75:147-158).
Enzymes involved in beta-oxidation include acyl CoA synthetase, carnitine acylfransferase, acyl CoA dehydrogenases, enoyl CoA hydratases, L-3-hydroxyacyl CoA dehydrogenase, β-ketothiolase, 2,4-dienoyl CoA reductase, and isomerase. Lipid Cleavage and Degradation Triglycerides are hydrolyzed to fatty acids and glycerol by Upases. Lysophospholipases
(LPLs) are widely distributed enzymes that metabolize intracellular lipids, and occur in numerous isoforms. Small isoforms, approximately 15-30 kD, function as hydrolases; large isoforms, those exceeding 60 kD, function both as hydrolases and transacylases. A particular substrate for LPLs, lysophosphatidylchoUne, causes lysis of cell membranes when it is formed or imported into a cell. LPLs are regulated by lipid factors including acylcarnitine, arachidonic acid, and phosphatidic acid. These lipid factors are signaUng molecules important in numerous pathways, including the inflammatory response. (Anderson, R. et al. (1994) Toxicol. Appl. Pharmacol. 125:176-183; Selle, H. et al. (1993); Eur. J. Biochem. 212:411-416.)
The secretory phospholipase A2 (PLA2) superfamily comprises a number of heterogeneous enzymes whose common feature is to hydrolyze the sn-2 fatty acid acyl ester bond of phosphoglycerides. Hydrolysis of the glycerophospholipids releases free fatty acids and lysophospholipids. PLA2 activity generates precursors for the biosynthesis of biologically active lipids, hydroxy fatty acids, and platelet-activating factor. PLA2 hydrolysis of the sn-2 ester bond in phosphoUpids generates free fatty acids, such as arachidonic acid and lysophospholipids. Carbon and Carbohydrate Metabolism Carbohydrates, including sugars or saccharides, starch, and cellulose, are aldehyde or ketone compounds with multiple hydroxyl groups. The importance of carbohydrate metaboUsm is demonstrated by the sensitive regulatory system in place for maintenance of blood glucose levels. Two pancreatic hormones, insulin and glucagon, promote increased glucose uptake and storage by cells, and 5 increased glucose release from cells, respectively. Carbohydrates have three important roles in mammaUan cells. First, carbohydrates are used as energy stores, fuels, and metabolic intermediates. Carbohydrates are broken down to form energy in glycolysis and are stored as glycogen for later use. Second, the sugars deoxyribose and ribose form part of the structural support of DNA and RNA, respectively. Third, carbohydrate modifications are added to secreted and membrane proteins and lipids 0 as they traverse the secretory pathway. Cell surface carbohydrate-containing macromolecules, including glycoproteins, glycolipids, and transmembrane proteoglycans, mediate adhesion with other cells and with components of the extracellular matrix. The extracellular mafrix is comprised of diverse glycoproteins, glycosaminoglycans (GAGs), and carbohydrate-binding proteins which are secreted from the cell and assembled into an organized meshwork in close association with the cell surface. The 5 interaction of the cell with the surrounding matrix profoundly influences cell shape, strength, flexibility, motility, and adhesion. These dynamic properties are intimately associated with signal transduction pathways conttolUng cell proliferation and differentiation, tissue construction, and embryonic development.
Carbohydrate metabolism is altered in several disorders including diabetes melUtus, o hyperglycemia, hypoglycemia, galactosemia, galactokinase deficiency, and UDP-galactose-4-epimerase deficiency (Fauci, A.S. et al. (1998) Harrison's Principles of Internal Medicine, McGraw-Hill, New York NY, pp. 2208-2209). Altered carbohydrate metabolism is associated with cancer. Reduced GAG and proteoglycan expression is associated with human lung carcinomas (Nackaerts, K. et al. (1997) Int. J. Cancer 74:335-345). The carbohydrate determinants sialyl Lewis A and sialyl Lewis X are 5 frequently expressed on human cancer cells (Kannagi, R. (1997) Glycoconj. J. 14:577-584).
Alterations of the N-linked carbohydrate core structure of cell surface glycoproteins are linked to colon and pancreatic cancers (Schwarz, R.E. et al. (1996) Cancer Lett. 107:285-291). Reduced expression of the Sda blood group carbohydrate structure in cell surface glycolipids and glycoproteins is observed in gastrointestinal cancer (Dohi, T. et al. (1996) Int. J. Cancer 67:626-663). (Carbon and o carbohydrate metabolism is reviewed in Stryer, L. (1995) Biochemistry W.H. Freeman and Company,
New York NY; Lehninger, A.L. (1982) Principles of Biochemistry Worth Publishers Inc., New York NY; and Lodish, H. et al. (1995) Molecular Cell Biology Scientific American Books, New York NY.) Glycolysis
Enzymes of the glycolytic pathway convert the sugar glucose to pyruvate while simultaneously 5 producing ATP. The pathway also provides building blocks for the synthesis of cellular components such as long-chain fatty acids. After glycolysis, pyrvuate is converted to acetyl-Coenzyme A, which, in aerobic organisms, enters the citric acid cycle. Glycolytic enzymes include hexokinase, phosphoglucose isomerase, phosphofructokinase, aldolase, triose phosphate isomerase, glyceraldehyde 3 -phosphate dehydrogenase, phosphoglycerate kinase, phosphoglyceromutase, enolase, and pyruvate kinase. Of 5 these, phosphofructokinase, hexokinase, and pyruvate kinase are important in regulating the rate of glycolysis. Gluconeogenesis
Gluconeogenesis is the synthesis of glucose from noncarbohydrate precursors such as lactate and amino acids. The pathway, which functions mainly in times of starvation and intense exercise, o occurs mostly in the liver and kidney. Responsible enzymes include pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose 1,6-bisphosphatase, and glucose-6-phosphatase. Pentose Phosphate Pathway
Pentose phosphate pathway enzymes are responsible for generating the reducing agent NADPH, while at the same time oxidizing glucose-6-phosphate to ribose- -phosphate. Ribose-5- 5 phosphate and its derivatives become part of important biological molecules such as ATP, Coenzyme A, NAD+, FAD, RNA, and DNA. The pentose phosphate pathway has both oxidative and non- oxidative branches. The oxidative branch steps, which are catalyzed by the enzymes glucose-6- phosphate dehydrogenase, lactonase, and 6-phosphogluconate dehydrogenase, convert glucose-6- phosphate and NADP+ to ribulose-6-phosphate and NADPH. The non-oxidative branch steps, which 0 are catalyzed by the enzymes phosphopentose isomerase, phosphopentose epimerase, fransketolase, and fransaldolase, allow the interconversion of three-, four-, five-, six-, and seven-carbon sugars. Glucouronate Metabolism
Glucuronate is a monosaccharide which, in the form of D-glucuronic acid, is found in the GAGs chondroitin and dermatan. D-glucuronic acid is also important in the detoxification and 5 excretion of foreign organic compounds such as phenol. Enzymes involved in glucuronate metabolism include UDP-glucose dehydrogenase and glucuronate reductase. Disaccharide Metabolism
Disaccharides must be hydrolyzed to monosaccharides to be digested. Lactose, a disaccharide found in milk, is hydrolyzed to galactose and glucose by the enzyme lactase. Maltose is derived from o plant starch and is hydrolyzed to glucose by the enzyme maltase. Sucrose is derived from plants and is hydrolyzed to glucose and fructose by the enzyme sucrase. Trehalose, a disaccharide found mainly in insects and mushrooms, is hydrolyzed to glucose by the enzyme trehalase (OMIM *275360 Trehalase; Ruf, J. et al. (1990) J. Biol. Chem. 265:15034-15039). Lactase, maltase, sucrase, and trehalase are bound to mucosal cells lining the small intestine, where they participate in the digestion of dietary 5 disaccharides. The enzyme lactose synthetase, composed of the catalytic subunit galactosylfransferase and the modifier subunit α-lactalbumin, converts UDP-galactose and glucose to lactose in the mammary glands.
Glycogen, Starch, and Chitin MetaboUsm
Glycogen is the storage form of carbohydrates in mammals. Mobilization of glycogen 5 maintains glucose levels between meals and during muscular activity. Glycogen is stored mainly in the Uver and in skeletal muscle in the form of cytoplasmic granules. These granules contain enzymes that catalyze the synthesis and degradation of glycogen, as well as enzymes that regulate these processes. Enzymes that catalyze the degradation of glycogen include glycogen phosphorylase, a transferase, α- 1,6-glucosidase, and phosphoglucomutase. Enzymes that catalyze the synthesis of glycogen include o UDP-glucose pyrophosphorylase, glycogen synthetase, a branching enzyme, and nucleoside diphosphokinase. The enzymes of glycogen synthesis and degradation are tightly regulated by the hormones insuUn, glucagon, and epinephrine. Starch, a plant-derived polysaccharide, is hydrolyzed to maltose, maltotriose, and α-dexfrin by α-amylase, an enzyme secreted by the salivary glands and pancreas. Chitin is a polysaccharide found in insects and Crustacea. A chitofriosidase is secreted by 5 macrophages and may play a role in the degradation of chitin-containing pathogens (Boot, R.G. et al. (1995) J. Biol. Chem. 270:26252-26256). Peptidoglvcans and Glycosaminoglvcans
Glycosaminoglycans (GAGs) are anionic linear unbranched polysaccharides composed of repetitive disaccharide units. These repetitive units contain a derivative of an amino sugar, either o glucosamine or galactosamine. GAGs exist free or as part of proteoglycans, large molecules composed of a core protein attached to one or more GAGs. GAGs are found on the cell surface, inside cells, and in the extracellular mafrix. Changes in GAG levels are associated with several autoimmune diseases including autoimmune thyroid disease, autoimmune diabetes mellitus, and systemic lupus eryfhematosus (Hansen, C. et al. (1996) Clin. Exp. Rheum. 14 (Suppl. 15):S59-S67). GAGs include 5 chondroitin sulfate, keratan sulfate, heparin, heparan sulfate, dermatan sulfate, and hyaluronan.
The GAG hyaluronan (HA) is found in the extracellular matrix of many cells, especially in soft connective tissues, and is abundant in synovial fluid (Pitsillides, A.A. et al. (1993) Int. J. Exp. Pathol. 74:27-34). HA seems to play important roles in cell regulation, development, and differentiation (Laurent, T.C and J.R. Fraser (1992) FASEB J. 6:2397-2404). Hyaluronidase is an enzyme that o degrades HA to oUgosaccharides. Hyaluronidases may function in cell adhesion, infection, angiogenesis, signal transduction, reproduction, cancer, and inflammation.
Proteoglycans, also known as peptidoglycans, are found in the extracellular matrix of connective tissues such as cartilage and are essential for distributing the load in weight-bearing joints. Cell-surface-attached proteoglycans anchor cells to the extracellular matrix. Both extracellular and 5 cell-surface proteoglycans bind growth factors, faciUtating their binding to cell-surface receptors and subsequent triggering of signal transduction pathways. Amino Acid and Nitrogen Metabolism
NH4 + is assimilated into amino acids by the actions of two enzymes, glutamate dehydrogenase and glutamine synthetase. The carbon skeletons of amino acids come from the intermediates of glycolysis, the pentose phosphate pathway, or the citric acid cycle. Of the twenty amino acids used in proteins, humans can synthesize only thirteen (nonessential amino acids). The remaining nine must come from the diet (essential amino acids). Enzymes involved in nonessential amino acid biosynthesis include glutamate kinase dehydrogenase, pyrroline carboxylate reductase, asparagine synthetase, phenylalanine oxygenase, methionine adenosylttansferase, adenosylhomocysteinase, cystathionine β-synthase, cystathionine γ-lyase, phosphoglycerate dehydrogenase, phosphoserine fransaminase, phosphoserine phosphatase, serine hydroxylmethyltransferase, and glycine synthase.
Metabolism of amino acids takes place almost entirely in the liver, where the amino group is removed by aminofransferases (transaminases), for example, alanine aminotransferase. The amino group is transferred to α-ketoglutarate to form glutamate. Glutamate dehydrogenase converts glutamate to NH4 + and α-ketoglutarate. NH4 +is converted to urea by the urea cycle which is catalyzed by the enzymes arginase, ornithine transcarbamoylase, arginosuccinate synthetase, and arginosuccinase. Carbamoyl phosphate synthetase is also involved in urea formation. Enzymes involved in the metabolism of the carbon skeleton of amino acids include serine dehydratase, asparaginase, glutaminase, propionyl CoA carboxylase, methylmalonyl CoA mutase, branched-chain α-keto dehydrogenase complex, isovaleryl CoA dehydrogenase, β-methylcrotonyl CoA carboxylase, phenylalanine hydroxylase, p-hydroxylphenylpyruvate hydroxylase, and homogentisate oxidase.
Polyamines, which include spermidine, pufrescine, and spermine, bind tightly to nucleic acids and are abundant in rapidly proliferating cells. Enzymes involved in polyamine synthesis include ornithine decarboxylase.
Diseases involved in amino acid and nitrogen metabolism include hyperammonemia, carbamoyl phosphate synthetase deficiency, urea cycle enzyme deficiencies, methylmalonic aciduria, maple syrup disease, alcaptonuria, and phenylketonuria. Energy Metabolism Cells derive energy from metabolism of ingested compounds that may be roughly categorized as carbohydrates, fats, or proteins. Energy is also stored in polymers such as triglycerides (fats) and glycogen (carbohydrates). Metabolism proceeds along separate reaction pathways connected by key intermediates such as acetyl coenzyme A (acetyl-CoA). Metabolic pathways feature anaerobic and aerobic degradation, coupled with the energy-requiring reactions such as phosphorylation of adenosine diphosphate (ADP) to the friphosphate (ATP) or analogous phosphorylations of guanosine (GDP/GTP). uridine (UDP/UTP), or cytidine (CDP/CTP). Subsequent dephosphorylation of the friphosphate drives reactions needed for cell maintenance, growth, and proliferation.
Digestive enzymes convert carbohydrates and sugars to glucose; fructose and galactose are converted in the Uver to glucose. Enzymes involved in these conversions include galactose- 1 - 5 phosphate uridyl fransferase and UDP-galactose-4 epimerase. In the cytoplasm, glycolysis converts glucose to pyruvate in a series of reactions coupled to ATP synthesis.
Pyruvate is transported into the mitochondria and converted to acetyl-CoA for oxidation via the citric acid cycle, involving pyruvate dehydrogenase components, dihydrolipoyl fransacetylase, and dihydrolipoyl dehydrogenase. Enzymes involved in the citric acid cycle include: citrate synthetase, 0 aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including franssuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate dehydrogenase. Acetyl CoA is oxidized to C02 with concomitant formation of NADH, FADH2, and GTP. In oxidative phosphorylation, the transport of electrons from NADH and FADH2 to oxygen by dehydrogenases is coupled to the synthesis of ATP from ADP and P. by the FQF, ATPase complex in 5 the mitochondrial inner membrane. Enzyme complexes responsible for electron fransport and ATP synthesis include the F0Fi ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone reductase, cytochrome b, cytochrome c]( FeS protein, and cytochrome c oxidase.
Triglycerides are hydrolyzed to fatty acids and glycerol by Upases. Glycerol is then phosphorylated to glycerol -3 -phosphate by glycerol kinase and glycerol phosphate dehydrogenase, 0 and degraded by the glycolysis. Fatty acids are transported into the mitochondria as fatty acylcarnitine esters and undergo oxidative degradation.
In addition to metabolic disorders such as diabetes and obesity, disorders of energy metabolism are associated with cancers (Dorward, A. et al. (1997) J. Bioenerg. Biomembr. 29:385- 392), autism (Lombard, J. (1998) Med. Hypotheses 50:497-500), neurodegenerative disorders (Alexi, 5 T. et al. (1998) Neuroreport 9:R57-64), and neuromuscular disorders (DiMauro, S. et al. (1998) Biochim. Biophys. Acta 1366:199-210). The myocardium is heavily dependent on oxidative metabolism, so metabolic dysfunction often leads to heart disease (DiMauro, S. and M. Hirano (1998) Curr. Opin. Cardiol. 13: 190-197).
For a review of energy metabolism enzymes and intermediates, see Stryer, L. et al. (1995) o Biochemistry. W.H. Freeman and Co., San Francisco CA, pp. 443-652. For a review of energy metabolism regulation, see Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York NY, pp. 744-770. Cofactor Metabolism
Cofactors, including coenzymes and prosthetic groups, are small molecular weight inorganic 5 or organic compounds that are required for the action of an enzyme. Many cofactors contain vitamins as a component. Cofactors include thiamine pyrophosphate, flavin adenine dinucleotide, flavin mononucleotide, nicotinamide adenine dinucleotide, pyridoxal phosphate, coenzyme A, tetrahydrofolate, lipoamide, and heme. The vitamins biotin and cobalamin are associated with enzymes as well. Heme, a prosthetic group found in myoglobin and hemoglobin, consists of 5 protopoφhyrin group bound to iron. Poφhyrin groups contain four substituted pyrroles covalentiy joined in a ring, often with a bound metal atom. Enzymes involved in poφhyrin synthesis include δ- aminolevulinate synthase, δ-aminolevulinate dehydrase, poφhobilinogen deaminase, and cosynthase. Deficiencies in heme formation cause poφhyrias. Heme is broken down as a part of erythrocyte turnover. Enzymes involved in heme degradation include heme oxygenase and biliverdin reductase. o Iron is a required cofactor for many enzymes. Besides the heme-containing enzymes, iron is found in iron-sulfur clusters in proteins including aconitase, succinate dehydrogenase, and NADH-Q reductase. Iron is transported in the blood by the protein transferrin. Binding of transferrin to the fransferrin receptor on cell surfaces allows uptake by receptor mediated endocytosis. Cytosolic iron is bound to ferritin protein. 5 A molybdenum-containing cofactor (molybdopterin) is found in enzymes including sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. Molybdopterin biosynthesis is performed by two molybdenum cofactor synthesizing enzymes. Deficiencies in these enzymes cause mental retardation and lens dislocation. Other diseases caused by defects in cofactor metabolism include pernicious anemia and methylmalonic aciduria. 0 Secretion and Trafficking
Eukaryotic cells are bound by a lipid bilayer membrane and subdivided into functionally distinct, membrane bound compartments. The membranes maintain the essential differences between the cytosol, the exfracellular environment, and the lumenal space of each intracellular organelle. As lipid membranes are highly impermeable to most polar molecules, transport of essential nutrients, 5 metabolic waste products, cell signaling molecules, macromolecules and proteins across lipid membranes and between organelles must be mediated by a variety of transport-associated molecules. Protein Trafficking
In eukaryotes, some proteins are synthesized on ER-bound ribosomes, co-franslationally imported into the ER, delivered from the ER to the Golgi complex for post-translational processing and o sorting, and fransported from the Golgi to specific intracellular and extracellular destinations. All cells possess a constitutive transport process which maintains homeostasis between the cell and its environment. In many differentiated cell types, the basic machinery is modified to carry out specific fransport functions. For example, in endocrine glands, hormones and other secreted proteins are packaged into secretory granules for regulated exocytosis to the cell exterior. In macrophage, foreign 5 extracellular material is engulfed (phagocytosis) and delivered to lysosomes for degradation. In fat and muscle cells, glucose transporters are stored in vesicles which fuse with the plasma membrane only in response to insutin stimulation. The Secretory Pathway
Synthesis of most integral membrane proteins, secreted proteins, and proteins destined for the lumen of a particular organelle occurs on ER-bound ribosomes. These proteins are co-translationally imported into the ER. The proteins leave the ER via membrane-bound vesicles which bud off the ER at specific sites and fuse with each other (homotypic fusion) to form the ER-Golgi Intermediate Compartment (ERGIC). The ERGIC matures progressively through the cis, medial, and trans cisternal stacks of the Golgi, modifying the enzyme composition by retrograde transport of specific Golgi enzymes. In this way, proteins moving through the Golgi undergo post-franslational modification, such as glycosylation. The final Golgi compartment is the Trans-Golgi Network (TGN), where both membrane and lumenal proteins are sorted for their final destination. Transport vesicles destined for intracellular compartments, such as the lysosome, bud off the TGN. What remains is a secretory vesicle which contains proteins destined for the plasma membrane, such as receptors, adhesion molecules, and ion channels, and secretory proteins, such as hormones, neurofransmitters, and digestive enzymes. Secretory vesicles eventually fuse with the plasma membrane (GUck, B.S. and V. Malhofra (1998) Cell 95:883-889).
The secretory process can be constitutive or regulated. Most cells have a constitutive pathway for secretion, whereby vesicles derived from maturation of the TGN require no specific signal to fuse with the plasma membrane. In many cells, such as endocrine cells, digestive cells, and neuroas, vesicle pools derived from the TGN collect in the cytoplasm and do not fuse with the plasma membrane until they are directed to by a specific signal. Endocytosis
Endocytosis, wherein cells internalize material from the extracellular environment, is essential for transmission of neuronal, metabolic, and proliferative signals; uptake of many essential nutrients; and defense against invading organisms. Most cells exhibit two forms of endocytosis. The first, phagocytosis, is an actin-driven process exemplified in macrophage and neutrophils. Material to be endocytosed contacts numerous cell surface receptors which stimulate the plasma membrane to extend and surround the particle, enclosing it in a membrane-bound phagosome. In the mammalian immune system, IgG-coated particles bind Fc receptors on the surface of phagocytic leukocytes. Activation of the Fc receptors initiates a signal cascade involving src-family cytosolic kinases and the monomeric GTP-binding (G) protein Rho. The resulting actin reorganization leads to phagocytosis of the particle. This process is an important component of the humoral immune response, allowing the processing and presentation of bacterial-derived peptides to antigen-specific T-lymphocytes. The second form of endocytosis, pinocytosis, is a more generalized uptake of material from the external miUeu. Like phagocytosis, pinocytosis is activated by Ugand binding to cell surface receptors. Activation of individual receptors stimulates an internal response that includes coalescence of the receptor-ligand complexes and formation of clathrin-coated pits. Imagination of the plasma membrane at clathrin-coated pits produces an endocytic vesicle within the cell cytoplasm. These vesicles undergo homotypic fusion to form an early endosomal (EE) compartment. The tubulovesicular EE serves as a sorting site for incoming material. ATP-driven proton pumps in the EE membrane lowers the pH of the EE lumen (pH 6.3-6.8). The acidic environment causes many hgands to dissociate from their receptors. The receptors, along with membrane and other integral membrane proteins, are recycled back to the plasma membrane by budding off the tubular extensions of the EE in recycling vesicles (RV). This selective removal of recycled components produces a carrier vesicle containing ligand and other material from the external environment. The carrier vesicle fuses with TGN-derived vesicles which contain hydrolytic enzymes. The acidic environment of the resulting late endosome (LE) activates the hydrolytic enzymes which degrade the ligands and other material. As digestion takes place, the LE fuses with the lysosome where digestion is completed (Mellman, I. (1996) Annu. Rev. Cell Dev. Biol. 12:575-625).
RecycUng vesicles may return directly to the plasma membrane. Receptors internalized and returned directly to the plasma membrane have a turnover rate of 2-3 minutes. Some RVs undergo microtubule-directed relocation to a perinuclear site, from which they then return to the plasma membrane. Receptors following this route have a turnover rate of 5-10 minutes. Still other RVs are retained within the cell until an appropriate signal is received (Mellman, supra; and James, D.E. et al. (1994) Trends Cell Biol. 4:120-126). Vesicle Formation
Several steps in the transit of material along the secretory and endocytic pathways require the formation of transport vesicles. Specifically, vesicles form at the transitional endoplasmic reticulum (tER), the rim of Golgi cisternae, the face of the Trans-Golgi Network (TGN), the plasma membrane (PM), and tubular extensions of the endosomes. The process begins with the budding of a vesicle out of the donor membrane. The membrane-bound vesicle contains proteins to be fransported and is surrounded by a protective coat made up of protein subunits recruited from the cytosol. The initial budding and coating processes are controlled by a cytosolic ras-like GTP-binding protein, ADP- ribosylating factor (Arf), and adapter proteins (AP). Different isoforms of both Arf and AP are involved at different sites of budding. Another small G-protein, dynamin, forms a ring complex around the neck of the forming vesicle and may provide the mechanochemical force to accomplish the final step of the budding process. The coated vesicle complex is then transported through the cytosol. During the transport process, Arf -bound GTP is hydrolyzed to GDP and the coat dissociates from the transport vesicle (West, M.A. et al. (1997) J. Cell Biol. 138:1239-1254). Two different classes of coat protein have also been identified. Clathrin coats form on the TGN and PM surfaces, whereas coatomer or COP coats form on the ER and Golgi. COP coats can further be distinguished as COPI, involved in retrograde traffic through the Golgi and from the Golgi to the ER, and COPII, involved in anterograde traffic from the ER to the Golgi (Mellman, supra). The COP coat consists of two major components, a 5 G-protein (Arf or Sar) and coat protomer (coatomer). Coatomer is an equimolar complex of seven proteins, termed alpha-, beta-, beta'-, gamma-, delta-, epsilon- and zeta-COP. (Harter, C. and F.T. Wieland (1998) Proc. Nati. Acad. Sci. USA 95:11649-11654.) Membrane Fusion
Transport vesicles undergo homotypic or heterotypic fusion in the secretory and endocytotic 0 pathways. Molecules required for appropriate targeting and fusion of vesicles with their target membrane include proteins incoφorated in the vesicle membrane, the target membrane, and proteins recruited from the cytosol. During budding of the vesicle from the donor compartment, an integral membrane protein, VAMP (vesicle-associated membrane protein) is incoφorated into the vesicle. Soon after the vesicle uncoats, a cytosolic prenylated GTP-binding protein, Rab (a member of the Ras 5 superfamily), is inserted into the vesicle membrane. GTP-bound Rab proteins are directed into nascent fransport vesicles where they interact with VAMP. Following vesicle fransport, GTPase activating proteins (GAPs) in the target membrane convert Rab proteins to the GDP-bound form. A cytosolic protein, guanine-nucleotide dissociation inhibitor (GDI) helps return GDP-bound Rab proteins to their membrane of origin. Several Rab isoforms have been identified and appear to associate with specific o compartments within the cell. Rab proteins appear to play a role in mediating the function of a viral gene, Rev, which is essential for replication of HIV-1, the virus responsible for AIDS (Flavell, R.A. et al. (1996) Proc. Nati. Acad. Sci. USA 93:4421-4424).
Docking of the fransport vesicle with the target membrane involves the formation of a complex between the vesicle SNAP receptor (v-SNARE), target membrane (t-) SNAREs, and certain other 5 membrane and cytosolic proteins. Many of these other proteins have been identified although their exact functions in the docking complex remain uncertain (Tellam, J.T. et al. (1995) J. Biol. Chem. 270:5857-63; and Hata, Y. and T.C Sudhof (1995) J. Biol. Chem. 270:13022-28). N-ethylmaleimide sensitive factor (NSF) and soluble NSF-attachment protein (α-SNAP and β-SNAP) are two such proteins that are conserved from yeast to man and function in most intracellular membrane fusion o reactions. Seel represents a family of yeast proteins that function at many different stages in the secretory pathway including membrane fusion. Recently, mammalian homologs of Seel , called Munc-18 proteins, have been identified (Katagiri, H. et al. (1995) J. Biol. Chem. 270:4963-4966; Hata et al. supra).
The SNARE complex involves three SNARE molecules, one in the vesicular membrane and 5 two in the target membrane. Synaptotagmin is an integral membrane protein in the synaptic vesicle which associates with the t-SNARE syntaxin in the docking complex. Synaptotagmin binds calcium in a complex with negatively charged phospholipids, which allows the cytosolic SNAP protein to displace synaptotagmin from syntaxin and fusion to occur. Thus, synaptotagmin is a negative regulator of fusion in the neuron (Littleton, J.T. et al. (1993) Cell 74:1125-1134). The most abundant membrane 5 protein of synaptic vesicles appears to be the glycoprotein synaptophysin, a 38 kDa protein with four transmembrane domains.
Specificity between a vesicle and its target is derived from the v-SNARE, t-SNAREs, and associated proteins involved. Different isoforms of SNAREs and Rabs show distinct cellular and subcellular distributions. VAMP-1/synaptobrevin, membrane-anchored synaptosome-associated 0 protein of 25 kDa (SNAP-25), syntaxin-1, Rab3A, Rabl5, and Rab23 are predominantly expressed in the brain and nervous system. Different syntaxin, VAMP, and Rab proteins are associated with distinct subcellular compartments and their vesicular carriers. Nuclear Transport
Transport of proteins and RNA between the nucleus and the cytoplasm occurs through nuclear 5 pore complexes (NPCs). NPC-mediated transport occurs in both directions through the nuclear envelope. All nuclear proteins are imported from the cytoplasm, their site of synthesis. tRNA and mRNA are exported from the nucleus, their site of synthesis, to the cytoplasm, their site of function. Processing of small nuclear RNAs involves export into the cytoplasm, assembly with proteins and modifications such as hypermethylation to produce small nuclear ribonuclear proteins (snRNPs), and o subsequent import of the snRNPs back into the nucleus. The assembly of ribosomes requires the initial import of ribosomal proteins from the cytoplasm, their incorporation with RNA into ribosomal subunits, and export back to the cytoplasm. (Gorlich, D. and l.W. Mattaj (1996) Science 271 :1513- 1518.)
The transport of proteins and mRNAs across the NPC is selective, dependent on nuclear 5 localization signals, and generally requires association with nuclear transport factors. Nuclear localization signals (NLS) consist of short stretches of amino acids enriched in basic residues. NLS are found on proteins that are targeted to the nucleus, such as the glucocorticoid receptor. The NLS is recognized by the NLS receptor, importin, which then interacts with the monomeric GTP-binding protein Ran. This NLS protein/receptor/Ran complex navigates the nuclear pore with the help of the o homodimeric protein nuclear transport factor 2 (NTF2). NTF2 binds the GDP-bound form of Ran and to multiple proteins of the nuclear pore complex containing FXFG repeat motifs, such as p62. (Paschal, B. et al. (1997) J. Biol. Chem. 272:21534-21539; and Wong, D.H. et al. (1997) Mol. Cell Biol. 17:3755-3767). Some proteins are dissociated before nuclear mRNAs are fransported across the NPC while others are dissociated shortly after nuclear mRNA transport across the NPC and are 5 reimported into the nucleus. Disease Correlation
The etiology of numerous human diseases and disorders can be attributed to defects in the fransport or secretion of proteins. For example, abnormal hormonal secretion is Unked to disorders such as diabetes insipidus (vasopressin), hyper- and hypoglycemia (insutin, glucagon), Grave's disease 5 and goiter (thyroid hormone), and Cushing's and Addison's diseases (adrenocorticotropic hormone, ACTH). Moreover, cancer cells secrete excessive amounts of hormones or other biologically active peptides. Disorders related to excessive secretion of biologically active peptides by tumor cells include fasting hypoglycemia due to increased insuUn secretion from insulinoma-islet cell tumors; hypertension due to increased epinephrine and norepinephrine secreted from pheochromocytomas of the adrenal 0 medulla and sympathetic paraganglia; and carcinoid syndrome, which is characterized by abdominal cramps, diarrhea, and valvular heart disease caused by excessive amounts of vasoactive substances such as serotonin, bradykinin, histamine, prostaglandins, and polypeptide hormones, secreted from intestinal tumors. Biologically active peptides that are ectopically synthesized in and secreted from tumor cells include ACTH and vasopressin (lung and pancreatic cancers); parathyroid hormone (lung 5 and bladder cancers); calcitonin (lung and breast cancers); and thyroid-stimulating hormone (medullary thyroid carcinoma). Such peptides may be useful as diagnostic markers for tumorigenesis (Schwartz, M.Z. (1997) Semin. Pediatr. Surg. 3:141-146; and Said, S.I. and GR. Faloona (1975) N. Engl. J. Med. 293:155-160).
Defective nuclear transport may play a role in cancer. The BRCA1 protein contains three o potential NLSs which interact with importin alpha, and is fransported into the nucleus by the importin/NPC pathway. In breast cancer cells the BRCA1 protein is aberrantly localized in the cytoplasm. The mislocation of the BRCA1 protein in breast cancer cells may be due to a defect in the NPC nuclear import pathway (Chen, C.F. et al. (1996) J. Biol. Chem. 271:32863-32868).
It has been suggested that in some breast cancers, the tumor-suppressing activity of p53 is 5 inactivated by the sequesfration of the protein in the cytoplasm, away from its site of action in the cell nucleus. Cytoplasmic wild-type p53 was also found in human cervical carcinoma cell lines. (Moll, U.M. et al. (1992) Proc. Nati. Acad. Sci. USA 89:7262-7266; and Liang, X.H. et al. (1993) Oncogene 8:2645-2652.) Environmental Responses o Organisms respond to the environment by a number of pathways. Heat shock proteins, including hsp 70, hsp60, hsp90, and hsp 40, assist organisms in coping with heat damage to cellular proteins.
Aquaporins (AQP) are channels that fransport water and, in some cases, nonionic small solutes such as urea and glycerol. Water movement is important for a number of physiological processes 5 including renal fluid filtration, aqueous humor generation in the eye, cerebrospinal fluid production in the brain, and appropriate hydration of the lung. Aquaporins are members of the major intrinsic protein (MIP) family of membrane transporters (King, L.S. and P. Agre (1996) Annu. Rev. Physiol. 58:619- 648; Ishibasbi, K. et al. (1997) J. Biol. Chem. 272:20782-20786). The study of aquaporins may have relevance to understanding edema formation and fluid balance in both normal physiology and disease 5 states (King, supra). Mutations in AQP2 cause autosomal recessive nephrogenic diabetes insipidus (OMIM *107777 Aquaporin 2; AQP2). Reduced AQP4 expression in skeletal muscle may be associated with Duchenne muscular dystrophy (Frigeri, A. et al. (1998) J. CUn. Invest. 102:695-703). Mutations in AQP0 cause autosomal dominant cataracts in the mouse (OMIM *154050 Major Intrinsic Protein of Lens Fiber; MIP). o The metallothioneins (MTs) are a group of small (61 amino acids), cysteine-rich proteins that bind heavy metals such as cadmium, zinc, mercury, lead, and copper and are thought to play a role in metal detoxification or the metabolism and homeostasis of metals. Arsenite-resistance proteins have been identified in hamsters that are resistant to toxic levels of arsenite (Rossman, T.G. et al. (1997) Mutat. Res. 386:307-314). 5 Humans respond to light and odors by specific protein pathways. Proteins involved in light perception include rhodopsin, fransducin, and cGMP phosphodiesterase. Proteins involved in odor perception include multiple olfactory receptors. Other proteins are important in human Circadian rhythms and responses to wounds. Immunity and Host Defense 0 All vertebrates have developed sophisticated and complex immune systems that provide protection from viral, bacterial, fungal and parasitic infections. Included in these systems are the processes of humoral immunity, the complement cascade and the inflammatory response (Paul, W.E. (1993) Fundamental Immunology, Raven Press, Ltd., New York NY, pp.1-20).
The cellular components of the humoral immune system include six different types of 5 leukocytes: monocytes, lymphocytes, polymoφhonuclear granulocytes (consisting of neufrophils, eosinophils, and basopbils) and plasma cells. Additionally, fragments of megakaryocytes, a seventh type of white blood cell in the bone marrow, occur in large numbers in the blood as platelets.
Leukocytes are formed from two stem cell lineages in bone marrow. The myeloid stem cell line produces granulocytes and monocytes and, the lymphoid stem cell produces lymphocytes. o Lymphoid cells fravel to the thymus, spleen and lymph nodes, where they mature and differentiate into lymphocytes. Leukocytes are responsible for defending the body against invading pathogens. Neufrophils and monocytes attack invading bacteria, viruses, and other pathogens and destroy them by phagocytosis. Monocytes enter tissues and differentiate into macrophages which are extremely phagocytic. Lymphocytes and plasma cells are a part of the immune system which recognizes 5 specific foreign molecules and organisms and inactivates them, as well as signals other cells to attack the invaders.
Granulocytes and monocytes are formed and stored in the bone marrow until needed. Megakaryocytes are produced in bone marrow, where they fragment into platelets and are released into the bloodstream. The main function of platelets is to activate the blood clotting mechanism. 5 Lymphocytes and plasma cells are produced in various lymphogenous organs, including the lymph nodes, spleen, thymus, and tonsils.
Both neufrophils and macrophages exhibit chemotaxis towards sites of inflammation. Tissue inflammation in response to pathogen invasion results in production of chemo-attractants for leukocytes, such as endotoxins or other bacterial products, prostaglandins, and products of leukocytes 0 or platelets.
Basophils participate in the release of the chemicals involved in the inflammatory process. The main function of basophils is secretion of these chemicals to such a degree that they have been referred to as "unicellular endocrine glands". A distinct aspect of basopbilic secretion is that the contents of granules go directly into the extracellular environment, not into vacuoles as occurs with 5 neufrophils, eosinophils and monocytes. Basophils have receptors for the Fc fragment of immunoglobuhn E (IgE) that are not present on other leukocytes. Crosslinking of membrane IgE with anti-IgE or other ligands triggers degranulation.
Eosinophils are bi- or multi-nucleated white blood cells which contain eosinophilic granules. Their plasma membrane is characterized by Ig receptors, particularly IgG and IgE. Generally, o eosinophils are stored in the bone marrow until recruited for use at a site of inflammation or invasion. They have specific functions in parasitic infections and allergic reactions, and are thought to detoxify some of the substances released by mast cells and basophils which cause inflammation. Additionally, they phagocytize antigen-antibody complexes and further help prevent spread of the inflammation.
Macrophages are monocytes that have left the blood stream to settle in tissue. Once 5 monocytes have migrated into tissues, they do not re-enter the bloodstream. The mononuclear phagocyte system is comprised of precursor cells in the bone marrow, monocytes in circulation, and macrophages in tissues. The system is capable of very fast and extensive phagocytosis. A macrophage may phagocytize over 100 bacteria, digest them and extrude residues, and then survive for many more months. Macrophages are also capable of ingesting large particles, including red o blood cells and malarial parasites. They increase several-fold in size and transform into macrophages that are characteristic of the tissue they have entered, surviving in tissues for several months.
Mononuclear phagocytes are essential in defending the body against invasion by foreign pathogens, particularly intracellular microorganisms such as M. tuberculosis, listeria, leishmania and toxoplasma. Macrophages can also control the growth of tumorous cells, via both phagocytosis and 5 secretion of hydrolytic enzymes. Another important function of macrophages is that of processing antigen and presenting them in a biochemically modified form to lymphocytes.
The immune system responds to invading microorganisms in two major ways: antibody production and cell mediated responses. Antibodies are immunoglobuhn proteins produced by B-lymphocytes which bind to specific antigens and cause inactivation or promote destruction of the antigen by other cells. Cell-mediated immune responses involve T-lymphocytes (T cells) that react with foreign antigen on the surface of infected host cells. Depending on the type of T cell, the infected cell is either killed or signals are secreted which activate macrophages and other cells to destroy the infected cell (Paul, supra).
T-lymphocytes originate in the bone marrow or liver in fetuses. Precursor cells migrate via the blood to the thymus, where they are processed to mature into T-lymphocytes. This processing is crucial because of positive and negative selection of T cells that will react with foreign antigen and not with self molecules. After processing, T cells continuously circulate in the blood and secondary lymphoid tissues, such as lymph nodes, spleen, certain epithelium-associated tissues in the gastrointestinal tract, respiratory tract and skin. When T-lymphocytes are presented with the complementary antigen, they are stimulated to proliferate and release large numbers of activated T cells into the lymph system and the blood system. These activated T cells can survive and circulate for several days. At the same time, T memory cells are created, which remain in the lymphoid tissue for months or years. Upon subsequent exposure to that specific antigen, these memory cells will respond more rapidly and with a stronger response than induced by the original antigen. This creates an "immunological memory" that can provide immunity for years.
There are two major types of T cells: cytotoxic T cells destroy infected host cells, and helper T cells activate other white blood cells via chemical signals. One class of helper cell, TH1, activates macrophages to destroy ingested microorganisms, while another, TH2, stimulates the production of antibodies by B cells. Cytotoxic T cells directly attack the infected target cell. In virus-infected cells, peptides derived from viral proteins are generated by the proteasome. These peptides are transported into the ER by the transporter associated with antigen processing (TAP) (Pamer, E. and P. Cress well (1998) Annu. Rev. Immunol. 16:323-358). Once inside the ER, the peptides bind MHC I chains, and the peptide/MHC I complex is transported to the cell surface. Receptors on the surface of T cells bind to antigen presented on cell surface MHC molecules. Once activated by binding to antigen, T cells secrete γ-interferon, a signal molecule that induces the expression of genes necessary for presenting viral (or other) antigens to cytotoxic T cells. Cytotoxic T cells kill the infected cell by stimulating programmed cell death.
Helper T cells constitute up to 75% of the total T cell population. They regulate the immune functions by producing a variety of lymphokines that act on other cells in the immune system and on bone marrow. Among these lymphokines are: interleukins-2,3,4,5,6; granulocyte-monocyte colony stimulating factor, and γ-interferon.
Helper T cells are required for most B cells to respond to antigen. When an activated helper cell contacts a B cell, its centrosome and Golgi apparatus become oriented toward the B cell, aiding the directing of signal molecules, such as fransmembrane-bound protein called CD40 ligand, onto the B cell surface to interact with the CD40 transmembrane protein. Secreted signals also help B cells to proliferate and mature and, in some cases, to switch the class of antibody being produced.
B-lymphocytes (B cells) produce antibodies which react with specific antigenic proteins presented by pathogens. Once activated, B cells become filled with extensive rough endoplasmic reticulum and are known as plasma cells. As with T cells, interaction of B cells with antigen stimulates proliferation of only those B cells which produce antibody specific to that antigen. There are five classes of antibodies, known as immunoglobulins, which together comprise about 20% of total plasma protein. Each class mediates a characteristic biological response after antigen binding. Upon activation by specific antigen B cells switch from making membrane-bound antibody to secretion of that antibody.
Antibodies, or immunoglobuUns (Ig), are the founding members of the Ig superfamily and the central components of the humoral immune response. Antibodies are either expressed on the surface of B cells or secreted by B cells into the circulation. Antibodies bind and neutralize blood-borne foreign antigens. The prototypical antibody is a tetramer consisting of two identical heavy polypeptide chains (H-chains) and two identical light polypeptide chains (L-chains) interlinked by disulfide bonds. This arrangement confers the characteristic Y-shape to antibody molecules. Antibodies are classified based on their H-chain composition. The five antibody classes, IgA, IgD, IgE, IgG and IgM, are defined by the α, δ, e, γ, and μ H-chain types. There are two types of L- chains, K and λ, either of which may associate as a pair with any H-chain pair. IgG, the most common class of antibody found in the circulation, is tettameric, while the other classes of antibodies are generally variants or multimers of this basic structure.
H-chains and L-chains each contain an N-terminal variable region and a C-terminal constant region. Both H-chains and L-chains contain repeated Ig domains. For example, a typical H-chain contains four Ig domains, three of which occur within the constant region and one of which occurs within the variable region and contributes to the formation of the antigen recognition site. Likewise, a typical L-chain contains two Ig domains, one of which occurs within the constant region and one of which occurs within the variable region. In addition, H chains such as μ have been shown to associate with other polypeptides during differentiation of the B cell.
Antibodies can be described in terms of their two main functional domains. Antigen recognition is mediated by the Fab (antigen binding fragment) region of the antibody, while effector functions are mediated by the Fc (crystallizable fragment) region. Binding of antibody to an antigen, such as a bacterium, triggers the destruction of the antigen by phagocytic white blood cells such as macrophages and neufrophils. These cells express surface receptors that specifically bind to the antibody Fc region and allow the phagocytic cells to engulf, ingest, and degrade the antibody-bound 5 antigen. The Fc receptors expressed by phagocytic cells are single-pass transmembrane glycoproteins of about 300 to 400 amino acids (Sears, D.W. et al. (1990) J. Immunol. 144:371-378). The extracellular portion of the Fc receptor typically contains two or three Ig domains.
Diseases which cause over- or under-abundance of any one type of leukocyte usually result in the entire immune defense system becoming involved. A well-known autoimmune disease is AIDS l o (Acquired Immunodeficiency Syndrome) where the number of helper T cells is depleted, leaving the patient susceptible to infection by microorganisms and parasites. Another widespread medical condition attributable to the immune system is that of allergic reactions to certain antigens. Allergic reactions include: hay fever, asthma, anaphylaxis, and urticaria (hives). Leukemias are an excess production of white blood cells, to the point where a major portion of the body' s metabolic resources
15 are directed solely at proUferation of white blood cells, leaving other tissues to starve. Leukopenia or agranulocytosis occurs when the bone marrow stops producing white blood cells. This leaves the body unprotected against foreign microorganisms, including those which normally inhabit skin, mucous membranes, and gastrointestinal tract. If all white blood cell production stops completely, infection will occur within two days and death may follow only 1 to 4 days later. 0 Impaired phagocytosis occurs in several diseases, including monocytic leukemia, systemic lupus, and granulomatous disease. In such a situation, macrophages can phagocytize normally, but the enveloped organism is not killed. A defect in the plasma membrane enzyme which converts oxygen to lethally reactive forms results in abscess formation in liver, lungs, spleen, lymph nodes, and beneath the skin. Eosinophilia is an excess of eosinophils commonly observed in patients with 5 allergies (hay fever, asthma), allergic reactions to drugs, rheumatoid arthritis, and cancers (Hodgkin' s disease, lung, and liver cancer) (Isselbacher, K.J. et al. (1994) Harrison's Principles of Internal Medicine. McGraw-Hill, Inc., New York NY).
Host defense is further augmented by the complement system. The complement system serves as an effector system and is involved in infectious agent recognition. It can function as an o independent immune network or in conjunction with other humoral immune responses. The complement system is comprised of numerous plasma and membrane proteins that act in a cascade of reaction sequences whereby one component activates the next. The result is a rapid and amplified response to infection through either an inflammatory response or increased phagocytosis.
The complement system has more than 30 protein components which can be divided into 5 functional groupings including modified serine proteases, membrane-binding proteins and regulators of complement activation. Activation occurs through two different pathways the classical and the alternative. Both pathways serve to destroy infectious agents through distinct triggering mechanisms that eventually merge with the involvement of the component C3.
The classical pathway requires antibody binding to infectious agent antigens. The antibodies 5 serve to define the target and initiate the complement system cascade, culminating in the destruction of the infectious agent. In this pathway, since the antibody guides initiation of the process, the complement can be seen as an effector arm of the humoral immune system.
The alternative pathway of the complement system does not require the presence of preexisting antibodies for targeting infectious agent destruction. Rather, this pathway, through low o levels of an activated component, remains constantly primed and provides surveillance in the non- immune host to enable targeting and destruction of infectious agents. In this case foreign material triggers the cascade, thereby facilitating phagocytosis or lysis (Paul, supra, pp.918-919).
Another important component of host defense is the process of inflammation. Inflammatory responses are divided into four categories on the basis of pathology and include allergic 5 inflammation, cytotoxic antibody mediated inflammation, immune complex mediated inflammation and monocyte mediated inflammation. Inflammation manifests as a combination of each of these forms with one predominating.
Allergic acute inflammation is observed in individuals wherein specific antigens stimulate IgE antibody production. Mast cells and basophils are subsequently activated by the attachment of o antigen-IgE complexes, resulting in the release of cytoplasmic granule contents such as histamine.
The products of activated mast cells can increase vascular permeability and constrict the smooth muscle of breathing passages, resulting in anaphylaxis or asthma. Acute inflammation is also mediated by cytotoxic antibodies and can result in the destruction of tissue through the binding of complement-fixing antibodies to cells. The responsible antibodies are of the IgG or IgM types. 5 Resultant clinical disorders include autoimmune hemolytic anemia and thrombocytopenia as associated with systemic lupus erythematosis.
Immune complex mediated acute inflammation involves the IgG or IgM antibody types which combine with antigen to activate the complement cascade. When such immune complexes bind to neufrophils and macrophages they activate the respiratory burst to form protein- and vessel- o damaging agents such as hydrogen peroxide, hydroxyl radical, hypochlorous acid, and chloramines.
Clinical manifestations include rheumatoid arthritis and systemic lupus erythematosus.
In chronic inflammation or delayed-type hypersensitivity, macrophages are activated and process antigen for presentation to T cells that subsequently produce lymphokines and monokines. This type of inflammatory response is likely important for defense against intracellular parasites and 5 certain viruses. Clinical associations include, granulomatous disease, tuberculosis, leprosy, and sarcoidosis (Paul, W.E., supra, pp.1017-1018).
Extracellular Information Transmission Molecules
Intercellular communication is essential for the growth and survival of multicellular organisms, and in particular, for the function of the endocrine, nervous, and immune systems. In addition, intercellular communication is critical for developmental processes such as tissue construction and organogenesis, in which cell proliferation, cell differentiation, and moφhogenesis must be spatially and temporally regulated in a precise and coordinated manner. Cells communicate with one another through the secretion and uptake of diverse types of signaling molecules such as hormones, growth factors, neuropeptides, and cytokines. Hormones
Hormones are signaUng molecules that coordinately regulate basic physiological processes from embryogenesis throughout adulthood. These processes include metaboUsm, respiration, reproduction, excretion, fetal tissue differentiation and organogenesis, growth and development, homeostasis, and the stress response. Hormonal secretions and the nervous system are tightly integrated and interdependent. Hormones are secreted by endocrine glands, primarily the hypothalamus and pituitary, the thyroid and parathyroid, the pancreas, the adrenal glands, and the ovaries and testes.
The secretion of hormones into the circulation is tightly controlled. Hormones are often secreted in diurnal, pulsatile, and cyclic patterns. Hormone secretion is regulated by perturbations in blood biochemisfry, by other upsfream-acting hormones, by neural impulses, and by negative feedback loops. Blood hormone concentrations are constantly monitored and adjusted to maintain optimal, steady-state levels. Once secreted, hormones act only on those target cells that express specific receptors.
Most disorders of the endocrine system are caused by either hyposecretion or hypersecretion of hormones. Hyposecretion often occurs when a hormone's gland of origin is damaged or otherwise impaired. Hypersecretion often results from the proliferation of tumors derived from hormone-secreting cells. Inappropriate hormone levels may also be caused by defects in regulatory feedback loops or in the processing of hormone precursors. Endocrine malfunction may also occur when the target cell fails to respond to the hormone. Hormones can be classified biochemically as polypeptides, steroids, eicosanoids, or amines.
Polypeptides, which include diverse hormones such as insulin and growth hormone, vary in size and function and are often synthesized as inactive precursors that are processed infracellularly into mature, active forms. Amines, which include epinephrine and dopamine, are amino acid derivatives that function in neuroendocrine signaUng. Steroids, which include the cholesterol-derived hormones estrogen and testosterone, function in sexual development and reproduction. Eicosanoids, which include prostaglandins and prostacyclins, are fatty acid derivatives that function in a variety of processes. Most polypeptides and some amines are soluble in the circulation where they are highly susceptible to proteolytic degradation within seconds after their secretion. Steroids and lipids are insoluble and must be fransported in the circulation by carrier proteins. The following discussion will 5 focus primarily on polypeptide hormones.
Hormones secreted by the hypothalamus and pituitary gland play a critical role in endocrine function by coordinately regulating hormonal secretions from other endocrine glands in response to neural signals. Hypothalamic hormones include thyrofropin-releasing hormone, gonadofropin-releasing hormone, somatostatin, growth-hormone releasing factor, corticofropin-releasing hormone, substance P, 0 dopamine, and prolactin-releasing hormone. These hormones directly regulate the secretion of hormones from the anterior lobe of the pituitary. Hormones secreted by the anterior pituitary include adrenocorticofropic hormone (ACTH), melanocyte-stimulating hormone, somatofropic hormones such as growth hormone and prolactin, glycoprotein hormones such as thyroid-stimulating hormone, luteinizing hormone (LH), and follicle-stimulating hormone (FSH), β-lipofropin, and β-endoφhins. 5 These hormones regulate hormonal secretions from the thyroid, pancreas, and adrenal glands, and act directly on the reproductive organs to stimulate ovulation and spermatogenesis. The posterior pituitary synthesizes and secretes antidiuretic hormone (ADH, vasopressin) and oxytocin.
Disorders of the hypothalamus and pituitary often result from lesions such as primary brain tumors, adenomas, infarction associated with pregnancy, hypophysectomy, aneurysms, vascular o malformations, thrombosis, infections, immunological disorders, and complications due to head frauma. Such disorders have profound effects on the function of other endocrine glands. Disorders associated with hypopituitarism include hypogonadism, Sheehan syndrome, diabetes insipidus, Kallman's disease, Hand-SchuUer-Christian disease, Letterer-Siwe disease, sarcoidosis, empty sella syndrome, and dwarfism. Disorders associated with hypeφituitarism include acromegaly, giantism, and syndrome of 5 inappropriate ADH secretion (SIADH), often caused by benign adenomas.
Hormones secreted by the thyroid and parathyroid primarily control metabolic rates and the regulation of serum calcium levels, respectively. Thyroid hormones include calcitonin, somatostatin, and thyroid hormone. The parathyroid secretes parathyroid hormone. Disorders associated with hypothyroidism include goiter, myxedema, acute thyroiditis associated with bacterial infection, o subacute thyroiditis associated with viral infection, autoimmune thyroiditis (Hashimoto's disease), and cretinism. Disorders associated with hyperthyroidism include thyrotoxicosis and its various forms, Grave's disease, pretibial myxedema, toxic multinodular goiter, thyroid carcinoma, and Plummer's disease. Disorders associated with hypeφarathyroidism include Conn disease (chronic hypercalemia) leading to bone resoφtion and parathyroid hypeφlasia. 5 Hormones secreted by the pancreas regulate blood glucose levels by modulating the rates of carbohydrate, fat, and protein metabolism. Pancreatic hormones include insulin, glucagon, amyUn, γ- aminobutyric acid, gasfrin, somatostatin, and pancreatic polypeptide. The principal disorder associated with pancreatic dysfunction is diabetes mellitus caused by insufficient insulin activity. Diabetes melUtus is generally classified as either Type I (insulin-dependent, juvenile diabetes) or Type II (non- 5 insuUn-dependent, adult diabetes). The treatment of both forms by insulin replacement therapy is well known. Diabetes melUtus often leads to acute compUcations such as hypoglycemia (insulin shock), coma, diabetic ketoacidosis, lactic acidosis, and chronic complications leading to disorders of the eye, kidney, skin, bone, joint, cardiovascular system, nervous system, and to decreased resistance to infection. 0 The anatomy, physiology, and diseases related to hormonal function are reviewed in McCance,
K.L. and S.E. Huether (1994) Pathophysiology: The Biological Basis for Disease in Adults and Children, Mosby-Year Book, Inc., St. Louis MO; Greenspan, F.S. and J.D. Baxter (1994) Basic and Clinical Endocrinology, Appleton and Lange, East Norwalk CT. Growth Factors 5 Growth factors are secreted proteins that mediate intercellular communication. Unlike hormones, which fravel great distances via the circulatory system, most growth factors are primarily local mediators that act on neighboring cells. Most growth factors contain a hydrophobic N-terminal signal peptide sequence which directs the growth factor into the secretory pathway. Most growth factors also undergo post-franslational modifications within the secretory pathway. These o modifications can include proteolysis, glycosylation, phosphorylation, and inframolecular disulfide bond formation. Once secreted, growth factors bind to specific receptors on the surfaces of neighboring target cells, and the bound receptors trigger intracellular signal transduction pathways. These signal transduction pathways eUcit specific cellular responses in the target cells. These responses can include the modulation of gene expression and the stimulation or inhibition of cell division, cell differentiation, 5 and cell motility.
Growth factors fall into at least two broad and overlapping classes. The broadest class includes the large polypeptide growth factors, which are wide-ranging in their effects. These factors include epidermal growth factor (EGF), fibroblast growth factor (FGF), transforming growth factor-β (TGF-β), insulin-Uke growth factor (IGF), nerve growth factor (NGF), and platelet-derived growth o factor (PDGF), each defining a family of numerous related factors. The large polypeptide growth factors, with the exception of NGF, act as mitogens on diverse cell types to stimulate wound healing, bone synthesis and remodeling, extracellular matrix synthesis, and proliferation of epithelial, epidermal, and connective tissues. Members of the TGF-β, EGF, and FGF families also function as inductive signals in the differentiation of embryonic tissue. NGF functions specifically as a 5 neurotrophic factor, promoting neuronal growth and differentiation. Another class of growth factors includes the hematopoietic growth factors, which are narrow in their target specificity. These factors stimulate the proUferation and differentiation of blood cells such as B-lymphocytes, T-lymphocytes, erythrocytes, platelets, eosinophils, basophils, neufrophils, macrophages, and their stem cell precursors. These factors include the colony-stimulating factors (G- CSF, M-CSF, GM-CSF, and CSF1-3), eryfhropoietin, and the cytokines. The cytokines are speciaUzed hematopoietic factors secreted by cells of the immune system and are discussed in detail below.
Growth factors play critical roles in neoplastic transformation of cells in vitro and in tumor progression in vivo. Overexpression of the large polypeptide growth factors promotes the proliferation and transformation of cells in culture. Inappropriate expression of these growth factors by tumor cells in vivo may confribute to tumor vascularization and metastasis. Inappropriate activity of hematopoietic growth factors can result in anemias, leukemias, and lymphomas. Moreover, growth factors are both structurally and functionally related to oncoproteins, the potentially cancer-causing products of proto-oncogenes. Certain FGF and PDGF family members are themselves homologous to oncoproteins, whereas receptors for some members of the EGF, NGF, and FGF families are encoded by proto-oncogenes. Growth factors also affect the ttanscriptional regulation of both proto-oncogenes and oncosuppressor genes (Pimentel, E. (1994) Handbook of Growth Factors, CRC Press, Ann Arbor MI; McKay, I. and I. Leigh, eds. (1993) Growth Factors: A Practical Approach, Oxford University Press, New York NY; Habenicht, A., ed. (1990) Growth Factors, Differentiation Factors, and Cytokines, Springer- Verlag, New York NY). In addition, some of the large polypeptide growth factors play crucial roles in the induction of the primordial germ layers in the developing embryo. This induction ultimately results in the formation of the embryonic mesoderm, ectoderm, and endoderm which in turn provide the framework for the entire adult body plan. Disruption of this inductive process would be catastrophic to embryonic development. Small Peptide Factors - Neuropeptides and Vasomediators
Neuropeptides and vasomediators (NP/VM) comprise a family of small peptide factors, typically of 20 amino acids or less. These factors generally function in neuronal excitation and inhibition of vasoconstriction/vasodilation, muscle contraction, and hormonal secretions from the brain and other endocrine tissues. Included in this family are neuropeptides and neuropeptide hormones such as bombesin, neuropeptide Y, neurotensin, neuromedin N, melanocortins, opioids, galanin, somatostatin, tachykinins, urotensin II and related peptides involved in smooth muscle stimulation, vasopressin, vasoactive intestinal peptide, and circulatory system-borne signaling molecules such as angiotensin, complement, calcitonin, endotheUns, formyl-methionyl peptides, glucagon, cholecystokinin, gastrin, and many of the peptide hormones discussed above. NP/VMs can transduce signals directly, modulate the activity or release of other neurofransmitters and hormones, and act as catalytic enzymes in signaUng cascades. The effects of NP/VMs range from extremely brief to long-lasting. (Reviewed in Martin, C.R. et al. (1985) Endocrine Physiology, Oxford University Press, New York NY, pp. 57-62.) Cytokines Cytokines comprise a family of signaUng molecules that modulate the immune system and the inflammatory response. Cytokines are usually secreted by leukocytes, or white blood cells, in response to injury or infection. Cytokines function as growth and differentiation factors that act primarily on cells of the immune system such as B- and T-lymphocytes, monocytes, macrophages, and granulocytes. Like other signaUng molecules, cytokines bind to specific plasma membrane receptors and trigger intracellular signal transduction pathways which alter gene expression patterns. There is considerable potential for the use of cytokines in the treatment of inflammation and immune system disorders.
Cytokine structure and function have been extensively characterized in vitro. Most cytokines are small polypeptides of about 30 kilodaltons or less. Over 50 cytokines have been identified from human and rodent sources. Examples of cytokine subfamiUes include the interferons (IFN-α, -β, and - γ), the interleukins (IL1-IL13), the tumor necrosis factors (TNF-α and -β), and the chemokines. Many cytokines have been produced using recombinant DNA techniques, and the activities of individual cytokines have been determined in vitro. These activities include regulation of leukocyte proliferation, differentiation, and motiUty.
The activity of an individual cytokine in vitro may not reflect the full scope of that cytokine' s activity in vivo. Cytokines are not expressed individually in vivo but are instead expressed in combination with a multitude of other cytokines when the organism is challenged with a stimulus. Together, these cytokines collectively modulate the immune response in a manner appropriate for that particular stimulus. Therefore, the physiological activity of a cytokine is determined by the stimulus itself and by complex interactive networks among co-expressed cytokines which may demonstrate both synergistic and antagonistic relationships.
Chemokines comprise a cytokine subfamily with over 30 members. (Reviewed in Wells, T. N.C. and M.C Peitsch (1997) J. Leukoc. Biol. 61:545-550.) Chemokines were initially identified as chemotactic proteins that recruit monocytes and macrophages to sites of inflammation. Recent evidence indicates that chemokines may also play key roles in hematopoiesis and HIV-1 infection. Chemokines are small proteins which range from about 6-15 kilodaltons in molecular weight. Chemokines are further classified as C, CC, CXC, or CX3C based on the number and position of critical cysteine residues. The CC chemokines, for example, each contain a conserved motif consisting of two consecutive cysteines followed by two additional cysteines which occur downstream at 24- and 16- residue intervals, respectively (ExPASy PROSITE database, documents PS00472 and PDOC00434). The presence and spacing of these four cysteine residues are highly conserved, whereas the intervening residues diverge significantly. However, a conserved tyrosine located about 15 residues downstream of the cysteine doublet seems to be important for chemotactic activity. Most of the human genes encoding CC chemokines are clustered on chromosome 17, although there are a few examples of CC chemokine genes that map elsewhere. Other chemokines include lymphotactin (C chemokine); macrophage 5 chemotactic and activating factor (MCAF/MCP-1 ; CC chemokine); platelet factor 4 and IL-8 (CXC chemokines); and fractalkine and neurotractin (CX3C chemokines). (Reviewed in Luster, A.D. (1998) N. Engl. J. Med. 338:436-445.)
Receptor Molecules 0 SEQ ID NO:6 and SEQ ID NO:7 encode, for example, receptor molecules.
The term receptor describes proteins that specifically recognize other molecules. The category is broad and includes proteins with a variety of functions. The bulk of receptors are cell surface proteins which bind exfracellular ligands and produce cellular responses in the areas of growth, differentiation, endocytosis, and immune response. Other receptors facilitate the selective fransport of 5 proteins out of the endoplasmic reticulum and localize enzymes to particular locations in the cell. The term may also be applied to proteins which act as receptors for ligands with known or unknown chemical composition and which interact with other cellular components. For example, the steroid hormone receptors bind to and regulate transcription of DNA.
Regulation of cell proliferation, differentiation, and migration is important for the formation o and function of tissues. Regulatory proteins such as growth factors coordinately confrol these cellular processes and act as mediators in cell-cell signaling pathways. Growth factors are secreted proteins that bind to specific cell-surface receptors on target cells. The bound receptors trigger intracellular signal transduction pathways which activate various downstream effectors that regulate gene expression, cell division, cell differentiation, cell motility, and other cellular processes. 5 Cell surface receptors are typically integral plasma membrane proteins. These receptors recognize hormones such as catecholamines; peptide hormones; growth and differentiation factors; small peptide factors such as thyrotropin-releasing hormone; galanin, somatostatin, and tachykinins; and circulatory system-borne signaling molecules. Cell surface receptors on immune system cells recognize antigens, antibodies, and major histocompatibility complex (MHC)-bound peptides. Other o cell surface receptors bind ligands to be internalized by the cell. This receptor-mediated endocytosis functions in the uptake of low density lipoproteins (LDL), transferrin, glucose- or mannose-terminal glycoproteins, galactose-terminal glycoproteins, immunoglobulins, phosphovitellogenins, fibrin, proteinase-inhibitor complexes, plasminogen activators, and thrombospondin (Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York NY, p. 723; Mikhailenko, I. et al. 5 (1997) J. Biol. Chem. 272:6784-6791). Receptor Protein Kinases
Many growth factor receptors, including receptors for epidermal growth factor, platelet-derived growth factor, fibroblast growth factor, as well as the growth modulator α-thrombin, contain intrinsic protein kinase activities. When growth factor binds to the receptor, it triggers the autophosphorylation of a serine, threonine, or tyrosine residue on the receptor. These phosphorylated sites are recognition sites for the binding of other cytoplasmic signaUng proteins. These proteins participate in signaling pathways that eventually Unk the initial receptor activation at the cell surface to the activation of a specific intracellular target molecule. In the case of tyrosine residue autophosphorylation, these signaling proteins contain a common domain referred to as a Src homology (SH) domain. SH2 domains and SH3 domains are found in phospholipase C-γ, PI-3-K p85 regulatory subunit, Ras-GTPase activating protein, and pp60c"src (Lowenstein, E.J. et al. (1992) Cell 70:431 -442). The cytokine family of receptors share a different common binding domain and include transmembrane receptors for growth hormone (GH), interleukins, erythropoietin, and prolactin.
Other receptors and second messenger-binding proteins have intrinsic serine/threonine protein kinase activity. These include activin/TGF-β/BMP-superfamily receptors, calcium- and diacylglycerol- activated/phospholipid-dependant protein kinase (PK-C), and RNA-dependant protein kinase (PK-R). In addition, other serine/threonine protein kinases, including nematode Twitchin, have fibronectin-like, immunoglobulin C2-Uke domains. G-Protein Coupled Receptors G-protein coupled receptors (GPCRs) are integral membrane proteins characterized by the presence of seven hydrophobic transmembrane domains which span the plasma membrane and form a bundle of antiparallel alpha (α) heUces. These proteins range in size from under 400 to over 1000 amino acids (Strosberg, AD. (1991) Eur. J. Biochem. 196:1-10; Coughlin, S.R. (1994) Curr. Opin. Cell Biol. 6:191-197). The amino-terminus of the GPCR is extracellular, of variable length and often glycosylated; the carboxy-terminus is cytoplasmic and generally phosphorylated. Exfracellular loops of the GPCR alternate with intracellular loops and link the transmembrane domains. The most conserved domains of GPCRs are the transmembrane domains and the first two cytoplasmic loops. The transmembrane domains account for structural and functional features of the receptor. In most cases, the bundle of α helices forms a binding pocket. In addition, the extracellular N-terminal segment or one or more of the three exfracellular loops may also participate in ligand binding. Ligand binding activates the receptor by inducing a conformational change in intracellular portions of the receptor. The activated receptor, in turn, interacts with an intracellular heterotrimeric guanine nucleotide binding (G) protein complex which mediates further intracellular signaling activities, generally the production of second messengers such as cyclic AMP (cAMP), phospholipase C, inositol friphosphate, or interactions with ion channel proteins (Baldwin, J.M. (1994) Curr. Opin. Cell Biol. 6:180-190). GPCRs include those for acetylchoUne, adenosine, epinephrine and norepinephrine, bombesin, bradykinin, chemokines, dopamine, endothelin, γ-aminobutyric acid (GABA), follicle-stimulating hormone (FSH), glutamate, gonadotropin-releasing hormone (GnRH), hepatocyte growth factor, histamine, leukotrienes, melanocortins, neuropeptide Y, opioid peptides, opsins, prostanoids, serotonin, 5 somatostatin, tachykinins, thrombin, thyrottopin-releasing hormone (TRH), vasoactive intestinal polypeptide family, vasopressin and oxytocin, and oφhan receptors.
GPCR mutations, which may cause loss of function or constitutive activation, have been associated with numerous human diseases (Coughlin, supra). For instance, retinitis pigmentosa may arise from mutations in the rhodopsin gene. Rhodopsin is the retinal photoreceptor which is located 0 within the discs of the eye rod cell. Parma, J. et al. (1993, Nature 365:649-651) report that somatic activating mutations in the thyrofropin receptor cause hyperfunctioning thyroid adenomas and suggest that certain GPCRs susceptible to constitutive activation may behave as protooncogenes. Nuclear Receptors
Nuclear receptors bind small molecules such as hormones or second messengers, leading to 5 increased receptor-binding affinity to specific chromosomal DNA elements. In addition the affinity for other nuclear proteins may also be altered. Such binding and protein-protein interactions may regulate and modulate gene expression. Examples of such receptors include the steroid hormone receptors family, the retinoic acid receptors family, and the thyroid hormone receptors family. Ligand-Gated Receptor Ion Channels o Ligand-gated receptor ion channels fall into two categories. The first category, exfracellular
Ugand-gated receptor ion channels (ELGs), rapidly transduce neurotransmitter-binding events into electrical signals, such as fast synaptic neurofransmission. ELG function is regulated by post- franslational modification. The second category, intracellular ligand-gated receptor ion channels (ILGs), are activated by many intracellular second messengers and do not require post-franslational 5 modification(s) to effect a channel-opening response.
ELGs depolarize excitable cells to the threshold of action potential generation. In non-excitable cells, ELGs permit a limited calcium ion-influx during the presence of agonist. ELGs include channels directly gated by neurofransmitters such as acetylcholine, L-glutamate, glycine, ATP, serotonin, GABA, and histamine. ELG genes encode proteins having strong structural and functional similarities. o ILGs are encoded by distinct and unrelated gene families and include receptors for cAMP, cGMP, calcium ions, ATP, and metabolites of arachidonic acid. Macrophage Scavenger Receptors
Macrophage scavenger receptors with broad ligand specificity may participate in the binding of low density lipoproteins (LDL) and foreign antigens. Scavenger receptors types I and II are trimeric 5 membrane proteins with each subunit containing a small N-terminal intracellular domain, a transmembrane domain, a large extracellular domain, and a C-terminal cysteine-rich domain. The extracellular domain contains a short spacer domain, an α-helical coiled-coil domain, and a friple helical collagenous domain. These receptors have been shown to bind a spectrum of ligands, including chemically modified lipoproteins and albumin, polyribonucleotides, polysaccharides, phosphoUpids, and 5 asbestos (Matsumoto, A. et al. (1990) Proc. Nati. Acad. Sci. USA 87:9133-9137; Elomaa, O. et al. (1995) Cell 80:603-609). The scavenger receptors are thought to play a key role in atherogenesis by mediating uptake of modified LDL in arterial walls, and in host defense by binding bacterial endotoxins, bacteria, and protozoa. T-Cell Receptors 0 T cells play a dual role in the immune system as effectors and regulators, coupUng antigen recognition with the transmission of signals that induce cell death in infected cells and stimulate proliferation of other immune cells. Although a population of T cells can recognize a wide range of different antigens, an individual T cell can only recognize a single antigen and only when it is presented to the T cell receptor (TCR) as a peptide complexed with a major histocompatibility molecule (MHC) 5 on the surface of an antigen presenting cell. The TCR on most T cells consists of immunoglobulin-like integral membrane glycoproteins containing two polypeptide subunits, α and β, of similar molecular weight. Both TCR subunits have an exfracellular domain containing both variable and constant regions, a transmembrane domain that traverses the membrane once, and a short intracellular domain (Saito, H. et al. (1984) Nature 309:757-762). The genes for the TCR subunits are constructed through o somatic rearrangement of different gene segments. Interaction of antigen in the proper MHC context with the TCR initiates signaling cascades that induce the proliferation, maturation, and function of cellular components of the immune system (Weiss, A. (1991) Annu. Rev. Genet. 25:487-510). Rearrangements in TCR genes and alterations in TCR expression have been noted in lymphomas, leukemias, autoimmune disorders, and immunodeficiency disorders (Aisenberg, A.C. et al. (1985) N. 5 Engl. J. Med. 313:529-533; Weiss, supra).
Intracellular Signaling Molecules
SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO.l l, and SEQ ID NO:12 encode, for example, intracellular signaling molecules. o Intracellular signaling is the general process by which cells respond to extracellular signals
(hormones, neurofransmitters, growth and differentiation factors, etc.) through a cascade of biochemical reactions that begins with the binding of a signaling molecule to a cell membrane receptor and ends with the activation of an intracellular target molecule. Intermediate steps in the process involve the activation of various cytoplasmic proteins by phosphorylation via protein kinases, 5 and their deactivation by protein phosphatases, and the eventual translocation of some of these activated proteins to the cell nucleus where the transcription of specific genes is triggered. The intracellular signaUng process regulates all types of cell functions including cell proliferation, cell differentiation, and gene transcription, and involves a diversity of molecules including protein kinases and phosphatases, and second messenger molecules, such as cyclic nucleotides, calcium-calmodulin, 5 inositol, and various mitogens, that regulate protein phosphorylation. Protein Phosphorylation
Protein kinases and phosphatases play a key role in the intracellular signaling process by controlling the phosphorylation and activation of various signaling proteins. The high energy phosphate for this reaction is generally transferred from the adenosine friphosphate molecule (ATP) to 0 a particular protein by a protein kinase and removed from that protein by a protein phosphatase. Protein kinases are roughly divided into two groups: those that phosphorylate tyrosine residues (protein tyrosine kinases, PTK) and those that phosphorylate serine or threonine residues (serine/threonine kinases, STK). A few protein kinases have dual specificity for serine/threonine and tyrosine residues. Almost all kinases contain a conserved 250-300 amino acid catalytic domain 5 containing specific residues and sequence motifs characteristic of the kinase family (Hardie, G. and S. Hanks (1995) The Protein Kinase Facts Books, Vol 1:7-20, Academic Press, San Diego CA).
STKs include the second messenger dependent protein kinases such as the cyclic- AMP dependent protein kinases (PKA), involved in mediating hormone-induced cellular responses; calcium-calmodulin (CaM) dependent protein kinases, involved in regulation of smooth muscle o confraction, glycogen breakdown, and neurofransmission; and the mitogen- activated protein kinases (MAP) which mediate signal transduction from the cell surface to the nucleus via phosphorylation cascades. Altered PKA expression is implicated in a variety of disorders and diseases including cancer, thyroid disorders, diabetes, atherosclerosis, and cardiovascular disease (Isselbacher, K.J. et al. (1994) Harrison's Principles of Internal Medicine McGraw-Hill, New York NY, pp. 416-431, 1887). 5 PTKs are divided into transmembrane, receptor PTKs and nonfransmembrane, non-receptor
PTKs. Transmembrane PTKs are receptors for most growth factors. Non-receptor PTKs lack transmembrane regions and, instead, form complexes with the intracellular regions of cell surface receptors. Receptors that function through non-receptor PTKs include those for cytokines and hormones (growth hormone and prolactin) and antigen-specific receptors on T and B lymphocytes. o Many of these PTKs were first identified as the products of mutant oncogenes in cancer cells in which their activation was no longer subject to normal cellular controls. In fact, about one third of the known oncogenes encode PTKs, and it is well known that cellular transformation (oncogenesis) is often accompanied by increased tyrosine phosphorylation activity (Charbonneau, H. and N.K. Tonks (1992) Annu. Rev. Cell Biol. 8:463-493). 5 An additional family of protein kinases previously thought to exist only in procaryotes is the histidine protein kinase family (HPK). HPKs bear little homology with mammalian STKs or PTKs but have distinctive sequence motifs of their own (Davie, J.R. et al. (1995) J. Biol. Chem. 270: 19861 - 19867). A histidine residue in the N-terminal half of the molecule (region I) is an autophosphorylation site. Three additional motifs located in the C-terminal half of the molecule include an invariant asparagine residue in region II and two glycine-rich loops characteristic of nucleotide binding domains in regions III and IV. Recently a branched chain alpha-ketoacid dehydrogenase kinase has been found with characteristics of HPK in rat (Davie, supra).
Protein phosphatases regulate the effects of protein kinases by removing phosphate groups from molecules previously activated by kinases. The two principal categories of protein phosphatases are the protein (serine/threonine) phosphatases (PPs) and the protein tyrosine phosphatases (PTPs). PPs dephosphorylate phosphoserine/threonine residues and are important regulators of many cAMP-mediated hormone responses (Cohen, P. (1989) Annu. Rev. Biochem. 58:453-508). PTPs reverse the effects of protein tyrosine kinases and play a significant role in cell cycle and cell signaling processes (Charbonneau, supra). As previously noted, many PTKs are encoded by oncogenes, and oncogenesis is often accompanied by increased tyrosine phosphorylation activity. It is therefore possible that PTPs may prevent or reverse cell transformation and the growth of various cancers by controlling the levels of tyrosine phosphorylation in cells. This hypothesis is supported by studies showing that overexpression of PTPs can suppress transformation in cells, and that specific inhibition of PTPs can enhance cell transformation (Charbonneau, supra). Phospholipid and Inositol -Phosphate Signaling
Inositol phosphoUpids (phosphoinositides) are involved in an intracellular signaling pathway that begins with binding of a signaling molecule to a G-protein linked receptor in the plasma membrane. This leads to the phosphorylation of phosphatidylinositol (PI) residues on the inner side of the plasma membrane to the biphosphate state (PIP2) by inositol kinases. Simultaneously, the G- protein linked receptor binding stimulates a trimeric G-protein which in turn activates a phosphoinositi de-specific phospholipase C-β. Phospholipase C-β then cleaves PIP2 into two products, inositol friphosphate (IP3) and diacylglycerol. These two products act as mediators for separate signaling events. IP3 diffuses through the plasma membrane to induce calcium release from the endoplasmic reticulum (ER), while diacylglycerol remains in the membrane and helps activate protein kinase C, an STK that phosphorylates selected proteins in the target cell. The calcium response initiated by IP3 is terminated by the dephosphorylation of IP3 by specific inositol phosphatases. Cellular responses that are mediated by this pathway are glycogen breakdown in the liver in response to vasopressin, smooth muscle contraction in response to acetylcholine, and thrombin-induced platelet aggregation. Cyclic Nucleotide Signaling Cyclic nucleotides (cAMP and cGMP) function as intracellular second messengers to transduce a variety of exfracellular signals including hormones, light, and neurofransmitters. In particular, cyclic-AMP dependent protein kinases (PKA) are thought to account for all of the effects of cAMP in most mammalian cells, including various hormone-induced cellular responses. Visual 5 excitation and the photottansmission of light signals in the eye is controlled by cyclic-GMP regulated, Ca2+-specific channels. Because of the importance of cellular levels of cyclic nucleotides in mediating these various responses, regulating the synthesis and breakdown of cyclic nucleotides is an important matter. Thus adenylyl cyclase, which synthesizes cAMP from AMP, is activated to increase cAMP levels in muscle by binding of adrenaline to β-andrenergic receptors, while activation 0 of guanylate cyclase and increased cGMP levels in photoreceptors leads to reopening of the
Ca2+-specific channels and recovery of the dark state in the eye. In contrast, hydrolysis of cyclic nucleotides by cAMP and cGMP-specific phosphodiesterases (PDEs) produces the opposite of these and other effects mediated by increased cyclic nucleotide levels. PDEs appear to be particularly important in the regulation of cyclic nucleotides, considering the diversity found in this family of 5 proteins. At least seven families of mammalian PDEs (PDE1 -7) have been identified based on substrate specificity and affinity, sensitivity to cofactors, and sensitivity to inhibitory drugs (Beavo, J.A. (1995) Physiological Reviews 75:725-48). PDE inhibitors have been found to be particularly useful in treating various clinical disorders. Rolipram, a specific inhibitor of PDE4, has been used in the treatment of depression, and similar inhibitors are undergoing evaluation as anti-inflammatory o agents. Theophylline is a nonspecific PDE inhibitor used in the treatment of bronchial asthma and other respiratory diseases (Banner, KH. and C.P. Page (1995) Eur. Respir. J. 8:996-1000). G-Protein Si naling
Guanine nucleotide binding proteins (G-proteins) are critical mediators of signal transduction between a particular class of extracellular receptors, the G-protein coupled receptors (GPCR), and 5 intracellular second messengers such as cAMP and Ca2+. G-proteins are linked to the cytosolic side of a GPCR such that activation of the GPCR by ligand binding stimulates binding of the G-protein to GTP, inducing an "active" state in the G-protein. In the active state, the G-protein acts as a signal to trigger other events in the cell such as the increase of cAMP levels or the release of Ca2+ into the cytosol from the ER, which, in turn, regulate phosphorylation and activation of other intracellular o proteins. Recycling of the G-protein to the inactive state involves hydrolysis of the bound GTP to
GDP by a GTPase activity in the G-protein. (See Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing, Inc., New York NY, pp.734-759.) Two structurally distinct classes of G- proteins are recognized: heterotrimeric G-proteins, consisting of three different subunits, and monomeric, low molecular weight (LMW), G-proteins consisting of a single polypeptide chain. 5 The three polypeptide subunits of heterotrimeric G-proteins are the ct, β, and γ subunits. The cc subunit binds and hydrolyzes GTP. The β and γ subunits form a tight complex that anchors the protein to the inner side of the plasma membrane. The β subunits, also known as G-β proteins or β fransducins, contain seven tandem repeats of the WD-repeat sequence motif, a motif found in many proteins with regulatory functions. Mutations and variant expression of β fransducin proteins are 5 linked with various disorders (Neer, E.J. et al. (1994) Nature 371 :297-300; Margottin, F. et al. (1998) Mol. Cell 1:565-574).
LMW GTP-proteins are GTPases which regulate cell growth, cell cycle confrol, protein secretion, and intracellular vesicle interaction. They consist of single polypeptides which, like the α subunit of the heterotrimeric G-proteins, are able to bind and hydrolyze GTP, thus cycling between an o inactive and an active state. At least sixty members of the LMW G-protein superfamily have been identified and are currently grouped into the six subfamilies of ras, rho, arf, sari, ran, and rab. Activated ras genes were initially found in human cancers, and subsequent studies confirmed that ras function is critical in determining whether cells continue to grow or become differentiated. Other members of the LMW G-protein superfamily have roles in signal transduction that vary with the 5 function of the activated genes and the locations of the G-proteins.
Guanine nucleotide exchange factors regulate the activities of LMW G-proteins by determining whether GTP or GDP is bound. GTPase-activating protein (GAP) binds to GTP-ras and induces it to hydrolyze GTP to GDP. In contrast, guanine nucleotide releasing protein (GNRP) binds to GDP-ras and induces the release of GDP and the binding of GTP. o Other regulators of G-protein signaling (RGS) also exist that act primarily by negatively regulating the G-protein pathway by an unknown mechanism (Druey, K.M. et al. (1996) Nature 379:742-746). Some 15 members of the RGS family have been identified. RGS family members are related structurally through similarities in an approximately 120 amino acid region termed the RGS domain and functionally by their ability to inhibit the interleukin (cytokine) induction of MAP kinase 5 in cultured mammaUan 293T cells (Druey, supra).
Calcium Signaling Molecules
Ca+2 is another second messenger molecule that is even more widely used as an intracellular mediator than cAMP. Two pathways exist by which Ca+2 can enter the cytosol in response to exfracellular signals: One pathway acts primarily in nerve signal transduction where Ca+2 enters a o nerve terminal through a voltage-gated Ca+2 channel. The second is a more ubiquitous pathway in which Ca+2 is released from the ER into the cytosol in response to binding of an exfracellular signaling molecule to a receptor. Ca2+ directly activates regulatory enzymes, such as protein kinase C, which trigger signal transduction pathways. Ca2+ also binds to specific Ca2+-binding proteins (CBPs) such as calmodulin (CaM) which then activate multiple target proteins in the cell including enzymes, 5 membrane fransport pumps, and ion channels. CaM interactions are involved in a multitude of cellular processes including, but not limited to, gene regulation, DNA synthesis, cell cycle progression, mitosis, cytokinesis, cytoskeletal organization, muscle contraction, signal transduction, ion homeostasis, exocytosis, and metabolic regulation (Celio, M.R. et al. (1996) Guidebook to Calcium-binding Proteins, Oxford University Press, Oxford, UK, pp. 15-20). Some CBPs can serve 5 as a storage depot for Ca2+ in an inactive state. Calsequestrin is one such CBP that is expressed in isoforms specific to cardiac muscle and skeletal muscle. It is suggested that calsequestrin binds Ca2+ in a rapidly exchangeable state that is released during Ca2+ -signaling conditions (Celio, M.R. et al. (1996) Guidebook to Calcium-binding Proteins, Oxford University Press, New York NY, pp. 222- 224). 0 Cyclins
Cell division is the fundamental process by which all living things grow and reproduce. In most organisms, the cell cycle consists of three principle steps; inteφhase, mitosis, and cytokinesis. Inteφhase, involves preparations for cell division, replication of the DNA and production of essential proteins. In mitosis, the nuclear material is divided and separates to opposite sides of the cell. 5 Cytokinesis is the final division and fission of the cell cytoplasm to produce the daughter cells.
The entry and exit of a cell from mitosis is regulated by the synthesis and destruction of a family of activating proteins called cyclins. Cyclins act by binding to and activating a group of cyclin-dependent protein kinases (Cdks) which then phosphorylate and activate selected proteins involved in the mitotic process. Several types of cyclins exist. (Ciechanover, A. (1994) Cell 0 79: 13-21.) Two principle types are mitotic cyclin, or cyclin B, which confrols entry of the cell into mitosis, and Gl cyclin, which confrols events that drive the cell out of mitosis. Signal Complex Scaffolding Proteins
Ceretain proteins in intracellular signaling pathways serve to link or cluster other proteins involved in the signaling cascade. A conserved protein domain called the PDZ domain has been 5 identified in various membrane-associated signaling proteins. This domain has been implicated in receptor and ion channel clustering and in the targeting of multiprotein signaling complexes to specialized functional regions of the cytosolic face of the plasma membrane. (For a review of PDZ domain-containing proteins, see Ponting, C.P. et al. (1997) Bioessays 19:469-479.) A large proportion of PDZ domains are found in the eukaryotic MAGUK (membrane-associated guanylate o kinase) protein family, members of which bind to the infracellular domains of receptors and channels.
However, PDZ domains are also found in diverse membrane-localized proteins such as protein tyrosine phosphatases, serine/threonine kinases, G-protein cofactors, and synapse-associated proteins such as syntrophins and neuronal nitric oxide synthase (nNOS). Generally, about one to three PDZ domains are found in a given protein, although up to nine PDZ domains have been identified in a 5 single protein. Membrane Transport Molecules
SEQ ID NO: 13 encodes, for example, a membrane transport molecule. The plasma membrane acts as a barrier to most molecules. Transport between the cytoplasm and the exfracellular environment, and between the cytoplasm and lumenal spaces of cellular 5 organelles requires specific transport proteins. Each transport protein carries a particular class of molecule, such as ions, sugars, or amino acids, and often is specific to a certain molecular species of the class. A variety of human inherited diseases are caused by a mutation in a fransport protein. For example, cystinuria is an inherited disease that results from the inability to fransport cystine, the disulfide-linked dimer of cysteine, from the urine into the blood. Accumulation of cystine in the l o urine leads to the formation of cystine stones in the kidneys.
Transport proteins are multi-pass transmembrane proteins, which either actively transport molecules across the membrane or passively allow them to cross. Active fransport involves directional pumping of a solute across the membrane, usually against an electrochemical gradient. Active fransport is tightly coupled to a source of metabolic energy, such as ATP hydrolysis or an
15 elecfrochemically favorable ion gradient. Passive transport involves the movement of a solute down its electrochemical gradient. Transport proteins can be further classified as either carrier proteins or channel proteins. Carrier proteins, which can function in active or passive fransport, bind to a specific solute to be fransported and undergo a conformational change which transfers the bound solute across the membrane. Channel proteins, which only function in passive transport, form hydrophihc pores
20 across the membrane. When the pores open, specific solutes, such as inorganic ions, pass through the membrane and down the electrochemical gradient of the solute.
Carrier proteins which transport a single solute from one side of the membrane to the other are called uniporters. In contrast, coupled transporters link the fransfer of one solute with simultaneous or sequential fransfer of a second solute, either in the same direction (symport) or in the 5 opposite direction (antiport). For example, intestinal and kidney epithelium contains a variety of symporter systems driven by the sodium gradient that exists across the plasma membrane. Sodium moves into the cell down its electrochemical gradient and brings the solute into the cell with it. The sodium gradient that provides the driving force for solute uptake is maintained by the ubiquitous Na7K+ ATPase. Sodium-coupled transporters include the mammalian glucose transporter (SGLT1), o iodide fransporter (NIS), and multivitamin transporter (SMVT). All three transporters have twelve putative transmembrane segments, extracellular glycosylation sites, and cytoplasmically-oriented N- and C-termini. NIS plays a crucial role in the evaluation, diagnosis, and treatment of various thyroid pathologies because it is the molecular basis for radioiodide thyroid-imaging techniques and for specific targeting of radioisotopes to the thyroid gland (Levy, O. et al. (1997) Proc. Nati. Acad. Sci. 5 USA 94:5568-5573). SMVT is expressed in the intestinal mucosa, kidney, and placenta, and is implicated in the transport of the water-soluble vitamins, e.g., biotin and pantothenate (Prasad, P.D. et al. (1998) J. Biol. Chem. 273:7501-7506).
Transporters play a major role in the regulation of pH, excretion of drugs, and the cellular K+/Na+ balance. Monocarboxylate anion transporters are proton-coupled symporters with a broad 5 substrate specificity that includes L-lactate, pyruvate, and the ketone bodies acetate, acetoacetate, and beta-hydroxybutyrate. At least seven isoforms have been identified to date. The isoforms are predicted to have twelve transmembrane (TM) helical domains with a large intracellular loop between TM6 and TM7, and play a critical role in maintaining infracellular pH by removing the protons that are produced stoichiomefrically with lactate during glycolysis. The best characterized H(+)-monocarboxylate o fransporter is that of the erythrocyte membrane, which fransports L-lactate and a wide range of other aliphatic monocarboxylates. Other cells possess H(+)-linked monocarboxylate transporters with differing substrate and inhibitor selectivities. In particular, cardiac muscle and tumor cells have transporters that differ in their Kra values for certain substrates, including stereoselectivity for L- over D-lactate, and in their sensitivity to inhibitors. There are Na(+)-monocarboxylate cofransporters on the 5 luminal surface of intestinal and kidney epitheUa, which allow the uptake of lactate, pyruvate, and ketone bodies in these tissues. In addition, there are specific and selective transporters for organic cations and organic anions in organs including the kidney, intestine and liver. Organic anion transporters are selective for hydrophobic, charged molecules with electron-attracting side groups. Organic cation transporters, such as the ammonium transporter, mediate the secretion of a variety of o drugs and endogenous metabolites, and confribute to the maintenance of intercellular pH. (Poole, R.C. and AP. Halestrap (1993) Am. J. Physiol. 264:C761-C782; Price, N.T. et al. (1998) Biochem. J. 329:321-328; and Martinelle, K. and I. Haggsfrom (1993) J. Biotechnol. 30: 339-350.)
The largest and most diverse family of transport proteins known is the ATP-binding cassette (ABC) transporters. As a family, ABC transporters can fransport substances that differ markedly in 5 chemical structure and size, ranging from small molecules such as ions, sugars, amino acids, peptides, and phosphoUpids, to lipopeptides, large proteins, and complex hydrophobic drugs. ABC proteins consist of four modules: two nucleotide-binding domains (NBD), which hydrolyze ATP to supply the energy required for fransport, and two membrane-spanning domains (MSD), each containing six putative transmembrane segments. These four modules may be encoded by a single gene, as is the case o for the cystic fibrosis transmembrane regulator (CFTR), or by separate genes. When encoded by separate genes, each gene product contains a single NBD and MSD. These "half-molecules" form homo- and heterodimers, such as Tapl and Tap2, the endoplasmic reticulum-based major histocompatibility (MHC) peptide transport system. Several genetic diseases are attributed to defects in ABC transporters, such as the following diseases and their corresponding proteins: cystic fibrosis 5 (CFTR, an ion channel), adrenoleukodysttophy (adrenoleukodystrophy protein, ALDP), Zellweger syndrome (peroxisomal membrane protein-70, PMP70), and hyperinsuUnemic hypoglycemia (sulfonylurea receptor, SUR). Overexpression of the multidrug resistance (MDR) protein, another ABC fransporter, in human cancer cells makes the cells resistant to a variety of cytotoxic drugs used in chemotherapy (Taglight, D. and S. Michaelis (1998) Meth. Enzymol. 292:131-163). Transport of fatty acids across the plasma membrane can occur by diffusion, a high capacity, low affinity process. However, under normal physiological conditions a significant fraction of fatty acid fransport appears to occur via a high affinity, low capacity protein-mediated fransport process. Fatty acid fransport protein (FATP), an integral membrane protein with four transmembrane segments, is expressed in tissues exhibiting high levels of plasma membrane fatty acid flux, such as muscle, heart, and adipose. Expression of FATP is upregulated in 3T3-L1 cells during adipose conversion, and expression in COS7 fibroblasts elevates uptake of long-chain fatty acids (Hui, T.Y. et al. (1998) J. Biol. Chem. 273:27420-27429). Ion Channels
The elecfrical potential of a cell is generated and maintained by controlling the movement of ions across the plasma membrane. The movement of ions requires ion channels, which form an ion- selective pore within the membrane. There are two basic types of ion channels, ion transporters and gated ion channels. Ion fransporters utitize the energy obtained from ATP hydrolysis to actively fransport an ion against the ion's concentration gradient. Gated ion channels allow passive flow of an ion down the ion's electrochemical gradient under restricted conditions. Together, these types of ion channels generate, maintain, and utilize an elecfrochemical gradient that is used in 1) electrical impulse conduction down the axon of a nerve cell, 2) fransport of molecules into cells against concentration gradients, 3) initiation of muscle confraction, and 4) endocrine cell secretion.
Ion transporters generate and maintain the resting elecfrical potential of a cell. Utilizing the energy derived from ATP hydrolysis, they fransport ions against the ion's concentration gradient. These transmembrane ATPases are divided into three families. The phosphorylated (P) class ion transporters, including Na+-K+ ATPase, Ca2+-ATPase, and H+-ATPase, are activated by a phosphorylation event. P-class ion fransporters are responsible for maintaining resting potential distributions such that cytosolic concentrations of Na+ and Ca2+ are low and cytosolic concentration of K+ is high. The vacuolar (V) class of ion transporters includes H+ pumps on infracellular organelles, such as lysosomes and Golgi. V-class ion transporters are responsible for generating the low pH within the lumen of these organelles that is required for function. The coupling factor (F) class consists of H+ pumps in the mitochondria. F-class ion transporters utilize a proton gradient to generate ATP from ADP and inorganic phosphate (P_).
The resting potential of the cell is utilized in many processes involving carrier proteins and gated ion channels. Carrier proteins utilize the resting potential to fransport molecules into and out of the cell. Amino acid and glucose fransport into many cells is linked to sodium ion co-transport (symport) so that the movement of Na+ down an electrochemical gradient drives fransport of the other molecule up a concentration gradient. Similarly, cardiac muscle links fransfer of Ca 2+ out of the cell with fransport of Na+ into the cell (antiport). 5 Ion channels share common structural and mechanistic themes. The channel consists of four or five subunits or protein monomers that are arranged like a barrel in the plasma membrane. Each subunit typically consists of six potential fransmembrane segments (SI, S2, S3, S4, S5, and S6). The center of the barrel forms a pore lined by α-helices or β-sfrands. The side chains of the amino acid residues comprising the α-heUces or β-sttands establish the charge (cation or anion) selectivity of the 0 channel. The degree of selectivity, or what specific ions are allowed to pass through the channel, depends on the diameter of the narrowest part of the pore.
Gated ion channels control ion flow by regulating the opening and closing of pores. These channels are categorized according to the manner of regulating the gating function. Mechanically-gated channels open pores in response to mechanical stress, voltage-gated channels open pores in response to 5 changes in membrane potential, and ligand-gated channels open pores in the presence of a specific ion, nucleotide, or neurotransmitter.
Voltage-gated Na+ and K+ channels are necessary for the function of electrically excitable cells, such as nerve and muscle cells. Action potentials, which lead to neurotransmitter release and muscle confraction, arise from large, transient changes in the permeability of the membrane to Na+ and K+ ions. o Depolarization of the membrane beyond the threshold level opens voltage-gated Na+ channels. Sodium ions flow into the cell, further depolarizing the membrane and opening more voltage-gated Na+ channels, which propagates the depolarization down the length of the cell. Depolarization also opens voltage-gated potassium channels. Consequently, potassium ions flow outward, which leads to repolarization of the membrane. Voltage-gated channels utilize charged residues in the fourth 5 fransmembrane segment (S4) to sense voltage change. The open state lasts only about 1 millisecond, at which time the channel spontaneously converts into an inactive state that cannot be opened irrespective of the membrane potential. Inactivation is mediated by the channel's N-terminus, which acts as a plug that closes the pore. The transition from an inactive to a closed state requires a return to resting potential. o Voltage-gated Na+ channels are heterotrimeric complexes composed of a 260 kDa pore forming α subunit that associates with two smaller auxiliary subunits, βl and β2. The β2 subunit is an integral membrane glycoprotein that contains an exfracellular Ig domain, and its association with α and βl subunits correlates with increased functional expression of the channel, a change in its gating properties, and an increase in whole cell capacitance due to an increase in membrane surface area. 5 (Isom, L.L. et al. (1995) Cell 83:433-442.) Voltage-gated Ca 2+ channels are involved in presynaptic neurotransmitter release, and heart and skeletal muscle confraction. The voltage-gated Ca2+ channels from skeletal muscle (L-type) and brain (N-type) have been purified, and though their functions differ dramatically, they have similar subunit compositions. The channels are composed of three subunits. The _ subunit forms the 5 membrane pore and voltage sensor, while the o^δ and β subunits modulate the voltage-dependence, gating properties, and the current amphtude of the channel. These subunits are encoded by at least six α^ one α2δ, and four β genes. A fourth subunit, γ, has been identified in skeletal muscle. (Walker, D. et al. (1998) J. Biol. Chem. 273:2361-2367; and Jay, S.D. et al. (1990) Science 248:490-492.)
Chloride channels are necessary in endocrine secretion and in regulation of cytosolic and o organelle pH. In secretory epithelial cells, Cl " enters the cell across a basolateral membrane through an
Na+, K7C1 " cofransporter, accumulating in the cell above its electrochemical equilibrium concentration. Secretion of Cl " from the apical surface, in response to hormonal stimulation, leads to flow of Na+ and water into the secretory lumen. The cystic fibrosis fransmembrane conductance regulator (CFTR) is a chloride channel encoded by the gene for cystic fibrosis, a common fatal genetic disorder in humans. 5 Loss of CFTR function decreases ttansepithelial water secretion and, as a result, the layers of mucus that coat the respiratory free, pancreatic ducts, and intestine are dehydrated and difficult to clear. The resulting blockage of these sites leads to pancreatic insufficiency, "meconium ileus", and devastating "chronic obstructive pulmonary disease" (Al-Awqati, Q. et al. (1992) J. Exp. Biol. 172:245-266).
Many infracellular organelles contain H+- ATPase pumps that generate transmembrane pH and o elecfrochemical differences by moving protons from the cytosol to the organelle lumen. If the membrane of the organelle is permeable to other ions, then the electrochemical gradient can be abrogated without affecting the pH differential. In fact, removal of the elecfrochemical barrier allows more H + to be pumped across the membrane, increasing the pH differential. Cl " is the sole counterion of H + translocation in a number of organelles, including chromaffin granules, Golgi vesicles, 5 lysosomes, and endosomes. Functions that require a low vacuolar pH include uptake of small molecules such as biogenic amines in chromaffin granules, processing of vacuolar constituents such as pro-hormones by proteolytic enzymes, and protein degradation in lysosomes (Al-Awqati, supra).
Ligand-gated channels open their pores when an exfracellular or intracellular mediator binds to the channel. Neurottansmitter-gated channels are channels that open when a neurotransmitter binds to o their extracellular domain. These channels exist in the postsynaptic membrane of nerve or muscle cells.
There are two types of neurofransmitter-gated channels. Sodium channels open in response to excitatory neurofransmitters, such as acetylcholine, glutamate, and serotonin. This opening causes an influx of Na+ and produces the initial localized depolarization that activates the voltage-gated channels and starts the action potential. Chloride channels open in response to inhibitory neurofransmitters, such 5 as γ-aminobutyric acid (GABA) and glycine, leading to hyperpolarization of the membrane and the subsequent generation of an action potential.
Ligand-gated channels can be regulated by infracellular second messengers. Calcium-activated K+ channels are gated by internal calcium ions. In nerve cells, an influx of calcium during depolarization opens K+ channels to modulate the magnitude of the action potential (Ishi, T.M. et al. (1997) Proc. Nati. Acad. Sci. USA 94:11651-11656). Cyclic nucleotide-gated (CNG) channels are gated by cytosoUc cycUc nucleotides. The best examples of these are the cAMP-gated Na + channels involved in olfaction and the cGMP-gated cation channels involved in vision. Both systems involve Ugand-mediated activation of a G-protein coupled receptor which then alters the level of cycUc nucleotide within the cell. Ion channels are expressed in a number of tissues where they are implicated in a variety of processes. CNG channels, while abundantly expressed in photoreceptor and olfactory sensory cells, are also found in kidney, lung, pineal, retinal ganglion cells, testis, aorta, and brain. Calcium-activated K+ channels may be responsible for the vasodilatory effects of bradykinin in the kidney and for shunting excess K+ from brain capillary endothehal cells into the blood. They are also implicated in repolarizing granulocytes after agonist-stimulated depolarization (Ishi, supra). Ion channels have been the target for many drug therapies. Neurofransmitter-gated channels have been targeted in therapies for treatment of insomnia, anxiety, depression, and schizophrenia. Voltage-gated channels have been targeted in therapies for arrhythmia, ischemic stroke, head frauma, and neurodegenerative disease (Taylor, C.P. and L.S. Narasimhan (1997) Adv. Pharmacol. 39:47-98). Disease Correlation
The etiology of numerous human diseases and disorders can be attributed to defects in the fransport of molecules across membranes. Defects in the trafficking of membrane-bound fransporters and ion channels are associated with several disorders, e.g. cystic fibrosis, glucose-galactose malabsoφtion syndrome, hypercholesterolemia, von Gierke disease, and certain forms of diabetes mellitus. Single-gene defect diseases resulting in an inability to fransport small molecules across membranes include, e.g., cystinuria, iminoglycinuria, Hartup disease, and Fanconi disease (van't Hoff, W.G. (1996) Exp. Nephrol. 4:253-262; Talente, G.M. et al. (1994) Ann. Intern. Med. 120:218-226; and Chillon, M. et al. (1995) New Engl. J. Med. 332:1475-1480).
Protein Modification and Maintenance Molecules
The cellular processes regulating modification and maintenance of protein molecules coordinate their conformation, stabilization, and degradation. Each of these processes is mediated by key enzymes or proteins such as proteases, protease inhibitors, transferases, isomerases, and molecular chaperones. Proteases Proteases cleave proteins and peptides at the peptide bond that forms the backbone of the peptide and protein chain. Proteolytic processing is essential to cell growth, differentiation, remodeling, and homeostasis as well as inflammation and immune response. Typical protein half- lives range from hours to a few days, so that within all living cells, precursor proteins are being 5 cleaved to their active form, signal sequences proteolytically removed from targeted proteins, and aged or defective proteins degraded by proteolysis. Proteases function in bacterial, parasitic, and viral invasion and replication within a host. Four principal categories of mammalian proteases have been identified based on active site structure, mechanism of action, and overall three-dimensional structure. (Beynon, R.J. and J.S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University 0 Press, New York NY, pp. 1-5).
The serine proteases (SPs) have a serine residue, usually within a conserved sequence, in an active site composed of the serine, an aspartate, and a histidine residue. SPs include the digestive enzymes trypsin and chymotrypsin, components of the complement cascade and the blood-clotting cascade, and enzymes that confrol extracellular protein degradation. The main SP sub-families are 5 trypases, which cleave after arginine or lysine; aspartases, which cleave after aspartate; chymases, which cleave after phenylalanine or leucine; metases, which cleavage after methionine; and serases which cleave after serine. Enterokinase, the initiator of intestinal digestion, is a serine protease found in the intestinal brush border, where it cleaves the acidic propeptide from trypsinogen to yield active trypsin (Kitamoto, Y. et al. (1994) Proc. Nati. Acad. Sci. USA 91:7588-7592). o Prolylcarboxypeptidase, a lysosomal serine peptidase that cleaves peptides such as angiotensin II and III and [des-Arg9] bradykinin, shares sequence homology with members of both the serine carboxypeptidase and prolylendopeptidase families (Tan, F. et al. (1993) J. Biol. Chem. 268:16631- 16638).
Cysteine proteases (CPs) have a cysteine as the major catalytic residue at an active site where 5 catalysis proceeds via an intermediate thiol ester and is facilitated by adjacent histidine and aspartic acid residues. CPs are involved in diverse cellular processes ranging from the processing of precursor proteins to intracellular degradation. Mammalian CPs include lysosomal cathepsins and cytosolic calcium activated proteases, calpains. CPs are produced by monocytes, macrophages and other cells of the immune system which migrate to sites of inflammation and secrete molecules involved in o tissue repair. Overabundance of these repair molecules plays a role in certain disorders. In autoimmune diseases such as rheumatoid arthritis, secretion of the cysteine peptidase cathepsin C degrades collagen, laminin, elastin and other structural proteins found in the extracellular mafrix of bones.
Aspartic proteases are members of the cathepsin family of lysosomal proteases and include 5 pepsin A, gasfricsin, chymosin, renin, and cathepsins D and E. Aspartic proteases have a pair of aspartic acid residues in the active site, and are most active in the pH 2 - 3 range, in which one of the aspartate residues is ionized, the other un-ionized. Aspartic proteases include bacterial penicillopepsin, mammalian pepsin, renin, chymosin, and certain fungal proteases. Abnormal regulation and expression of cathepsins is evident in various inflammatory disease states. In cells 5 isolated from inflamed synovia, the mRNA for sfromelysin, cytokines, TIMP-1, cathepsin, gelatinase, and other molecules is preferentially expressed. Expression of cathepsins L and D is elevated in synovial tissues from patients with rheumatoid arthritis and osteoarthritis. Cathepsin L expression may also confribute to the influx of mononuclear cells which exacerbates the destruction of the rheumatoid synovium. (Keyszer, G.M. (1995) Arthritis Rheum. 38:976-984.) The increased expression and o differential regulation of the cathepsins are linked to the metastatic potential of a variety of cancers and as such are of therapeutic and prognostic interest (Chambers, A.F. et al. (1993) Crit. Rev. Oncog. 4:95-114).
Metalloproteases have active sites that include two glutamic acid residues and one histidine residue that serve as binding sites for zinc. Carboxypeptidases A and B are the principal mammalian 5 metalloproteases. Both are exoproteases of similar structure and active sites. Carboxypeptidase A, like chymofrypsin, prefers C-terminal aromatic and aliphatic side chains of hydrophobic nature, whereas carboxypeptidase B is directed toward basic arginine and lysine residues. Glycoprotease (GCP), or O-sialoglycoprotein endopeptidase, is a metallopeptidase which specifically cleaves O-sialoglycoproteins such as glycophorin A. Another metallopeptidase, placental leucine 0 aminopeptidase (P-LAP) degrades several peptide hormones such as oxytocin and vasopressin, suggesting a role in maintaining homeostasis during pregnancy, and is expressed in several tissues (Rogi, T. et al. (1996) J. Biol. Chem. 271 :56-61).
Ubiquitin proteases are associated with the ubiquitin conjugation system (UCS), a major pathway for the degradation of cellular proteins in eukaryotic cells and some bacteria. The UCS 5 mediates the elimination of abnormal proteins and regulates the half-lives of important regulatory proteins that confrol cellular processes such as gene transcription and cell cycle progression. In the UCS pathway, proteins targeted for degradation are conjugated to a ubiquitin, a small heat stable protein. The ubiquitinated protein is then recognized and degraded by proteasome, a large, multisubunit proteolytic enzyme complex, and ubiquitin is released for reutilization by ubiquitin o protease. The UCS is implicated in the degradation of mitotic cyclic kinases, oncoproteins, tumor suppressor genes such as p53, viral proteins, cell surface receptors associated with signal transduction, franscriptional regulators, and mutated or damaged proteins (Ciechanover, A. (1994) Cell 79:13-21). A murine proto-oncogene, Unp, encodes a nuclear ubiquitin protease whose overexpression leads to oncogenic transformation of NIH3T3 cells, and the human homolog of this 5 gene is consistently elevated in small cell tumors and adenocarcinomas of the lung (Gray, D. A. (1995) Oncogene 10:2179-2183). Signal Peptidases
The mechanism for the translocation process into the endoplasmic reticulum (ER) involves the recognition of an N-terminal signal peptide on the elongating protein. The signal peptide directs 5 the protein and attached ribosome to a receptor on the ER membrane. The polypeptide chain passes through a pore in the ER membrane into the lumen while the N-terminal signal peptide remains attached at the membrane surface. The process is completed when signal peptidase located inside the ER cleaves the signal peptide from the protein and releases the protein into the lumen. Protease Inhibitors o Protease inhibitors and other regulators of protease activity confrol the activity and effects of proteases. Protease inhibitors have been shown to control pathogenesis in animal models of proteolytic disorders (Muφhy, G. (1991) Agents Actions Suppl. 35:69-76). Low levels of the cystatins, low molecular weight inhibitors of the cysteine proteases, correlate with malignant progression of tumors. (Calkins, C. et al (1995) Biol. Biochem. Hoppe Seyler 376:71-80). Seφins 5 are inhibitors of mammalian plasma serine proteases. Many seφins serve to regulate the blood clotting cascade and/or the complement cascade in mammals. Sp32 is a positive regulator of the mammalian acrosomal protease, acrosin, that binds the proenzyme, proacrosin, and thereby aides in packaging the enzyme into the acrosomal mafrix (Baba, T. et al. (1994) J. Biol. Chem. 269:10133- 10140). The Kunitz family of serine protease inhibitors are characterized by one or more "Kunitz o domains" containing a series of cysteine residues that are regularly spaced over approximately 50 amino acid residues and form three intrachain disulfide bonds. Members of this family include aprotinin, tissue factor pathway inhibitor (TFPI-1 and TFPI-2), inter-α-frypsin inhibitor, and bikunin. (Marlor, C.W. et al. (1997) J. Biol. Chem. 272:12202-12208.) Members of this family are potent inhibitors (in the nanomolar range) against serine proteases such as kallikrein and plasmin. Aprotinin 5 has cUnical utility in reduction of perioperative blood loss.
A major portion of all proteins synthesized in eukaryotic cells are synthesized on the cytosolic surface of the endoplasmic reticulum (ER). Before these immature proteins are distributed to other organelles in the cell or are secreted, they must be transported into the interior lumen of the ER where post-franslational modifications are performed. These modifications include protein folding o and the formation of disulfide bonds, and N-linked glycosylations.
Protein Isomerases
Protein folding in the ER is aided by two principal types of protein isomerases, protein disulfide isomerase (PDI), and peptidyl-prolyl isomerase (PPI). PDI catalyzes the oxidation of free sulfhydryl groups in cysteine residues to form inframolecular disulfide bonds in proteins. PPI, an 5 enzyme that catalyzes the isomerization of certain proline imidic bonds in oligopeptides and proteins, is considered to govern one of the rate limiting steps in the folding of many proteins to their final functional conformation. The cyclophilins represent a major class of PPI that was originally identified as the major receptor for the immunosuppressive drug cyclosporin A (Handschumacher, R.E. et al. (1984) Science 226: 544-547). Protein Glycosylation
The glycosylation of most soluble secreted and membrane-bound proteins by oligosaccharides linked to asparagine residues in proteins is also performed in the ER. This reaction is catalyzed by a membrane-bound enzyme, oligosaccharyl transferase. Although the exact puφose of this "N-linked" glycosylation is unknown, the presence of oligosaccharides tends to make a glycoprotein resistant to protease digestion. In addition, oligosaccharides attached to cell-surface proteins called selectins are known to function in cell-cell adhesion processes (Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing Co., New York NY, p.608). "O-linked" glycosylation of proteins also occurs in the ER by the addition of N-acetylgalactosamine to the hydroxyl group of a serine or threonine residue followed by the sequential addition of other sugar residues to the first. This process is catalysed by a series of glycosyltransferases each specific for a particular donor sugar nucleotide and acceptor molecule (Lodish, H. et al. (1995) Molecular Cell Biology, W.H. Freeman and Co., New York NY, ppJ00-708). In many cases, both N- and O-linked oligosaccharides appear to be required for the secretion of proteins or the movement of plasma membrane glycoproteins to the cell surface. An additional glycosylation mechanism operates in the ER specifically to target lysosomal enzymes to lysosomes and prevent their secretion. Lysosomal enzymes in the ER receive an N-linked oligosaccharide, like plasma membrane and secreted proteins, but are then phosphorylated on one or two mannose residues. The phosphorylation of mannose residues occurs in two steps, the first step being the addition of an N-acetylglucosamine phosphate residue by N-acetylglucosamine phosphotransferase, and the second the removal of the N-acetylglucosamine group by phosphodiesterase. The phosphorylated mannose residue then targets the lysosomal enzyme to a mannose 6-phosphate receptor which transports it to a lysosome vesicle (Lodish, supra, pp. 708-711). Chaperones
Molecular chaperones are proteins that aid in the proper folding of immature proteins and refolding of improperly folded ones, the assembly of protein subunits, and in the fransport of unfolded proteins across membranes. Chaperones are also called heat-shock proteins (hsp) because of their tendency to be expressed in dramatically increased amounts following brief exposure of cells to elevated temperatures. This latter property most likely reflects their need in the refolding of proteins that have become denatured by the high temperatures. Chaperones may be divided into several classes according to their location, function, and molecular weight, and include hsp60, TCPl , hsp70, hsp40 (also called DnaJ), and hsp90. For example, hsp90 binds to steroid hormone receptors, represses franscription in the absence of the ligand, and provides proper folding of the ligand-binding domain of the receptor in the presence of the hormone (Burston, S.G. and A.R. Clarke (1995) Essays Biochem. 29:125-136). Hsp60 and hsp70 chaperones aid in the fransport and folding of newly 5 synthesized proteins. Hsp70 acts early in protein folding, binding a newly synthesized protein before it leaves the ribosome and transporting the protein to the mitochondria or ER before releasing the folded protein. Hsp60, along with hsp 10, binds misfolded proteins and gives them the opportunity to refold correctly. All chaperones share an affinity for hydrophobic patches on incompletely folded proteins and the ability to hydrolyze ATP. The energy of ATP hydrolysis is used to release the hsp- 0 bound protein in its properly folded state (Alberts, supra, pp 214, 571-572).
Nucleic Acid Synthesis and Modification Molecules
SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO: 16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO: 19, and SEQ ID NO:20 encode, for example, nucleic acid synthesis and modification molecules. 5 Polymerases
DNA and RNA replication are critical processes for cell replication and function. DNA and RNA replication are mediated by the enzymes DNA and RNA polymerase, respectively, by a "templating" process in which the nucleotide sequence of a DNA or RNA strand is copied by complementary base-pairing into a complementary nucleic acid sequence of either DNA or RNA. o However, there are fundamental differences between the two processes.
DNA polymerase catalyzes the stepwise addition of a deoxyribonucleotide to the 3'-OH end of a polynucleotide strand (the primer strand) that is paired to a second (template) strand. The new DNA strand therefore grows in the 5' to 3' direction (Alberts, B. et al. (1994) The Molecular Biology of the Cell, Garland Publishing Inc., New York NY, pp. 251-254). The substrates for the polymerization 5 reaction are the corresponding deoxynucleotide triphosphates which must base-pair with the correct nucleotide on the template strand in order to be recognized by the polymerase. Because DNA exists as a double-stranded hehx, each of the two strands may serve as a template for the formation of a new complementary strand. Each of the two daughter cells of the dividing cell therefore inherits a new DNA double helix containing one old and one new strand. Thus, DNA is said to be replicated o "semiconservatively" by DNA polymerase. In addition to the synthesis of new DNA, DNA polymerase is also involved in the repair of damaged DNA as discussed below under "Ligases."
In contrast to DNA polymerase, RNA polymerase uses a DNA template strand to "transcribe" DNA into RNA using ribonucleotide triphosphates as substrates. Like DNA polymerization, RNA polymerization proceeds in a 5' to 3' direction by addition of a ribonucleoside monophosphate to the 3'- 5 OH end of a growing RNA chain. DNA franscription generates messenger RNAs (mRNA) that carry information for protein synthesis, as well as the transfer, ribosomal, and other RNAs that have structural or catalytic functions. In eukaryotes, three discrete RNA polymerases synthesize the three different types of RNA (Alberts, supra, pp. 367-368). RNA polymerase I makes the large ribosomal RNAs, RNA polymerase II makes the mRNAs that will be translated into proteins, and RNA 5 polymerase III makes a variety of small, stable RNAs, including 5S ribosomal RNA and the transfer RNAs (tRNA). In all cases, RNA synthesis is initiated by binding of the RNA polymerase to a promoter region on the DNA and synthesis begins at a start site within the promoter. Synthesis is completed at a broad, general stop or termination region in the DNA where both the polymerase and the completed RNA chain are released. 0 Ligases
DNA repair is the process by which accidental base changes, such as those produced by oxidative damage, hydrolytic attack, or uncontrolled methylation of DNA are corrected before replication or franscription of the DNA can occur. Because of the efficiency of the DNA repair process, fewer than one in one thousand accidental base changes causes a mutation (Alberts, supra, pp. 5 245-249). The three steps common to most types of DNA repair are (1 ) excision of the damaged or altered base or nucleotide by DNA nucleases, leaving a gap; (2) insertion of the correct nucleotide in this gap by DNA polymerase using the complementary strand as the template; and (3) sealing the break left between the inserted nucleotide(s) and the existing DNA strand by DNA ligase. In the last reaction, DNA ligase uses the energy from ATP hydrolysis to activate the 5 ' end of the broken phosphodiester o bond before forming the new bond with the 3'-OH of the DNA strand. In Bloom' s syndrome, an inherited human disease, individuals are partially deficient in DNA ligation and consequently have an increased incidence of cancer (Alberts, supra, p. 247).
Nucleases
Nucleases comprise both enzymes that hydrolyze DNA (DNase) and RNA (RNase). They 5 serve different puφoses in nucleic acid metabolism. Nucleases hydrolyze the phosphodiester bonds between adjacent nucleotides either at internal positions (endonucleases) or at the terminal 3' or 5' nucleotide positions (exonucleases). A DNA exonuclease activity in DNA polymerase, for example, serves to remove improperly paired nucleotides attached to the 3'-OH end of the growing DNA strand by the polymerase and thereby serves a "proofreading" function. As mentioned above, DNA o endonuclease activity is involved in the excision step of the DNA repair process.
RNases also serve a variety of functions. For example, RNase P is a ribonucleoprotein enzyme which cleaves the 5' end of pre-tRNAs as part of their maturation process. RNase H digests the RNA strand of an RNA/DNA hybrid. Such hybrids occur in cells invaded by refroviruses, and RNase H is an important enzyme in the retroviral replication cycle. Pancreatic RNase secreted by the pancreas into 5 the intestine hydrolyzes RNA present in ingested foods. RNase activity in serum and cell extracts is elevated in a variety of cancers and infectious diseases (Schein, CH. (1997) Nat. Biotechnol. 15:529- 536). Regulation of RNase activity is being investigated as a means to control tumor angiogenesis, allergic reactions, viral infection and repUcation, and fungal infections. Methylases 5 Methylation of specific nucleotides occurs in both DNA and RNA, and serves different functions in the two macromolecules. Methylation of cytosine residues to form 5-methyl cytosine in DNA occurs specifically at CG sequences which are base-paired with one another in the DNA double- hehx. This pattern of methylation is passed from generation to generation during DNA replication by an enzyme called "maintenance methylase" that acts preferentially on those CG sequences that are base- o paired with a CG sequence that is already methylated. Such methylation appears to distinguish active from inactive genes by preventing the binding of regulatory proteins that "turn on" the gene, but permit the binding of proteins that inactivate the gene (Alberts, supra, pp. 448-451). In RNA metabolism, "tRNA methylase" produces one of several nucleotide modifications in tRNA that affect the conformation and base-pairing of the molecule and facilitate the recognition of the appropriate mRNA 5 codons by specific tRNAs. The primary methylation pattern is the dimethylation of guanine residues to form N,N-dimethyl guanine. Helicases and Single-Stranded Binding Proteins
Helicases are enzymes that destabilize and unwind double helix structures in both DNA and RNA. Since DNA replication occurs more or less simultaneously on both strands, the two strands must o first separate to generate a replication "fork" for DNA polymerase to act on. Two types of replication proteins confribute to this process, DNA helicases and single-stranded binding proteins. DNA helicases hydrolyze ATP and use the energy of hydrolysis to separate the DNA strands. Single-stranded binding proteins (SSBs) then bind to the exposed DNA strands without covering the bases, thereby temporarily stabilizing them for templating by the DNA polymerase (Alberts, supra, pp. 255-256). 5 RNA heUcases also alter and regulate RNA conformation and secondary structure. Like the
DNA helicases, RNA helicases utilize energy derived from ATP hydrolysis to destabilize and unwind RNA duplexes. The most well-characterized and ubiquitous family of RNA helicases is the DEAD-box family, so named for the conserved B-type ATP-binding motif which is diagnostic of proteins in this family. Over 40 DEAD-box helicases have been identified in organisms as diverse as bacteria, insects, o yeast, amphibians, mammals, and plants. DEAD-box helicases function in diverse processes such as translation initiation, splicing, ribosome assembly, and RNA editing, fransport, and stability. Some DEAD-box helicases play tissue- and stage-specific roles in spermatogenesis and embryogenesis. Overexpression of the DEAD-box 1 protein (DDX1) may play a role in the progression of neuroblastoma (Nb) and retinoblastoma (Rb) tumors (Godbout, R. et al. (1998) J. Biol. Chem. 5 273:21161-21168). These observations suggest that DDX1 may promote or enhance tumor progression by altering the normal secondary structure and expression levels of RNA in cancer cells. Other DEAD-box heUcases have been implicated either directly or indirectly in tumorigenesis (Discussed in Godbout, supra). For example, murine p68 is mutated in ultraviolet Ught-induced tumors, and human DDX6 is located at a chromosomal breakpoint associated with B-cell lymphoma. Similarly, a chimeric protein comprised of DDX10 and NUP98, a nucleoporin protein, may be involved in the pathogenesis of certain myeloid maUgnancies. Topoisomerases
Besides the need to separate DNA strands prior to replication, the two strands must be "unwound" from one another prior to their separation by DNA helicases. This function is performed by proteins known as DNA topoisomerases. DNA topoisomerase effectively acts as a reversible nuclease that hydrolyzes a phosphodiesterase bond in a DNA strand, permitting the two strands to rotate freely about one another to remove the strain of the heUx, and then rejoins the original phosphodiester bond between the two strands. Two types of DNA topoisomerase exist, types I and II. DNA Topoisomerase
I causes a single-strand break in a DNA helix to allow the rotation of the two strands of the helix about the remaining phosphodiester bond in the opposite strand. DNA topoisomerase II causes a transient break in both strands of a DNA helix where two double helices cross over one another. This type of topoisomerase can efficiently separate two interlocked DNA circles (Alberts, supra, pp.260-262). Type
II topoisomerases are largely confined to proliferating cells in eukaryotes, such as cancer cells. For this reason they are targets for anticancer drugs. Topoisomerase II has been implicated in multi-drug resistance (MDR) as it appears to aid in the repair of DNA damage inflicted by DNA binding agents such as doxorubicin and vincristine. Recombinases
Genetic recombination is the process of rearranging DNA sequences within an organism's genome to provide genetic variation for the organism in response to changes in the environment. DNA recombination allows variation in the particular combination of genes present in an individual' s genome, as well as the timing and level of expression of these genes (see Alberts, supra, pp. 263-273). Two broad classes of genetic recombination are commonly recognized, general recombination and site- specific recombination. General recombination involves genetic exchange between any homologous pair of DNA sequences usually located on two copies of the same chromosome. The process is aided by enzymes called recombinases that "nick" one strand of a DNA duplex more or less randomly and permit exchange with the complementary strand of another duplex. The process does not normally change the arrangement of genes on a chromosome. In site-specific recombination, the recombinase recognizes specific nucleotide sequences present in one or both of the recombining molecules. Base- pairing is not involved in this form of recombination and therefore does not require DNA homology between the recombining molecules. Unlike general recombination, this form of recombination can alter the relative positions of nucleotide sequences in chromosomes. Splicing Factors
Various proteins are necessary for processing of transcribed RNAs in the nucleus. Pre-mRNA processing steps include capping at the 5' end with methylguanosine, polyadenylating the 3' end, and 5 spUcing to remove introns. The primary RNA transcript from DNA is a faithful copy of the gene containing both exon and intron sequences, and the latter sequences must be cut out of the RNA transcript to produce an mRNA that codes for a protein. This "splicing" of the mRNA sequence takes place in the nucleus with the aid of a large, multicomponent ribonucleoprotein complex known as a spUceosome. The spUceosomal complex is composed of five small nuclear ribonucleoprotein particles 0 (snRNPs) designated Ul, U2, U4, U5, and U6, and a number of additional proteins. Each snRNP contains a single species of snRNA and about ten proteins. The RNA components of some snRNPs recognize and base pair with intron consensus sequences. The protein components mediate spliceosome assembly and the splicing reaction. Autoantibodies to snRNP proteins are found in the blood of patients with systemic lupus erythematosus (Stryer, L. (1995) Biochemistry, W.H. Freeman and 5 Company, New York NY, p. 863).
Adhesion Molecules
SEQ ID NO:21 and SEQ ID NO:22 encode, for example, adhesion molecules.
The surface of a cell is rich in fransmembrane proteoglycans, glycoproteins, glycolipids, and o receptors. These macromolecules mediate adhesion with other cells and with components of the exfracellular mafrix (ECM). The interaction of the cell with its surroundings profoundly influences cell shape, strength, flexibility, motility, and adhesion. These dynamic properties are intimately associated with signal transduction pathways controlling cell proUferation and differentiation, tissue construction, and embryonic development. 5 Cadherins
Cadherins comprise a family of calcium-dependent glycoproteins that function in mediating cell-cell adhesion in virtually all solid tissues of multicellular organisms. These proteins share multiple repeats of a cadherin-specific motif, and the repeats form the folding units of the cadherin exfracellular domain. Cadherin molecules cooperate to form focal contacts, or adhesion plaques, between adjacent o epithelial cells. The cadherin family includes the classical cadherins and protocadherins. Classical cadherins include the E-cadherin, N-cadherin, and P-cadherin subfamilies. E-cadherin is present on many types of epitheUal cells and is especially important for embryonic development. N-cadherin is present on nerve, muscle, and lens cells and is also critical for embryonic development. P-cadherin is present on cells of the placenta and epidermis. Recent studies report that protocadherins are involved in 5 a variety of cell-cell interactions (Suzuki, S.T. (1996) J. Cell Sci. 109:2609-2611). The infracellular anchorage of cadherins is regulated by their dynamic association with catenins, a family of cytoplasmic signal transduction proteins associated with the actin cytoskeleton. The anchorage of cadherins to the actin cytoskeleton appears to be regulated by protein tyrosine phosphorylation, and the cadherins are the target of phosphorylation-inducedjunctional disassembly (Aberle, H. et al. (1996) J. Cell. Biochem. 5 61:514-523). Integrins
Integrins are ubiquitous fransmembrane adhesion molecules that link the ECM to the internal cytoskeleton. Integrins are composed of two noncovalently associated fransmembrane glycoprotein subunits called α and β. Integrins function as receptors that play a role in signal transduction. For o example, binding of integrin to its extracellular ligand may stimulate changes in infracellular calcium levels or protein kinase activity (Sjaastad, M.D. and W.J. Nelson (1997) BioEssays 19:47-55). At least ten cell surface receptors of the integrin family recognize the ECM component fibronectin, which is involved in many different biological processes including cell migration and embryogenesis (Johansson, S. et al. (1997) Front. Biosci. 2:D126-D146). 5 Lectins
Lectins comprise a ubiquitous family of exfracellular glycoproteins which bind cell surface carbohydrates specifically and reversibly, resulting in the agglutination of cells (reviewed in Drickamer, K. and M.E. Taylor (1993) Annu. Rev. Cell Biol. 9:237-264). This function is particularly important for activation of the immune response. Lectins mediate the agglutination and mitogenic stimulation of 0 lymphocytes at sites of inflammation (Lasky, L.A. (1991) J. Cell. Biochem. 45:139-146; Paietta, E. et al. (1989) J. Immunol. 143:2850-2857).
Lectins are further classified into subfamilies based on carbohydrate-binding specificity and other criteria. The galectin subfamily, in particular, includes lectins that bind β-galactoside carbohydrate moieties in a thiol-dependent manner (reviewed in Hadari, Y.R. et al. (1998) J. Biol. 5 Chem. 270:3447-3453). Galectins are widely expressed and developmentaUy regulated. Because all galectins lack an N-terminal signal peptide, it is suggested that galectins are externalized through an atypical secretory mechanism. Two classes of galectins have been defined based on molecular weight and oligomerization properties. Small galectins form homodimers and are about 14 to 16 kilodaltons in mass, while large galectins are monomeric and about 29-37 kilodaltons. o Galectins contain a characteristic carbohydrate recognition domain (CRD). The CRD is about
140 amino acids and contains several stretches of about 1 - 10 amino acids which are highly conserved among all galectins. A particular 6-amino acid motif within the CRD contains conserved tryptophan and arginine residues which are critical for carbohydrate binding. The CRD of some galectins also contains cysteine residues which may be important for disulfide bond formation. Secondary structure 5 predictions indicate that the CRD forms several β-sheets. Galectins play a number of roles in diseases and conditions associated with cell-cell and cell- matrix interactions. For example, certain galectins associate with sites of inflammation and bind to cell surface immunoglobulin E molecules. In addition, galectins may play an important role in cancer metastasis. Galectin overexpression is correlated with the metastatic potential of cancers in humans 5 and mice. Moreover, anti-galectin antibodies inhibit processes associated with cell fransformation, such as cell aggregation and anchorage-independent growth (See, for example, Su, Z.-Z. et al. (1996) Proc. Nati. Acad. Sci. USA 93:7252-7257). Selectins
Selectins, or LEC-CAMs, comprise a specialized lectin subfamily involved primarily in o inflammation and leukocyte adhesion (Reviewed in Lasky, supra). Selectins mediate the recruitment of leukocytes from the circulation to sites of acute inflammation and are expressed on the surface of vascular endothelial cells in response to cytokine signaling. Selectins bind to specific ligands on the leukocyte cell membrane and enable the leukocyte to adhere to and migrate along the endothehal surface. Binding of selectin to its ligand leads to polarized rearrangement of the actin cytoskeleton and 5 stimulates signal transduction within the leukocyte (Brenner, B. et al. (1997) Biochem. Biophys. Res. Commun. 231 :802-807; Hidari, K.I. et al. (1997) J. Biol. Chem. 272:28750-28756). Members of the selectin family possess three characteristic motifs: a lectin or carbohydrate recognition domain; an epidermal growth factor-Uke domain; and a variable number of short consensus repeats (scr or "sushi" repeats) which are also present in complement regulatory proteins. The selectins include lymphocyte 0 adhesion molecule- 1 (Lam-1 or L-selectin), endothelial leukocyte adhesion molecule- 1 (ELAM-1 or E- selectin), and granule membrane protein- 140 (GMP-140 or P-selectin) (Johnston, G.I. et al. (1989) Cell 56:1033-1044).
Antigen Recognition Molecules 5 All vertebrates have developed sophisticated and complex immune systems that provide protection from viral, bacterial, fungal, and parasitic infections. A key feature of the immune system is its ability to distinguish foreign molecules, or antigens, from "self molecules. This ability is mediated primarily by secreted and fransmembrane proteins expressed by leukocytes (white blood cells) such as lymphocytes, granulocytes, and monocytes. Most of these proteins belong to the o immunoglobulin (Ig) superfamily, members of which contain one or more repeats of a conserved structural domain. This Ig domain is comprised of antiparallel β sheets joined by a disulfide bond in an arrangement called the Ig fold. Members of the Ig superfamily include T-cell receptors, major histocompatibility (MHC) proteins, antibodies, and immune cell-specific surface markers such as CD4, CD8, and CD28. 5 MHC proteins are cell surface markers that bind to and present foreign antigens to T cells. MHC molecules are classified as either class I or class II. Class I MHC molecules (MHC I) are expressed on the surface of almost all cells and are involved in the presentation of antigen to cytotoxic T cells. For example, a cell infected with virus will degrade intracellular viral proteins and express the protein fragments bound to MHC I molecules on the cell surface. The MHC I/antigen 5 complex is recognized by cytotoxic T-cells which destroy the infected cell and the virus within. Class II MHC molecules are expressed primarily on specialized antigen-presenting cells of the immune system, such as B-cells and macrophages. These cells ingest foreign proteins from the exfracellular fluid and express MHC H/antigen complex on the cell surface. This complex activates helper T-cells, which then secrete cytokines and other factors that stimulate the immune response. o MHC molecules also play an important role in organ rejection following fransplantation. Rejection occurs when the recipient's T-cells respond to foreign MHC molecules on the transplanted organ in the same way as to self MHC molecules bound to foreign antigen. (Reviewed in Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing, New York NY, pp. 1229-1246.)
Antibodies, or immunoglobuUns, are either expressed on the surface of B-cells or secreted by 5 B-cells into the circulation. Antibodies bind and neutralize foreign antigens in the blood and other exfracellular fluids. The prototypical antibody is a teframer consisting of two identical heavy polypeptide chains (H-chains) and two identical light polypeptide chains (L-chains) interlinked by disulfide bonds. This arrangement confers the characteristic Y-shape to antibody molecules. Antibodies are classified based on their H-chain composition. The five antibody classes, IgA, IgD, o IgE, IgG and IgM, are defined by the α, δ, e, γ, and μ H-chain types. There are two types of L- chains, K and λ, either of which may associate as a pair with any H-chain pair. IgG, the most common class of antibody found in the circulation, is tettameric, while the other classes of antibodies are generally variants or multimers of this basic structure.
H-chains and L-chains each contain an N-terminal variable region and a C-terminal constant 5 region. The constant region consists of about 110 amino acids in L-chains and about 330 or 440 amino acids in H-chains. The amino acid sequence of the constant region is nearly identical among H- or L-chains of a particular class. The variable region consists of about 110 amino acids in both H- and L-chains. However, the amino acid sequence of the variable region differs among H- or L-chains of a particular class. Within each H- or L-chain variable region are three hypervariable regions of o extensive sequence diversity, each consisting of about 5 to 10 amino acids. In the antibody molecule, the H- and L-chain hypervariable regions come together to form the antigen recognition site. (Reviewed in Alberts, supra, pp. 1206-1213 and 1216-1217.)
Both H-chains and L-chains contain repeated Ig domains. For example, a typical H-chain contains four Ig domains, three of which occur within the constant region and one of which occurs 5 within the variable region and contributes to the formation of the antigen recognition site. Likewise, a typical L-chain contains two Ig domains, one of which occurs within the constant region and one of which occurs within the variable region.
The immune system is capable of recognizing and responding to any foreign molecule that enters the body. Therefore, the immune system must be armed with a full repertoire of antibodies 5 against all potential antigens. Such antibody diversity is generated by somatic rearrangement of gene segments encoding variable and constant regions. These gene segments are joined together by site- specific recombination which occurs between highly conserved DNA sequences that flank each gene segment. Because there are hundreds of different gene segments, millions of unique genes can be generated combinatorially. In addition, imprecise joining of these segments and an unusually high 0 rate of somatic mutation within these segments further contribute to the generation of a diverse antibody population.
T-cell receptors are both structurally and functionally related to antibodies. (Reviewed in Alberts, supra, pp. 1228-1229.) T-cell receptors are cell surface proteins that bind foreign antigens and mediate diverse aspects of the immune response. A typical T-cell receptor is a heterodimer comprised 5 of two disulfide-linked polypeptide chains called α and β. Each chain is about 280 amino acids in length and contains one variable region and one constant region. Each variable or constant region folds into an Ig domain. The variable regions from the α and β chains come together in the heterodimer to form the antigen recognition site. T-cell receptor diversity is generated by somatic rearrangement of gene segments encoding the α and β chains. T-cell receptors recognize small peptide antigens that are o expressed on the surface of antigen-presenting cells and pathogen-infected cells. These peptide antigens are presented on the cell surface in association with major histocompatibility proteins which provide the proper context for antigen recognition.
Secreted and Extracellular Matrix Molecules 5 SEQ ID NO:25 encodes, for example, a secreted/extracellular matrix molecule.
Protein secretion is essential for cellular function. Protein secretion is mediated by a signal peptide located at the amino terminus of the protein to be secreted. The signal peptide is comprised of about ten to twenty hydrophobic amino acids which target the nascent protein from the ribosome to the endoplasmic reticulum (ER). Proteins targeted to the ER may either proceed through the secretory o pathway or remain in any of the secretory organelles such as the ER, Golgi apparatus, or lysosomes.
Proteins that transit through the secretory pathway are either secreted into the exfracellular space or retained in the plasma membrane. Secreted proteins are often synthesized as inactive precursors that are activated by post-franslational processing events during transit through the secretory pathway. Such events include glycosylation, proteolysis, and removal of the signal peptide by a signal peptidase. 5 Other events that may occur during protein fransport include chaperone-dependent unfolding and folding of the nascent protein and interaction of the protein with a receptor or pore complex. Examples of secreted proteins with amino terminal signal peptides include receptors, exfracellular mafrix molecules, cytokines, hormones, growth and differentiation factors, neuropeptides, vasomediators, ion channels, transporters/pumps, and proteases. (Reviewed in Alberts, B. et al. (1994) Molecular Biology 5 of The Cell. Garland PubUshing, New York NY, pp. 557-560, 582-592.)
The exfracellular mafrix (ECM) is a complex network of glycoproteins, polysaccharides, proteoglycans, and other macromolecules that are secreted from the cell into the exfracellular space. The ECM remains in close association with the cell surface and provides a supportive meshwork that profoundly influences cell shape, motility, strength, flexibility, and adhesion. In fact, adhesion of a 0 cell to its surrounding mafrix is required for cell survival except in the case of metastatic tumor cells, which have overcome the need for cell-ECM anchorage. This phenomenon suggests that the ECM plays a critical role in the molecular mechanisms of growth confrol and metastasis. (Reviewed in Ruoslahti, E. (1996) Sci. Am. 275:72-77.) Furthermore, the ECM determines the structure and physical properties of connective tissue and is particularly important for moφhogenesis and other 5 processes associated with embryonic development and pattern formation.
The collagens comprise a family of ECM proteins that provide structure to bone, teeth, skin, Ugaments, tendons, cartilage, blood vessels, and basement membranes. Multiple collagen proteins have been identified. Three collagen molecules fold together in a friple helix stabilized by interchain disulfide bonds. Bundles of these friple helices then associate to form fibrils. Collagen primary structure o consists of hundreds of (Gly-X-Y) repeats where about a third of the X and Y residues are Pro.
Glycines are crucial to helix formation as the bulkier amino acid sidechains cannot fold into the friple helical conformation. Because of these strict sequence requirements, mutations in collagen genes have severe consequences. Osteogenesis imperfecta patients have brittle bones that fracture easily; in severe cases patients die in utero or at birth. Ehlers-Danlos syndrome patients have hyperelastic skin, 5 hypermobile joints, and susceptibility to aortic and intestinal rupture. Chondrodysplasia patients have short stature and ocular disorders. Alport syndrome patients have hematuria, sensorineural deafness, and eye lens deformation. (Isselbacher, K.J. et al. (1994) Harrison's Principles of Internal Medicine, McGraw-Hill, Inc., New York NY, pp. 2105-2117; and Creighton, T.E. (1984) Proteins, Structures and Molecular Principles, W.H. Freeman and Company, New York NY, pp. 191-197.) o Elastin and related proteins confer elasticity to tissues such as skin, blood vessels, and lungs.
Elastin is a highly hydrophobic protein of about 750 amino acids that is rich in proline and glycine residues. Elastin molecules are highly cross-linked, forming an extensive extracellular network of fibers and sheets. Elastin fibers are surrounded by a sheath of microfibrils which are composed of a number of glycoproteins, including fibrillin. Mutations in the gene encoding fibrillin are responsible for 5 Marfan's syndrome, a genetic disorder characterized by defects in connective tissue. In severe cases, the aortas of afflicted individuals are prone to rupture. (Reviewed in Alberts, supra, pp. 984-986.)
Fibronectin is a large ECM glycoprotein found in all vertebrates. Fibronectin exists as a dimer of two subunits, each containing about 2,500 amino acids. Each subunit folds into a rod-like structure containing multiple domains. The domains each contain multiple repeated modules, the most common of which is the type III fibronectin repeat. The type III fibronectin repeat is about 90 amino acids in length and is also found in other ECM proteins and in some plasma membrane and cytoplasmic proteins. Furthermore, some type III fibronectin repeats contain a characteristic fripeptide consisting of Arginine-Glycine- Aspartic acid (RGD). The RGD sequence is recognized by the integrin family of cell surface receptors and is also found in other ECM proteins. Disruption of both copies of the gene encoding fibronectin causes early embryonic lethality in mice. The mutant embryos display extensive moφhological defects, including defects in the formation of the notochord, somites, heart, blood vessels, neural tube, and exfraembryonic structures. (Reviewed in Alberts, supra, pp. 986-987.)
Laminin is a major glycoprotein component of the basal lamina which underlies and supports epithelial cell sheets. Laminin is one of the first ECM proteins synthesized in the developing embryo. Laminin is an 850 kilodalton protein composed of three polypeptide chains joined in the shape of a cross by disulfide bonds. Laminin is especially important for angiogenesis and in particular, for guiding the formation of capillaries. (Reviewed in Alberts, supra, pp. 990-991.)
There are many other types of proteinaceous ECM components, most of which can be classified as proteoglycans. Proteoglycans are composed of unbranched polysaccharide chains (glycosaminoglycans) attached to protein cores. Common proteoglycans include aggrecan, betaglycan, decorin, perlecan, serglycin, and syndecan-1. Some of these molecules not only provide mechanical support, but also bind to extracellular signaling molecules, such as fibroblast growth factor and transforming growth factor β, suggesting a role for proteoglycans in cell-cell communication and cell growth. (Reviewed in Alberts, supra, pp. 973-978.) Likewise, the glycoproteins tenascin-C and tenascin-R are expressed in developing and lesioned neural tissue and provide stimulatory and anti- adhesive (inhibitory) properties, respectively, for axonal growth. (Faissner, A. (1997) Cell Tissue Res. 290:331-341.)
Cytoskeletal Molecules SEQ ID NO:26 and SEQ ID NO:27 encode, for example, cytoskeletal molecules.
The cytoskeleton is a cytoplasmic network of protein fibers that mediate cell shape, structure, and movement. The cytoskeleton supports the cell membrane and forms tracks along which organelles and other elements move in the cytosol. The cytoskeleton is a dynamic structure that allows cells to adopt various shapes and to carry out directed movements. Major cytoskeletal fibers include the microtubules, the microfilaments, and the intermediate filaments. Motor proteins, including myosin, dynein, and kinesin, drive movement of or along the fibers. The motor protein dynamin drives the formation of membrane vesicles. Accessory or associated proteins modify the structure or activity of the fibers while cytoskeletal membrane anchors connect the fibers to the cell membrane. Tubulins
Microtubules, cytoskeletal fibers with a diameter of about 24 nm, have multiple roles in the cell. Bundles of microtubules form cilia and flagella, which are whip-like extensions of the cell membrane that are necessary for sweeping materials across an epithelium and for swimming of sperm, respectively. Marginal bands of microtubules in red blood cells and platelets are important for these cells' pliability. Organelles, membrane vesicles, and proteins are transported in the cell along tracks of microtubules. For example, microtubules run through nerve cell axons, allowing bidirectional transport of materials and membrane vesicles between the cell body and the nerve terminal. Failure to supply the nerve terminal with these vesicles blocks the transmission of neural signals. Microtubules are also critical to chromosomal movement during cell division. Both stable and short-lived populations of microtubules exist in the cell.
Microtubules are polymers of GTP-binding tubulin protein subunits. Each subunit is a heterodimer of α- and β- tubulin, multiple isoforms of which exist. The hydrolysis of GTP is linked to the addition of tubulin subunits at the end of a microtubule. The subunits interact head to tail to form protofilaments; the protofilaments interact side to side to form a microtubule. A microtubule is polarized, one end ringed with α-tubulin and the other with β-tubulin, and the two ends differ in their rates of assembly. Generally, each microtubule is composed of 13 protofilaments although 11 or 15 protofilament-microtubules are sometimes found. Cilia and flagella contain doublet microtubules. Microtubules grow from specialized structures known as centrosomes or microtubule-organizing centers (MTOCs). MTOCs may contain one or two centrioles, which are pinwheel arrays of triplet microtubules. The basal body, the organizing center located at the base of a cilium or flagellum, contains one centriole. Gamma tubulin present in the MTOC is important for nucleating the polymerization of α- and β- tubulin heterodimers but does not polymerize into microtubules. Microtubule- Associated Proteins
Microtubule-associated proteins (MAPs) have roles in the assembly and stabilization of microtubules. One major family of MAPs, assembly MAPs, can be identified in neurons as well as non-neuronal cells. Assembly MAPs are responsible for cross-linking microtubules in the cytosol. These MAPs are organized into two domains: a basic microtubule-binding domain and an acidic projection domain. The projection domain is the binding site for membranes, intermediate filaments, or other microtubules. Based on sequence analysis, assembly MAPs can be further grouped into two types: Type I and Type II. Type I MAPs, which include MAPI A and MAPIB, are large, filamentous molecules that co-purify with microtubules and are abundantly expressed in brain and testes. Type I MAPs contain several repeats of a positively-charged amino acid sequence motif that binds and neutraUzes negatively charged tubulin, leading to stabilization of microtubules. MAPI A and MAPIB are each derived from a single precursor polypeptide that is subsequently proteolytically processed to 5 generate one heavy chain and one Ught chain.
Another light chain, LC3, is a 16.4 kDa molecule that binds MAPI A, MAPIB, and microtubules. It is suggested that LC3 is synthesized from a source other than the MAPI A or MAPIB transcripts, and that the expression of LC3 may be important in regulating the microtubule binding activity of MAPI A and MAPIB during cell proliferation (Mann, S.S. et al. (1994) J. Biol. Chem. 0 269:11492-11497).
Type II MAPs, which include MAP2a, MAP2b, MAP2c, MAP4, and Tau, are characterized by three to four copies of an 18-residue sequence in the microtubule-binding domain. MAP2a, MAP2b, and MAP2c are found only in dendrites, MAP4 is found in non-neuronal cells, and Tau is found in axons and dendrites of nerve cells. Alternative splicing of the Tau mRNA leads to the existence of 5 multiple forms of Tau protein. Tau phosphorylation is altered in neurodegenerative disorders such as Alzheimer's disease, Pick's disease, progressive supranuclear palsy, corticobasal degeneration, and familial frontotemporal dementia and Parkinsonism linked to chromosome 17. The altered Tau phosphorylation leads to a collapse of the microtubule network and the formation of intraneuronal Tau aggregates (Spillantini, M.G. and M. Goedert (1998) Trends Neurosci. 21 :428-433). o The protein pericentrin is found in the MTOC and has a role in microtubule assembly.
Actins
Microfilaments, cytoskeletal filaments with a diameter of about 7-9 nm, are vital to cell locomotion, cell shape, cell adhesion, cell division, and muscle confraction. Assembly and disassembly of the microfilaments allow cells to change their moφhology. Microfilaments are the 5 polymerized form of actin, the most abundant infracellular protein in the eukaryotic cell. Human cells contain six isoforms of actin. The three α-actins are found in different kinds of muscle, nonmuscle β- actin and nonmuscle γ-actin are found in nonmuscle cells, and another γ-actin is found in intestinal smooth muscle cells. G-actin, the monomeric form of actin, polymerizes into polarized, helical F- actin filaments, accompanied by the hydrolysis of ATP to ADP. Actin filaments associate to form o bundles and networks, providing a framework to support the plasma membrane and determine cell shape. These bundles and networks are connected to the cell membrane. In muscle cells, thin filaments containing actin slide past thick filaments containing the motor protein myosin during contraction. A family of actin-related proteins exist that are not part of the actin cytoskeleton, but rather associate with microtubules and dynein. 5 Actin-Associated Proteins Actin-associated proteins have roles in cross-linking, severing, and stabilization of actin filaments and in sequestering actin monomers. Several of the actin-associated proteins have multiple functions. Bundles and networks of actin filaments are held together by actin cross-linking proteins. These proteins have two actin-binding sites, one for each filament. Short cross-linking proteins 5 promote bundle formation while longer, more flexible cross-linking proteins promote network formation. Calmodulin-like calcium-binding domains in actin cross-linking proteins allow calcium regulation of cross-linking. Group I cross-linking proteins have unique actin-binding domains and include the 30 kD protein, EF-la, fascin, and scruin. Group II cross-linking proteins have a 7,000- MW actin-binding domain and include villin and dematin. Group III cross-linking proteins have 0 pairs of a 26,000-MW actin-binding domain and include fimbrin, spectrin, dysfrophin, ABP 120, and filamin.
Severing proteins regulate the length of actin filaments by breaking them into short pieces or by blocking their ends. Severing proteins include gCAP39, severin (fragmin), gelsolin, and villin. Capping proteins can cap the ends of actin filaments, but cannot break filaments. Capping proteins 5 include CapZ and fropomodulin. The proteins thymosin and profilin sequester actin monomers in the cytosol, allowing a pool of unpolymerized actin to exist. The actin-associated proteins tropomyosin, froponin, and caldesmon regulate muscle confraction in response to calcium. Intermediate Filaments and Associated Proteins
Intermediate filaments (IFs) are cytoskeletal fibers with a diameter of about 10 nm, o intermediate between that of microfilaments and microtubules. IFs serve structural roles in the cell, reinforcing cells and organizing cells into tissues. IFs are particularly abundant in epidermal cells and in neurons. IFs are extremely stable, and, in contrast to microfilaments and microtubules, do not function in cell motility.
Five types of IF proteins are known in mammals. Type I and Type II proteins are the acidic 5 and basic keratins, respectively. Heterodimers of the acidic and basic keratins are the building blocks of keratin IFs. Keratins are abundant in soft epitheUa such as skin and cornea, hard epithelia such as nails and hair, and in epitheUa that line internal body cavities. Mutations in keratin genes lead to epithelial diseases including epidermolysis buUosa simplex, bullous congenital ichthyosiform erythroderma (epidermolytic hyperkeratosis), non-epidermolytic and epidermolytic palmoplantar o keratoderma, ichthyosis bullosa of Siemens, pachyonychia congenita, and white sponge nevus. Some of these diseases result in severe skin blistering. (See, e.g., Wawersik, M. et al. (1997) J. Biol. Chem. 272:32557-32565; and Corden L.D. and W.H. McLean (1996) Exp. Dermatol. 5:297-307.)
Type III IF proteins include desmin, glial fibrillary acidic protein, vimentin, and peripherin. Desmin filaments in muscle cells link myofibrils into bundles and stabilize sarcomeres in contracting 5 muscle. GUal fibrillary acidic protein filaments are found in the glial cells that surround neurons and astrocytes. Vimentin filaments are found in blood vessel endothelial cells, some epitheUal cells, and mesenchymal cells such as fibroblasts, and are commonly associated with microtubules. Vimentin filaments may have roles in keeping the nucleus and other organelles in place in the cell. Type IV IFs include the neurofilaments and nestin. Neurofilaments, composed of three polypeptides NF-L, NF-M, and NF-H, are frequently associated with microtubules in axons. Neurofilaments are responsible for the radial growth and diameter of an axon, and ultimately for the speed of nerve impulse transmission. Changes in phosphorylation and metabolism of neurofilaments are observed in neurodegenerative diseases including amyofrophic lateral sclerosis, Parkinson's disease, and Alzheimer's disease (Julien, J.P. and W.E. Mushynski (1998) Prog. Nucleic Acid Res. Mol. Biol. 61:1-23). Type V IFs, the lamins, are found in the nucleus where they support the nuclear membrane.
IFs have a central α-helical rod region interrupted by short nonhelical linker segments. The rod region is bracketed, in most cases, by non-hehcal head and tail domains. The rod regions of intermediate filament proteins associate to form a coiled-coil dimer. A highly ordered assembly process leads from the dimers to the IFs. Neither ATP nor GTP is needed for IF assembly, unlike that of microfilaments and microtubules.
IF-associated proteins (IFAPs) mediate the interactions of IFs with one another and with other cell structures. IFAPs cross-link IFs into a bundle, into a network, or to the plasma membrane, and may cross-link IFs to the microfilament and microtubule cytoskeleton. Microtubules and IFs are in particular closely associated. IFAPs include BPAG1, plakoglobin, desmoplakin I, desmoplakin II, plectin, ankyrin, filaggrin, and lamin B receptor. Cytoskeletal -Membrane Anchors
Cytoskeletal fibers are attached to the plasma membrane by specific proteins. These attachments are important for maintaining cell shape and for muscle confraction. In erythrocytes, the spectrin- actin cytoskeleton is attached to cell membrane by three proteins, band 4J, ankyrin, and adducin. Defects in this attachment result in abnormally shaped cells which are more rapidly degraded by the spleen, leading to anemia. In platelets, the spectrin-actin cytoskeleton is also linked to the membrane by ankyrin; a second actin network is anchored to the membrane by filamin. In muscle cells the protein dysfrophin links actin filaments to the plasma membrane; mutations in the dysfrophin gene lead to Duchenne muscular dystrophy. In adherens junctions and adhesion plaques the peripheral membrane proteins α-actinin and vinculin attach actin filaments to the cell membrane.
IFs are also attached to membranes by cytoskeletal-membrane anchors. The nuclear lamina is attached to the inner surface of the nuclear membrane by the lamin B receptor. Vimentin IFs are attached to the plasma membrane by ankyrin and plectin. Desmosome and hemidesmosome membrane junctions hold together epithelial cells of organs and skin. These membrane junctions allow shear forces to be distributed across the entire epithelial cell layer, thus providing strength and rigidity to the epithelium. IFs in epithelial cells are attached to the desmosome by plakoglobin and desmoplakins. The proteins that link IFs to hemidesmosomes are not known. Desmin IFs surround the sarcomere in muscle and are linked to the plasma membrane by paranemin, synemin, and ankyrin. Myosin-related Motor Proteins 5 Myosins are actin-activated ATPases, found in eukaryotic cells, that couple hydrolysis of
ATP with motion. Myosin provides the motor function for muscle confraction and intracellular movements such as phagocytosis and rearrangement of cell contents during mitotic cell division (cytokinesis). The contractile unit of skeletal muscle, termed the sarcomere, consists of highly ordered arrays of thin actin-containing filaments and thick myosin-containing filaments. Crossbridges form o between the thick and thin filaments, and the ATP-dependent movement of myosin heads within the thick filaments pulls the thin filaments, shortening the sarcomere and thus the muscle fiber.
Myosins are composed of one or two heavy chains and associated light chains. Myosin heavy chains contain an amino-terminal motor or head domain, a neck that is the site of light-chain binding, and a carboxy-terminal tail domain. The tail domains may associate to form an α-helical 5 coiled coil. Conventional myosins, such as those found in muscle tissue, are composed of two myosin heavy-chain subunits, each associated with two light-chain subunits that bind at the neck region and play a regulatory role. Unconventional myosins, believed to function in infracellular motion, may contain either one or two heavy chains and associated light chains. There is evidence for about 25 myosin heavy chain genes in vertebrates, more than half of them unconventional. 0 Dynein-related Motor Proteins
Dyneins are (-) end-directed motor proteins which act on microtubules. Two classes of dyneins, cytosolic and axonemal, have been identified. Cytosolic dyneins are responsible for translocation of materials along cytoplasmic microtubules, for example, fransport from the nerve terminal to the cell body and fransport of endocytic vesicles to lysosomes. Cytoplasmic dyneins are 5 also reported to play a role in mitosis. Axonemal dyneins are responsible for the beating of flagella and ciUa. Dynein on one microtubule doublet walks along the adjacent microtubule doublet. This sliding force produces bending forces that cause the flagellum or cilium to beat. Dyneins have a native mass between 1000 and 2000 kDa and contain either two or three force-producing heads driven by the hydrolysis of ATP. The heads are linked via stalks to a basal domain which is composed of a highly o variable number of accessory intermediate and Ught chains.
Kinesin-related Motor Proteins
Kinesins are (+) end-directed motor proteins which act on microtubules. The prototypical kinesin molecule is involved in the transport of membrane-bound vesicles and organelles. This function is particularly important for axonal fransport in neurons. Kinesin is also important in all cell types for 5 the fransport of vesicles from the Golgi complex to the endoplasmic reticulum. This role is critical for maintaining the identity and functionality of these secretory organelles.
Kinesins define a ubiquitous, conserved family of over 50 proteins that can be classified into at least 8 subfamiUes based on primary amino acid sequence, domain structure, velocity of movement, and cellular function. (Reviewed in Moore, J.D. and S.A Endow (1996) Bioessays 18:207-219; and Hoyt, A.M. (1994) Curr. Opin. Cell Biol. 6:63-68.) The prototypical kinesin molecule is a heteroteframer comprised of two heavy polypeptide chains (KHCs) and two light polypeptide chains (KLCs). The KHC subunits are typically referred to as "kinesin." KHC is about 1000 amino acids in length, and KLC is about 550 amino acids in length. Two KHCs dimerize to form a rod-shaped molecule with three distinct regions of secondary structure. At one end of the molecule is a globular motor domain that functions in ATP hydrolysis and microtubule binding. Kinesin motor domains are highly conserved and share over 70% identity. Beyond the motor domain is an α-helical coiled-coil region which mediates dimerization. At the other end of the molecule is a fan-shaped tail that associates with molecular cargo. The tail is formed by the interaction of the KHC C-termini with the two KLCs. Members of the more divergent subfamilies of kinesins are called kinesin-related proteins (KRPs), many of which function during mitosis in eukaryotes (Hovt, supra). Some KRPs are required for assembly of the mitotic spindle. In vivo and in vitro analyses suggest that these KRPs exert force on microtubules that comprise the mitotic spindle, resulting in the separation of spindle poles. Phosphorylation of KRP is required for this activity. Failure to assemble the mitotic spindle results in abortive mitosis and chromosomal aneuploidy, the latter condition being characteristic of cancer cells. In addition, a unique KRP, centromere protein E, localizes to the kinetochore of human mitotic chromosomes and may play a role in their segregation to opposite spindle poles. Dynamin-related Motor Proteins
Dynamin is a large GTPase motor protein that functions as a "molecular pinchase," generating a mechanochemical force used to sever membranes. This activity is important in forming clathrin-coated vesicles from coated pits in endocytosis and in the biogenesis of synaptic vesicles in neurons. Binding of dynamin to a membrane leads to dynamin' s self-assembly into spirals that may act to constrict a flat membrane surface into a tubule. GTP hydrolysis induces a change in conformation of the dynamin polymer that pinches the membrane tubule, leading to severing of the membrane tubule and formation of a membrane vesicle. Release of GDP and inorganic phosphate leads to dynamin disassembly. Following disassembly the dynamin may either dissociate from the membrane or remain associated to the vesicle and be fransported to another region of the cell. Three homologous dynamin genes have been discovered, in addition to several dynamin-related proteins. Conserved dynamin regions are the N-terminal GTP-binding domain, a central pleckstrin homology domain that binds membranes, a central coiled-coil region that may activate dynamin' s GTPase activity, and a C-terminal proline-rich domain that contains several motifs that bind SH3 domains on other proteins. Some dynamin-related proteins do not contain the pleckstrin homology domain or the proline-rich domain. (See McNiven, M.A. (1998) Cell 94:151-154; Scaife, R.M. and R.L. Margolis (1997) Cell. Signal. 9:395-401.)
The cytoskeleton is reviewed in Lodish, H. et al. (1995) Molecular Cell Biology, Scientific 5 American Books, New York NY.
Ribosomal Molecules
SEQ ID NO:30 and SEQ ID NO:31 encode, for example, ribosomal molecules. Ribosomal RNAs (rRNAs) are assembled, along with ribosomal proteins, into ribosomes, o which are cytoplasmic particles that franslate messenger RNA into polypeptides. The eukaryotic ribosome is composed of a 60S (large) subunit and a 40S (small) subunit, which together form the 80S ribosome. In addition to the 18S, 28S, 5S, and 5.8S rRNAs, the ribosome also contains more than fifty proteins. The ribosomal proteins have a prefix which denotes the subunit to which they belong, either L (large) or S (small). Ribosomal protein activities include binding rRNA and 5 organizing the conformation of the junctions between rRNA helices (Woodson, S.A. and N.B .
Leontis (1998) Curr. Opin. Struct. Biol. 8:294-300; Ramakrishnan, V. and S.W. White (1998) Trends Biochem. Sci. 23:208-212.) Three important sites are identified on the ribosome. The aminoacyl- tRNA site (A site) is where charged tRNAs (with the exception of the initiator-tRNA) bind on arrival at the ribosome. The peptidyl-tRNA site (P site) is where new peptide bonds are formed, as well as o where the initiator tRNA binds. The exit site (E site) is where deacylated tRNAs bind prior to their release from the ribosome. (The ribosome is reviewed in Stryer, L. (1995) Biochemistry W.H. Freeman and Company, New York NY, pp. 888-908; and Lodish, H. et al. (1995) Molecular Cell Biology Scientific American Books, New York NY. pp. 119-138.)
5 Chromatin Molecules
The nuclear DNA of eukaryotes is organized into chromatin. Two types of chromatin are observed: euchromatin, some of which may be transcribed, and heterochromatin so densely packed that much of it is inaccessible to franscription. Chromatin packing thus serves to regulate protein expression in eukaryotes. Bacteria lack chromatin and the chromatin-packing level of gene regulation. o The fundamental unit of chromatin is the nucleosome of 200 DNA base pairs associated with two copies each of histones H2A, H2B, H3, and H4. Adjascent nucleosomes are linked by another class of histones, HI. Low molecular weight non-histone proteins called the high mobility group (HMG), associated with chromatin, may function in the unwinding of DNA and stabilization of single- stranded DNA. Chromodomain proteins function in compaction of chromatin into its franscriptionally 5 silent heterochromatin form. During mitosis, all DNA is compacted into heterochromatin and franscription ceases. Transcription in inteφhase begins with the activation of a region of chromatin. Active chromatin is decondensed. Decondensation appears to be accompanied by changes in binding coefficient, phosphorylation and acetylation states of chromatin histones. HMG proteins HMG13 and HMG 17 5 selectively bind activated chromatin. Topoisomerases remove superhelical tension on DNA. The activated region decondenses, allowing gene regulatory proteins and franscription factors to assemble on the DNA.
Patterns of chromatin structure can be stably inherited, producing heritable patterns of gene expression. In mammals, one of the two X chromosomes in each female cell is inactivated by l o condensation to heterochromatin during zygote development. The inactive state of this chromosome is inherited, so that adult females are mosaics of clusters of paternal-X and maternal-X clonal cell groups. The condensed X chromosome is reactivated in meiosis.
Chromatin is associated with disorders of protein expression such as thalassemia, a genetic anemia resulting from the removal of the locus confrol region (LCR) required for decondensation of the 15 globin gene locus .
For a review of chromatin structure and function see Alberts, B. et al. (1994) Molecular Cell Biology, third edition, Garland Publishing, Inc., New York NY, pp. 351-354, 433-439.
Electron Transfer Associated Molecules
20 SEQ ID NO:23 and SEQ ID NO:24 encode, for example, electron transfer associated molecules.
Electron carriers such as cytochromes accept electrons from NADH or FADH, and donate them to other electron carriers. Most electron-transferring proteins, except ubiquinone, are prosthetic groups such as flavins, heme, FeS clusters, and copper, bound to inner membrane proteins. 5 Adrenodoxin, for example, is an FeS protein that forms a complex with NADPH :adrenodoxin reductase and cytochrome p450. Cytochromes contain a heme prosthetic group, a poφhyrin ring containing a tightly bound iron atom. Electron fransfer reactions play a crucial role in cellular energy production.
Energy is produced by the oxidation of glucose and fatty acids. Glucose is initially converted 0 to pyruvate in the cytoplasm. Fatty acids and pyruvate are fransported to the mitochondria for complete oxidation to C02 coupled by enzymes to the fransport of electrons from NADH and FADH2 to oxygen and to the synthesis of ATP (oxidative phosphorylation) from ADP and P..
Pyruvate is transported into the mitochondria and converted to acetyl-CoA for oxidation via the citric acid cycle, involving pyruvate dehydrogenase components, dihydrolipoyl fransacetylase, and 5 dihydrolipoyl dehydrogenase. Enzymes involved in the cifric acid cycle include: citrate synthetase, aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including transsuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate dehydrogenase. Acetyl CoA is oxidized to C02 with concomitant formation of NADH, FADH2, and GTP. In oxidative phosphorylation, the fransfer of electrons from NADH and FADH2 to oxygen by 5 dehydrogenases is coupled to the synthesis of ATP from ADP and P; by the F0F, ATPase complex in the mitochondrial inner membrane. Enzyme complexes responsible for electron transport and ATP synthesis include the FQFJ ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone reductase, cytochrome b, cytochrome Cj, FeS protein, and cytochrome c oxidase.
ATP synthesis requires membrane fransport enzymes including the phosphate fransporter and 0 the ATP- ADP antiport protein. The ATP-binding casette (ABC) superfamily has also been suggested as belonging to the mitochondrial fransport group (Hogue, D.L. et al. (1999) J. Mol. Biol. 285:379- 389). Brown fat uncoupling protein dissipates oxidative energy as heat, and may be involved the fever response to infection and frauma (Cannon, B. et al. (1998) Ann. NY Acad. Sci. 856:171-187).
Mitochondria are oval-shaped organelles comprising an outer membrane, a tightly folded 5 inner membrane, an intermembrane space between the outer and inner membranes, and a matrix inside the inner membrane. The outer membrane contains many porin molecules that allow ions and charged molecules to enter the intermembrane space, while the inner membrane contains a variety of fransport proteins that transfer only selected molecules. Mitochondria are the primary sites of energy production in cells. o Mitochondria contain a small amount of DNA. Human mitochondrial DNA encodes 13 proteins, 22 tRNAs, and 2 rRNAs. Mitochondrial-DNA encoded proteins include NADH-Q reductase, a cytochrome reductase subunit, cytochrome oxidase subunits, and ATP synthase subunits.
Electron-transfer reactions also occur outside the mitochondria in locations such as the endoplasmic reticulum, which plays a crucial role in lipid and protein biosynthesis. Cytochrome b5 5 is a cenfral electron donor for various reductive reactions occurring on the cytoplasmic surface of liver endoplasmic reticulum. Cytochrome b5 has been found in Golgi, plasma, endoplasmic reticulum (ER), and microbody membranes.
For a review of mitochondrial metabolism and regulation, see Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York NY, pp. 745-797 and Stryer (1995) 0 Biochemistry. W.H. Freeman and Co., San Francisco CA. pp 529-558, 988-989.
The majority of mitochondrial proteins are encoded by nuclear genes, are synthesized on cytosolic ribosomes, and are imported into the mitochondria. Nuclear-encoded proteins which are destined for the mitochondrial matrix typically contain positively-charged amino terminal signal sequences. Import of these preproteins from the cytoplasm requires a multisubunit protein complex in the outer membrane known as the translocase of outer mitochondrial membrane (TOM; previously designated MOM; Pfanner, N. et al. (1996) Trends Biochem. Sci. 21 :51-52) and at least three inner membrane proteins which comprise the translocase of inner mitochondrial membrane (TIM; previously designated MIM; Pfanner, supra). An inside-negative membrane potential across the inner mitochondrial membrane is also required for preprotein import. Preproteins are recognized by surface receptor components of the TOM complex and are translocated through a proteinaceous pore formed by other TOM components. Proteins targeted to the matrix are then recognized by the import machinery of the TIM complex. The import systems of the outer and inner membranes can function independently (Segui-Real, B. et al. (1993) EMBO J. 12:2211-2218).
Once precursor proteins are in the mitochondria, the leader peptide is cleaved by a signal peptidase to generate the mature protein. Most leader peptides are removed in a one step process by a protease termed mitochondrial processing peptidase (MPP) (Paces, V. et al. (1993) Proc. Nati. Acad. Sci. USA 90:5355-5358). In some cases a two-step process occurs in which MPP generates an intermediate precursor form which is cleaved by a second enzyme, mitochondrial intermediate peptidase, to generate the mature protein. Mitochondrial dysfunction leads to impaired calcium buffering, generation of free radicals that may participate in deleterious infracellular and exfracellular processes, changes in mitochondrial permeability and oxidative damage which is observed in several neurodegenerative diseases. Neurodegenerative diseases Unked to mitochondrial dysfunction include some forms of Alzheimer's disease, Friedreich's ataxia, familial amyofrophic lateral sclerosis, and Huntington's disease (Beal, M.F. (1998) Biochim. Biophys. Acta 1366:211-213). The myocardium is heavily dependent on oxidative metabolism, so mitochondrial dysfunction often leads to heart disease (DiMauro, S. and M. Hirano (1998) Curr. Opin. Cardiol 13:190-197). Mitochondria are implicated in disorders of cell proliferation, since they play an important role in a cell's decision to proliferate or self-destruct through apoptosis. The oncoprotein Bcl-2, for example, promotes cell proliferation by stabilizing mitochondrial membranes so that apoptosis signals are not released (Susin, S.A. (1998) Biochim.
Biophys. Acta 1366:151-165).
Transcription Factor Molecules
SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, and SEQ ID NO:43 encode, for example, franscription factor molecules.
Multicellular organisms are comprised of diverse cell types that differ dramatically both in structure and function. The identity of a cell is determined by its characteristic pattern of gene expression, and different cell types express overlapping but distinctive sets of genes throughout development. Spatial and temporal regulation of gene expression is critical for the control of cell proliferation, cell differentiation, apoptosis, and other processes that contribute to organismal development. Furthermore, gene expression is regulated in response to exfracellular signals that mediate cell-cell communication and coordinate the activities of different cell types. Appropriate gene regulation also ensures that cells function efficiently by expressing only those genes whose 5 functions are required at a given time.
Transcriptional regulatory proteins are essential for the confrol of gene expression. Some of these proteins function as transcription factors that initiate, activate, repress, or terminate gene franscription. Transcription factors generally bind to the promoter, enhancer, and upstream regulatory regions of a gene in a sequence-specific manner, although some factors bind regulatory elements l o within or downsfream of a gene's coding region. Transcription factors may bind to a specific region of DNA singly or as a complex with other accessory factors. (Reviewed in Lewin, B. (1990) Genes IV, Oxford University Press, New York NY, and Cell Press, Cambridge MA, pp. 554-570.)
The double helix structure and repeated sequences of DNA create topological and chemical features which can be recognized by franscription factors. These features are hydrogen bond donor 15 and acceptor groups, hydrophobic patches, major and minor grooves, and regular, repeated stretches of sequence which induce distinct bends in the helix. Typically, franscription factors recognize specific DNA sequence motifs of about 20 nucleotides in length. Multiple, adjacent franscription factor-binding motifs may be required for gene regulation.
Many transcription factors incoφorate DNA-binding structural motifs which comprise either 0 heUces or β sheets that bind to the major groove of DNA. Four well -characterized structural motifs are helix-turn-helix, zinc finger, leucine zipper, and helix-loop-helix. Proteins containing these motifs may act alone as monomers, or they may form homo- or heterodimers that interact with DNA.
The helix-turn-helix motif consists of two α helices connected at a fixed angle by a short chain of amino acids. One of the helices binds to the major groove. Helix-turn-helix motifs are 5 exemplified by the homeobox motif which is present in homeodomain proteins. These proteins are critical for specifying the anterior-posterior body axis during development and are conserved throughout the animal kingdom. The Antennapedia and Ultrabithorax proteins of Drosophila melanogaster are prototypical homeodomain proteins (Pabo, CO. and R.T. Sauer (1992) Annu. Rev. Biochem. 61 :1053-1095). o The zinc finger motif, which binds zinc ions, generally contains tandem repeats of about 30 amino acids consisting of periodically spaced cysteine and histidine residues. Examples of this sequence pattern, designated C2H2 and C3HC4 ("RING" finger), have been described (Lewin, supra). Zinc finger proteins each contain an α helix and an antiparallel β sheet whose proximity and conformation are maintained by the zinc ion. Contact with DNA is made by the arginine prece ding 5 the α helix and by the second, third, and sixth residues of the α hehx. Variants of the zinc finger motif include poorly defined cysteine-rich motifs which bind zinc or other metal ions. These motifs may not contain histidine residues and are generally nonrepetitive.
The leucine zipper motif comprises a stretch of amino acids rich in leucine which can form an amphipathic α hehx. This structure provides the basis for dimerization of two leucine zipper proteins. The region adjacent to the leucine zipper is usually basic, and upon protein dimerization, is optimally positioned for binding to the major groove. Proteins containing such motifs are generally referred to as bZIP franscription factors.
The helix-loop-helix motif (HLH) consists of a short α hehx connected by a loop to a longer αhetix. The loop is flexible and allows the two helices to fold back against each other and to bind to DNA. The transcription factor Myc contains a prototypical HLH motif.
Most franscription factors contain characteristic DNA binding motifs, and variations on the above motifs and new motifs have been and are currently being characterized (Faisst, S. and S. Meyer
(1992) Nucleic Acids Res. 20:3-26).
Many neoplastic disorders in humans can be attributed to inappropriate gene expression. Malignant cell growth may result from either excessive expression of tumor promoting genes or insufficient expression of tumor suppressor genes (Cleary, M.L. (1992) Cancer Surv. 15:89-104).
Chromosomal franslocations may also produce chimeric loci which fuse the coding sequence of one gene with the regulatory regions of a second unrelated gene. Such an arrangement likely results in inappropriate gene franscription, potentially contributing to malignancy. In addition, the immune system responds to infection or frauma by activating a cascade of events that coordinate the progressive selection, amplification, and mobilization of cellular defense mechanisms. A complex and balanced program of gene activation and repression is involved in this process. However, hyperactivity of the immune system as a result of improper or insufficient regulation of gene expression may result in considerable tissue or organ damage. This damage is well documented in immunological responses associated with arthritis, allergens, heart attack, sfroke, and infections (Isselbacher, K.J. et al. (1996) Harrison's Principles of Internal Medicine, 13/e, McGraw
Hill, Inc. and Teton Data Systems Software).
Furthermore, the generation of multicellular organisms is based upon the induction and coordination of cell differentiation at the appropriate stages of development. Central to this process is differential gene expression, which confers the distinct identities of cells and tissues throughout the body. Failure to regulate gene expression during development can result in developmental disorders.
Human developmental disorders caused by mutations in zinc finger-type franscriptional regulators include: urogenenital developmental abnormalities associated with WT1; Greig cephalopolysyndactyly, Pallister-Hall syndrome, and postaxial polydactyly type A (GLI3); and Townes-Brocks syndrome, characterized by anal, renal, limb, and ear abnormalities (SALL1) (Engelkamp, D. and V. van Heyningen (1996) Curr. Opin. Genet. Dev. 6:334-342; Kohlhase, J. et al. (1999) Am. J. Hum. Genet. 64:435-445).
CeU Membrane Molecules SEQ ID NO:28 and SEQ ID NO:29 encode, for example, cell membrane molecules.
Eukaryotic cells are surrounded by plasma membranes which enclose the cell and maintain an environment inside the cell that is distinct from its surroundings. In addition, eukaryotic organisms are distinct from prokaryotes in possessing many intracellular organelle and vesicle structures. Many of the metabolic reactions which distinguish eukaryotic biochemistry from prokaryotic biochemistry take place within these structures. The plasma membrane and the membranes surrounding organelles and vesicles are composed of phosphoglycerides, fatty acids, cholesterol, phosphoUpids, glycolipids, proteoglycans, and proteins. These components confer identity and functionality to the membranes with which they associate. Integral Membrane Proteins The majority of known integral membrane proteins are fransmembrane proteins (TM) which are characterized by an exfracellular, a transmembrane, and an infracellular domain. TM domains are typically comprised of 15 to 25 hydrophobic amino acids which are predicted to adopt an α-helical conformation. TM proteins are classified as bitopic (Types I and II) and polytopic (Types III and IV) (Singer, S.J. (1990) Annu. Rev. Cell Biol. 6:247-296). Bitopic proteins span the membrane once while polytopic proteins contain multiple membrane-spanning segments. TM proteins function as cell-surface receptors, receptor-interacting proteins, fransporters of ions or metabolites, ion channels, cell anchoring proteins, and cell type- specific surface antigens.
Many membrane proteins (MPs) contain amino acid sequence motifs that target these proteins to specific subcellular sites. Examples of these motifs include PDZ domains, KDEL, RGD, NGR, and GSL sequence motifs, von Willebrand factor A (vWFA) domains, and EGF-like domains. RGD,
NGR, and GSL motif-containing peptides have been used as drug delivery agents in targeted cancer treatment of tumor vasculature (Arap, W. et al. (1998) Science 279:377-380). Furthermore, MPs may also contain amino acid sequence motifs, such as the carbohydrate recognition domain (CRD), that mediate interactions with exfracellular or infracellular molecules. G-Protein Coupled Receptors
G-protein coupled receptors (GPCR) are a superfamily of integral membrane proteins which transduce extracellular signals. GPCRs include receptors for biogenic amines, lipid mediators of inflammation, peptide hormones, and sensory signal mediators. The structure of these highly-conserved receptors consists of seven hydrophobic fransmembrane regions, an extracellular N-terminus, and a cytoplasmic C-terminus. Three extracellular loops alternate with three infracellular loops to link the seven transmembrane regions. Cysteine disulfide bridges connect the second and third extracellular loops. The most conserved regions of GPCRs are the transmembrane regions and the first two cytoplasmic loops. A conserved, acidic-Arg-aromatic residue triplet present in the second cytoplasmic loop may interact with G proteins. A GPCR consensus pattern is characteristic of 5 most proteins belonging to this superfamily (ExPASy PROSITE document PS00237; and Watson, S. and S. Arkinstall (1994) The G-protein Linked Receptor Facts Book, Academic Press, San Diego CA, pp. 2-6). Mutations and changes in franscriptional activation of GPCR-encoding genes have been associated with neurological disorders such as schizophrenia, Parkinson's disease, Alzheimer's disease, drug addiction, and feeding disorders. 0 Scavenger Receptors
Macrophage scavenger receptors with broad ligand specificity may participate in the binding of low density lipoproteins (LDL) and foreign antigens. Scavenger receptors types I and II are trimeric membrane proteins with each subunit containing a small N-terminal infracellular domain, a fransmembrane domain, a large exfracellular domain, and a C-terminal cysteine-rich domain. The 5 exfracellular domain contains a short spacer region, an α-helical coiled-coil region, and a triple helical collagen-like region. These receptors have been shown to bind a spectrum of ligands, including chemically modified lipoproteins and albumin, polyribonucleotides, polysaccharides, phosphoUpids, and asbestos (Matsumoto, A. et al. (1990) Proc. Nati. Acad. Sci. USA 87:9133-9137; and Elomaa, O. et al. (1995) Cell 80:603-609). The scavenger receptors are thought to play a key role in o atherogenesis by mediating uptake of modified LDL in arterial walls, and in host defense by binding bacterial endotoxins, bacteria, and protozoa. Tetraspan Family Proteins
The fransmembrane 4 superfamily (TM4SF) or tetraspan family is a multigene family encoding type III integral membrane proteins (Wright, M.D. and M.G. Tomlinson (1994) Immunol. 5 Today 15 :588-594). The TM4SF is comprised of membrane proteins which traverse the cell membrane four times. Members of the TM4SF include platelet and endothelial cell membrane proteins, melanoma-associated antigens, leukocyte surface glycoproteins, colonal carcinoma antigens, tumor-associated antigens, and surface proteins of the schistosome parasites (Jankowski, S.A. (1994) Oncogene 9:1205-1211). Members of the TM4SF share about 25-30% amino acid sequence identity o with one another.
A number of TM4SF members have been implicated in signal transduction, confrol of cell adhesion, regulation of cell growth and proliferation, including development and oncogenesis, and cell motility, including tumor cell metastasis. Expression of TM4SF proteins is associated with a variety of tumors and the level of expression may be altered when cells are growing or activated. 5 Tumor Antigens Tumor antigens are cell surface molecules that are differentially expressed in tumor cells relative to normal cells. Tumor antigens distinguish tumor cells immunologically from normal cells and provide diagnostic and therapeutic targets for human cancers (Takagi, S. et al. (1995) Int. J. Cancer 61:706-715; Liu, E. et al. (1992) Oncogene 7:1027-1032). 5 Leukocyte Antigens
Other types of cell surface antigens include those identified on leukocytic cells of the immune system. These antigens have been identified using systematic, monoclonal antibody (mAb)-based "shot gun" techniques. These techniques have resulted in the production of hundreds of mAbs directed against unknown cell surface leukocytic antigens. These antigens have been grouped into o "clusters of differentiation" based on common immunocytochemical localization patterns in various differentiated and undifferentiated leukocytic cell types. Antigens in a given cluster are presumed to identify a single cell surface protein and are assigned a "cluster of differentiation" or "CD" designation. Some of the genes encoding proteins identified by CD antigens have been cloned and verified by standard molecular biology techniques. CD antigens have been characterized as both 5 fransmembrane proteins and cell surface proteins anchored to the plasma membrane via covalent attachment to fatty acid-containing glycolipids such as glycosylphosphatidylinositol (GPI). (Reviewed in Barclay, A.N. et al. (1995) The Leucocyte Antigen Facts Book, Academic Press, San Diego CA, pp. 17-20.) Ion Channels o Ion channels are found in the plasma membranes of virtually every cell in the body. For example, chloride channels mediate a variety of cellular functions including regulation of membrane potentials and absoφtion and secretion of ions across epithelial membranes. Chloride channels also regulate the pH of organelles such as the Golgi apparatus and endosomes (see, e.g., Greger, R. (1988) Annu. Rev. Physiol. 50:111-122). Elecfrophysiological and pharmacological properties of chloride 5 channels, including ion conductance, current-voltage relationships, and sensitivity to modulators, suggest that different chloride channels exist in muscles, neurons, fibroblasts, epithelial cells, and lymphocytes.
Many ion channels have sites for phosphorylation by one or more protein kinases including protein kinase A, protein kinase C, tyrosine kinase, and casein kinase II, all of which regulate ion o channel activity in cells. Inappropriate phosphorylation of proteins in cells has been linked to changes in cell cycle progression and cell differentiation. Changes in the cell cycle have been linked to induction of apoptosis or cancer. Changes in cell differentiation have been linked to diseases and disorders of the reproductive system, immune system, skeletal muscle, and other organ systems. Proton Pumps 5 Proton ATPases comprise a large class of membrane proteins that use the energy of ATP hydrolysis to generate an electrochemical proton gradient across a membrane. The resultant gradient may be used to transport other ions across the membrane (Na+, K+, or Cl") or to maintain organelle pH. Proton ATPases are further subdivided into the mitochondrial F- ATPases, the plasma membrane ATPases, and the vacuolar ATPases. The vacuolar ATPases establish and maintain an acidic pH 5 within various organelles involved in the processes of endocytosis and exocytosis (Mellman, I. et al. (1986) Annu. Rev. Biochem. 55:663-700).
Proton-coupled, 12 membrane-spanning domain transporters such as PEPT 1 and PEPT 2 are responsible for gastrointestinal absoφtion and for renal reabsoφtion of peptides using an elecfrochemical H+ gradient as the driving force. Another type of peptide transporter, the TAP o fransporter, is a heterodimer consisting of TAP 1 and TAP 2 and is associated with antigen processing. Peptide antigens are fransported across the membrane of the endoplasmic reticulum by TAP so they can be expressed on the cell surface in association with MHC molecules. Each TAP protein consists of multiple hydrophobic membrane spanning segments and a highly conserved ATP-binding cassette (Boll, M. et al. (1996) Proc. Nati. Acad. Sci. USA 93:284-289). Pathogenic 5 microorganisms, such as herpes simplex virus, may encode inhibitors of TAP-mediated peptide transport in order to evade immune surveillance (Marusina, K. and J.J Manaco (1996) Curr. Opin. Hematol. 3:19-26). ABC Transporters
The ATP-binding cassette (ABC) fransporters, also called the "traffic ATPases", comprise a o superfamily of membrane proteins that mediate fransport and channel functions in prokaryotes and eukaryotes (Higgins, C.F. (1992) Annu. Rev. Cell Biol. 8:67-113). ABC proteins share a similar overall structure and significant sequence homology. All ABC proteins contain a conserved domain of approximately two hundred amino acid residues which includes one or more nucleotide binding domains. Mutations in ABC transporter genes are associated with various disorders, such as 5 hyperbilirubinemia II/Dubin- Johnson syndrome, recessive Stargardt's disease, X-linked adrenoleukodysfrophy, multidrug resistance, celiac disease, and cystic fibrosis. Peripheral and Anchored Membrane Proteins
Some membrane proteins are not membrane-spanning but are attached to the plasma membrane via membrane anchors or interactions with integral membrane proteins. Membrane o anchors are covalentiy joined to a protein post-franslationally and include such moieties as prenyl, myristyl, and glycosylphosphatidyl inositol groups. Membrane localization of peripheral and anchored proteins is important for their function in processes such as receptor-mediated signal transduction. For example, prenylation of Ras is required for its localization to the plasma membrane and for its normal and oncogenic functions in signal transduction. 5 Vesicle Coat Proteins Intercellular communication is essential for the development and survival of multicellular organisms. Cells communicate with one another through the secretion and uptake of protein signaling molecules. The uptake of proteins into the cell is achieved by the endocytic pathway, in which the interaction of exfracellular signaling molecules with plasma membrane receptors results in 5 the formation of plasma membrane-derived vesicles that enclose and transport the molecules into the cytosol. These transport vesicles fuse with and mature into endosomal and lysosomal (digestive) compartments. The secretion of proteins from the cell is achieved by exocytosis, in which molecules inside of the cell proceed through the secretory pathway. In this pathway, molecules transit from the ER to the Golgi apparatus and finally to the plasma membrane, where they are secreted from the cell. o Several steps in the transit of material along the secretory and endocytic pathways require the formation of transport vesicles. Specifically, vesicles form at the transitional endoplasmic reticulum (tER), the rim of Golgi cisternae, the face of the Trans-Golgi Network (TGN), the plasma membrane (PM), and tubular extensions of the endosomes. Vesicle formation occurs when a region of membrane buds off from the donor organelle. The membrane-bound vesicle contains proteins to be 5 fransported and is surrounded by a proteinaceous coat, the components of which are recruited from the cytosol. Two different classes of coat protein have been identified. Clathrin coats form on vesicles derived from the TGN and PM, whereas coatomer (COP) coats form on vesicles derived from the ER and Golgi. COP coats can be further classified as COPI, involved in retrograde traffic through the Golgi and from the Golgi to the ER, and COPII, involved in anterograde traffic from the 0 ER to the Golgi (Mellman, supra).
In clathrin-based vesicle formation, adapter proteins bring vesicle cargo and coat proteins together at the surface of the budding membrane. Adapter protein- 1 and -2 select cargo from the TGN and plasma membrane, respectively, based on molecular information encoded on the cytoplasmic tail of integral membrane cargo proteins. Adapter proteins also recruit clathrin to the bud 5 site. Clathrin is a protein complex consisting of three large and three small polypeptide chains arranged in a three-legged structure called a friskelion. Multiple triskelions and other coat proteins appear to self-assemble on the membrane to form a coated pit. This assembly process may serve to deform the membrane into a budding vesicle. GTP-bound ADP-ribosylation factor (Arf) is also incoφorated into the coated assembly. Another small G-protein, dynamin, forms a ring complex o around the neck of the forming vesicle and may provide the mechanochemical force to seal the bud, thereby releasing the vesicle. The coated vesicle complex is then transported through the cytosol. During the fransport process, Arf-bound GTP is hydrolyzed to GDP, and the coat dissociates from the fransport vesicle (West, M.A. et al. (1997) J. Cell Biol. 138:1239-1254).
Vesicles which bud from the ER and the Golgi are covered with a protein coat similar to the 5 clathrin coat of endocytic and TGN vesicles. The coat protein (COP) is assembled from cytosolic precursor molecules at specific budding regions on the organelle. The COP coat consists of two major components, a G-protein (Arf or Sar) and coat protomer (coatomer). Coatomer is an equimolar complex of seven proteins, termed alpha-, beta-, beta'-, gamma-, delta-, epsilon- and zeta-COP. The coatomer complex binds to dilysine motifs contained on the cytoplasmic tails of integral membrane 5 proteins. These include the KKXX retrieval motif of membrane proteins of the ER and dibasic/diphenylamine motifs of members of the p24 family. The p24 family of type I membrane proteins represent the major membrane proteins of COPI vesicles (Harter, C and F.T. Wieland (1998) Proc. Nati. Acad. Sci. USA 95:11649-11654).
0 Organelle Associated Molecules
SEQ ID NO:44, SEQ ID NO:45, and SEQ ID NO:46 encode, for example, organelle associated molecules.
Eukaryotic cells are organized into various cellular organelles which has the effect of separating specific molecules and their functions from one another and from the cytosol. Within the 5 cell, various membrane structures surround and define these organelles while allowing them to interact with one another and the cell environment through both active and passive fransport processes. Important cell organelles include the nucleus, the Golgi apparatus, the endoplasmic reticulum, mitochondria, peroxisomes, lysosomes, endosomes, and secretory vesicles. Nucleus o The cell nucleus contains all of the genetic information of the cell in the form of DNA, and the components and machinery necessary for replication of DNA and for franscription of DNA into RNA. (See Alberts, B. et al. (1994) Molecular Biology of the Cell, Garland Publishing Inc., New York NY, pp. 335-399.) DNA is organized into compact structures in the nucleus by interactions with various DNA-binding proteins such as histones and non-histone chromosomal proteins. 5 DNA-specific nucleases, DNAses, partially degrade these compacted structures prior to DNA replication or franscription. DNA replication takes place with the aid of DNA helicases which unwind the double-stranded DNA helix, and DNA polymerases that duplicate the separated DNA strands.
Transcriptional regulatory proteins are essential for the control of gene expression. Some of o these proteins function as franscription factors that initiate, activate, repress, or terminate gene transcription. Transcription factors generally bind to the promoter, enhancer, and upstream regulatory regions of a gene in a sequence-specific manner, although some factors bind regulatory elements within or downstream of a gene's coding region. Transcription factors may bind to a specific region of DNA singly or as a complex with other accessory factors. (Reviewed in Lewin, B. (1990) 5 Genes IV, Oxford University Press, New York NY, and Cell Press, Cambridge MA, pp. 554-570.) Many transcription factors incoφorate DNA-binding structural motifs which comprise either α helices or β sheets that bind to the major groove of DNA. Four well-characterized structural motifs are helix-turn-heUx, zinc finger, leucine zipper, and helix-loop-helix. Proteins containing these motifs may act alone as monomers, or they may form homo- or heterodimers that interact with DNA. 5 Many neoplastic disorders in humans can be attributed to inappropriate gene expression.
Malignant cell growth may result from either excessive expression of tumor promoting genes or insufficient expression of tumor suppressor genes (Cleary, M.L. (1992) Cancer Surv. 15:89-104). Chromosomal franslocations may also produce chimeric loci which fuse the coding sequence of one gene with the regulatory regions of a second unrelated gene. Such an arrangement likely results in o inappropriate gene franscription, potentially contributing to malignancy.
In addition, the immune system responds to infection or frauma by activating a cascade of events that coordinate the progressive selection, amplification, and mobilization of cellular defense mechanisms. A complex and balanced program of gene activation and repression is involved in this process. However, hyperactivity of the immune system as a result of improper or insufficient 5 regulation of gene expression may result in considerable tissue or organ damage. This damage is well documented in immunological responses associated with arthritis, allergens, heart attack, sfroke, and infections (Isselbacher, KJ. et al. (1996) Harrison's Principles of Internal Medicine, 13/e, McGraw Hill, Inc. and Teton Data Systems Software).
Transcription of DNA into RNA also takes place in the nucleus catalyzed by RNA o polymerases. Three types of RNA polymerase exist. RNA polymerase I makes large ribosomal
RNAs, while RNA polymerase III makes a variety of small, stable RNAs including 5S ribosomal RNA and the fransfer RNAs (tRNA). RNA polymerase II transcribes genes that will be translated into proteins. The primary transcript of RNA polymerase II is called heterogenous nuclear RNA (hnRNA), and must be further processed by splicing to remove non-coding sequences called introns. 5 RNA splicing is mediated by small nuclear ribonucleoprotein complexes, or snRNPs, producing mature messenger RNA (mRNA) which is then fransported out of the nucleus for translation into proteins.
Nucleolus
The nucleolus is a highly organized subcompartment in the nucleus that contains high o concenfrations of RNA and proteins and functions mainly in ribosomal RNA synthesis and assembly
(Alberts, et al. supra, pp. 379-382). Ribosomal RNA (rRNA) is a structural RNA that is complexed with proteins to form ribonucleoprotein structures called ribosomes. Ribosomes provide the platform on which protein synthesis takes place.
Ribosomes are assembled in the nucleolus initially from a large, 45S rRNA combined with a 5 variety of proteins imported from the cytoplasm, as well as smaller, 5S rRNAs. Later processing of the immature ribosome results in formation of smaller ribosomal subunits which are transported from the nucleolus to the cytoplasm where they are assembled into functional ribosomes. Endoplasmic Reticulum
In eukaryotes, proteins are synthesized within the endoplasmic reticulum (ER), delivered from 5 the ER to the Golgi apparatus for post-franslational processing and sorting, and transported from the Golgi to specific infracellular and exfracellular destinations. Synthesis of integral membrane proteins, secreted proteins, and proteins destined for the lumen of a particular organelle occurs on the rough endoplasmic reticulum (ER). The rough ER is so named because of the rough appearance in electron micrographs imparted by the attached ribosomes on which protein synthesis proceeds. Synthesis of l o proteins destined for the ER actually begins in the cytosol with the synthesis of a specific signal peptide which directs the growing polypeptide and its attached ribosome to the ER membrane where the signal peptide is removed and protein synthesis is completed. Soluble proteins destined for the ER lumen, for secretion, or for transport to the lumen of other organelles pass completely into the ER lumen. Transmembrane proteins destined for the ER or for other cell membranes are translocated
15 across the ER membrane but remain anchored in the lipid bilayer of the membrane by one or more membrane-spanning α-helical regions.
Translocated polypeptide chains destined for other organelles or for secretion also fold and assemble in the ER lumen with the aid of certain "resident" ER proteins. Protein folding in the ER is aided by two principal types of protein isomerases, protein disulfide isomerase (PDI), and peptidyl-
20 prolyl isomerase (PPI). PDI catalyzes the oxidation of free sulfhydryl groups in cysteine residues to form inframolecular disulfide bonds in proteins. PPI, an enzyme that catalyzes the isomerization of certain proline imide bonds in oligopeptides and proteins, is considered to govern one of the rate limiting steps in the folding of many proteins to their final functional conformation. The cyclophilins represent a major class of PPI that was originally identified as the major receptor for the 5 immunosuppressive drug cyclosporin A (Handschumacher, R.E. et al. (1984) Science 226:544-547). Molecular "chaperones" such as BiP (binding protein) in the ER recognize incorrectly folded proteins as well as proteins not yet folded into their final form and bind to them, both to prevent improper aggregation between them, and to promote proper folding.
The "N-linked" glycosylation of most soluble secreted and membrane-bound proteins by o oligosacchrides linked to asparagine residues in proteins is also performed in the ER. This reaction is catalyzed by a membrane-bound enzyme, oligosaccharyl transferase. Golgi Apparatus
The Golgi apparatus is a complex structure that lies adjacent to the ER in eukaryotic cells and serves primarily as a sorting and dispatching station for products of the ER (Alberts, et al. supra, pp. 5 600-610). Additional postfranslational processing, principally additional glycosylation, also occurs in the Golgi. Indeed, the Golgi is a major site of carbohydrate synthesis, including most of the glycosaminoglycans of the extracellular matrix. N-linked oligosaccharides, added to proteins in the ER, are also further modified in the Golgi by the addition of more sugar residues to form complex N- linked oligosaccharides. "O-linked" glycosylation of proteins also occurs in the Golgi by the 5 addition of N-acetylgalactosamine to the hydroxyl group of a serine or threonine residue followed by the sequential addition of other sugar residues to the first. This process is catalyzed by a series of glycosyltransferases each specific for a particular donor sugar nucleotide and acceptor molecule (Lodish, H. et al. (1995) Molecular Cell Biology. W.H. Freeman and Co., New York NY, pp.700- 708). In many cases, both N- and O-linked oligosaccharides appear to be required for the secretion of o proteins or the movement of plasma membrane glycoproteins to the cell surface.
The terminal compartment of the Golgi is the Trans-Golgi Network (TGN), where both membrane and lumenal proteins are sorted for their final destination. Transport (or secretory) vesicles destined for infracellular compartments, such as lysosomes, bud off of the TGN. Other fransport vesicles bud off containing proteins destined for the plasma membrane, such as receptors, adhesion 5 molecules, and ion channels, and secretory proteins, such as hormones, neurofransmitters, and digestive enzymes. Vacuoles
The vacuole system is a collection of membrane bound compartments in eukaryotic cells that functions in the processes of endocytosis and exocytosis. They include phagosomes, lysosomes, 0 endosomes, and secretory vesicles. Endocytosis is the process in cells of internalizing nufrients, solutes or small particles (pinocytosis) or large particles such as internalized receptors, viruses, bacteria, or bacterial toxins (phagocytosis). Exocytosis is the process of transporting molecules to the cell surface. It facilitates placement or localization of membrane-bound receptors or other membrane proteins and secretion of hormones, neurofransmitters, digestive enzymes, wastes, etc. 5 A common property of all of these vacuoles is an acidic pH environment ranging from approximately pH 4.5-5.0. This acidity is maintained by the presence of a proton ATPase that uses the energy of ATP hydrolysis to generate an elecfrochemical proton gradient across a membrane (Mellman, I. et al. (1986) Annu. Rev. Biochem. 55:663-700). Eukaryotic vacuolar proton ATPase (vp-ATPase) is a multimeric enzyme composed of 3-10 different subunits. One of these subunits is a highly o hydrophobic polypeptide of approximately 16 kDa that is similar to the proteolipid component of vp-
ATPases from eubacteria, fungi, and plant vacuoles (Mandel, M. et al. (1988) Proc. Nati. Acad. Sci. USA 85 :5521 -5524). The 16 kDa proteolipid component is the major subunit of the membrane portion of vp-ATPase and functions in the fransport of protons across the membrane. Lysosomes 5 Lysosomes are membranous vesicles containing various hydrolytic enzymes used for the controlled intracellular digestion of macromolecules. Lysosomes contain some 40 types of enzymes including proteases, nucleases, glycosidases, Upases, phospholipases, phosphatases, and sulfatases, all of which are acid hydrolases that function at a pH of about 5. Lysosomes are surrounded by a unique membrane containing fransport proteins that allow the final products of macromolecule degradation, 5 such as sugars, amino acids, and nucleotides, to be fransported to the cytosol where they may be either excreted or reutilized by the cell. A vp-ATPase, such as that described above, maintains the acidic environment necessary for hydrolytic activity (Alberts, supra, pp. 610-611). Endosomes
Endosomes are another type of acidic vacuole that is used to transport substances from the 0 cell surface to the interior of the cell in the process of endocytosis. Like lysosomes, endosomes have an acidic environment provided by a vp-ATPase (Alberts et al. supra, pp. 610-618). Two types of endosomes are apparent based on tracer uptake studies that distinguish their time of formation in the cell and their cellular location. Early endosomes are found near the plasma membrane and appear to function primarily in the recycling of internalized receptors back to the cell surface. Late endosomes 5 appear later in the endocytic process close to the Golgi apparatus and the nucleus, and appear to be associated with delivery of endocytosed material to lysosomes or to the TGN where they may be recycled. Specific proteins are associated with particular transport vesicles and their target compartments that may provide selectivity in targeting vesicles to their proper compartments. A cytosolic prenylated GTP-binding protein, Rab, is one such protein. Rabs 4, 5, and 11 are associated o with the early endosome, whereas Rabs 7 and 9 associate with the late endosome. Mitochondria
Mitochondria are oval-shaped organelles comprising an outer membrane, a tightly folded inner membrane, an intermembrane space between the outer and inner membranes, and a matrix inside the inner membrane. The outer membrane contains many porin molecules that allow ions and 5 charged molecules to enter the intermembrane space, while the inner membrane contains a variety of fransport proteins that fransfer only selected molecules. Mitochondria are the primary sites of energy production in cells.
Energy is produced by the oxidation of glucose and fatty acids. Glucose is initially converted to pyruvate in the cytoplasm. Fatty acids and pyruvate are fransported to the mitochondria for o complete oxidation to C02 coupled by enzymes to the transport of elecfrons from NADH and FADH2 to oxygen and to the synthesis of ATP (oxidative phosphorylation) from ADP and P..
Pyruvate is fransported into the mitochondria and converted to acetyl-CoA for oxidation via the citric acid cycle, involving pyruvate dehydrogenase components, dihydrolipoyl fransacetylase, and dihydrolipoyl dehydrogenase. Enzymes involved in the cifric acid cycle include: citrate synthetase, 5 aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including ttanssuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate dehydrogenase. Acetyl CoA is oxidized to C02 with concomitant formation of NADH, FADH2, and GTP. In oxidative phosphorylation, the fransfer of electrons from NADH and FADH2 to oxygen by dehydrogenases is coupled to the synthesis of ATP from ADP and P; by the F0F, ATPase complex in 5 the mitochondrial inner membrane. Enzyme complexes responsible for electron transport and ATP synthesis include the F0Fl ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone reductase, cytochrome b, cytochrome c,, FeS protein, and cytochrome c oxidase. Peroxisomes
Peroxisomes, like mitochondria, are a major site of oxygen utilization. They contain one or o more enzymes, such as catalase and urate oxidase, that use molecular oxygen to remove hydrogen atoms from specific organic substrates in an oxidative reaction that produces hydrogen peroxide (Alberts, supra, pp. 574-577). Catalase oxidizes a variety of substrates including phenols, formic acid, formaldehyde, and alcohol and is important in peroxisomes of liver and kidney cells for detoxifying various toxic molecules that enter the bloodstream. Another major function of oxidative 5 reactions in peroxisomes is the breakdown of fatty acids in a process called β oxidation, β oxidation results in shortening of the alkyl chain of fatty acids by blocks of two carbon atoms that are converted to acetyl CoA and exported to the cytosol for reuse in biosynthetic reactions.
Also like mitochondria, peroxisomes import their proteins from the cytosol using a specific signal sequence located near the C-terminus of the protein. The importance of this import process is o evident in the inherited human disease Zellweger syndrome, in which a defect in importing proteins into perixosomes leads to a perixosomal deficiency resulting in severe abnormalities in the brain, liver, and kidneys, and death soon after birth. One form of this disease has been shown to be due to a mutation in the gene encoding a perixosomal integral membrane protein called peroxisome assembly factor- 1. 5 The discovery of new human molecules for diagnostics and therapeutics satisfies a need in the art by providing new compositions which are useful in the diagnosis, study, prevention, and treatment of diseases associated with human molecules.
SUMMARY OF THE INVENTION o The present invention relates to nucleic acid sequences comprising human diagnostic and therapeutic polynucleotides (dithp) as presented in the Sequence Listing. Some of the dithp uniquely identify genes encoding human structural, functional, and regulatory molecules.
The invention provides an isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of 5 SEQ ID NOJ-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). In one alternative, the polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52. In another alternative, the polynucleotide comprises at least 60 contiguous nucleotides of a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). The invention further provides a composition for the detection of expression of human diagnostic and therapeutic polynucleotides, comprising at least one isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 -52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 -52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d); and a detectable label.
The invention also provides a method for detecting a target polynucleotide in a sample, said target polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 -52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). The method comprises a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof. In one alternative, the probe comprises at least 30 contiguous nucleotides. In another alternative, the probe comprises at least 60 contiguous nucleotides.
The invention further provides a recombinant polynucleotide comprising a promoter sequence operably Unked to an isolated polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 - 52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). In one alternative, the invention provides a cell transformed with the recombinant polynucleotide. In another alternative, the invention provides a transgenic organism comprising the recombinant polynucleotide. In a further alternative, the invention provides a method 5 for producing a human diagnostic and therapeutic polypeptide, the method comprising a) culturing a cell under conditions suitable for expression of the human diagnostic and therapeutic polypeptide, wherein said cell is transformed with the recombinant polynucleotide, and b) recovering the human diagnostic and therapeutic polypeptide so expressed.
The invention also provides a purified human diagnostic and therapeutic polypeptide (DITHP) o encoded by at least one polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52. Additionally, the invention provides an isolated antibody which specifically binds to the human diagnostic and therapeutic polypeptide. The invention further provides a method of identifying a test compound which specifically binds to the human diagnostic and therapeutic polypeptide, the method comprising the steps of a) providing a test compound; b) combining 5 the human diagnostic and therapeutic polypeptide with the test compound for a sufficient time and under suitable conditions for binding; and c) detecting binding of the human diagnostic and therapeutic polypeptide to the test compound, thereby identifying the test compound which specifically binds the human diagnostic and therapeutic polypeptide.
The invention further provides a microarray wherein at least one element of the microarray is 0 an isolated polynucleotide comprising at least 60 contiguous nucleotides of a polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence 5 complementary to b); and e) an RNA equivalent of a) through d). The invention also provides a method for generating a transcript image of a sample which contains polynucleotides. The method comprises a) labeling the polynucleotides of the sample, b) contacting the elements of the microarray with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample. o Additionally, the invention provides a method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ 5 ID NOJ-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). The method comprises a) exposing a sample comprising the target polynucleotide to a compound, and b) detecting altered expression of the target polynucleotide.
The invention further provides a method for detecting a target polynucleotide in a sample for toxicity testing of a compound, said target polynucleotide comprising a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52; c) a polynucleotide sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d). The method comprises a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide, b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof, and c) comparing the presence, absence or amount of said target polynucleotide in a first biological sample and a second biological sample, wherein said first biological sample has been contacted with said compound, and said second sample is a confrol, whereby a change in presence, absence or amount of said target polynucleotide in said first sample, as compared with said second sample, is indicative of toxic response to said compound.
DESCRIPTION OF THE TABLES
Table 1 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with their GenBank hits (GI Numbers), probability scores, and functional annotations corresponding to the GenBank hits.
Table 2 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with polynucleotide segments of each template sequence as defined by the indicated "start" and "stop" nucleotide positions. The reading frames of the polynucleotide segments and the Pfam hits, Pfam descriptions, and E- values corresponding to the polypeptide domains encoded by the polynucleotide segments are indicated.
Table 3 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with polynucleotide segments of each template sequence as defined by the indicated "start" and "stop" nucleotide positions. The reading frames of the polynucleotide segments are shown, and the polypeptides encoded by the polynucleotide segments constitute either signal peptide (SP) or fransmembrane (TM) domains, as indicated.
Table 4 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template IDs) corresponding to the polynucleotides of the present invention, along with 5 component sequence identification numbers (component IDs) corresponding to each template. The component sequences, which were used to assemble the template sequences, are defined by the indicated "start" and "stop" nucleotide positions along each template.
Table 5 summarizes the bioinformatics tools which are useful for analysis of the polynucleotides of the present invention. The first column of Table 5 lists analytical tools, programs, o and algorithms, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are incoφorated by reference herein in their entirety, and the fourth column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score, the greater the homology between two sequences). 5
DETAILED DESCRIPTION OF THE INVENTION
Before the nucleic acid sequences and methods are presented, it is to be understood that this invention is not limited to the particular machines, methods, and materials described. Although particular embodiments are described, machines, methods, and materials similar or equivalent to these o embodiments may be used to practice the invention. The preferred machines, methods, and materials set forth are not intended to limit the scope of the invention which is limited only by the appended claims.
The singular forms "a", "an", and "the" include plural reference unless the context clearly dictates otherwise. All technical and scientific terms have the meanings commonly understood by one 5 of ordinary skill in the art. All publications are incoφorated by reference for the puφose of describing and disclosing the cell lines, vectors, and methodologies which are presented and which might be used in connection with the invention. Nothing in the specification is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.
0 Definitions
As used herein, the lower case "dithp" refers to a nucleic acid sequence, while the upper case "DITHP" refers to an amino acid sequence encoded by dithp. A "full-length" dithp refers to a nucleic acid sequence containing the entire coding region of a gene endogenously expressed in human tissue.
"Adjuvants" are materials such as Freund's adjuvant, mineral gels (aluminum hydroxide), and 5 surface active substances (lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole Umpet hemocyanin, and dinifrophenol) which may be administered to increase a host's immunological response.
"Allele" refers to an alternative form of a nucleic acid sequence. Alleles result from a "mutation," a change or an alternative reading of the genetic code. Any given gene may have none, one, or many allelic forms. Mutations which give rise to alleles include deletions, additions, or substitutions of nucleotides. Each of these changes may occur alone, or in combination with the others, one or more times in a given nucleic acid sequence. The present invention encompasses allelic dithp.
"Amino acid sequence" refers to a peptide, a polypeptide, or a protein of either natural or synthetic origin. The amino acid sequence is not limited to the complete, endogenous amino acid sequence and may be a fragment, epitope, variant, or derivative of a protein expressed by a nucleic acid sequence.
"Amplification" refers to the production of additional copies of a sequence and is carried out using polymerase chain reaction (PCR) technologies well known in the art.
"Antibody" refers to intact molecules as well as to fragments thereof, such as Fab, F(ab')2, and Fv fragments, which are capable of binding the epitopic determinant. Antibodies that bind DITHP polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen. The polypeptide or peptide used to immunize an animal (e.g., a mouse, a rat, or a rabbit) can be derived from the translation of RNA, or synthesized chemically, and can be conjugated to a carrier protein if desired. Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobuUn, and keyhole limpet hemocyanin (KLH). The coupled peptide is then used to immunize the animal.
"Antisense sequence" refers to a sequence capable of specifically hybridizing to a target sequence. The antisense sequence may include DNA, RNA, or any nucleic acid mimic or analog such as peptide nucleic acid (PNA); oligonucleotides having modified backbone linkages such as phosphorothioates, methylphosphonates, or benzylphosphonates; oligonucleotides having modified sugar groups such as 2'-methoxyethyl sugars or 2'-methoxyethoxy sugars; or oligonucleotides having modified bases such as 5-methyl cytosine, 2'-deoxyuracil, or 7-deaza-2'-deoxyguanosine.
"Antisense sequence" refers to a sequence capable of specifically hybridizing to a target sequence. The antisense sequence can be DNA, RNA, or any nucleic acid mimic or analog. "Antisense technology" refers to any technology which relies on the specific hybridization of an antisense sequence to a target sequence.
A "bin" is a portion of computer memory space used by a computer program for storage of data, and bounded in such a manner that data stored in a bin may be retrieved by the program.
"Biologically active" refers to an amino acid sequence having a structural, regulatory, or biochemical function of a naturally occurring amino acid sequence. "Clone joining" is a process for combining gene bins based upon the bins' containing sequence information from the same clone. The sequences may assemble into a primary gene transcript as well as one or more splice variants.
"Complementary" describes the relationship between two single-stranded nucleic acid sequences that anneal by base-pairing (5'-A-G-T-3' pairs with its complement 3'-T-C-A-5').
A "component sequence" is a nucleic acid sequence selected by a computer program such as PHRED and used to assemble a consensus or template sequence from one or more component sequences.
A "consensus sequence" or "template sequence" is a nucleic acid sequence which has been assembled from overlapping sequences, using a computer program for fragment assembly such as the GEL VIEW fragment assembly system (Genetics Computer Group (GCG), Madison WI) or using a relational database management system (RDMS).
"Conservative amino acid substitutions" are those substitutions that, when made, least interfere with the properties of the original protein, i.e., the structure and especially the function of the protein is conserved and not significantly changed by such substitutions. The table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative substitutions.
Original Residue Conservative Substitution Ala Gly, Ser
Arg His, Lys
Asn Asp, Gin, His
Asp Asn, Glu
Cys Ala, Ser Gin Asn, Glu, His
Glu Asp, Gin, His
Gly Ala
His Asn, Arg, Gin, Glu
He Leu, Val Leu He, Val
Lys Arg, Gin, Glu Met Leu, He Phe His, Met, Leu, Trp, Tyr Ser Cys, Thr Thr Ser, Val Tφ Phe, Tyr Tyr His, Phe, Tφ Val He, Leu, Thr
Conservative substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.
"Deletion" refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or amino acid residue, respectively, is absent. 5 "Derivative" refers to the chemical modification of a nucleic acid sequence, such as by replacement of hydrogen by an alkyl, acyl, amino, hydroxyl, or other group.
"E-value" refers to the statistical probability that a match between two sequences occurred by chance.
A "fragment" is a unique portion of dithp or DITHP which is identical in sequence to but o shorter in length than the parent sequence. A fragment may comprise up to the entire length of the defined sequence, minus one nucleotide/amino acid residue. For example, a fragment may comprise from 10 to 1000 contiguous amino acid residues or nucleotides. A fragment used as a probe, primer, antigen, therapeutic molecule, or for other puφoses, may be at least 5, 10, 15, 16, 20, 25, 30, 40, 50, 60, 75, 100, 150, 250 or at least 500 contiguous amino acid residues or nucleotides in length. 5 Fragments may be preferentially selected from certain regions of a molecule. For example, a polypeptide fragment may comprise a certain length of contiguous amino acids selected from the first 250 or 500 amino acids (or first 25% or 50%) of a polypeptide as shown in a certain defined sequence. Clearly these lengths are exemplary, and any length that is supported by the specification, including the Sequence Listing and the figures, may be encompassed by the present embodiments. 0 A fragment of dithp comprises a region of unique polynucleotide sequence that specifically identifies dithp, for example, as distinct from any other sequence in the same genome. A fragment of dithp is useful, for example, in hybridization and amplification technologies and in analogous methods that distinguish dithp from related polynucleotide sequences. The precise length of a fragment of dithp and the region of dithp to which the fragment corresponds are routinely determinable by one of ordinary 5 skill in the art based on the intended puφose for the fragment.
A fragment of DITHP is encoded by a fragment of dithp. A fragment of DITHP comprises a region of unique amino acid sequence that specifically identifies DITHP. For example, a fragment of DITHP is useful as an immunogenic peptide for the development of antibodies that specifically recognize DITHP. The precise length of a fragment of DITHP and the region of DITHP to which the o fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended puφose for the fragment.
A "full length" nucleotide sequence is one containing at least a start site for translation to a protein sequence, followed by an open reading frame and a stop site, and encoding a "full length" polypeptide. 5 "Hit" refers to a sequence whose annotation will be used to describe a given template. Criteria for selecting the top hit are as follows: if the template has one or more exact nucleic acid matches, the top hit is the exact match with highest percent identity. If the template has no exact matches but has significant protein hits, the top hit is the protein hit with the lowest E-value. If the template has no significant protein hits, but does have significant non-exact nucleotide hits, the top hit is the nucleotide hit with the lowest E-value.
"Homology" refers to sequence similarity either between a reference nucleic acid sequence and at least a fragment of a dithp or between a reference amino acid sequence and a fragment of a DITHP.
"Hybridization" refers to the process by which a strand of nucleotides anneals with a complementary strand through base pairing. Specific hybridization is an indication that two nucleic acid sequences share a high degree of identity. Specific hybridization complexes form under defined annealing conditions, and remain hybridized after the "washing" step. The defined hybridization conditions include the annealing conditions and the washing step(s), the latter of which is particularly important in determining the stringency of the hybridization process, with more stringent conditions allowing less non-specific binding, i.e., binding between pairs of nucleic acid probes that are not perfectly matched. Permissive conditions for annealing of nucleic acid sequences are routinely determinable and may be consistent among hybridization experiments, whereas wash conditions may be varied among experiments to achieve the desired stringency.
Generally, stringency of hybridization is expressed with reference to the temperature under which the wash step is carried out. Generally, such wash temperatures are selected to be about 5°C to 20°C lower than the thermal melting point (T„) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. An equation for calculating Tm and conditions for nucleic acid hybridization is well known and can be found in Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor Press, Plainview NY; specifically see volume 2, chapter 9.
High stringency conditions for hybridization between polynucleotides of the present invention include wash conditions of 68°C in the presence of about 0.2 x SSC and about 0J % SDS, for 1 hour. Alternatively, temperatures of about 65°C, 60°C, or 55°C may be used. SSC concentration may be varied from about 0.2 to 2 x SSC, with SDS being present at about 0.1%. Typically, blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, denatured salmon sperm DNA at about 100-200 μg/ml. Useful variations on these conditions will be readily apparent to those skilled in the art. Hybridization, particularly under high stringency conditions, may be suggestive of evolutionary similarity between the nucleotides. Such similarity is strongly indicative of a similar role for the nucleotides and their resultant proteins. Other parameters, such as temperature, salt concentration, and detergent concentration may be varied to achieve the desired stringency. Denaturants, such as formamide at a concentration of about 35-50% v/v, may also be used under particular circumstances, such as RNA:DNA hybridizations. Appropriate hybridization conditions are routinely determinable by one of ordinary skill in the art.
"Immunogenic" describes the potential for a natural, recombinant, or synthetic peptide, epitope, 5 polypeptide, or protein to induce antibody production in appropriate animals, cells, or cell Unes.
"Insertion" or "addition" refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or residue, respectively, is added to the sequence.
"LabeUng" refers to the covalent or noncovalent joining of a polynucleotide, polypeptide, or antibody with a reporter molecule capable of producing a detectable or measurable signal. 0 "Microarray" is any arrangement of nucleic acids, amino acids, antibodies, etc., on a substrate.
The substrate may be a solid support such as beads, glass, paper, nitrocellulose, nylon, or an appropriate membrane.
The terms "element" and "array element" refer to a polynucleotide, polypeptide, or other chemical compound having a unique and defined position on a microarray. 5 "Linkers" are short stretches of nucleotide sequence which may be added to a vector or a dithp to create resfriction endonuclease sites to facilitate cloning. "Polylinkers" are engineered to incorporate multiple resfriction enzyme sites and to provide for the use of enzymes which leave 5' or 3' overhangs (e.g., BamHI, EcoRI, and Hindlll) and those which provide blunt ends (e.g., EcoRV, SnaBI, and Stul).
"Naturally occurring" refers to an endogenous polynucleotide or polypeptide that may be o isolated from viruses or prokaryotic or eukaryotic cells.
"Nucleic acid sequence" refers to the specific order of nucleotides joined by phosphodiester bonds in a linear, polymeric arrangement. Depending on the number of nucleotides, the nucleic acid sequence can be considered an oligomer, oligonucleotide, or polynucleotide. The nucleic acid can be DNA, RNA, or any nucleic acid analog, such as PNA, may be of genomic or synthetic origin, may be 5 either double-stranded or single-stranded, and can represent either the sense or antisense (complementary) strand.
"Oligomer" refers to a nucleic acid sequence of at least about 6 nucleotides and as many as about 60 nucleotides, preferably about 15 to 40 nucleotides, and most preferably between about 20 and 30 nucleotides, that may be used in hybridization or amplification technologies. Oligomers may be used o as, e.g., primers for PCR, and are usually chemically synthesized.
"Operably linked" refers to the situation in which a first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences may be in close proximity or contiguous and, 5 where necessary to join two protein coding regions, in the same reading frame. "Peptide nucleic acid" (PNA) refers to a DNA mimic in which nucleotide bases are attached to a pseudopeptide backbone to increase stability. PNAs, also designated antigene agents, can prevent gene expression by targeting complementary messenger RNA.
The phrases "percent identity" and "% identity", as applied to polynucleotide sequences, refer 5 to the percentage of residue matches between at least two polynucleotide sequences aUgned using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize ahgnment between two sequences, and therefore achieve a more meaningful comparison of the two sequences.
Percent identity between polynucleotide sequences may be determined using the default o parameters of the CLUSTAL V algorithm as incoφorated into the MEG ALIGN version 3J 2e sequence ahgnment program. This program is part of the LASERGENE software package, a suite of molecular biological analysis programs (DNASTAR, Madison WI). CLUSTAL V is described in Higgins, D.G. and Shaφ, P.M. (1989) CABIOS 5:151-153 and in Higgins, D.G. et al. (1992) CABIOS 8:189-191.
For pairwise alignments of polynucleotide sequences, the default parameters are set as follows: 5 Ktuple=2, gap penalty=5, window=4, and "diagonals saved"=4. The "weighted" residue weight table is selected as the default. Percent identity is reported by CLUSTAL V as the "percent similarity" between aligned polynucleotide sequence pairs.
Alternatively, a suite of commonly used and freely available sequence comparison algorithms is provided by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search 0 Tool (BLAST) (Altschul, S.F. et al. (1990) J. Mol. Biol. 215:403-410), which is available from several sources, including the NCBI, Bethesda, MD, and on the Internet at http://www.ncbi.nlm.nih.gov/BLAST/. The BLAST software suite includes various sequence analysis programs including "blastn," that is used to determine alignment between a known polynucleotide sequence and other sequences on a variety of databases. Also available is a tool called "BLAST 2 5 Sequences" that is used for direct pairwise comparison of two nucleotide sequences. "BLAST 2
Sequences" can be accessed and used interactively at http://www.ncbi.nlm.nih.gov/gorf/bl2/. The "BLAST 2 Sequences" tool can be used for both blastn and blastp (discussed below). BLAST programs are commonly used with gap and other parameters set to default settings. For example, to compare two nucleotide sequences, one may use blastn with the "BLAST 2 Sequences" tool Version o 2.0.9 (May-07-1999) set at default parameters. Such default parameters may be, for example:
Matrix: BLOSUM62 Reward for match: 1 Penalty for mismatch: -2 Open Gap: 5 and Extension Gap: 2 penalties 5 Gap x drop-off: 50 Expect: 10
Word Size: 11
Filter: on
Percent identity may be measured over the length of an entire defined sequence, for example, as 5 defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined sequence, for instance, a fragment of at least 20, at least 30, at least 40, at least 50, at least 70, at least 100, or at least 200 contiguous nucleotides. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage o identity may be measured.
Nucleic acid sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequences that all encode substantially the same protein. 5 The phrases "percent identity" and "% identity", as applied to polypeptide sequences, refer to the percentage of residue matches between at least two polypeptide sequences aligned using a standardized algorithm. Methods of polypeptide sequence alignment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail above, generally preserve the hydrophobicity and acidity of the substituted o residue, thus preserving the structure (and therefore function) of the folded polypeptide.
Percent identity between polypeptide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incoφorated into the MEGALIGN version 3J2e sequence alignment program (described and referenced above). For pairwise alignments of polypeptide sequences using CLUSTAL V, the default parameters are set as follows: Ktuple=l , gap penalty=3, window=5, and 5 "diagonals saved"=5. The PAM250 mafrix is selected as the default residue weight table. As with polynucleotide alignments, the percent identity is reported by CLUSTAL V as the "percent similarity" between aUgned polypeptide sequence pairs.
Alternatively the NCBI BLAST software suite may be used. For example, for a pairwise comparison of two polypeptide sequences, one may use the "BLAST 2 Sequences" tool Version 2.0.9 o (May-07-1999) with blastp set at default parameters. Such default parameters may be, for example:
Matrix: BLOSUM62
Open Gap: 11 and Extension Gap: 1 penalty Gap x drop-off: 50 Expect: 10 5 Word Size: 3 Filter: on
Percent identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, 5 a fragment of at least 15, at least 20, at least 30, at least 40, at least 50, at least 70 or at least 150 contiguous residues. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage identity may be measured.
"Post-franslational modification" of a DITHP may involve lipidation, glycosylation, 0 phosphorylation, acetylation, racemization, proteolytic cleavage, and other modifications known in the art. These processes may occur synthetically or biochemically. Biochemical modifications will vary by cell type depending on the enzymatic milieu and the DITHP.
"Probe" refers to dithp or fragments thereof, which are used to detect identical, allelic or related nucleic acid sequences. Probes are isolated oligonucleotides or polynucleotides attached to a detectable 5 label or reporter molecule. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes. "Primers" are short nucleic acids, usually DNA oligonucleotides, which may be annealed to a target polynucleotide by complementary base-pairing. The primer may then be extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification (and identification) of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR). 0 Probes and primers as used in the present invention typically comprise at least 15 contiguous nucleotides of a known sequence. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20, 30, 40, 50, 60, 70, 80, 90, 100, or at least 150 consecutive nucleotides of the disclosed nucleic acid sequences. Probes and primers may be considerably longer than these examples, and it is understood that any length supported by the 5 specification, including the figures and Sequence Listing, may be used.
Methods for preparing and using probes and primers are described in the references, for example Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor Press, Plainview NY; Ausubel et al.,1987, Current Protocols in Molecular Biology, Greene Publ. Assoc. & Wiley-Intersciences, New York NY; Innis et al., 1990, PCR Protocols. A Guide o to Methods and Applications, Academic Press, San Diego CA. PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, 1991, Whitehead Institute for Biomedical Research, Cambridge MA).
Oligonucleotides for use as primers are selected using software known in the art for such purpose. For example, OLIGO 4.06 software is useful for the selection of PCR primer pairs of up to 5 100 nucleotides each, and for the analysis of oligonucleotides and larger polynucleotides of up to 5,000 nucleotides from an input polynucleotide sequence of up to 32 kilobases. Similar primer selection programs have incoφorated additional features for expanded capabilities. For example, the PrimOU primer selection program (available to the public from the Genome Center at University of Texas South West Medical Center, Dallas TX) is capable of choosing specific primers from megabase sequences 5 and is thus useful for designing primers on a genome- wide scope. The Primer3 primer selection program (available to the public from the Whitehead Institute/MIT Center for Genome Research, Cambridge MA) allows the user to input a "mispriming library ' in which sequences to avoid as primer binding sites are user-specified. Primer3 is useful, in particular, for the selection of oligonucleotides for microarrays. (The source code for the latter two primer selection programs may also be obtained from o their respective sources and modified to meet the user ' s specific needs.) The PrimeGen program
(available to the public from the UK Human Genome Mapping Project Resource Centre, Cambridge UK) designs primers based on multiple sequence alignments, thereby allowing selection of primers that hybridize to either the most conserved or least conserved regions of aligned nucleic acid sequences. Hence, this program is useful for identification of both unique and conserved oligonucleotides and 5 polynucleotide fragments. The oligonucleotides and polynucleotide fragments identified by any of the above selection methods are useful in hybridization technologies, for example, as PCR or sequencing primers, microarray elements, or specific probes to identify fully or partially complementary polynucleotides in a sample of nucleic acids. Methods of oligonucleotide selection are not limited to those described above. o "Purified" refers to molecules, either polynucleotides or polypeptides that are isolated or separated from their natural environment and are at least 60% free, preferably at least 75% free, and most preferably at least 90% free from other compounds with which they are naturally associated.
A "recombinant nucleic acid" is a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two or more otherwise separated segments of sequence. 5 This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques such as those described in Sambrook, supra. The term recombinant includes nucleic acids that have been altered solely by addition, substitution, or deletion of a portion of the nucleic acid. Frequently, a recombinant nucleic acid may include a nucleic acid sequence operably linked to a promoter sequence. o Such a recombinant nucleic acid may be part of a vector that is used, for example, to transform a cell.
Alternatively, such recombinant nucleic acids may be part of a viral vector, e.g., based on a vaccinia virus, that could be use to vaccinate a mammal wherein the recombinant nucleic acid is expressed, inducing a protective immunological response in the mammal.
"Regulatory element" refers to a nucleic acid sequence from nontranslated regions of a gene, 5 and includes enhancers, promoters, introns, and 3' untranslated regions, which interact with host proteins to carry out or regulate transcription or ttanslation.
"Reporter" molecules are chemical or biochemical moieties used for labeUng a nucleic acid, an amino acid, or an antibody. They include radionuclides; enzymes; fluorescent, chemiluminescent, or chromogenic agents; substrates; cofactors; inhibitors; magnetic particles; and other moieties known in 5 the art.
An "RNA equivalent," in reference to a DNA sequence, is composed of the same linear sequence of nucleotides as the reference DNA sequence with the exception that all occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose instead of deoxyribose. 0 "Sample" is used in its broadest sense. Samples may contain nucleic or amino acids, antibodies, or other materials, and may be derived from any source (e.g., bodily fluids including, but not Umited to, saliva, blood, and urine; chromosome(s), organelles, or membranes isolated from a cell; genomic DNA, RNA, or cDNA in solution or bound to a subsfrate; and cleared cells or tissues or blots or imprints from such cells or tissues). 5 "Specific binding" or "specifically binding" refers to the interaction between a protein or peptide and its agonist, antibody, antagonist, or other binding partner. The interaction is dependent upon the presence of a particular structure of the protein, e.g., the antigenic determinant or epitope, recognized by the binding molecule. For example, if an antibody is specific for epitope "A," the presence of a polypeptide containing epitope A, or the presence of free unlabeled A, in a reaction o containing free labeled A and the antibody will reduce the amount of labeled A that binds to the antibody.
"Substitution" refers to the replacement of at least one nucleotide or amino acid by a different nucleotide or amino acid.
"Subsfrate" refers to any suitable rigid or semi-rigid support including, e.g., membranes, filters, 5 chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles or capillaries. The subsfrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which polynucleotides or polypeptides are bound.
A "transcript image" refers to the collective pattern of gene expression by a particular tissue or cell type under given conditions at a given time. o "Transformation" refers to a process by which exogenous DNA enters a recipient cell.
Transformation may occur under natural or artificial conditions using various methods well known in the art. Transformation may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method is selected based on the host cell being transformed. 5 "Transformants" include stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as cells which transiently express inserted DNA or RNA.
A "transgenic organism," as used herein, is any organism, including but not limited to animals and plants, in which one or more of the cells of the organism contains heterologous nucleic acid 5 introduced by way of human intervention, such as by transgenic techniques well known in the art. The nucleic acid is introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by microinjection or by infection with a recombinant virus. The term genetic manipulation does not include classical cross-breeding, or in vitro fertilization, but rather is directed to the introduction of a recombinant DNA molecule. The transgenic organisms o contemplated in accordance with the present invention include bacteria, cyanobacteria, fungi, and plants and animals. The isolated DNA of the present invention can be introduced into the host by methods known in the art, for example infection, transfection, fransformation or fransconjugation. Techniques for transferring the DNA of the present invention into such organisms are widely known and provided in references such as Sambrook et al. (1989), supra. 5 A "variant" of a particular nucleic acid sequence is defined as a nucleic acid sequence having at least 25% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the "BLAST 2 Sequences" tool Version 2.0.9 (May-07-1999) set at default parameters. Such a pair of nucleic acids may show, for example, at least 30%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or even at least 98% or o greater sequence identity over a certain defined length. The variant may result in "conservative" amino acid changes which do not affect structural and/or chemical properties. A variant may be described as, for example, an "allelic" (as defined above), "splice," "species," or "polymoφhic" variant. A splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of exons during mRNA processing. The 5 corresponding polypeptide may possess additional functional domains or lack domains that are present in the reference molecule. Species variants are polynucleotide sequences that vary from one species to another. The resulting polypeptides generally will have significant amino acid identity relative to each other. A polymoφhic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species. Polymoφhic variants also may encompass "single nucleotide o polymoφhisms" (SNPs) in which the polynucleotide sequence varies by one base. The presence of
SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.
In an alternative, variants of the polynucleotides of the present invention may be generated through recombinant methods. One possible method is a DNA shuffling technique such as 5 MOLECULARBREEDING (Maxygen Inc. , Santa Clara C A; described in U. S . Patent Number 5,837,458; Chang, C-C. et al. (1999) Nat. Biotechnol. 17:793-797; Christians, F.C et al. (1999) Nat. Biotechnol. 17:259-264; and Crameri, A. et al. (1996) Nat. Biotechnol. 14:315-319) to alter or improve the biological properties of DITHP, such as its biological or enzymatic activity or its ability to bind to other molecules or compounds. DNA shuffling is a process by which a hbrary of gene variants is produced using PCR-mediated recombination of gene fragments. The library is then subjected to selection or screening procedures that identify those gene variants with the desired properties. These preferred variants may then be pooled and further subjected to recursive rounds of DNA shuffling and selection/screening. Thus, genetic diversity is created through "artificial" breeding and rapid molecular evolution. For example, fragments of a single gene containing random point mutations may be recombined, screened, and then reshuffled until the desired properties are optimized. Alternatively, fragments of a given gene may be recombined with fragments of homologous genes in the same gene family, either from the same or different species, thereby maximizing the genetic diversity of multiple naturally occurring genes in a directed and controllable manner.
A "variant" of a particular polypeptide sequence is defined as a polypeptide sequence having at least 40% sequence identity to the particular polypeptide sequence over a certain length of one of the polypeptide sequences using blastp with the "BLAST 2 Sequences" tool Version 2.0.9 (May-07- 1999) set at default parameters. Such a pair of polypeptides may show, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 98% or greater sequence identity over a certain defined length of one of the polypeptides.
THE INVENTION
In a particular embodiment, cDNA sequences derived from human tissues and cell lines were aligned based on nucleotide sequence identity and assembled into "consensus" or "template" sequences which are designated by the template identification numbers (template IDs) in column 2 of Table 1. The sequence identification numbers (SEQ ID NO:s) corresponding to the template IDs are shown in column 1. The template sequences have similarity to GenBank sequences, or "hits," as designated by the GI Numbers in column 3. The statistical probability of each GenBank hit is indicated by a probability score in column 4, and the functional annotation corresponding to each GenBank hit is listed in column 5. The invention incoφorates the nucleic acid sequences of these templates as disclosed in the
Sequence Listing and the use of these sequences in the diagnosis and treatment of disease states characterized by defects in human molecules. The invention further utilizes these sequences in hybridization and amplification technologies, and in particular, in technologies which assess gene expression patterns correlated with specific cells or tissues and their responses in vivo or in vitro to pharmaceutical agents, toxins, and other treatments. In this manner, the sequences of the present invention are used to develop a transcript image for a particular cell or tissue.
Derivation of Nucleic Acid Sequences cDNA was isolated from libraries constructed using RNA derived from normal and diseased human tissues and cell hnes. The human tissues and cell lines used for cDNA library construction were selected from a broad range of sources to provide a diverse population of cDNAs representative of gene franscription throughout the human body. Descriptions of the human tissues and cell Unes used for cDNA library construction are provided in the LIFESEQ database (Incyte Genomics, Inc. (Incyte), Palo Alto CA). Human tissues were broadly selected from, for example, cardiovascular, dermatologic, endocrine, gastrointestinal, hematopoietic/immune system, musculoskeletal, neural, reproductive, and urologic sources.
Cell lines used for cDNA library construction were derived from, for example, leukemic cells, teratocarcinomas, neuroepitheliomas, cervical carcinoma, lung fibroblasts, and endothelial cells. Such cell lines include, for example, THP-1, Jurkat, HUVEC, hNT2, WI38, HeLa, and other cell lines commonly used and available from public depositories (American Type Culture Collection, Manassas VA). Prior to mRNA isolation, cell Unes were untreated, treated with a pharmaceutical agent such as 5'-aza-2'-deoxycytidine, treated with an activating agent such as lipopolysaccharide in the case of leukocytic cell lines, or, in the case of endothelial cell lines, subjected to shear stress.
Sequencing of the cDNAs
Methods for DNA sequencing are well known in the art. Conventional enzymatic methods employ the Klenow fragment of DNA polymerase I, SEQUENASE DNA polymerase (U.S. Biochemical Coφoration, Cleveland OH), Taq polymerase (PE Biosystems, Foster City CA), thermostable T7 polymerase (Amersham Pharmacia Biotech, Inc. (Amersham Pharmacia Biotech), Piscataway NJ), or combinations of polymerases and proofreading exonucleases such as those found in the ELONGASE amplification system (Life Technologies Inc. (Life Technologies), Gaithersburg MD), to extend the nucleic acid sequence from an oligonucleotide primer annealed to the DNA template of interest. Methods have been developed for the use of both single-stranded and double-stranded templates. Chain termination reaction products may be elecfrophoresed on urea-poly acrylamide gels and detected either by autoradiography (for radioisotope-labeled nucleotides) or by fluorescence (for fluorophore-labeled nucleotides). Automated methods for mechanized reaction preparation, sequencing, and analysis using fluorescence detection methods have been developed. Machines used to prepare cDNAs for sequencing can include the MICROLAB 2200 liquid transfer system (Hamilton Company (Hamilton), Reno NV), Peltier thermal cycler (PTC200; MJ Research, Inc. (MJ Research), Watertown MA), and ABI CATALYST 800 thermal cycler (PE Biosystems). Sequencing can be carried out using, for example, the ABI 373 or 377 (PE Biosystems) or MEGABACE 1000 (Molecular Dynamics, Inc. (Molecular Dynamics), Sunnyvale CA) DNA sequencing systems, or other automated and manual sequencing systems well known in the art.
The nucleotide sequences of the Sequence Listing have been prepared by current, state-of-the- art, automated methods and, as such, may contain occasional sequencing errors or unidentified nucleotides. Such unidentified nucleotides are designated by an N. These infrequent unidentified bases do not represent a hindrance to practicing the invention for those skilled in the art. Several methods employing standard recombinant techniques may be used to correct errors and complete the missing sequence information. (See, e.g., those described in Ausubel, F.M. et al. (1997) Short Protocols in Molecular Biology, John Wiley & Sons, New York NY; and Sambrook, J. et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview NY.)
Assembly of cDNA Sequences
Human polynucleotide sequences may be assembled using programs or algorithms well known in the art. Sequences to be assembled are related, wholly or in part, and may be derived from a single or many different transcripts. Assembly of the sequences can be performed using such programs as PHRAP (Phils Revised Assembly Program) and the GEL VIEW fragment assembly system (GCG), or other methods known in the art.
Alternatively, cDNA sequences are used as "component" sequences that are assembled into "template" or "consensus" sequences as follows. Sequence chromatograms are processed, verified, and quatity scores are obtained using PHRED. Raw sequences are edited using an editing pathway known as Block 1 (See, e.g., the LIFESEQ Assembled User Guide, Incyte Genomics, Palo Alto, CA). A series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucleotide repeats, Alu repeats, etc.) are replaced by "n's", or masked, to prevent spurious matches. Mitochondrial and ribosomal RNA sequences are also removed. The processed sequences are then loaded into a relational database management system (RDMS) which assigns edited sequences to existing templates, if available. When additional sequences are added into the RDMS, a process is initiated which modifies existing templates or creates new templates from works in progress (i.e., nonfinal assembled sequences) containing queued sequences or the sequences themselves. After the new sequences have been assigned to templates, the templates can be merged into bins. If multiple templates exist in one bin, the bin can be split and the templates reannotated.
Once gene bins have been generated based upon sequence alignments, bins are "clone joined" based upon clone information. Clone joining occurs when the 5' sequence of one clone is present in one bin and the 3' sequence from the same clone is present in a different bin, indicating that the two bins should be merged into a single bin. Only bins which share at least two different clones are merged. A resultant template sequence may contain either a partial or a full length open reading frame, or all or part of a genetic regulatory element. This variation is due in part to the fact that the full length cDNAs of many genes are several hundred, and sometimes several thousand, bases in length. With current technology, cDNAs comprising the coding regions of large genes cannot be cloned because of vector Umitations, incomplete reverse franscription of the mRNA, or incomplete "second strand" synthesis. Template sequences may be extended to include additional contiguous sequences derived from the parent RNA transcript using a variety of methods known to those of skill in the art. Extension may thus be used to achieve the full length coding sequence of a gene.
Analysis of the cDNA Sequences
The cDNA sequences are analyzed using a variety of programs and algorithms which are well known in the art. (See, e.g., Ausubel, 1997, supra. Chapter 7.7; Meyers, R.A. (Ed.) (1995) Molecular Biology and Biotechnology, Wiley VCH, New York NY, pp. 856-853; and Table 5.) These analyses comprise both reading frame determinations, e.g., based on triplet codon periodicity for particular organisms (Fickett, J.W. (1982) Nucleic Acids Res. 10:5303-5318); analyses of potential start and stop codons; and homology searches.
Computer programs known to those of skill in the art for performing computer-assisted searches for amino acid and nucleic acid sequence similarity, include, for example, Basic Local Ahgnment Search Tool (BLAST; Altschul, S.F. (1993) J. Mol. Evol. 36:290-300; Altschul, S.F. et al. (1990) J. Mol. Biol. 215:403-410). BLAST is especially useful in determining exact matches and comparing two sequence fragments of arbitrary but equal lengths, whose alignment is locally maximal and for which the alignment score meets or exceeds a threshold or cutoff score set by the user (Karlin, S. et al. (1988) Proc. Nati. Acad. Sci. USA 85:841-845). Using an appropriate search tool (e.g., BLAST or HMM), GenBank, SwissProt, BLOCKS, PFAM and other databases may be searched for sequences containing regions of homology to a query dithp or DITHP of the present invention. Other approaches to the identification, assembly, storage, and display of nucleotide and polypeptide sequences are provided in "Relational Database for Storing Biomolecule Information," U.S.S.N. 08/947,845, filed October 9, 1997; "Project-Based Full-Length Biomolecular Sequence Database," U.S.S.N. 08/811,758, filed March 6, 1997; and "Relational Database and System for Storing Information Relating to Biomolecular Sequences," U.S.S.N. 09/034,807, filed March 4, 1998, all of which are incoφorated by reference herein in their entirety.
Protein hierarchies can be assigned to the putative encoded polypeptide based on, e.g., motif, BLAST, or biological analysis. Methods for assigning these hierarchies are described, for example, in "Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data," U.S.S.N. 08/812,290, filed March 6, 1997, incorporated herein by reference. Identification of Human Diagnostic and Therapeutic Molecules Encoded by dithp
The identities of the DITHP encoded by the dithp of the present invention were obtained by analysis of the assembled cDNA sequences. SEQ ID NOJ, SEQ ID NO:2, SEQ ID NOJ, SEQ ID NO:4, and SEQ ID NO:5 encode, for example, human enzyme molecules. SEQ ID NO:6 and SEQ ID NO:7 encode, for example, receptor molecules. SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11 , and SEQ ID NO: 12 encode, for example, infracellular signaling molecules. SEQ ID NO:13 encodes, for example, a membrane transport molecule. SEQ ID NO:14, SEQ ID NOJ5, SEQ ID NOJ6, SEQ ID NO:17, SEQ ID NOJ8, SEQ ID NOJ9, and SEQ ID NO:20 encode, for example, nucleic acid synthesis and modification molecules. SEQ ID NO:21 and SEQ ID NO:22 encode, for example, adhesion molecules. SEQ ID NO:23 and SEQ ID NO:24 encode, for example, electron fransfer associated molecules. SEQ ID NO:25 encodes, for example, a secreted/extracellular matrix molecule. SEQ ID NO:26 and SEQ ID NO:27 encode, for example, cytoskeletal molecules. SEQ ID NO:28 and SEQ ID NO:29 encode, for example, cell membrane molecules. SEQ ID NO:30 and SEQ ID NO:31 encode, for example, ribosomal molecules. SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, and SEQ ID NO:43 encode, for example, transcription factor molecules. SEQ ID NO:44, SEQ ID NO:45, and SEQ ID NO:46 encode, for example, organelle associated molecules. SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, and SEQ ID NO:50 encode, for example, biochemical pathway molecules. SEQ ID NO:51 and SEQ ID NO:52 encode, for example, molecules associated with growth and development.
Sequences of Human Diagnostic and Therapeutic Molecules
The dithp of the present invention may be used for a variety of diagnostic and therapeutic puφoses. For example, a dithp may be used to diagnose a particular condition, disease, or disorder associated with human molecules. Such conditions, diseases, and disorders include, but are not limited to, a cell proliferative disorder, such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, a cancer of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; an autoimmune/inflammatory disorder, such as inflammation, actinic keratosis, acquired immunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, arteriosclerosis, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, bronchitis, bursitis, cholecystitis, cirrhosis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes melUtus, emphysema, erythroblastosis fetalis, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, paroxysmal nocturnal hemoglobinuria, hepatitis, hypereosinophilia, irritable bowel syndrome, episodic lymphopenia with lymphocytotoxins, mixed connective tissue disease (MCTD), multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, myelofibrosis, osteoarthritis, osteoporosis, pancreatitis, polycythemia vera, polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjogren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, primary thrombocythemia, thrombocytopenic p pura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and extracoφoreal circulation, frauma, and hematopoietic cancer including lymphoma, leukemia, and myeloma; an infection caused by a viral agent classified as adenovirus, arenavirus, bunyavirus, calicivirus, coronavirus, filovirus, hepadnavirus, heφesvirus, fiavivirus, orthomyxovirus, parvovirus, papovavirus, paramyxovirus, picomavirus, poxvirus, reovirus, refrovirus, rhabdovirus, or togavirus; an infection caused by a bacterial agent classified as pneumococcus, staphylococcus, streptococcus, bacillus, corynebacterium, clostridium, meningococcus, gonococcus, listeria, moraxella, kingella, haemophilus, legionella, bordetella, gram- negative enterobacterium including shigella, salmonella, or campylobacter, pseudomonas, vibrio, brucella, francisella, yersinia, bartonella, norcardium, actinomyces, mycobacterium, spirochaetale, rickettsia, chlamydia, or mycoplasma; an infection caused by a fungal agent classified as aspergillus, blastomyces, dermatophytes, cryptococcus, coccidioides, malasezzia, histoplasma, or other mycosis- causing fungal agent; and an infection caused by a parasite classified as plasmodium or malaria- causing, parasitic entamoeba, leishmania, trypanosoma, toxoplasma, pneumocystis carinii, intestinal protozoa such as giardia, trichomonas, tissue nematode such as frichinella, intestinal nematode such as ascaris, lymphatic filarial nematode, frematode such as schistosoma, and cesfrode such as tapeworm; a developmental disorder such as renal tubular acidosis, anemia, Cushing's syndrome, achondroplastic dwarfism, Duchenne and Becker muscular dystrophy, epilepsy, gonadal dysgenesis, WAGR syndrome (Wilms' tumor, aniridia, genitourinary abnormalities, and mental retardation), Smith-Magenis syndrome, myelodysplastic syndrome, hereditary mucoepithelial dysplasia, hereditary keratodermas, hereditary neuropathies such as Charcot-Marie-Tooth disease and neurofibromatosis, hypothyroidism, hydrocephalus, seizure disorders such as Syndenham's chorea and cerebral palsy, spina bifida, anencephaly, craniorachischisis, congenital glaucoma, cataract, and sensorineural hearing loss; an endocrine disorder such as a disorder of the hypothalamus and/or pituitary resulting from lesions such as a primary brain tumor, adenoma, infarction associated with pregnancy, hypophysectomy, aneurysm, vascular malformation, thrombosis, infection, immunological disorder, and complication due to head trauma; a disorder associated with hypopituitarism including hypogonadism, Sheehan syndrome, diabetes insipidus, Kallman's disease, Hand-Schuller-Christian disease, Letterer- Siwe disease, sarcoidosis, empty sella syndrome, and dwarfism; a disorder associated with hypeφituitarism including acromegaly, giantism, and syndrome of inappropriate antidiuretic hormone (ADH) secretion (SIADH) often caused by benign adenoma; a disorder associated with hypothyroidism including goiter, myxedema, acute thyroiditis associated with bacterial infection, subacute thyroiditis associated with viral infection, autoimmune thyroiditis (Hashimoto's disease), and cretinism; a disorder associated with hyperthyroidism including thyrotoxicosis and its various forms, Grave's disease, pretibial myxedema, toxic multinodular goiter, thyroid carcinoma, and Plummer 's disease; a disorder associated with hypeφarathyroidism including Conn disease (chronic hypercalemia); a pancreatic disorder such as Type I or Type II diabetes melUtus and associated compUcations; a disorder associated with the adrenals such as hypeφlasia, carcinoma, or adenoma of the adrenal cortex, hypertension associated with alkalosis, amyloidosis, hypokalemia, Cushing's disease, Liddle's syndrome, and Arnold-Healy-Gordon syndrome, pheochromocytoma tumors, and Addison's disease; a disorder associated with gonadal steroid hormones such as: in women, abnormal prolactin production, infertility, endomefriosis, perturbation of the menstrual cycle, polycystic ovarian disease, hypeφrolactinemia, isolated gonadofropin deficiency, amenorrhea, galactorrhea, hermaphroditism, hirsutism and virilization, breast cancer, and, in post-menopausal women, osteoporosis; and, in men, Leydig cell deficiency, male climacteric phase, and germinal cell aplasia, a hypergonadal disorder associated with Leydig cell tumors, androgen resistance associated with absence of androgen receptors, syndrome of 5 α-reductase, and gynecomastia; a metabolic disorder such as Addison's disease, cerebrotendinous xanthomatosis, congenital adrenal hypeφlasia, coumarin resistance, cystic fibrosis, diabetes, fatty hepatocirrhosis, fructose- 1,6-diphosphatase deficiency, galactosemia, goiter, glucagonoma, glycogen storage diseases, hereditary fructose intolerance, hyperadrenalism, hypoadrenalism, hypeφarathyroidism, hypoparathyroidism, hypercholesterolemia, hyperthyroidism, hypoglycemia, hypothyroidism, hyperhpidemia, hyperlipemia, lipid myopathies, lipodystrophies, lysosomal storage diseases, mannosidosis, neuraminidase deficiency, obesity, pentosuria phenylketonuria, pseudovitamin D-deficiency rickets; disorders of carbohydrate metabolism such as congenital type II dyserythropoietic anemia, diabetes, insulin-dependent diabetes mellitus, non-insulin-dependent diabetes melUtus, fructose- 1,6-diphosphatase deficiency, galactosemia, glucagonoma, hereditary fructose intolerance, hypoglycemia, mannosidosis, neuraminidase deficiency, obesity, galactose epimerase deficiency, glycogen storage diseases, lysosomal storage diseases, fructosuria, pentosuria, and inherited abnormalities of pyruvate metabolism; disorders of lipid metabolism such as fatty liver, cholestasis, primary biliary cirrhosis, carnitine deficiency, carnitine palmitoylttansferase deficiency, myoadenylate deaminase deficiency, hypertriglyceridemia, lipid storage disorders such Fabry's disease, Gaucher's disease, Niemann-Pick' s disease, metachromatic leukodysttophy, adrenoleukodystrophy, GM2 gangliosidosis, and ceroid hpofuscinosis, abetalipoproteinemia, Tangier disease, hyperlipoproteinemia, diabetes mellitus, 5 lipodysfrophy, lipomatoses, acute panniculitis. disseminated fat necrosis, adiposis dolorosa, lipoid adrenal hypeφlasia, minimal change disease, lipomas, atherosclerosis, hypercholesterolemia, hypercholesterolemia with hypertriglyceridemia, primary hypoalphalipoproteinemia, hypothyroidism, renal disease, liver disease, lecithin holesterol acylfransferase deficiency, cerebrotendinous xanthomatosis, sitosterolemia, hypocholesterolemia, Tay-Sachs disease, Sandhoff s disease, o hyperlipidemia, hyperlipemia, lipid myopathies, and obesity; and disorders of copper metabolism such as Menke's disease, Wilson's disease, and Ehlers-Danlos syndrome type IX; a neurological disorder such as epilepsy, ischemic cerebrovascular disease, stroke, cerebral neoplasms, Alzheimer's disease, Pick's disease, Huntington's disease, dementia, Parkinson's disease and other exfrapyramidal disorders, amyottophic lateral sclerosis and other motor neuron disorders, progressive neural muscular 5 atrophy, retinitis pigmentosa, hereditary ataxias, multiple sclerosis and other demyehnating diseases, bacterial and viral meningitis, brain abscess, subdural empyema, epidural abscess, suppurative intracranial thrombophlebitis, myehtis and radiculitis, viral cenfral nervous system disease, prion diseases including kuru, Creutzfeldt-Jakob disease, and Gerstmann-Sfraussler-Scheinker syndrome, fatal familial insomnia, nutritional and metabolic diseases of the nervous system, neurofibromatosis, 0 tuberous sclerosis, cerebelloretinal hemangioblastomatosis, encephalofrigeminal syndrome, mental retardation and other developmental disorder of the cenfral nervous system, cerebral palsy, a neuroskeletal disorder, an autonomic nervous system disorder, a cranial nerve disorder, a spinal cord disease, muscular dysfrophy and other neuromuscular disorder, a peripheral nervous system disorder, dermatomyositis and polymyositis, inherited, metabohc, endocrine, and toxic myopathy, myasthenia 5 gravis, periodic paralysis, a mental disorder including mood, anxiety, and schizophrenic disorders, seasonal affective disorder (SAD), akathesia, amnesia, catatonia, diabetic neuropathy, tardive dyskinesia, dystonias, paranoid psychoses, postheφetic neuralgia, and Tourette's disorder; a gastrointestinal disorder including ulcerative colitis, gastric and duodenal ulcers, cystinuria, dibasicaminoaciduria, hypercystinuria, lysinuria, hartnup disease, tryptophan malabsoφtion, o methionine malabsoφtion, histidinuria, iminoglycinuria, dicarboxylicaminoaciduria, cystinosis, renal glycosuria, hypouricemia, familial hypophophatemic rickets, congenital chloridorrhea, distal renal tubular acidosis, Menkes' disease, Wilson's disease, lethal diarrhea, juvenile pernicious anemia, folate malabsoφtion, adrenoleukodystrophy, hereditary myoglobinuria, and Zellweger syndrome; a transport disorder such as akinesia, amyottophic lateral sclerosis, ataxia telangiectasia, cystic fibrosis, 5 Becker's muscular dystrophy, Bell's palsy, Charcot-Marie Tooth disease, diabetes mellitus, diabetes insipidus, diabetic neuropathy, Duchenne muscular dysfrophy, hyperkalemic periodic paralysis, normokalemic periodic paralysis, Parkinson's disease, malignant hyperthermia, multidrug resistance, myasthenia gravis, myotonic dysfrophy, catatonia, tardive dyskinesia, dystonias, peripheral neuropathy, cerebral neoplasms, prostate cancer, cardiac disorders associated with transport, e.g., 5 angina, bradyarrythmia, tachyarrythmia, hypertension, Long QT syndrome, myocarditis, cardiomyopathy, nemaline myopathy, cenfronuclear myopathy, lipid myopathy, mitochondrial myopathy, thyrotoxic myopathy, ethanol myopathy, dermatomyositis, inclusion body myositis, infectious myositis, and polymyositis, neurological disorders associated with fransport, e.g., Alzheimer's disease, amnesia, bipolar disorder, dementia, depression, epilepsy, Tourette's disorder, 0 paranoid psychoses, and schizophrenia, and other disorders associated with fransport, e.g., neurofibromatosis, postheφetic neuralgia, trigeminal neuropathy, sarcoidosis, sickle cell anemia, cataracts, infertility, pulmonary artery stenosis, sensorineural autosomal deafness, hyperglycemia, hypoglycemia, Grave's disease, goiter, glucose-galactose malabsoφtion syndrome, hypercholesterolemia, Cushing's disease, and Addison's disease; and a connective tissue disorder 5 such as osteogenesis imperfecta, Ehlers-Danlos syndrome, chondrodysplasias, Marfan syndrome, Alport syndrome, familial aortic aneurysm, achondroplasia, mucopolysaccharidoses, osteoporosis, osteopefrosis, Paget's disease, rickets, osteomalacia, hypeφarathyroidism, renal osteodysfrophy, osteonecrosis, osteomyelitis, osteoma, osteoid osteoma, osteoblastoma, osteosarcoma, osteochondroma, chondroma, chondroblastoma, chondromyxoid fibroma, chondrosarcoma, fibrous o cortical defect, nonossifying fibroma, fibrous dysplasia, fibrosarcoma, malignant fibrous histiocytoma, Ewing's sarcoma, primitive neuroectodermal tumor, giant cell tumor, osteoarthritis, rheumatoid arthritis, ankylosing spondyloarthritis, Reiter's syndrome, psoriatic arthritis, enteropathic arthritis, infectious arthritis, gout, gouty arthritis, calcium pyrophosphate crystal deposition disease, ganglion, synovial cyst, villonodular synovitis, systemic sclerosis, Dupuytren's contracture, hepatic 5 fibrosis, lupus erythematosus, mixed connective tissue disease, epidermolysis bullosa simplex, bullous congenital ichthyosiform erythroderma (epidermolytic hyperkeratosis), non-epidermolytic and epidermolytic palmoplantar keratoderma, ichthyosis bullosa of Siemens, pachyonychia congenita, and white sponge nevus. The dithp can be used to detect the presence of, or to quantify the amount of, a dithp-related polynucleotide in a sample. This information is then compared to information obtained o from appropriate reference samples, and a diagnosis is established. Alternatively, a polynucleotide complementary to a given dithp can inhibit or inactivate a therapeutically relevant gene related to the dithp.
Analysis of dithp Expression Patterns 5 The expression of dithp may be routinely assessed by hybridization-based methods to determine, for example, the tissue-specificity, disease-specificity, or developmental stage-specificity of dithp expression. For example, the level of expression of dithp may be compared among different cell types or tissues, among diseased and normal cell types or tissues, among cell types or tissues at different developmental stages, or among cell types or tissues undergoing various treatments. This type 5 of analysis is useful, for example, to assess the relative levels of dithp expression in fully or partially differentiated cells or tissues, to determine if changes in dithp expression levels are correlated with the development or progression of specific disease states, and to assess the response of a cell or tissue to a specific therapy, for example, in pharmacological or toxicological studies. Methods for the analysis of dithp expression are based on hybridization and amplification technologies and include membrane- 0 based procedures such as northern blot analysis, high-throughput procedures that utilize, for example, microarrays, and PCR-based procedures.
Hybridization and Genetic Analysis
The dithp, their fragments, or complementary sequences, may be used to identify the presence 5 of and/or to determine the degree of similarity between two (or more) nucleic acid sequences. The dithp may be hybridized to naturally occurring or recombinant nucleic acid sequences under appropriately selected temperatures and salt concenfrations. Hybridization with a probe based on the nucleic acid sequence of at least one of the dithp allows for the detection of nucleic acid sequences, including genomic sequences, which are identical or related to the dithp of the Sequence Listing. Probes may be o selected from non-conserved or unique regions of at least one of the polynucleotides of SEQ ID NO: 1 -
52 and tested for their ability to identify or amplify the target nucleic acid sequence using standard protocols.
Polynucleotide sequences that are capable of hybridizing, in particular, to those shown in SEQ ID NOJ-52 and fragments thereof, can be identified using various conditions of stringency. (See, e.g., 5 Wahl, G.M. and S.L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A.R. (1987) Methods Enzymol. 152:507-511.) Hybridization conditions are discussed in "Definitions."
A probe for use in Southern or northern hybridization may be derived from a fragment of a dithp sequence, or its complement, that is up to several hundred nucleotides in length and is either single-stranded or double-stranded. Such probes may be hybridized in solution to biological materials o such as plasmids, bacterial, yeast, or human artificial chromosomes, cleared or sectioned tissues, or to artificial substrates containing dithp. Microarrays are particularly suitable for identifying the presence of and detecting the level of expression for multiple genes of interest by examining gene expression correlated with, e.g., various stages of development, treatment with a drug or compound, or disease progression. An array analogous to a dot or slot blot may be used to arrange and link polynucleotides 5 to the surface of a subsfrate using one or more of the following: mechanical (vacuum), chemical, thermal, or UV bonding procedures. Such an array may contain any number of dithp and may be produced by hand or by using available devices, materials, and machines.
Microarrays may be prepared, used, and analyzed using methods known in the art. (See, e.g., Brennan, T.M. et al. (1995) U.S. Patent No. 5,474,796; Schena, M. et al. (1996) Proc. Nati. Acad. Sci. 5 USA 93:10614-10619; Baldeschweiler et al. (1995) PCT application W095/251116; Shalon, D. et al. (1995) PCT appUcation WO95/35505; Heller, R.A. et al. (1997) Proc. Nati. Acad. Sci. USA 94:2150- 2155; and Heller, M.J. et al. (1997) U.S. Patent No. 5,605,662.)
Probes may be labeled by either PCR or enzymatic techniques using a variety of commercially available reporter molecules. For example, commercial kits are available for radioactive and o chemiluminescent labeUng (Amersham Pharmacia Biotech) and for alkaline phosphatase labeling (Life
Technologies). Alternatively, dithp may be cloned into commercially available vectors for the production of RNA probes. Such probes may be transcribed in the presence of at least one labeled nucleotide (e.g., 32P-ATP, Amersham Pharmacia Biotech).
Additionally the polynucleotides of SEQ ID NOJ-52 or suitable fragments thereof can be used 5 to isolate full length cDNA sequences utilizing hybridization and/or amplification procedures well known in the art, e.g., cDNA library screening, PCR amplification, etc. The molecular cloning of such full length cDNA sequences may employ the method of cDNA library screening with probes using the hybridization, stringency, washing, and probing strategies described above and in Ausubel, supra. Chapters 3, 5, and 6. These procedures may also be employed with genomic libraries to isolate o genomic sequences of dithp in order to analyze, e.g., regulatory elements.
Genetic Mapping
Gene identification and mapping are important in the investigation and treatment of almost all conditions, diseases, and disorders. Cancer, cardiovascular disease, Alzheimer's disease, arthritis, 5 diabetes, and mental illnesses are of particular interest. Each of these conditions is more complex than the single gene defects of sickle cell anemia or cystic fibrosis, with select groups of genes being predictive of predisposition for a particular condition, disease, or disorder. For example, cardiovascular disease may result from malfunctioning receptor molecules that fail to clear cholesterol from the bloodstream, and diabetes may result when a particular individual's immune system is o activated by an infection and attacks the insulin-producing cells of the pancreas. In some studies,
Alzheimer's disease has been linked to a gene on chromosome 21 ; other studies predict a different gene and location. Mapping of disease genes is a complex and reiterative process and generally proceeds from genetic linkage analysis to physical mapping.
As a condition is noted among members of a family, a genetic linkage map traces parts of 5 chromosomes that are inherited in the same pattern as the condition. Statistics link the inheritance of particular conditions to particular regions of chromosomes, as defined by RFLP or other markers. (See, for example, Lander, E. S. and Botstein, D. (1986) Proc. Nati. Acad. Sci. USA 83:7353-7357.) Occasionally, genetic markers and their locations are known from previous studies. More often, however, the markers are simply stretches of DNA that differ among individuals. Examples of genetic linkage maps can be found in various scientific journals or at the Online Mendelian Inheritance in Man (OMIM) World Wide Web site.
In another embodiment of the invention, dithp sequences may be used to generate hybridization probes useful in chromosomal mapping of naturally occurring genomic sequences. Either coding or noncoding sequences of dithp may be used, and in some instances, noncoding sequences may be preferable over coding sequences. For example, conservation of a dithp coding sequence among members of a multi-gene family may potentially cause undesired cross hybridization during chromosomal mapping. The sequences may be mapped to a particular chromosome, to a specific region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial PI constructions, or single chromosome cDN A libraries. (See, e.g., Harrington, JJ. et al. (1997) Nat. Genet. 15:345-355; Price, CM. (1993) Blood Rev. 7:127-134; and Trask, BJ. (1991) Trends Genet. 7:149-154.)
Fluorescent in situ hybridization (FISH) may be correlated with other physical chromosome mapping techniques and genetic map data. (See, e.g., Meyers, supra, pp. 965-968.) Correlation between the location of dithp on a physical chromosomal map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA associated with that disorder. The dithp sequences may also be used to detect polymoφhisms that are genetically linked to the inheritance of a particular condition, disease, or disorder.
In situ hybridization of chromosomal preparations and genetic mapping techniques, such as linkage analysis using established chromosomal markers, may be used for extending existing genetic maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the number or arm of the corresponding human chromosome is not known. These new marker sequences can be mapped to human chromosomes and may provide valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once a disease or syndrome has been crudely correlated by genetic linkage with a particular genomic region, e.g., ataxia-telangiectasia to 1 lq22-23, any sequences mapping to that area may represent associated or regulatory genes for further investigation. (See, e.g., Gatti, R.A. et al. (1988) Nature 336:577-580.) The nucleotide sequences of the subject invention may also be used to detect differences in chromosomal architecture due to translocation, inversion, etc., among normal, carrier, or affected individuals. Once a disease-associated gene is mapped to a chromosomal region, the gene must be cloned in order to identify mutations or other alterations (e.g., franslocations or inversions) that may be correlated with disease. This process requires a physical map of the chromosomal region containing the disease- gene of interest along with associated markers. A physical map is necessary for determining the nucleotide sequence of and order of marker genes on a particular chromosomal region. Physical mapping techniques are well known in the art and require the generation of overlapping sets of cloned DNA fragments from a particular organelle, chromosome, or genome. These clones are analyzed to reconstruct and catalog their order. Once the position of a marker is determined, the DNA from that region is obtained by consulting the catalog and selecting clones from that region. The gene of interest is located through positional cloning techniques using hybridization or similar methods.
Diagnostic Uses
The dithp of the present invention may be used to design probes useful in diagnostic assays. Such assays, well known to those skilled in the art, may be used to detect or confirm conditions, disorders, or diseases associated with abnormal levels of dithp expression. Labeled probes developed from dithp sequences are added to a sample under hybridizing conditions of desired stringency. In some instances, dithp, or fragments or oligonucleotides derived from dithp, may be used as primers in amplification steps prior to hybridization. The amount of hybridization complex formed is quantified and compared with standards for that cell or tissue. If dithp expression varies significantly from the standard, the assay indicates the presence of the condition, disorder, or disease. Qualitative or quantitative diagnostic methods may include northern, dot blot, or other membrane or dip-stick based technologies or multiple-sample format technologies such as PCR, enzyme-linked immunosorbent assay (ELISA)-like, pin, or chip-based assays.
The probes described above may also be used to monitor the progress of conditions, disorders, or diseases associated with abnormal levels of dithp expression, or to evaluate the efficacy of a particular therapeutic treatment. The candidate probe may be identified from the dithp that are specific to a given human tissue and have not been observed in GenBank or other genome databases. Such a probe may be used in animal studies, preclinical tests, clinical trials, or in monitoring the treatment of an individual patient. In a typical process, standard expression is established by methods well known in the art for use as a basis of comparison, samples from patients affected by the disorder or disease are combined with the probe to evaluate any deviation from the standard profile, and a therapeutic agent is administered and effects are monitored to generate a treatment profile. Efficacy is evaluated by determining whether the expression progresses toward or returns to the standard normal pattern. Treatment profiles may be generated over a period of several days or several months. Statistical methods well known to those skilled in the art may be use to determine the significance of such therapeutic agents.
The polynucleotides are also useful for identifying individuals from minute biological samples, for example, by matching the RFLP pattern of a sample's DNA to that of an individual's DNA. The polynucleotides of the present invention can also be used to determine the actual base-by-base DNA sequence of selected portions of an individual's genome. These sequences can be used to prepare PCR primers for ampUfying and isolating such selected DNA, which can then be sequenced. Using this technique, an individual can be identified through a unique set of DNA sequences. Once a unique ID database is established for an individual, positive identification of that individual can be made from extremely small tissue samples. In a particular aspect, oligonucleotide primers derived from the dithp of the invention may be used to detect single nucleotide polymoφhisms (SNPs). SNPs are substitutions, insertions and deletions that are a frequent cause of inherited or acquired genetic disease in humans. Methods of SNP detection include, but are not limited to, single-stranded conformation polymoφhism (SSCP) and fluorescent SSCP (fSSCP) methods. In SSCP, oligonucleotide primers derived from the polynucleotide sequences encoding DITHP are used to amplify DNA using the polymerase chain reaction (PCR). The DNA may be derived, for example, from diseased or normal tissue, biopsy samples, bodily fluids, and the like. SNPs in the DNA cause differences in the secondary and tertiary structures of PCR products in single-stranded form, and these differences are detectable using gel elecfrophoresis in non-denaturing gels. In f'SCCP, the oUgonucleotide primers are fluorescently labeled, which allows detection of the amplimers in high-throughput equipment such as DNA sequencing machines. Additionally, sequence database analysis methods, termed in silico SNP (isSNP), are capable of identifying polymoφhisms by comparing the sequences of individual overlapping DNA fragments which assemble into a common consensus sequence. These computer-based methods filter out sequence variations due to laboratory preparation of DNA and sequencing errors using statistical models and automated analyses of DNA sequence chromatograms. In the alternative, SNPs may be detected and characterized by mass spectromefry using, for example, the high throughput MASSARRAY system (Sequenom, Inc., San Diego CA).
DNA-based identification techniques are critical in forensic technology. DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saliva, semen, etc., can be amplified using, e.g., PCR, to identify individuals. (See, e.g., Erlich, H. (1992) PCR Technology. Freeman and Co., New York, NY). Similarly, polynucleotides of the present invention can be used as polymoφhic markers.
There is also a need for reagents capable of identifying the source of a particular tissue. Appropriate reagents can comprise, for example, DNA probes or primers prepared from the sequences of the present invention that are specific for particular tissues. Panels of such reagents can identify tissue by species and/or by organ type. In a similar fashion, these reagents can be used to screen tissue cultures for contamination.
The polynucleotides of the present invention can also be used as molecular weight markers on nucleic acid gels or Southern blots, as diagnostic probes for the presence of a specific mRNA in a 5 particular cell type, in the creation of subfracted cDNA libraries which aid in the discovery of novel polynucleotides, in selection and synthesis of oligomers for attachment to an array or other support, and as an antigen to eUcit an immune response.
Disease Model Systems Using dithp o The dithp of the invention or their mammalian homologs may be "knocked out" in an animal model system using homologous recombination in embryonic stem (ES) cells. Such techniques are well known in the art and are useful for the generation of animal models of human disease. (See, e.g., U.S. Patent Number 5,175,383 and U.S. Patent Number 5,161,331.) For example, mouse ES cells, such as the mouse 129/SvJ cell line, are derived from the early mouse embryo and grown in culture. The ES 5 cells are fransformed with a vector containing the gene of interest disrupted by a marker gene, e.g., the neomycin phosphofransferase gene (neo; Capecchi, M.R. (1989) Science 244:1288-1292). The vector integrates into the corresponding region of the host genome by homologous recombination. Alternatively, homologous recombination takes place using the Cre-loxP system to knockout a gene of interest in a tissue- or developmental stage-specific manner (Marth, J.D. (1996) Clin. Invest. 97:1999- 0 2002; Wagner, K.U. et al. (1997) Nucleic Acids Res. 25:4323-4330). Transformed ES cells are identified and microinjected into mouse cell blastocysts such as those from the C57BL/6 mouse strain. The blastocysts are surgically transferred to pseudopregnant dams, and the resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains. Transgenic animals thus generated may be tested with potential therapeutic or toxic agents. 5 The dithp of the invention may also be manipulated in vitro in ES cells derived from human blastocysts. Human ES cells have the potential to differentiate into at least eight separate cell lineages including endoderm, mesoderm, and ectodermal cell types. These cell lineages differentiate into, for example, neural cells, hematopoietic lineages, and cardiomyocytes (Thomson, J.A. et al. (1998) Science 282:1145-1147). o The dithp of the invention can also be used to create "knockin" humanized animals (pigs) or transgenic animals (mice or rats) to model human disease. With knockin technology, a region of dithp is injected into animal ES cells, and the injected sequence integrates into the animal cell genome. Transformed cells are injected into blastulae, and the blastulae are implanted as described above. Transgenic progeny or inbred lines are studied and treated with potential pharmaceutical agents to 5 obtain information on treatment of a human disease. Alternatively, a mammal inbred to overexpress dithp, resulting, e.g., in the secretion of DITHP in its milk, may also serve as a convenient source of that protein (Janne, J. et al. (1998) Biotechnol. Annu. Rev. 4:55-74).
Screening Assays 5 DITHP encoded by polynucleotides of the present invention may be used to screen for molecules that bind to or are bound by the encoded polypeptides. The binding of the polypeptide and the molecule may activate (agonist), increase, inhibit (antagonist), or decrease activity of the polypeptide or the bound molecule. Examples of such molecules include antibodies, oligonucleotides, proteins (e.g., receptors), or small molecules. o Preferably, the molecule is closely related to the natural ligand of the polypeptide, e.g., a ligand or fragment thereof, a natural subsfrate, or a structural or functional mimetic. (See, Coligan et al., (1991) Current Protocols in Immunology 1(2): Chapter 5.) Similarly, the molecule can be closely related to the natural receptor to which the polypeptide binds, or to at least a fragment of the receptor, e.g., the active site. In either case, the molecule can be rationally designed using known techniques. 5 Preferably, the screening for these molecules involves producing appropriate cells which express the polypeptide, either as a secreted protein or on the cell membrane. Preferred cells include cells from mammals, yeast, Drosophila, or E. coli. Cells expressing the polypeptide or cell membrane fractions which contain the expressed polypeptide are then contacted with a test compound and binding, stimulation, or inhibition of activity of either the polypeptide or the molecule is analyzed. 0 An assay may simply test binding of a candidate compound to the polypeptide, wherein binding is detected by a fluorophore, radioisotope, enzyme conjugate, or other detectable label. Alternatively, the assay may assess binding in the presence of a labeled competitor.
Additionally, the assay can be carried out using cell-free preparations, polypeptide/molecule affixed to a soUd support, chemical libraries, or natural product mixtures. The assay may also simply 5 comprise the steps of mixing a candidate compound with a solution containing a polypeptide, measuring polypeptide/molecule activity or binding, and comparing the polypeptide/molecule activity or binding to a standard.
Preferably, an ELISA assay using, e.g., a monoclonal or polyclonal antibody, can measure polypeptide level in a sample. The antibody can measure polypeptide level by either binding, directly or o indirectly, to the polypeptide or by competing with the polypeptide for a subsfrate.
All of the above assays can be used in a diagnostic or prognostic context. The molecules discovered using these assays can be used to treat disease or to bring about a particular result in a patient (e.g., blood vessel growth) by activating or inhibiting the polypeptide/molecule. Moreover, the assays can discover agents which may inhibit or enhance the production of the polypeptide from 5 suitably manipulated cells or tissues. Transcript Imaging
Another embodiment relates to the use of dithp to develop a transcript image of a tissue or cell type. A transcript image is the collective pattern of gene expression by a particular tissue or cell type under given conditions and at a given time. This pattern of gene expression is defined by the number of 5 expressed genes, their abundance, and their function. Thus the dithp of the present invention may be used to develop a transcript image of a tissue or cell type by hybridizing, preferably in a microarray format, the dithp of the present invention to the totality of transcripts or reverse transcripts of a tissue or cell type. The resultant transcript image would provide a profile of gene activity pertaining to human molecules for diagnostics and therapeutics. o Transcript images which profile dithp expression may be generated using transcripts isolated from tissues, cell lines, biopsies, or other biological samples. The transcript image may thus reflect dithp expression in vivo, as in the case of a tissue or biopsy sample, or in vitro, as in the case of a cell line. Transcript images may be used to profile dithp expression in distinct tissue types. This process can be used to determine the activity of human diagnostic and therapeutic molecules in a particular 5 tissue type relative to this activity in a different tissue type. Transcript images may be used to generate a profile of dithp expression characteristic of diseased tissue. Transcript images of tissues before and after treatment may be used for diagnostic puφoses, to monitor the progression of disease, and to monitor the efficacy of drug treatments for diseases which affect the activity of human diagnostic and therapeutic molecules. o Transcript images which profile dithp expression may also be used in conjunction with in vitro model systems and preclinical evaluation of pharmaceuticals. Transcript images of cell lines can be used to assess the activity of human diagnostic and therapeutic molecules and/or to identify cell lines that lack or misregulate this activity. Such cell lines may then be treated with pharmaceutical agents, and a transcript image following treatment may indicate the efficacy of these agents in restoring desired 5 levels of this activity. A similar approach may be used to assess the toxicity of pharmaceutical agents as reflected by undesirable changes in the activity of human diagnostic and therapeutic molecules. Candidate pharmaceutical agents may be evaluated by comparing their associated transcript images with those of pharmaceutical agents of known effectiveness.
0 Antisense Molecules
The polynucleotides of the present invention are useful in antisense technology. Antisense technology or therapy relies on the modulation of expression of a target protein through the specific binding of an antisense sequence to a target sequence encoding the target protein or directing its expression. (See, e.g., Agrawal, S., ed. (1996) Antisense Therapeutics, Humana Press Inc., Totawa NJ; Alama, A. et al. (1997) Pharmacol. Res. 36(3):171-178; Crooke, S.T. (1997) Adv. Pharmacol. 40:1-49; Sharma, H.W. and R. Narayanan (1995) Bioessays 17(12):1055-1063; and Lavrosky, Y. et al. (1997) Biochem. Mol. Med. 62(1):11-22.) An antisense sequence is a polynucleotide sequence capable of specifically hybridizing to at least a portion of the target sequence. Antisense sequences bind to cellular mRNA and/or genomic DNA, affecting translation and/or franscription. Antisense 5 sequences can be DNA, RNA, or nucleic acid mimics and analogs. (See, e.g., Rossi, J.J. et al. (1991) Antisense Res. Dev. l(3):285-288; Lee, R. et al. (1998) Biochemistry 37(3):900-1010; Pardridge, W.M. et al. (1995) Proc. Nati. Acad. Sci. USA 92(12):5592-5596; and Nielsen, P. E. and Haaima, G. (1997) Chem. Soc. Rev. 96:73-78.) Typically, the binding which results in modulation of expression occurs through hybridization or binding of complementary base pairs. Antisense sequences can also l o bind to DNA duplexes through specific interactions in the major groove of the double helix.
The polynucleotides of the present invention and fragments thereof can be used as antisense sequences to modify the expression of the polypeptide encoded by dithp. The antisense sequences can be produced ex vivo, such as by using any of the ABI nucleic acid synthesizer series (PE Biosystems) or other automated systems known in the art. Antisense sequences can also be produced biologically,
15 such as by fransforming an appropriate host cell with an expression vector containing the sequence of interest. (See, e.g., Agrawal, supra.)
In therapeutic use, any gene deUvery system suitable for introduction of the antisense sequences into appropriate target cells can be used. Antisense sequences can be delivered infracellularly in the form of an expression plasmid which, upon franscription, produces a sequence complementary to at
20 least a portion of the cellular sequence encoding the target protein. (See, e.g., Slater, J.E., et al. (1998) J. Allergy Clin. Immunol. 102(3) .469-475; and Scanlon, K.J., et al. (1995) 9(13):1288-1296.) Antisense sequences can also be introduced infracellularly through the use of viral vectors, such as refrovirus and adeno-associated virus vectors. (See, e.g., Miller, A.D. (1990) Blood 76:271 ; Ausubel, F.M. et al. (1995) Current Protocols in Molecular Biology, John Wiley & Sons, New York NY; Uckert,
25 W. and W. Walther (1994) Pharmacol. Ther. 63(3):323-347.) Other gene delivery mechanisms include liposome-derived systems, artificial viral envelopes, and other systems known in the art. (See, e.g., Rossi, J.J. (1995) Br. Med. Bull. 51(l):217-225; Boado, R.J. et al. (1998) J. Pharm. Sci. 87(11):1308- 1315; and Morris, M.C. et al. (1997) Nucleic Acids Res. 25(14):2730-2736.)
30 Expression
In order to express a biologically active DITHP, the nucleotide sequences encoding DITHP or fragments thereof may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for ttanscriptional and franslational control of the inserted coding sequence in a suitable host. Methods which are well known to those skilled in the art may be used to construct
35 expression vectors containing sequences encoding DITHP and appropriate ttanscriptional and franslational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. (See, e.g., Sambrook, supra. Chapters 4, 8, 16, and 17; and Ausubel, supra. Chapters 9, 10, 13, and 16.)
A variety of expression vector/host systems may be utilized to contain and express sequences encoding DITHP. These include, but are not Umited to, microorganisms such as bacteria fransformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast fransformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems fransformed with viral expression vectors (e.g., cauUflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal (mammaUan) cell systems. (See, e.g., Sambrook, supra; Ausubel, 1995, supra. Van Heeke, G. and S.M. Schuster (1989) J. Biol. Chem. 264:5503-5509; Bitter, G.A. et al. (1987) Methods Enzymol.
153:516-544; Scorer, CA. et al. (1994) Bio/Technology 12:181-184; Engelhard, E.K. et al. (1994)
Proc. Nati. Acad. Sci. USA 91:3224-3227; Sandig, V. et al. (1996) Hum. Gene Ther. 7:1937-1945;
Takamatsu, N. (1987) EMBO J. 6:307-311; Coruzzi, G. et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; Winter, J. et al. (1991) Results Probl. Cell Differ. 17:85-105;
The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York NY, pp.
191-196; Logan, J. and T. Shenk (1984) Proc. Nati. Acad. Sci. USA 81 :3655-3659; and Harrington,
J.J. et al. (1997) Nat. Genet. 15:345-355.) Expression vectors derived from refroviruses, adenoviruses, or heφes or vaccinia viruses, or from various bacterial plasmids, may be used for delivery of nucleotide sequences to the targeted organ, tissue, or cell population. (See, e.g., Di Nicola, M. et al. (1998)
Cancer Gen. Ther. 5(6):350-356; Yu, M. et al., (1993) Proc. Nati. Acad. Sci. USA 90(13):6340-6344;
Buller, R.M. et al. (1985) Nature 317(6040):813-815; McGregor, D.P. et al. (1994) Mol. Immunol.
31(3):219-226; and Verma, I.M. and N. Somia (1997) Nature 389:239-242.) The invention is not
Umited by the host cell employed. For long term production of recombinant proteins in mammalian systems, stable expression of
DITHP in cell Unes is preferred. For example, sequences encoding DITHP can be transformed into cell Unes using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Any number of selection systems may be used to recover fransformed cell lines. (See, e.g., Wigler, M. et al. (1977) Cell 11:223-232; Lowy, I. et al. (1980) Cell 22:817-823.; Wigler, M. et al. (1980) Proc. Nati. Acad. Sci. USA 77:3567-3570; Colbere-Garapin, F. et al. (1981) J. Mol. Biol. 150:1-14; Hartman, S.C and R.CMulligan (1988) Proc. Nati. Acad. Sci. USA 85:8047-8051 ; Rhodes, CA (1995) Methods Mol. Biol. 55:121-131.)
Therapeutic Uses of dithp The dithp of the invention may be used for somatic or germhne gene therapy. Gene therapy may be performed to (i) correct a genetic deficiency (e.g., in the cases of severe combined immunodeficiency (SCID)-Xl disease characterized by X-linked inheritance (Cavazzana-Calvo, M. et al. (2000) Science 288:669-672), severe combined immunodeficiency syndrome associated with an 5 inherited adenosine deaminase (ADA) deficiency (Blaese, R.M. et al. (1995) Science 270:475-480; Bordignon, C et al. (1995) Science 270:470-475), cystic fibrosis (Zabner, J. et al. (1993) Cell 75:207- 216; Crystal, R.G. et al. (1995) Hum. Gene Therapy 6:643-666; Crystal, R.G. et al. (1995) Hum. Gene Therapy 6:667-703), thalassemias, familial hypercholesterolemia, and hemophilia resulting from Factor VIII or Factor IX deficiencies (Crystal, R.G. (1995) Science 270:404-410; Verma, I.M. and Somia, N. 0 (1997) Nature 389:239-242)), (ii) express a conditionally lethal gene product (e.g., in the case of cancers which result from unregulated cell proliferation), or (iii) express a protein which affords protection against infracellular parasites (e.g., against human refroviruses, such as human immunodeficiency virus (HIV) (Baltimore, D. (1988) Nature 335:395-396; Poeschla, E. et al. (1996) Proc. Nati. Acad. Sci. USA. 93:11395-11399), hepatitis B or C virus (HBV, HCV); fungal parasites, 5 such as Candida albicans and Paracoccidioides brasiliensis; and protozoan parasites such as
Plasmodium falciparum and Trvpanosoma cruzi). In the case where a genetic deficiency in dithp expression or regulation causes disease, the expression of dithp from an appropriate population of transduced cells may alleviate the clinical manifestations caused by the genetic deficiency.
In a further embodiment of the invention, diseases or disorders caused by deficiencies in dithp 0 are treated by constructing mammalian expression vectors comprising dithp and introducing these vectors by mechanical means into dithp-deficient cells. Mechanical fransfer technologies for use with cells in vivo or ex vitro include (i) direct DNA microinjection into individual cells, (ii) ballistic gold particle delivery, (iii) liposome-mediated transfection, (iv) receptor-mediated gene fransfer, and (v) the use of DNA fransposons (Morgan, R.A. and Anderson, W.F. (1993) Annu. Rev. Biochem. 62:191-217; 5 Ivies, Z. (1997) Cell 91:501-510; Boulay, J-L. and Recipon, H. (1998) Curr. Opin. Biotechnol. 9:445- 450).
Expression vectors that may be effective for the expression of dithp include, but are not limited to, the PCDNA 3.1, EPITAG, PRCCMV2, PREP, PVAX vectors (Invitrogen, Carlsbad CA), PCMV-SCRIPT, PCMV-TAG, PEGSH/PERV (Stratagene, La Jolla CA), and PTET-OFF, o PTET-ON, PTRE2, PTRE2-LUC, PTK-HYG (Clontech, Palo Alto CA). The dithp of the invention may be expressed using (i) a constitutively active promoter, (e.g., from cytomegalovirus (CMV), Rous sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or β-actin genes), (ii) an inducible promoter (e.g., the tetracycUne-regulated promoter (Gossen, M. and Bujard, H. (1992) Proc. Nati. Acad. Sci. U.S.A. 89:5547-5551 ; Gossen, M. et al., (1995) Science 268:1766-1769; Rossi, F.M.V. and Blau, 5 H.M. (1998) Curr. Opin. Biotechnol. 9:451-456), commercially available in the T-REX plasmid (Invitrogen)); the ecdysone-inducible promoter (available in the plasmids PVGRXR and PIND; Invitrogen); the FK506/rapamycin inducible promoter; or the RU486/mifepristone inducible promoter (Rossi, F.M.V. and Blau, H.M. supra)), or (iii) a tissue-specific promoter or the native promoter of the endogenous gene encoding DITHP from a normal individual. Commercially available liposome transformation kits (e.g., the PERFECT LIPID
TRANSFECTION KIT, available from Invitrogen) allow one with ordinary skill in the art to deliver polynucleotides to target cells in culture and require minimal effort to optimize experimental parameters. In the alternative, fransformation is performed using the calcium phosphate method (Graham, F.L. and Eb, A.J. (1973) Virology 52:456-467), or by electroporation (Neumann, E. et al. (1982) EMBO J. 1:841-845). The introduction of DNA to primary cells requires modification of these standardized mammaUan transfection protocols.
In another embodiment of the invention, diseases or disorders caused by genetic defects with respect to dithp expression are treated by constructing a refrovirus vector consisting of (i) the dithp of the invention under the confrol of an independent promoter or the refrovirus long terminal repeat (LTR) promoter, (ii) appropriate RNA packaging signals, and (iii) a Rev-responsive element (RRE) along with additional refrovirus cw-acting RNA sequences and coding sequences required for efficient vector propagation. Refrovirus vectors (e.g., PFB and PFBNEO) are commercially available (Sfratagene) and are based on published data (Riviere, I. et al. (1995) Proc. Nati. Acad. Sci. U.S.A. 92:6733-6737), incoφorated by reference herein. The vector is propagated in an appropriate vector producing cell Une (VPCL) that expresses an envelope gene with a fropism for receptors on the target cells or a promiscuous envelope protein such as VSVg (Armentano, D. et al. (1987) J. Virol. 61 :1647-1650; Bender, M.A. et al. (1987) J. Virol. 61:1639-1646; Adam, M.A. and Miller, AD. (1988) J. Virol. 62:3802-3806; Dull, T. et al. (1998) J. Virol. 72:8463-8471 ; Zufferey, R. et al. (1998) J. Virol. 72:9873-9880). U.S. Patent Number 5,910,434 to Rigg ("Method for obtaining refrovirus packaging cell lines producing high transducing efficiency retroviral supernatant") discloses a method for obtaining retrovirus packaging cell lines and is hereby incorporated by reference. Propagation of retrovirus vectors, transduction of a population of cells (e.g., CD4+ T-cells), and the return of transduced cells to a patient are procedures well known to persons skilled in the art of gene therapy and have been well documented (Ranga, U. et al. (1997) J. Virol. 71:7020-7029; Bauer, G. et al. (1997) Blood 89:2259-2267; Bonyhadi, M.L. (1997) J. Virol. 71 :4707-4716; Ranga, U. et al. (1998) Proc. Nati. Acad. Sci. U.S.A. 95:1201-1206; Su, L. (1997) Blood 89:2283-2290).
In the alternative, an adenovirus-based gene therapy delivery system is used to deliver dithp to cells which have one or more genetic abnormalities with respect to the expression of dithp. The construction and packaging of adenovirus-based vectors are well known to those with ordinary skill in the art. RepUcation defective adenovirus vectors have proven to be versatile for importing genes encoding immunoregulatory proteins into intact islets in the pancreas (Csete, M.E. et al. (1995) Transplantation 27:263-268). Potentially useful adenoviral vectors are described in U.S. Patent Number 5,707,618 to Armentano ("Adenovirus vectors for gene therapy"), hereby incoφorated by reference. For adenoviral vectors, see also Antinozzi, P.A. et al. (1999) Annu. Rev. Nufr. 19:511-544 and Verma, I.M. and Somia, N. (1997) Nature 18:389:239-242, both incoφorated by reference herein. In another alternative, a heφes-based, gene therapy delivery system is used to deliver dithp to target cells which have one or more genetic abnormalities with respect to the expression of dithp. The use of heφes simplex virus (HSV)-based vectors may be especially valuable for introducing dithp to cells of the cenfral nervous system, for which HSV has a tropism. The construction and packaging of heφes-based vectors are well known to those with ordinary skill in the art. A replication-competent heφes simplex virus (HSV) type 1 -based vector has been used to deliver a reporter gene to the eyes of primates (Liu, X. et al. (1999) Exp. Eye ResJ 69:385-395). The construction of a HSV-1 virus vector has also been disclosed in detail in U.S. Patent Number 5,804,413 to DeLuca ("Heφes simplex virus strains for gene transfer"), which is hereby incoφorated by reference. U.S. Patent Number 5,804,413 teaches the use of recombinant HSV d92 which consists of a genome containing at least one exogenous gene to be transferred to a cell under the confrol of the appropriate promoter for puφoses including human gene therapy. Also taught by this patent are the construction and use of recombinant HSV strains deleted for ICP4, ICP27 and ICP22. For HSV vectors, see also Goins, W. F. et al. 1999 J. Virol. 73:519-532 an Xu, H. et al., (1994) Dev. Biol. 163:152-161, hereby incoφorated by reference. The manipulation of cloned herpesvirus sequences, the generation of recombinant virus following the transfection of multiple plasmids containing different segments of the large herpesvirus genomes, the growth and propagation of heφesvirus, and the infection of cells with heφes virus are techniques well known to those of ordinary skill in the art.
In another alternative, an alphavirus (positive, single-stranded RNA virus) vector is used to deliver dithp to target cells. The biology of the prototypic alphavirus, Semliki Forest Virus (SFV), has been studied extensively and gene transfer vectors have been based on the SFV genome (Garoff, H. and Li, K-J. (1998) Curr. Opin. Biotech. 9:464-469). During alphavirus RNA replication, a subgenomic RNA is generated that normally encodes the viral capsid proteins. This subgenomic RNA replicates to higher levels than the full-length genomic RNA, resulting in the oveφroduction of capsid proteins relative to the viral proteins with enzymatic activity (e.g., protease and polymerase). Similarly, inserting dithp into the alphavirus genome in place of the capsid-coding region results in the production of a large number of dithp RNAs and the synthesis of high levels of DITHP in vector transduced cells. While alphavirus infection is typically associated with cell lysis within a few days, the ability to establish a persistent infection in hamster normal kidney cells (BHK-21) with a variant of Sindbis virus (SIN) indicates that the lytic repUcation of alphaviruses can be altered to suit the needs of the gene therapy application (Dryga, S.A. et al. (1997) Virology 228:74-83). The wide host range of alphaviruses will allow the introduction of DITHP into a variety of cell types. The specific transduction of a subset of cells in a population may require the sorting of cells prior to transduction. The methods of manipulating infectious cDNA clones of alphaviruses, performing alphavirus cDNA 5 and RNA fransfections, and performing alphavirus infections, are well known to those with ordinary skill in the art.
Antibodies
Anti-DITHP antibodies may be used to analyze protein expression levels. Such antibodies o include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, and Fab fragments. For descriptions of and protocols of antibody technologies, see, e.g., Pound, J.D. (1998) Immunochemical Protocols, Humana Press, Totowa, NJ.
The amino acid sequence encoded by the dithp of the Sequence Listing may be analyzed by appropriate software (e.g., LASERGENE NAVIGATOR software, DNASTAR) to determine regions 5 of high immunogenicity. The optimal sequences for immunization are selected from the C-terminus, the N-terminus, and those intervening, hydrophihc regions of the polypeptide which are likely to be exposed to the external environment when the polypeptide is in its natural conformation. Analysis used to select appropriate epitopes is also described by Ausubel (1997, supra. Chapter 11.7). Peptides used for antibody induction do not need to have biological activity; however, they must be antigenic. Peptides o used to induce specific antibodies may have an amino acid sequence consisting of at five amino acids, preferably at least 10 amino acids, and most preferably 15 amino acids. A peptide which mimics an antigenic fragment of the natural polypeptide may be fused with another protein such as keyhole limpet cyanin (KLH; Sigma, St. Louis MO) for antibody production. A peptide encompassing an antigenic region may be expressed from a dithp, synthesized as described above, or purified from human cells. 5 Procedures well known in the art may be used for the production of antibodies. Various hosts including mice, goats, and rabbits, may be immunized by injection with a peptide. Depending on the host species, various adjuvants may be used to increase immunological response.
In one procedure, peptides about 15 residues in length may be synthesized using an ABI 431 A peptide synthesizer (PE Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction 0 with M-maleimidobenzoyl-N-hydroxysuccinimide ester (Ausubel, 1995, supra). Rabbits are immunized with the peptide- KLH complex in complete Freund's adjuvant. The resulting antisera are tested for antipeptide activity by binding the peptide to plastic, blocking with 1 % bovine serum albumin (BSA), reacting with rabbit antisera, washing, and reacting with radioiodinated goat anti-rabbit IgG. Antisera with antipeptide activity are tested for anti-DITHP activity using protocols well known in the 5 art, including ELISA, radioimmunoassay (RIA), and immunoblotting. In another procedure, isolated and purified peptide may be used to immunize mice (about 100 μg of peptide) or rabbits (about 1 mg of peptide). Subsequently, the peptide is radioiodinated and used to screen the immunized animals' B-lymphocytes for production of antipeptide antibodies. Positive cells are then used to produce hybridomas using standard techniques. About 20 mg of peptide is 5 sufficient for labeUng and screening several thousand clones. Hybridomas of interest are detected by screening with radioiodinated peptide to identify those fusions producing peptide-specific monoclonal antibody. In a typical protocol, wells of a multi-well plate (FAST, Becton-Dickinson, Palo Alto, CA) are coated with affinity-purified, specific rabbit-anti-mouse (or suitable anti-species IgG) antibodies at 10 mg/ml. The coated wells are blocked with 1 % BSA and washed and exposed to supernatants from o hybridomas. After incubation, the wells are exposed to radiolabeled peptide at 1 mg/ml.
Clones producing antibodies bind a quantity of labeled peptide that is detectable above background. Such clones are expanded and subjected to 2 cycles of cloning. Cloned hybridomas are injected into pristane-freated mice to produce ascites, and monoclonal antibody is purified from the ascitic fluid by affinity chromatography on protein A (Amersham Pharmacia Biotech). Several 5 procedures for the production of monoclonal antibodies, including in vitro production, are described in Pound (supra). Monoclonal antibodies with antipeptide activity are tested for anti-DITHP activity using protocols well known in the art, including ELISA, RIA, and immunoblotting.
Antibody fragments containing specific binding sites for an epitope may also be generated. For example, such fragments include, but are not limited to, the F(ab')2 fragments produced by pepsin o digestion of the antibody molecule, and the Fab fragments generated by reducing the disulfide bridges of the F(ab')2 fragments. Alternatively, construction of Fab expression libraries in filamentous bacteriophage allows rapid and easy identification of monoclonal fragments with desired specificity (Pound, supra. Chaps. 45-47). Antibodies generated against polypeptide encoded by dithp can be used to purify and characterize full-length DITHP protein and its activity, binding partners, etc. 5
Assays Using Antibodies
Anti-DITHP antibodies may be used in assays to quantify the amount of DITHP found in a particular human cell. Such assays include methods utilizing the antibody and a label to detect expression level under normal or disease conditions. The peptides and antibodies of the invention may 0 be used with or without modification or labeled by joining them, either covalentiy or noncovalently, with a reporter molecule.
Protocols for detecting and measuring protein expression using either polyclonal or monoclonal antibodies are well known in the art. Examples include ELISA, RIA, and fluorescent activated cell sorting (FACS). Such immunoassays typically involve the formation of complexes between the DITHP 5 and its specific antibody and the measurement of such complexes. These and other assays are described in Pound (supra).
Without further elaboration, it is believed that one skilled in the art can, using the preceding description, utilize the present invention to its fullest extent. The following preferred specific embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of 5 the disclosure in any way whatsoever.
The disclosures of all patents, applications, and pubUcations mentioned above and below, in particular U.S. Ser. No. 60/137,109, U.S. Ser. No. 60/137,337, U.S. Ser. No. 60/137,258, U.S. Ser. No. 60/137,260, U.S. Ser. No. 60/137,113, U.S. Ser. No. 60 137,161, U.S. Ser. No. 60/137,417, U.S. Ser. No. 60/137,259, U.S. Ser. No. 60/137,396, U.S. Ser. No. 60/137,114, U.S. Ser. No. 60/137,173, 0 U.S. Ser. No. 60/137,411, U.S. Ser. No. 60/147,436, U.S. Ser. No. 60/147,549, U.S. Ser. No.
60/147,377, U.S. Ser. No. 60/147,527, U.S. Ser. No. 60/147,520, U.S. Ser. No. 60/147,536, U.S. Ser. No. 60/147,530, U.S. Ser. No. 60/147,547, U.S. Ser. No. 60/147,824, U.S. Ser. No. 60/147,541, U.S. Ser. No. 60/147,542, and U.S. Ser. No. 60/147,500, are hereby expressly incoφorated by reference.
5 EXAMPLES
I. Construction of cDNA Libraries
RNA was purchased from CLONTECH Laboratories, Inc. (Palo Alto CA) or isolated from various tissues. Some tissues were homogenized and lysed in guanidinium isothiocyanate, while others were homogenized and lysed in phenol or in a suitable mixture of denaturants, such as TRIZOL (Life o Technologies), a monophasic solution of phenol and guanidine isothiocyanate. The resulting lysates were cenfrifuged over CsCl cushions or extracted with chloroform. RNA was precipitated with either isopropanol or sodium acetate and ethanol, or by other routine methods.
Phenol extraction and precipitation of RNA were repeated as necessary to increase RNA purity. In most cases, RNA was treated with DNase. For most libraries, poly(A+) RNA was isolated 5 using oligo d(T)-coupled paramagnetic particles (Promega Coφoration (Promega), Madison WI),
OLIGOTEX latex particles (QIAGEN, Inc. (QIAGEN), Valencia CA), or an OLIGOTEX mRNA purification kit (QIAGEN). Alternatively, RNA was isolated directly from tissue lysates using other RNA isolation kits, e.g., the POLY(A)PURE mRNA purification kit (Ambion, Inc., Austin TX).
In some cases, Sfratagene was provided with RNA and constructed the corresponding cDNA o libraries. Otherwise, cDNA was synthesized and cDNA libraries were constructed with the UNIZAP vector system (Sfratagene Cloning Systems, Inc. (Sfratagene), La Jolla CA) or SUPERSCRIPT plasmid system (Life Technologies), using the recommended procedures or similar methods known in the art. (See, e.g., Ausubel, 1997, supra, Chapters 5J through 6.6.) Reverse transcription was initiated using oligo d(T) or random primers. Synthetic oligonucleotide adapters were ligated to double 5 stranded cDNA, and the cDNA was digested with the appropriate resfriction enzyme or enzymes. For most libraries, the cDNA was size-selected (300-1000 bp) using SEPHACRYL SI 000, SEPH AROSE CL2B, or SEPH AROSE CL4B column chromatography (Amersham Pharmacia Biotech) or preparative agarose gel elecfrophoresis. cDNAs were ligated into compatible restriction enzyme sites of the polylinker of a suitable plasmid, e.g., PBLUESCRIPT plasmid (Sfratagene), pSPORTl plasmid 5 (Life Technologies), or pINCY (Incyte). Recombinant plasmids were transformed into competent E. coli cells including XLl-Blue, XLl-BlueMRF, or SOLR from Sfratagene or DH5α, DH10B, or ElecfroMAX DH10B from Life Technologies.
II. Isolation of cDNA Clones o Plasmids were recovered from host cells by in vivo excision using the UNIZAP vector system
(Sfratagene) or by cell lysis. Plasmids were purified using at least one of the following: the Magic or WIZARD Minipreps DNA purification system (Promega); the AGTC Miniprep purification kit (Edge BioSystems, Gaithersburg MD); and the QIAWELL 8, QIAWELL 8 Plus, and QIAWELL 8 Ultra plasmid purification systems or the R.E.A.L. PREP 96 plasmid purification kit (QIAGEN). Following 5 precipitation, plasmids were resuspended in 0J ml of distilled water and stored, with or without lyophilization, at 4°C
Alternatively, plasmid DNA was amplified from host cell lysates using direct link PCR in a high-throughput format. (Rao, V.B. (1994) Anal. Biochem. 216:1-14.) Host cell lysis and thermal cycUng steps were carried out in a single reaction mixture. Samples were processed and stored in 384- o well plates, and the concenfration of amplified plasmid DNA was quantified fluoromefrically using
PICOGREEN dye (Molecular Probes, Inc. (Molecular Probes), Eugene OR) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy, Helsinki, Finland).
III. Sequencing and Analysis 5 cDNA sequencing reactions were processed using standard methods or high-throughput instrumentation such as the ABI CATALYST 800 thermal cycler (PE Biosystems) or the PTC-200 thermal cycler (MJ Research) in conjunction with the HYDRA microdispenser (Robbins Scientific Coφ., Sunnyvale CA) or the MICROLAB 2200 liquid fransfer system (Hamilton). cDNA sequencing reactions were prepared using reagents provided by Amersham Pharmacia Biotech or supplied in ABI 0 sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (PE Biosystems). Electrophoretic separation of cDNA sequencing reactions and detection of labeled polynucleotides were carried out using the MEGABACE 1000 DNA sequencing system (Molecular Dynamics); the ABI PRISM 373 or 377 sequencing system (PE Biosystems) in conjunction with standard ABI protocols and base calling software; or other sequence analysis systems known in the art. Reading frames within the cDNA sequences were identified using standard methods (reviewed in Ausubel, 1997, supra. Chapter 1.1). Some of the cDNA sequences were selected for extension using the techniques disclosed in Example VIII.
IV. Assembly and Analysis of Sequences
5 Component sequences from chromatograms were subject to PHRED analysis and assigned a quality score. The sequences having at least a required quaUty score were subject to various preprocessing editing pathways to eUminate, e.g., low quality 3' ends, vector and linker sequences, polyA tails, Alu repeats, mitochondrial and ribosomal sequences, bacterial contamination sequences, and sequences smaller than 50 base pairs. In particular, low-information sequences and repetitive elements 0 (e.g., dinucleotide repeats, Alu repeats, etc.) were replaced by "n's", or masked, to prevent spurious matches.
Processed sequences were then subject to assembly procedures in which the sequences were assigned to gene bins (bins). Each sequence could only belong to one bin. Sequences in each gene bin were assembled to produce consensus sequences (templates). Subsequent new sequences were added to 5 existing bins using BLASTn (v.1.4 WashU) and CROSSMATCH. Candidate pairs were identified as all BLAST hits having a quality score greater than or equal to 150. Alignments of at least 82% local identity were accepted into the bin. The component sequences from each bin were assembled using a version of PHRAP. Bins with several overlapping component sequences were assembled using DEEP PHRAP. The orientation (sense or antisense) of each assembled template was determined based on the o number and orientation of its component sequences. Template sequences as disclosed in the sequence listing correspond to sense strand sequences (the "forward" reading frames), to the best determination. The complementary (antisense) strands are inherently disclosed herein. The component sequences which were used to assemble each template consensus sequence are Usted in Table 4, along with their positions along the template nucleotide sequences. 5 Bins were compared against each other and those having local similarity of at least 82% were combined and reassembled. Reassembled bins having templates of insufficient overlap (less than 95% local identity) were re-split. Assembled templates were also subject to analysis by STITCHER/EXON MAPPER algorithms which analyze the probabilities of the presence of splice variants, alternatively spliced exons, splice junctions, differential expression of alternative spliced genes across tissue types or o disease states, etc. These resulting bins were subject to several rounds of the above assembly procedures.
Once gene bins were generated based upon sequence alignments, bins were clone joined based upon clone information. If the 5' sequence of one clone was present in one bin and the 3' sequence from the same clone was present in a different bin, it was likely that the two bins actually belonged together 5 in a single bin. The resulting combined bins underwent assembly procedures to regenerate the consensus sequences.
The final assembled templates were subsequently annotated using the following procedure. Template sequences were analyzed using BLASTn (v2.0, NCBI) versus gbpri (GenBank version 116). "Hits" were defined as an exact match having from 95% local identity over 200 base pairs through 5 100% local identity over 100 base pairs, or a homolog match having an E-value, i.e. a probability score, of < 1 x 10"8. The hits were subject to frameshift FASTx versus GENPEPT (GenBank version 116). (See Table 5). In this analysis, a homolog match was defined as having an E-value of < 1 x 10J The assembly method used above was described in "System and Methods for Analyzing Biomolecular Sequences," U.S.S.N. 09/276,534, filed March 25, 1999, and the LIFESEQ Gold user manual (Incyte) o both incoφorated by reference herein.
Following assembly, template sequences were subjected to motif, BLAST, and functional analyses, and categorized in protein hierarchies using methods described in, e.g., "Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data," U.S.S.N. 08/812,290, filed March 6, 1997; "Relational Database for Storing Biomolecule Information;' 5 U.S.S.N. 08/947,845, filed October 9, 1997; "Project-Based Full-Length Biomolecular Sequence Database," U.S.S.N. 08/811,758, filed March 6, 1997; and "Relational Database and System for Storing Information Relating to Biomolecular Sequences/' U.S.S.N. 09/034,807, filed March 4, 1998, all of which are incoφorated by reference herein.
The template sequences were further analyzed by translating each template in all three forward o reading frames and searching each franslation against the Pfam database of hidden Markov model- based protein families and domains using the HMMER software package (available to the public from Washington University School of Medicine, St. Louis MO). Regions of templates which, when translated, contain similarity to Pfam consensus sequences are reported in Table 2, along with descriptions of Pfam protein domains and families. Only those Pfam hits with an E-value of < 1 x 10"3 5 are reported. (See also World Wide Web site http://pfam.wustl.edu/ for detailed descriptions of Pfam protein domains and famiUes.)
Additionally, the template sequences were translated in all three forward reading frames, and each translation was searched against hidden Markov models for signal peptide and fransmembrane domains using the HMMER software package. Construction of hidden Markov models and their usage 0 in sequence analysis has been described. (See, for example, Eddy, S.R. (1996) Curr. Opin. Sfr. Biol. 6:361-365.) Regions of templates which, when translated, contain similarity to signal peptide or transmembrane domain consensus sequences are reported in Table 3. Only those signal peptide or transmembrane hits with a cutoff score of 11 bits or greater are reported. A cutoff score of 11 bits or greater corresponds to at least about 91-94% true-positives in signal peptide prediction, and at least 5 about 75 % true-positives in fransmembrane domain prediction. The results of HMMER analysis as reported in Tables 2 and 3 may support the results of BLAST analysis as reported in Table 1 or may suggest alternative or additional properties of template- encoded polypeptides not previously uncovered by BLAST or other analyses.
Template sequences are further analyzed using the bioinformatics tools Usted in Table 5, or using sequence analysis software known in the art such as MACDNASIS PRO software (Hitachi
Software Engineering, South San Francisco CA) and LASERGENE software (DNASTAR). Template sequences may be further queried against public databases such as the GenBank rodent, mammalian, vertebrate, prokaryote, and eukaryote databases.
V. Analysis of Polynucleotide Expression
Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound. (See, e.g., Sambrook, supra, ch. 7; Ausubel, 1995, supra, ch. 4 and 16.) Analogous computer techniques applying BLAST were used to search for identical or related molecules in cDNA databases such as GenBank or LIFESEQ (Incyte Pharmaceuticals). This analysis is much faster than multiple membrane-based hybridizations. In addition, the sensitivity of the computer search can be modified to determine whether any particular match is categorized as exact or similar. The basis of the search is the product score, which is defined as:
BLAST Score x Percent Identity 5 x minimum {length(Seq. 1), length(Seq. 2)}
The product score takes into account both the degree of similarity between two sequences and the length of the sequence match. The product score is a normalized value between 0 and 100, and is calculated as follows: the BLAST score is multiplied by the percent nucleotide identity and the product is divided by (5 times the length of the shorter of the two sequences). The BLAST score is calculated by assigning a score of +5 for every base that matches in a high-scoring segment pair (HSP), and -4 for every mismatch. Two sequences may share more than one HSP (separated by gaps). If there is more than one HSP, then the pair with the highest BLAST score is used to calculate the product score. The product score represents a balance between fractional overlap and quality in a BLAST alignment. For example, a product score of 100 is produced only for 100% identity over the entire length of the shorter of the two sequences being compared. A product score of 70 is produced either by 100% identity and 70% overlap at one end, or by 88% identity and 100% overlap at the other. A product score of 50 is produced either by 100% identity and 50% overlap at one end, or 79% identity and 100% overlap. VI. Tissue Distribution Profiling
A tissue distribution profile is determined for each template by compiling the cDNA library tissue classifications of its component cDNA sequences. Each component sequence, is derived from a 5 cDNA Ubrary constructed from a human tissue. Each human tissue is classified into one of the following categories: cardiovascular system; connective tissue; digestive system; embryonic structures; endocrine system; exocrine glands; genitaha, female; genitaUa, male; germ cells; hemic and immune system; liver; musculoskeletal system; nervous system; pancreas; respiratory system; sense organs; skin; stomatognathic system; unclassified mixed; or urinary tract. Template sequences, component o sequences, and cDNA library/tissue information are found in the LIFESEQ GOLD database (Incyte
Genomics, Palo Alto CA).
VII. Transcript Image Analysis
Transcript images are generated as described in Seilhamer et al., "Comparative Gene 5 Transcript Analysis," U.S. Patent Number 5,840,484, incoφorated herein by reference.
VIII. Extension of Polynucleotide Sequences and Isolation of a Full-length cDNA
Oligonucleotide primers designed using a dithp of the Sequence Listing are used to extend the nucleic acid sequence. One primer is synthesized to initiate 5' extension of the template, and the other o primer, to initiate 3' extension of the template. The initial primers may be designed using OLIGO 4.06 software (National Biosciences, Inc. (National Biosciences), Plymouth MN), or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68 °C to about 72°C Any stretch of nucleotides which would result in haiφin structures and primer-primer dimerizations are avoided. Selected human 5 cDNA libraries are used to extend the sequence. If more than one extension is necessary or desired, additional or nested sets of primers are designed.
High fidelity amplification is obtained by PCR using methods well known in the art. PCR is performed in 96-well plates using the PTC-200 thermal cycler (MJ Research). The reaction mix contains DNA template, 200 nmol of each primer, reaction buffer containing Mg2+, (NH4)2S04, and β- o mercaptoethanol, Taq DNA polymerase (Amersham Pharmacia Biotech), ELONGASE enzyme (Life
Technologies), and Pfu DNA polymerase (Sfratagene), with the following parameters for primer pair PCI A and PCI B: Step 1 : 94°C, 3 min; Step 2: 94°C, 15 sec; Step 3: 60°C, 1 min; Step 4: 68°C, 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68 °C, 5 min; Step 7: storage at 4°C In the alternative, the parameters for primer pair T7 and SK+ are as follows: Step 1 : 94°C, 3 min; Step 2: 5 94°C, 15 sec; Step 3: 57°C, 1 min; Step 4: 68°C, 2 min; Step 5: Steps 2, 3, and 4 repeate 20 times; Step 6: 68 °C, 5 min; Step 7: storage at 4°C
The concentration of DNA in each well is determined by dispensing 100 μl PICOGREEN quantitation reagent (0.25% (v/v); Molecular Probes) dissolved in IX Tris-EDTA (TE) and 0.5 μl of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Incoφorated (Corning), 5 Corning NY), allowing the DNA to bind to the reagent. The plate is scanned in a FLUOROSKAN II (Labsystems Oy) to measure the fluorescence of the sample and to quantify the concentration of DNA. A 5 μl to 10 μl aUquot of the reaction mixture is analyzed by electrophoresis on a 1 % agarose mini-gel to determine which reactions are successful in extending the sequence.
The extended nucleotides are desalted and concentrated, transferred to 384-well plates, o digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison WI), and sonicated or sheared prior to religation into pUC 18 vector (Amersham Pharmacia Biotech). For shotgun sequencing, the digested nucleotides are separated on low concenfration (0.6 to 0.8%) agarose gels, fragments are excised, and agar digested with AGAR ACE (Promega). Extended clones are religated using T4 ligase (New England Biolabs, Inc., Beverly MA) into pUC 18 vector (Amersham 5 Pharmacia Biotech), freated with Pfu DNA polymerase (Sfratagene) to fill-in resfriction site overhangs, and fransfected into competent E. coli cells. Transformed cells are selected on antibiotic-containing media, individual colonies are picked and cultured overnight at 37 °C in 384-well plates in LB/2x carbenicillin liquid media.
The cells are lysed, and DNA is ampUfied by PCR using Taq DNA polymerase (Amersham o Pharmacia Biotech) and Pfu DNA polymerase (Sfratagene) with the following parameters: Step 1 :
94°C, 3 min; Step 2: 94°C, 15 sec; Step 3: 60°C, 1 min; Step 4: 72°C, 2 min; Step 5: steps 2, 3, and 4 repeated 29 times; Step 6: 72°C, 5 min; Step 7: storage at 4°C DNA is quantified by PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries are reamplified using the same conditions as described above. Samples are diluted with 20% dimethysulfoxide (1:2, 5 v/v), and sequenced using DYENAMIC energy fransfer sequencing primers and the DYENAMIC DIRECT kit (Amersham Pharmacia Biotech) or the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (PE Biosystems).
In hke manner, the dithp is used to obtain regulatory sequences (promoters, introns, and enhancers) using the procedure above, oligonucleotides designed for such extension, and an appropriate o genomic library.
IX. Labeling of Probes and Southern Hybridization Analyses
Hybridization probes derived from the dithp of the Sequence Listing are employed for screening cDNAs, mRNAs, or genomic DNA. The labeling of probe nucleotides between 100 and 5 1000 nucleotides in length is specifically described, but essentially the same procedure may be used with larger cDNA fragments. Probe sequences are labeled at room temperature for 30 minutes using a T4 polynucleotide kinase, y2P-ATP, and 0.5X One-Phor-All Plus (Amersham Pharmacia Biotech) buffer and purified using a ProbeQuant G-50 Microcolumn (Amersham Pharmacia Biotech). The probe mixture is diluted to 107 dpm/μg/ml hybridization buffer and used in a typical membrane-based hybridization analysis.
The DNA is digested with a resfriction endonuclease such as Eco RV and is electtophoresed through a 0.7% agarose gel. The DNA fragments are transferred from the agarose to nylon membrane (NYTRAN Plus, Schleicher & Schuell, Inc., Keene NH) using procedures specified by the manufacturer of the membrane. Prehybridization is carried out for three or more hours at 68 °C, and hybridization is carried out overnight at 68 °C To remove non-specific signals, blots are sequentially washed at room temperature under increasingly stringent conditions, up to OJx saline sodium citrate (SSC) and 0.5% sodium dodecyl sulfate. After the blots are placed in a PHOSPHORIMAGER cassette (Molecular Dynamics) or are exposed to autoradiography film, hybridization patterns of standard and experimental lanes are compared. Essentially the same procedure is employed when screening RNA.
X. Chromosome Mapping of dithp
The cDNA sequences which were used to assemble SEQ ID NOJ-52 are compared with sequences from the Incyte LIFESEQ database and public domain databases using BLAST and other implementations of the Smith- Waterman algorithm. Sequences from these databases that match SEQ ID NO: 1 -52 are assembled into clusters of contiguous and overlapping sequences using assembly algorithms such as PHRAP (Table 5). Radiation hybrid and genetic mapping data available from public resources such as the Stanford Human Genome Center (SHGC), Whitehead Institute for Genome Research (WIGR), and Genethon are used to determine if any of the clustered sequences have been previously mapped. Inclusion of a mapped sequence in a cluster will result in the assignment of all sequences of that cluster, including its particular SEQ ID NO:, to that map location. The genetic map locations of SEQ ID NO: 1 -52 are described as ranges, or intervals, of human chromosomes. The map position of an interval, in centiMorgans, is measured relative to the terminus of the chromosome's p- arm. (The centiMorgan (cM) is a unit of measurement based on recombination frequencies between chromosomal markers. On average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA in humans, although this can vary widely due to hot and cold spots of recombination.) The cM distances are based on genetic markers mapped by Genethon which provide boundaries for radiation hybrid markers whose sequences were included in each of the clusters.
XI. Microarray Analysis Probe Preparation from Tissue or Cell Samples Total RNA is isolated from tissue samples using the guanidinium thiocyanate method and polyA+ RNA is purified using the ohgo (dT) cellulose method. Each polyA+ RNA sample is reverse transcribed using MMLV reverse-transcriptase, 0.05 pg/μl oligo-dT primer (21mer), IX first strand buffer, 0.03 units/μl RNase inhibitor, 500 μM dATP, 500 μM dGTP, 500 μM dTTP, 40 μM dCTP, 40 μM dCTP-Cy3 (BDS) or dCTP-Cy5 (Amersham Pharmacia Biotech). The reverse transcription reaction is performed in a 25 ml volume containing 200 ng polyA+ RNA with GEMBRIGHT kits (Incyte). Specific confrol polyA+ RNAs are synthesized by in vitro franscription from non-coding yeast genomic DNA (W. Lei, unpublished). As quantitative confrols, the confrol mRNAs at 0.002 ng, 0.02 ng, 0.2 ng, and 2 ng are diluted into reverse franscription reaction at ratios of 1 : 100,000, 1 : 10,000, 1:1000, 1 : 100 (w/w) to sample mRNA respectively. The confrol mRNAs are diluted into reverse franscription reaction at ratios of 1:3, 3:1, 1:10, 10:1, 1:25, 25:1 (w/w) to sample mRNA differential expression patterns. After incubation at 37° C for 2 hr, each reaction sample (one with Cy3 and another with Cy5 labeUng) is treated with 2.5 ml of 0.5M sodium hydroxide and incubated for 20 minutes at 85° C to the stop the reaction and degrade the RNA. Probes are purified using two successive CHROMA SPIN 30 gel filfration spin columns (CLONTECH Laboratories, Inc. (CLONTECH), Palo Alto CA) and after combining, both reaction samples are ethanol precipitated using 1 ml of glycogen (1 mg/ml), 60 ml sodium acetate, and 300 ml of 100% ethanol. The probe is then dried to completion using a SpeedVAC (Savant Instruments Inc., Holbrook NY) and resuspended in 14 μl 5X SSC/0.2% SDS.
Microarray Preparation
Sequences of the present invention are used to generate array elements. Each array element is amplified from bacterial cells containing vectors with cloned cDNA inserts. PCR amplification uses primers complementary to the vector sequences flanking the cDNA insert. Array elements are amplified in thirty cycles of PCR from an initial quantity of 1 -2 ng to a final quantity greater than 5 μg.
Amplified array elements are then purified using SEPHACRYL-400 (Amersham Pharmacia Biotech).
Purified array elements are immobilized on polymer-coated glass slides. Glass microscope slides (Corning) are cleaned by ultrasound in 0J % SDS and acetone, with extensive distilled water washes between and after treatments. Glass slides are etched in 4% hydrofluoric acid (VWR Scientific Products Coφoration (VWR), West Chester, PA), washed extensively in distilled water, and coated with 0.05% aminopropyl silane (Sigma) in 95% ethanol. Coated slides are cured in a 110°C oven. Array elements are applied to the coated glass substrate using a procedure described in US Patent No. 5,807,522, incoφorated herein by reference. 1 μl of the array element DNA, at an average concentration of 100 ng/μl, is loaded into the open capillary printing element by a high-speed robotic apparatus. The apparatus then deposits about 5 nl of array element sample per slide. Microarrays are UV-crosslinked using a STRATALINKER UV-crosslinker (Sfratagene). Microarrays are washed at room temperature once in 0.2% SDS and three times in distilled water. Non-specific binding sites are blocked by incubation of microarrays in 0.2% casein in phosphate buffered saUne (PBS) (Tropix, Inc., Bedford, MA) for 30 minutes at 60° C followed by washes in 0.2% SDS and distilled water as before.
Hybridization
Hybridization reactions contain 9 μl of probe mixture consisting of 0.2 μg each of Cy3 and Cy5 labeled cDNA synthesis products in 5X SSC, 0.2% SDS hybridization buffer. The probe mixture is heated to 65° C for 5 minutes and is aliquoted onto the microarray surface and covered with an 1.8 cm2 coversUp. The arrays are transferred to a wateφroof chamber having a cavity just slightly larger than a microscope shde. The chamber is kept at 100% humidity internally by the addition of 140 μl of 5x SSC in a corner of the chamber. The chamber containing the arrays is incubated for about 6.5 hours at 60° C The arrays are washed for 10 min at 45° C in a first wash buffer (IX SSC, 0.1 % SDS), three times for 10 minutes each at 45°C in a second wash buffer (0JX SSC), and dried.
Detection
Reporter-labeled hybridization complexes are detected with a microscope equipped with an Innova 70 mixed gas 10 W laser (Coherent, Inc., Santa Clara CA) capable of generating spectral lines at 488 nm for excitation of Cy3 and at 632 nm for excitation of Cy5. The excitation laser light is focused on the array using a 20X microscope objective (Nikon, Inc., Melville NY). The slide containing the array is placed on a computer-controlled X-Y stage on the microscope and raster- scanned past the objective. The 1.8 cm x 1.8 cm array used in the present example is scanned with a resolution of 20 micrometers. In two separate scans, a mixed gas multiline laser excites the two fluorophores sequentially.
Emitted light is split, based on wavelength, into two photomultiplier tube detectors (PMT R1477, Hamamatsu Photonics Systems, Bridgewater NJ) corresponding to the two fluorophores. Appropriate filters positioned between the array and the photomultiplier tubes are used to filter the signals. The emission maxima of the fluorophores used are 565 nm for Cy3 and 650 nm for Cy5. Each array is typically scanned twice, one scan per fluorophore using the appropriate filters at the laser source, although the apparatus is capable of recording the spectra from both fluorophores simultaneously. The sensitivity of the scans is typically calibrated using the signal intensity generated by a cDNA control species added to the probe mix at a known concentration. A specific location on the array contains a complementary DNA sequence, allowing the intensity of the signal at that location to be correlated with a weight ratio of hybridizing species of 1 : 100,000. When two probes from different sources (e.g., representing test and confrol cells), each labeled with a different fluorophore, are hybridized to a single array for the puφose of identifying genes that are differentially expressed, the caUbration is done by labeUng samples of the calibrating cDNA with the two fluorophores and adding identical amounts of each to the hybridization mixture. The output of the photomultiplier tube is digitized using a 12-bit RTI-835H analog-to-digital
(A/D) conversion board (Analog Devices, Inc., Norwood, MA) installed in an IBM-compatible PC computer. The digitized data are displayed as an image where the signal intensity is mapped using a linear 20-color fransformation to a pseudocolor scale ranging from blue (low signal) to red (high signal). The data is also analyzed quantitatively. Where two different fluorophores are excited and measured simultaneously, the data are first corrected for optical crosstalk (due to overlapping emission spectra) between the fluorophores using each fluorophore's emission spectrum.
A grid is superimposed over the fluorescence signal image such that the signal from each spot is centered in each element of the grid. The fluorescence signal within each element is then integrated to obtain a numerical value corresponding to the average intensity of the signal. The software used for signal analysis is the GEMTOOLS gene expression analysis program (Incyte).
XII. Complementary Nucleic Acids
Sequences complementary to the dithp are used to detect, decrease, or inhibit expression of the naturally occurring nucleotide. The use of oUgonucleotides comprising from about 15 to 30 base pairs is typical in the art. However, smaller or larger sequence fragments can also be used. Appropriate oligonucleotides are designed from the dithp using OLIGO 4.06 software (National Biosciences) or other appropriate programs and are synthesized using methods standard in the art or ordered from a commercial suppUer. To inhibit franscription, a complementary oligonucleotide is designed from the most unique 5 ' sequence and used to prevent franscription factor binding to the promoter sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding and processing of the transcript.
XIII. Expression of DITHP
Expression and purification of DITHP is accomplished using bacterial or virus-based expression systems. For expression of DITHP in bacteria, cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA franscription. Examples of such promoters include, but are not limited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator regulatory element. Recombinant vectors are transformed into suitable bacterial hosts, e.g., BL21 (DE3). Antibiotic resistant bacteria express DITHP upon induction with isopropyl beta-D- thiogalactopyranoside (IPTG). Expression of DITHP in eukaryotic cells is achieved by infecting insect or mammaUan cell lines with recombinant Autographica californica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus. The nonessential polyhedrin gene of baculovirus is replaced with cDNA encoding DITHP by either homologous recombination or bacterial-mediated fransposition involving fransfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA transcription. Recombinant baculovirus is used to infect Spodoptera frugiperda (Sf9) insect cells in most cases, or human hepatocytes, in some cases. Infection of the latter requires additional genetic modifications to baculovirus. (See e.g., Engelhard, supra; and Sandig, supra.) In most expression systems, DITHP is synthesized as a fusion protein with, e.g., glutathione S- fransferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crude cell lysates. GST, a 26-kilodalton enzyme from Schistosoma iaponicum, enables the purification of fusion proteins on immobilized glutathione under conditions that maintain protein activity and antigenicity (Amersham Pharmacia Biotech). Following purification, the GST moiety can be proteolytically cleaved from DITHP at specifically engineered sites. FLAG, an 8-amino acid peptide, enables immunoaffinity purification using commercially available monoclonal and polyclonal anti-FLAG antibodies (Eastman Kodak Company, Rochester NY). 6-His, a stretch of six consecutive histidine residues, enables purification on metal-chelate resins (QIAGEN). Methods for protein expression and purification are discussed in Ausubel (1995, supra, Chapters 10 and 16). Purified DITHP obtained by these methods can be used directly in the following activity assay.
XIV. Demonstration of DITHP Activity
DITHP activity is demonstrated through a variety of specific assays, some of which are outlined below.
Oxidoreductase activity of DITHP is measured by the increase in extinction coefficient of NAD(P)H coenzyme at 340 nmfor the measurement of oxidation activity, or the decrease in extinction coefficient of NAD(P)H coenzyme at 340 nmfor the measurement of reduction activity (Dalziel, K. (1963) J. Biol. Chem. 238:2850-2858). One of three substrates may be used: Asn-βGal, biocytidine, or ubiquinone- 10. The respective subunits of the enzyme reaction, for example, cytochtome c_ -b oxidoreductase and cytochrome c, are reconstituted. The reaction mixture contains a) 1-2 mg/ml DITHP; and b) 15 mM subsfrate, 2.4 mM NAD(P)+ in 0.1 M phosphate buffer, pH 7.1 (oxidation reaction), or 2.0 mM NAD(P)H, in 0.1 M Na2HP04 buffer, pH 1.4 ( reduction reaction); in a total volume of 0.1 ml. Changes in absorbance at 340 nm (A340) are measured at 23.5 ° C using a recording specfrophotometer (Shimadzu Scientific Insfruments, Inc., Pleasanton CA). The amount of NAD(P)H is stoichiomettically equivalent to the amount of substrate initially present, and the change in A340 is a direct measure of the amount of NAD(P)H produced; ΔA340 = 6620[NADH]. Oxidoreductase activity of DITHP activity is proportional to the amount of NAD(P)H present in the assay.
Transferase activity of DITHP is measured through assays such as a methyl transferase assay in which the transfer of radiolabeled methyl groups between a donor substrate and an acceptor substrate is measured (Bokar, J.A. et al. (1994) J. Biol. Chem. 269: 17697-17704). Reaction mixtures (50 μl final volume) contain 15 mM HEPES, pH 7.9, 1.5 mM MgCl 2, 10 mM dithiothreitol, 3% polyvinylalcohol, 1.5 μCi [metΛy/-3H]AdoMet (0.375 μM AdoMet) (DuPont-NEN), 0.6 μg DITHP, and acceptor substrate (0.4 μg [35S]RNA or 6-mercaptopurine (6-MP) to 1 mM final concentration). Reaction mixtures are incubated at 30°C for 30 minutes, then 65 °C for 5 minutes. The products are separated by chromatography or elecfrophoresis and the level of methyl fransferase activity is determined by quantification of methyl-3 recovery.
DITHP hydrolase activity is measured by the hydrolysis of appropriate synthetic peptide substrates conjugated with various chromogenic molecules in which the degree of hydrolysis is quantified by specfrophotomefric (or fluoromefric) absoφtion of the released chromophore. (Beynon, RJ. and J.S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University Press, New York NY, pp. 25-55) Peptide substrates are designed according to the category of protease activity as endopeptidase (serine, cysteine, aspartic proteases), animopeptidase (leucine aminopeptidase), or carboxypeptidase (Carboxypeptidase A and B, procollagen C-proteinase). DITHP isomerase activity such as peptidyl prolyl cis/trans isomerase activity can be assayed by an enzyme assay described by Rahfeld, J.U., et al. (1994) (FEBS Lett. 352: 180-184). The assay is performed at 10°C in 35 mM HEPES buffer, pH 7.8, containing chymottypsin (0.5 mg/ml) and DITHP at a variety of concentrations. Under these assay conditions, the substrate, Suc-Ala-Xaa-Pro- Phe-4-NA, is in equilibrium with respect to the prolyl bond, with 80-95% in trans and 5-20% in cis conformation. An aliquot (2 ul) of the substrate dissolved in dimethyl sulfoxide (10 mg/ml) is added to the reaction mixture described above. Only the cis isomer of the substrate is a substrate for cleavage by chymottypsin. Thus, as the substrate is isomerized by DITHP, the product is cleaved by chymottypsin to produce 4-nittOanilide, which is detected by it's absorbance at 390 nm. 4- Nitroanilide appears in a time-dependent and a DITHP concentration-dependent manner. An assay for DITHP activity associated with growth and development measures cell proliferation as the amount of newly initiated DNA synthesis in Swiss mouse 3T3 cells. A plasmid containing polynucleotides encoding DITHP is transfected into quiescent 3T3 cultured cells using methods well known in the art. The transiently fransfected cells are then incubated in the presence of [3H]thymidine, a radioactive DNA precursor. Where applicable, varying amounts of DITHP ligand are added to the fransfected cells. Incoφoration of [3H]thymidine into acid-precipitable DNA is measured over an appropriate time interval, and the amount incoφorated is directly proportional to the amount of newly synthesized DNA.
Growth factor activity of DITHP is measured by the stimulation of DNA synthesis in Swiss mouse 3T3 cells (McKay, I. and I. Leigh, eds. (1993) Growth Factors: A Practical Approach, Oxford 5 University Press, New York NY). Initiation of DNA synthesis indicates the cells' entry into the mitotic cycle and their commitment to undergo later division. 3T3 cells are competent to respond to most growth factors, not only those that are mitogenic, but also those that are involved in embryonic induction. This competence is possible because the in vivo specificity demonstrated by some growth factors is not necessarily inherent but is determined by the responding tissue. In this assay, varying o amounts of DITHP are added to quiescent 3T3 cultured cells in the presence of [3H]thymidine, a radioactive DNA precursor. DITHP for this assay can be obtained by recombinant means or from biochemical preparations. Incoφoration of [3H]thymidine into acid-precipitable DNA is measured over an appropriate time interval, and the amount incoφorated is directly proportional to the amount of newly synthesized DNA. A linear dose-response curve over at least a hundred-fold DITHP 5 concenfration range is indicative of growth factor activity. One unit of activity per milliUter is defined as the concenfration of DITHP producing a 50% response level, where 100% represents maximal incoφoration of [3H]thymidine into acid-precipitable DNA.
Alternatively, an assay for cytokine activity of DITHP measures the proliferation of leukocytes. In this assay, the amount of tritiated thymidine incoφorated into newly synthesized DNA 0 is used to estimate proliferative activity. Varying amounts of DITΗP are added to cultured leukocytes, such as granulocytes, monocytes, or lymphocytes, in the presence of [3H]thymidine, a radioactive DNA precursor. DITHP for this assay can be obtained by recombinant means or from biochemical preparations. Incoφoration of [3H]thymidine into acid-precipitable DNA is measured over an appropriate time interval, and the amount incoφorated is directly proportional to the amount 5 of newly synthesized DNA. A linear dose-response curve over at least a hundred-fold DITHP concentration range is indicative of DITHP activity. One unit of activity per milliliter is conventionally defined as the concenfration of DITHP producing a 50% response level, where 100% represents maximal incoφoration of [3H]thymidine into acid-precipitable DNA.
An alternative assay for DITHP cytokine activity utilizes a Boyden micro chamber o (Neuroprobe, Cabin John MD) to measure leukocyte chemotaxis (Vicari, supra). In this assay, about
105 migratory cells such as macrophages or monocytes are placed in cell culture media in the upper compartment of the chamber. Varying dilutions of DITHP are placed in the lower compartment. The two compartments are separated by a 5 or 8 micron pore polycarbonate filter (Nucleopore, Pleasanton CA). After incubation at 37 °C for 80 to 120 minutes, the filters are fixed in methanol and stained 5 with appropriate labeling agents. Cells which migrate to the other side of the filter are counted using standard microscopy. The chemotactic index is calculated by dividing the number of migratory cells counted when DITHP is present in the lower compartment by the number of migratory cells counted when only media is present in the lower compartment. The chemotactic index is proportional to the activity of DITHP. 5 Alternatively, cell Unes or tissues transformed with a vector containing dithp can be assayed for
DITHP activity by immunoblotting. Cells are denatured in SDS in the presence of β-mercaptoethanol, nucleic acids removed by ethanol precipitation, and proteins purified by acetone precipitation. Pellets are resuspended in 20 mM tris buffer at pH 7.5 and incubated with Protein G-Sepharose pre-coated with an antibody specific for DITHP. After washing, the Sepharose beads are boiled in elecfrophoresis i o sample buffer, and the eluted proteins subjected to SDS-PAGE. The SDS-PAGE is transferred to a nitrocellulose membrane for immunoblotting, and the DITHP activity is assessed by visualizing and quantifying bands on the blot using the antibody specific for DITHP as the primary antibody and 125I- labeled IgG specific for the primary antibody as the secondary antibody.
DITHP kinase activity is measured by phosphorylation of a protein subsfrate using γ-labeled
15 [32P]-ATP and quantitation of the incoφorated radioactivity using a radioisotope counter. DITHP is incubated with the protein subsfrate, [32P]-ATP, and an appropriate kinase buffer. The [32P] incoφorated into the product is separated from free [32P]-ATP by elecfrophoresis and the incoφorated [32P] is counted. The amount of [32P] recovered is proportional to the kinase activity of DITHP in the assay. A determination of the specific amino acid residue phosphorylated is made by
2 o phosphoamino acid analysis of the hydrolyzed protein.
In the alternative, DITHP activity is measured by the increase in cell proliferation resulting from transformation of a mammalian cell line such as COS7, HeLa or CHO with an eukaryotic expression vector encoding DITHP. Eukaryotic expression vectors are commercially available, and the techniques to introduce them into cells are well known to those skilled in the art. The cells are 5 incubated for 48-72 hours after transformation under conditions appropriate for the cell line to allow expression of DITHP. Phase microscopy is then used to compare the mitotic index of transformed versus control cells. An increase in the mitotic index indicates DITHP activity.
In a further alternative, an assay for DITHP signaling activity is based upon the ability of GPCR family proteins to modulate G protein-activated second messenger signal transduction 0 pathways (e.g., cAMP; Gaudin, P. et al. (1998) J. Biol. Chem. 273:4990-4996). A plasmid encoding full length DITHP is fransfected into a mammalian cell line (e.g., Chinese hamster ovary (CHO) or human embryonic kidney (HEK-293) cell lines) using methods well-known in the art. Transfected cells are grown in 12-well trays in culture medium for 48 hours, then the culture medium is discarded, and the attached cells are gently washed with PBS. The cells are then incubated in culture medium 5 with or without ligand for 30 minutes, then the medium is removed and cells lysed by treatment with 1 M perchloric acid. The cAMP levels in the lysate are measured by radioimmunoassay using methods well-known in the art. Changes in the levels of cAMP in the lysate from cells exposed to ligand compared to those without ligand are proportional to the amount of DITHP present in the fransfected cells. 5 Alternatively, an assay for DITHP protein phosphatase activity measures the hydrolysis of P- nifrophenyl phosphate (PNPP). DITHP is incubated together with PNPP in HEPES buffer pH 7.5, in the presence of OJ % β-mercaptoethanol at 37 ° C for 60 min. The reaction is stopped by the addition of 6 ml of 10 N NaOH, and the increase in Ught absorbance of the reaction mixture at 410 nm resulting from the hydrolysis of PNPP is measured using a specfrophotometer. The increase in light absorbance 0 is proportional to the phosphatase activity of DITHP in the assay (Diamond, R.H. et al (1994) Mol Cell Biol 14:3752-3762).
An alternative assay measures DITHP-mediated G-protein signaling activity by monitoring the mobilization of Ca++ as an indicator of the signal transduction pathway stimulation. (See, e.g., Grynkievicz, G. et al. (1985) J. Biol. Chem. 260:3440; McColl, S. et al. (1993) j. Immunol. 5 150:4550-4555; and Aussel, C et al. (1988) J. Immunol. 140:215-220). The assay requires preloading neufrophils or T cells with a fluorescent dye such as FURA-2 or BCECF (Universal Imaging Corp, Westchester PA) whose emission characteristics are altered by Ca++ binding. When the cells are exposed to one or more activating stimuli artificially (e.g., anti-CD3 antibody ligation of the T cell receptor) or physiologically (e.g., by allogeneic stimulation), Ca++ flux takes place. This o flux can be observed and quantified by assaying the cells in a fluorometer or fluorescent activated cell sorter. Measurements of Ca++ flux are compared between cells in their normal state and those fransfected with DITHP. Increased Ca++ mobilization attributable to increased DITHP concenfration is proportional to DITHP activity.
DITHP transport activity is assayed by measuring uptake of labeled substrates into Xenopus 5 laevis oocytes. Oocytes at stages V and VI are injected with DITHP mRNA (10 ng per oocyte) and incubated for 3 days at 18°C in OR2 medium (82.5mM NaCl, 2.5 mM KC1, lmM CaCl2, ImM MgCl2, ImM NaJrIPO.,, 5 mM Hepes, 3.8 mM NaOH, 50μg/ml gentamycin, pH 7.8) to allow expression of DITHP protein. Oocytes are then transferred to standard uptake medium (lOOmM NaCl, 2 mM KC1, ImM CaCl2, ImM MgCl2, 10 mM Hepes/Tris pH 7.5). Uptake of various substrates (e.g., amino o acids, sugars, drugs, ions, and neurofransmitters) is initiated by adding labeled substrate (e.g. radiolabeled with 3H, fluorescently labeled with rhodamine, etc.) to the oocytes. After incubating for 30 minutes, uptake is terminated by washing the oocytes three times in Na+-free medium, measuring the incoφorated label, and comparing with confrols. DITHP fransport activity is proportional to the level of internalized labeled subsfrate. 5 DITHP transferase activity is demonstrated by a test for galactosylttansferase activity. This can be determined by measuring the fransfer of radiolabeled galactose from UDP-galactose to a GlcNAc-terminated oUgosaccharide chain (Kolbinger, F. et al. (1998) J. Biol. Chem. 273:58-65). The sample is incubated with 14 μl of assay stock solution (180 mM sodium cacodylate, pH 6.5, 1 mg/ml bovine serum albumin, 0.26 mM UDP-galactose, 2 μl of UDP-[3H]galactose), 1 μl of MnCl2 (500 mM), and 2.5 μl of GlcNAcβO-(CH2)8-C02Me (37 mg/ml in dimethyl sulfoxide) for 60 minutes at 37 °C. The reaction is quenched by the addition of 1 ml of water and loaded on a C 18 Sep-Pak cartridge (Waters), and the column is washed twice with 5 ml of water to remove unreacted UDP- [Ηjgalactose. The [ΗJgalactosylated GlcNAcβO-(CH2)8-C02Me remains bound to the column during the water washes and is eluted with 5 ml of methanol. Radioactivity in the eluted material is measured by liquid scintillation counting and is proportional to galactosylfransferase activity in the starting sample.
In the alternative, DITHP induction by heat or toxins may be demonstrated using primary cultures of human fibroblasts or human cell lines such as CCL-13, HEK293, or HEP G2 (ATCC). To heat induce DITHP expression, aliquots of cells are incubated at 42 °C for 15, 30, or 60 minutes. Confrol aliquots are incubated at 37 °C for the same time periods. To induce DITHP expression by toxins, aliquots of cells are freated with 100 μM arsenite or 20 mM azetidine-2-carboxylic acid for 0, 3, 6, or 12 hours. After exposure to heat, arsenite, or the amino acid analogue, samples of the treated cells are harvested and cell lysates prepared for analysis by western blot. Cells are lysed in lysis buffer containing 1% Nonidet P-40, 0.15 M NaCl, 50 mM Tris-HCl, 5 mM EDTA, 2 mM N-ethylmaleimide, 2 mM phenylmethylsulfonyl fluoride, 1 mg/ml leupeptin, and 1 mg/ml pepstatin. Twenty micrograms of the cell lysate is separated on an 8% SDS-PAGE gel and transferred to a membrane. After blocking with 5% nonfat dry milk/phosphate- buffered saline for 1 h, the membrane is incubated overnight at 4°C or at room temperature for 2-4 hours with a 1 : 1000 dilution of anti-DITHP serum in 2% nonfat dry milk/phosphate-buffered saline. The membrane is then washed and incubated with a 1 : 1000 dilution of horseradish peroxidase-conjugated goat anti-rabbit IgG in 2% dry milk/phosphate-buffered saline. After washing with 0.1% Tween 20 in phosphate-buffered saline, the DITHP protein is detected and compared to controls using chemiluminescence.
Alternatively, DITHP protease activity is measured by the hydrolysis of appropriate synthetic peptide substrates conjugated with various chromogenic molecules in which the degree of hydrolysis is quantified by spectrophotomefric (or fluoromefric) absoφtion of the released chromophore
(Beynon, R.J. and J.S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University Press, New York, NY, pp.25-55). Peptide substrates are designed according to the category of protease activity as endopeptidase (serine, cysteine, aspartic proteases, or metalloproteases), aminopeptidase (leucine aminopeptidase), or carboxypeptidase (carboxypeptidases A and B, procollagen C-proteinase). Commonly used chromogens are 2-naphthylamine, 4-nitroaniline, and furylacrylic acid. Assays are performed at ambient temperature and contain an aliquot of the enzyme and the appropriate subsfrate in a suitable buffer. Reactions are carried out in an optical cuvette, and the increase/decrease in absorbance of the chromogen released during hydrolysis of the peptide subsfrate is measured. The change in absorbance is proportional to the DITHP protease activity in the 5 assay.
In the alternative, an assay for DITHP protease activity takes advantage of fluorescence resonance energy transfer (FRET) that occurs when one donor and one acceptor fluorophore with an appropriate spectral overlap are in close proximity. A flexible peptide Unker containing a cleavage site specific for PRTS is fused between a red-shifted variant (RSGFP4) and a blue variant (BFP5) of o Green Fluorescent Protein. This fusion protein has specfral properties that suggest energy fransfer is occurring from BFP5 to RSGFP4. When the fusion protein is incubated with DITHP, the subsfrate is cleaved, and the two fluorescent proteins dissociate. This is accompanied by a marked decrease in energy fransfer which is quantified by comparing the emission spectra before and after the addition of DITHP (Mitra, R.D. et al (1996) Gene 173:13-17). This assay can also be performed in living cells. 5 In this case the fluorescent substrate protein is expressed constitutively in cells and DITHP is introduced on an inducible vector so that FRET can be monitored in the presence and absence of DITHP (Sagot, I. et al (1999) FEBS Lett. 447:53-57).
A method to determine the nucleic acid binding activity of DITHP involves a polyacrylamide gel mobility-shift assay. In preparation for this assay, DITHP is expressed by fransforming a o mammalian cell Une such as COS7, HeLa or CHO with a eukaryotic expression vector containing
DITHP cDNA. The cells are incubated for 48-72 hours after fransformation under conditions appropriate for the cell line to allow expression and accumulation of DITHP. Extracts containing solubilized proteins can be prepared from cells expressing DITHP by methods well known in the art. Portions of the extract containing DITHP are added to [32P]-labeled RNA or DNA. Radioactive nucleic 5 acid can be synthesized in vifro by techniques well known in the art. The mixtures are incubated at
25 °C in the presence of RNase- and DNase-inhibitors under buffered conditions for 5-10 minutes. After incubation, the samples are analyzed by polyacrylamide gel electrophoresis followed by autoradiography. The presence of a band on the autoradiogram indicates the formation of a complex between DITHP and the radioactive transcript. A band of similar mobility will not be present in o samples prepared using control extracts prepared from untransformed cells.
In the alternative, a method to determine the methylase activity of a DITHP measures transfer of radiolabeled methyl groups between a donor substrate and an acceptor substrate. Reaction mixtures (50 μl final volume) contain 15 mM HEPES, pH 7.9, 1.5 mM MgCl2, 10 mM dithiothreitol, 3% polyvinylalcohol, 1.5 μCi [met/τy/-Η]AdoMet (0J75 μM AdoMet) (DuPont-NEN), 0.6 μg DITHP, 5 and acceptor substrate (e.g., 0.4 μg [35S]RNA, or 6-mercaptopurine (6-MP) to 1 mM final concenfration). Reaction mixtures are incubated at 30°C for 30 minutes, then 65 °C for 5 minutes. Analysis of [met/ϊyZ-3H]RNA is as follows: 1) 50 μl of 2 x loading buffer (20 mM Tris-HCl, pH 7.6, 1 M LiCl, 1 mM EDTA, 1% sodium dodecyl sulphate (SDS)) and 50 μl oligo d(T)-cellulose (10 mg/ml in 1 x loading buffer) are added to the reaction mixture, and incubated at ambient temperature with shaking for 30 minutes. 2) Reaction mixtures are transferred to a 96-well filfration plate attached to a vacuum apparatus. 3) Each sample is washed sequentially with three 2.4 ml aliquots of 1 x oligo d(T) loading buffer containing 0.5% SDS, 0.1 % SDS, or no SDS. and 4) RNA is eluted with 300 μl of water into a 96-well collection plate, transferred to scintillation vials containing liquid scintillant, and radioactivity determined. Analysis of [methyl-3H]6-MP is as follows: 1) 500 μl 0.5 M borate buffer, pH 10.0, and then 2.5 ml of 20% (v/v) isoamyl alcohol in toluene are added to the reaction mixtures. 2) The samples mixed by vigorous vortexing for ten seconds. 3) After centrifugation at 700g for 10 minutes, 1.5 ml of the organic phase is transferred to scintillation vials containing 0.5 ml absolute ethanol and liquid scintillant, and radioactivity determined, and 4) Results are corrected for the extraction of 6-MP into the organic phase (approximately 41 %). An assay for adhesion activity of DITHP measures the disruption of cytoskeletal filament networks upon overexpression of DITHP in cultured cell lines (Rezniczek, G.A. et al. (1998) J. Cell Biol. 141 :209-225). cDNA encoding DITHP is subcloned into a mammalian expression vector that drives high levels of cDNA expression. This construct is fransfected into cultured cells, such as rat kangaroo PtK2 or rat bladder carcinoma 804G cells. Actin filaments and intermediate filaments such as keratin and vimentin are visualized by immunofluorescence microscopy using antibodies and techniques well known in the art. The configuration and abundance of cytoskeletal filaments can be assessed and quantified using confocal imaging techniques. In particular, the bundling and collapse of cytoskeletal filament networks is indicative of DITHP adhesion activity.
Alternatively, an assay for DITHP activity measures the expression of DITHP on the cell surface. cDNA encoding DITHP is fransfected into a non-leukocytic cell line. Cell surface proteins are labeled with biotin (de la Fuente, M.A. et al. (1997) Blood 90:2398-2405). Immunoprecipitations are performed using DITHP-specific antibodies, and immunoprecipitated samples are analyzed using SDS- PAGE and immunoblotting techniques. The ratio of labeled immunoprecipitant to unlabeled immunoprecipitant is proportional to the amount of DITHP expressed on the cell surface. Alternatively, an assay for DITHP activity measures the amount of cell aggregation induced by overexpression of DITHP. In this assay, cultured cells such as NIH3T3 are fransfected with cDNA encoding DITHP contained within a suitable mammalian expression vector under confrol of a strong promoter. Cofransfection with cDNA encoding a fluorescent marker protein, such as Green Fluorescent Protein (CLONTECH), is useful for identifying stable fransfectants. The amount of cell agglutination, or clumping, associated with fransfected cells is compared with that associated with unfransfected cells. The amount of cell agglutination is a direct measure of DITHP activity.
DITHP may recognize and precipitate antigen from serum. This activity can be measured by the quantitative precipitin reaction (Golub, E.S. et al. (1987) Immunology: A Synthesis, Sinauer Associates, Sunderland MA, pages 113-115). DITHP is isotopically labeled using methods known in 5 the art. Various serum concenfrations are added to constant amounts of labeled DITHP. DITHP- antigen complexes precipitate out of solution and are collected by cenfrifugation. The amount of precipitable DITHP-antigen complex is proportional to the amount of radioisotope detected in the precipitate. The amount of precipitable DITHP-antigen complex is plotted against the serum concentration. For various serum concenfrations, a characteristic precipitation curve is obtained, in o which the amount of precipitable DITHP-antigen complex initially increases proportionately with increasing serum concenfration, peaks at the equivalence point, and then decreases proportionately with further increases in serum concenfration. Thus, the amount of precipitable DITHP-antigen complex is a measure of DITHP activity which is characterized by sensitivity to both limiting and excess quantities of antigen. 5 A microtubule motility assay for DITHP measures motor protein activity. In this assay, recombinant DITHP is immobilized onto a glass slide or similar substrate. Taxol-stabilized bovine brain microtubules (commercially available) in a solution containing ATP and cytosolic extract are perfused onto the shde. Movement of microtubules as driven by DITHP motor activity can be visualized and quantified using video-enhanced light microscopy and image analysis techniques. o DITHP motor protein activity is directly proportional to the frequency and velocity of microtubule movement.
Alternatively, an assay for DITHP measures the formation of protein filaments in vitro. A solution of DITHP at a concenfration greater than the "critical concenfration" for polymer assembly is applied to carbon-coated grids. Appropriate nucleation sites may be supplied in the solution. The 5 grids are negative stained with 0.7% (w/v) aqueous uranyl acetate and examined by electron microscopy. The appearance of filaments of approximately 25 nm (microtubules), 8 nm (actin), or 10 nm (intermediate filaments) is a demonstration of protein activity.
DITHP electron transfer activity is demonstrated by oxidation or reduction of NADP.
Substrates such as Asn-βGal, biocytidine, or ubiquinone-10 may be used. The reaction mixture 0 contains 1-2 mg/ml HORP, 15 mM substrate, and 2.4 mM NAD(P)+ in 0J M phosphate buffer, pH
7J (oxidation reaction), or 2.0 mM NAD(P)H, in 0J M Na2HP04 buffer, pH 7.4 (reduction reaction); in a total volume of 0.1 ml. FAD may be included with NAD, according to methods well known in the art. Changes in absorbance are measured using a recording specfrophotometer. The amount of
NAD(P)H is stoichiomefrically equivalent to the amount of substrate initially present, and the change in 5 A340 is a direct measure of the amount of NAD(P)H produced; ΔA340 = 6620[NADH]. DITHP activity is proportional to the amount of NAD(P)H present in the assay. The increase in extinction coefficient of NAD(P)H coenzyme at 340 nm is a measure of oxidation activity, or the decrease in extinction coefficient of NAD(P)H coenzyme at 340 nm is a measure of reduction activity (Dalziel, K. (1963) J. Biol. Chem. 238:2850-2858). 5 DITHP franscription factor activity is measured by its ability to stimulate franscription of a reporter gene (Liu, H.Y. et al. (1997) EMBO J. 16:5289-5298). The assay entails the use of a well characterized reporter gene construct, LexA^-LacZ, that consists of LexA DNA franscriptional control elements (LexA^) fused to sequences encoding the E. coli LacZ enzyme. The methods for constructing and expressing fusion genes, introducing them into cells, and measuring LacZ enzyme activity, are well 0 known to those skilled in the art. Sequences encoding DITHP are cloned into a plasmid that directs the synthesis of a fusion protein, LexA-DITHP, consisting of DITHP and a DNA binding domain derived from the LexA franscription factor. The resulting plasmid, encoding a LexA-DITHP fusion protein, is introduced into yeast cells along with a plasmid containing the LexA^-LacZ reporter gene. The amount of LacZ enzyme activity associated with LexA-DITHP fransfected cells, relative to confrol cells, is 5 proportional to the amount of franscription stimulated by the DITHP.
Chromatin activity of DITHP is demonstrated by measuring sensitivity to DNase I (Dawson, B.A. et al. (1989) J. Biol. Chem. 264:12830-12837). Samples are freated with DNase I, followed by insertion of a cleavable biotinylated nucleotide analog, 5-[(N-biotinamido)hexanoamido-ethyl-l,3- thiopropionyl-3-aminoallyl]-2'-deoxyuridine 5 -friphosphate using nick-repair techniques well known to o those skilled in the art. Following purification and digestion with EcoRI resfriction endonuclease, biotinylated sequences are affinity isolated by sequential binding to sfreptavidin and biotincellulose.
Another specific assay demonstrates the ion conductance capacity of DITHP using an elecfrophysiological assay. DITHP is expressed by transforming a mammalian cell line such as COS7, HeLa or CHO with a eukaryotic expression vector encoding DITHP. Eukaryotic expression 5 vectors are commercially available, and the techniques to introduce them into cells are well known to those skilled in the art. A small amount of a second plasmid, which expresses any one of a number of marker genes such as β-galactosidase, is co-transformed into the cells in order to allow rapid identification of those cells which have taken up and expressed the foreign DNA. The cells are incubated for 48-72 hours after transformation under conditions appropriate for the cell line to allow o expression and accumulation of DITHP and β-galactosidase. Transformed cells expressing β- galactosidase are stained blue when a suitable colorimetric substrate is added to the culture media under conditions that are well known in the art. Stained cells are tested for differences in membrane conductance due to various ions by elecfrophysiological techniques that are well known in the art. Untransformed cells, and/or cells transformed with either vector sequences alone or β-galactosidase 5 sequences alone, are used as controls and tested in parallel. The confribution of DITHP to cation or anion conductance can be shown by incubating the cells using antibodies specific for either DITHP. The respective antibodies will bind to the extracellular side of DITHP, thereby blocking the pore in the ion channel, and the associated conductance.
5 XV. Functional Assays
DITHP function is assessed by expressing dithp at physiologically elevated levels in mammaUan cell culture systems. cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression. Vectors of choice include pCMV SPORT (Life Technologies) and pCR3.1 (Invitrogen Coφoration, Carlsbad CA), both of which contain the o cytomegalovirus promoter. 5- 10 μg of recombinant vector are transiently ttansfected into a human cell
Une, preferably of endothelial or hematopoietic origin, using either liposome formulations or electroporation. 1-2 μg of an additional plasmid containing sequences encoding a marker protein are co-fransfected.
Expression of a marker protein provides a means to distinguish fransfected cells from 5 nonfransfected cells and is a reliable predictor of cDNA expression from the recombinant vector. Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP; CLONTECH), CD64, or a CD64-GFP fusion protein. Flow cytomefry (FCM), an automated laser optics-based technique, is used to identify ttansfected cells expressing GFP or CD64-GFP and to evaluate the apoptotic state of the cells and other cellular properties. o FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death. These events include changes in nuclear DNA content as measured by staining of DNA with propidium iodide; changes in cell size and granularity as measured by forward light scatter and 90 degree side light scatter; down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intracellular 5 proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods in flow cytomefry are discussed in Ormerod, M. G. (1994) Flow Cytomefry, Oxford, New York NY.
The influence of DITHP on gene expression can be assessed using highly purified populations 0 of cells ttansfected with sequences encoding DITHP and either CD64 or CD64-GFP. CD64 and
CD64-GFP are expressed on the surface of ttansfected cells and bind to conserved regions of human immunoglobulin G (IgG). Transfected cells are efficiently separated from nonfransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Inc., Lake Success NY). mRNA can be purified from the cells using methods well known by those of skill in the art. Expression of mRNA encoding DITHP and other genes of interest can be analyzed by northern analysis or microarray techniques.
XVI. Production of Antibodies
DITHP substantially purified using polyacrylamide gel elecfrophoresis (PAGE; see, e.g., Harrington, M.G. (1990) Methods Enzymol. 182:488-495), or other purification techniques, is used to immunize rabbits and to produce antibodies using standard protocols.
Alternatively, the DITHP amino acid sequence is analyzed using LASERGENE software (DNASTAR) to determine regions of high immunogenicity, and a corresponding peptide is synthesized and used to raise antibodies by means known to those of skill in the art. Methods for selection of appropriate epitopes, such as those near the C-terminus or in hydrophihc regions are well described in the art. (See, e.g., Ausubel, 1995, supra. Chapter 11.)
Typically, peptides 15 residues in length are synthesized using an ABI 431 A peptide synthesizer (PE Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction with N- maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increase immunogenicity. (See, e.g., Ausubel, supra.) Rabbits are immunized with the peptide- KLH complex in complete Freund's adjuvant. Resulting antisera are tested for antipeptide activity by, for example, binding the peptide to plastic, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radioiodinated goat anti-rabbit IgG. Antisera with antipeptide activity are tested for anti-DITHP activity using protocols well known in the art, including ELISA, RIA, and immunoblotting.
XVII. Purification of Naturally Occurring DITHP Using Specific Antibodies
Naturally occurring or recombinant DITHP is substantially purified by immunoaffinity chromatography using antibodies specific for DITHP. An immunoaffinity column is constructed by covalentiy coupling anti-DITHP antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupling, the resin is blocked and washed according to the manufacturer's instructions.
Media containing DITHP are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of DITHP (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/DITHP binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and DITHP is collected.
XVIII. Identification of Molecules Which Interact with DITHP
DITHP, or biologically active fragments thereof, are labeled with 125I Bolton-Hunter reagent. (See, e.g., Bolton, AE. and W.M. Hunter (1973) Biochem. J. 133:529-539.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled DITHP, washed, and any wells with labeled DITHP complex are assayed. Data obtained using different concenfrations of DITHP are used to calculate values for the number, affinity, and association of DITHP with the candidate molecules. 5 Alternatively, molecules interacting with DITHP are analyzed using the yeast two-hybrid system as described in Fields, S. and O. Song (1989) Nature 340:245-246, or using commercially available kits based on the two-hybrid system, such as the MATCHMAKER system (CLONTECH). DITHP may also be used in the PATHCALLING process (CuraGen Coφ., New Haven CT) which employs the yeast two-hybrid system in a high-throughput manner to determine all interactions o between the proteins encoded by two large libraries of genes (Nandabalan, K. et al. (2000) U.S. Patent
No. 6,057,101).
All pubUcations and patents mentioned in the above specification are herein incoφorated by reference. Various modifications and variations of the described method and system of the invention 5 will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the above-described modes for carrying out the invention which are obvious to those skilled in the field of molecular biology or related fields are intended to be within the o scope of the following claims.
TABLE 1
SEQ ID NO: Template ID Gl Number Probability Score Annotation 1 061149.1.J g3073775 3.20E-31 heparan-sulfate 6-sulfotransferase
2 404508.3.j g55535 1.30E-35 100 kDa protein 3 441227.2 g2896147 0 Human alpha-methylacyl-CoA racemase mRNA, complete cds. 4 277927.2 g2708639 2.80E-49 carbonic anhydrase precursor 5 475311.1 g6815284 0 Homo sapiens methionine adenosyltransferase regulatory beta subunit mRNA, complete cds.
6 13039.2 g35790 1.70E-12 protein-tyrosine phosphatase 7 238005.4 g4321όl9 9.40E-96 seven transmembrane domain orphan receptor 8 345322. l.j g206352 1.50E-15 protein phosphatase inhibitor- 1 protein 9 348094.6.J g3876117 3.80E-77 similarity to mouse nekl protein kinase 10 233678.1 gόl 79911 0 Homo sapiens ADP-ribosylation factor binding protein GGA1 (GGA1) mRNA, complete cds.
1 1 312243.1 g3925265 6.90E-21 similar to Probable rabGAP domains
12 425487.3 g6179913 1.00E-154 Homo sapiens ADP-ribosylation factor binding protein GGA2 (GGA2) mRNA, complete cds.
13 346813.3. j g2088550 Human hereditary haemochromatosis region, histone 2A-like protein gene, hereditary haemochromatosis (HLA-H) gene, RoRet gene, and sodium phosphate transporter (NPT3) gene, complete cds.
14 006861.l.j g1263080 4.00E-52 Human marinerl transposase gene, complete consensus sequence.
15 028008.3.j g2463648 5.00E-37 snRNP core Sm protein homolog Sm-X5
16 346078.5.J g3746839 0 Human 45kDa splicing factor mRNA, complete cds.
17 394637. l.j g1263080 0 Human marinerl transposase gene, complete consensus sequence.
18 222429.3 g337451 1.90E-17 hnRNP type A/B protein
19 366739.2 g5524926 0 Homo sapiens mRNA for deoxyribonuclease III (drn3 gene).
20 474635.6 g3880433 4.90E-16 similar to mitochondrial RNA splicing MSR4 like protein; cDNA EST EMBLC09217 comes from this gene
21 228470.1 j g514373 1.00E-80 Opioid-binding cell adhesion molecule
22 407090.5.J g500858 1.20E-10 50 kDa lectin
23 068194. l.j g397947 1.40E-23 thioredoxin
24 411449.2 g5295993 0 Homo sapiens SDHD gene for small subunit of cytochrome b of succinate dehydrogenase, complete cds.
TABLE 1 emplate ID Gl Number Probability Score Annotation
18549.2 g4455608 1.50E-20 dJ742C19.2 (APOBECl (Apolipoprotein B mRNA editing protein) and Phorbolin 1
LIKE)
236043.3 g562263 1.20E-94 fropomodulin
445433.2 g28251 6.00E-25 Human mRNA for beta-actin.
344630.7.J g40828 5.40E-30 Hyd gamma (homologous to the periplasmic hydrogenase)
257121.2 g550123 2 JOE-163 GEG-154
243794. l.j g36131 0 Human mRNA for ribosomal protein L32.
442085.1 j g437878 4.50E-25 ribosomal protein S24
370661.3.J gl016712 1.40E-28 Fos-related antigen
427939.17.J g488555 1.20E-85 zinc finger protein ZNF135
430569.2 g487784 9.00E-16 Human zinc finger protein ZNF136.
444689.1 j g487784 1.00E-26 Human zinc finger protein ZNF136.
445198. l.j g498152 3.70E-35 ha0946 protein is Kruppel-related
84399.1 g207696 2.80E-17 zinc finger protein
350044.1 g1613847 5.00E-10 Human zinc finger protein zfpό (ZF6) mRNA, partial cds.
441329.2 g3006231 4.10E-78 Zn-finger-like protein; similar to Z98745 (PID:g2924250)
442401.2 g498722 4.00E-62 Human HZF2 mRNA for zinc finger protein.
444933.2 g456269 1.80E-20 zinc finger protein 30
481129.4 g3876716 3.10E-15 similar to Zinc finger, C3HC4 type (RING finger)
481999.1 g4519269 3.00E-45 Human ZK1 mRNA for Kruppel-type zinc finger protein, complete cds.
233814. l.j g1326367 7.50E-11 Similar to the mitochondrial carrier family
351376.4.J g517226 7.40E-15 mitochondrial ATPase inhibitor
338992.1 g414797 2.80E-253 pyruvate dehydrogenase phosphatase
200587.3.J g722379 7.50E-23 similar to NIFS protein (nitrogen fixation)
246727.5.J g33745ό 4.00E-25 Human ribonucleoprotein (La) mRNA, 3' end.
407087.3.J gl 176422 7.40E-72 rhophilin
441779. l.j g1304381 8.10E-56 hemoglobin alpha chain
206603.1 g4101720 4.00E-14 lymphocyte specific formin related protein
435694.2 g4572570 3.00E-22 Homo sapiens jun dimerization protein gene, partial cds; cfos gene, complete cds; and unknown gene.
TABLE 2
SEQ ID NO: Template ID Start Stop Frame Pfam Hit Pfam Description E-value
6 13039.2 568 801 forward 1 fn3 Fibronectin type III domain 3.00E-09
9 348094.6.J 255 779 forward 3 pkinase Eukaryotic protein kinase domain 1.10E-53
9 348094.6.J 782 967 forward 2 pkinase Eukaryotic protein kinase domain 2.70E-08
10 233678.1 149 514 forward 2 VHS VHS domain 1.30E-06
1 1 312243.1 703 1263 forward 1 TBC TBC domain 2.20E-07
12 425487.3 78 407 forward 3 VHS VHS domain 2.90E-09
16 346078.5.j 844 978 forward 1 G-patch G-patch domain 8.00E-08
20 474635.6 258 530 forward 3 mito_carr Mitochondrial carrier proteins 4.10E-17
20 474635.6 2449 2652 forward 1 mito_carr Mitochondrial carrier proteins 2.40E-10
21 228470.1.j 312 515 forward 3 ig Immunoglobulin domain 6.20E-08
29 257121 .2 344 541 forward 2 IBR IBR domain 7.70E-23
30 243794. l .j 456 740 forward 3 Ribosomal_L32e Ribosomal protein L32 8.00E-20
30 243794.1 .j 231 326 forward 3 Ribosomal_S14 Ribosomal protein S14p/S29e 1 .40E-12
31 442085.1 .j 149 400 forward 2 Ribosomal_S24e Ribosomal protein S24e 4.70E-40
_ 33 427939.17.J 1002 1070 forward 3 zf-C2H2 Zinc finger, C2H2 type 1 .70E-07
--4
33 427939.17.j 589 657 forward 1 zf-C2H2 Zinc finger, C2H2 type 4.80E-07
35 444689.1 j 170 274 forward 2 KRAB KRAB box 8.70E-06
36 445198. l .j 80 268 forward 2 KRAB KRAB box 2.90E-42
38 350044.1 76 240 forward 1 KRAB KRAB box 4.40E-12
38 350044.1 895 963 forward 1 zf-C2H2 Zinc finger, C2H2 type 8.40E-06
39 441329.2 684 965 forward 3 SCAN SCAN domain 5.30E-48
40 442401.2 206 394 forward 2 KRAB KRAB box 2.40E-41
41 444933.2 292 480 forward 1 KRAB KRAB box 1.40E-41
43 481999.1 371 547 forward 2 KRAB KRAB box 1.90E-15
43 481999.1 839 907 forward 2 zf-C2H2 Zinc finger, C2H2 type 1 .40E-04
44 233814. l .j 356 625 forward 2 mito_carr Mitochondrial carrier proteins 2.10E-19
46 338992.1 1 156 1680 forward 1 PP2C Protein phosphatase 2C 1.90E-54
46 338992.1 840 1 184 forward 3 PP2C Protein phosphatase 2C 3.30E-10
47 200587.3. j 146 1276 forward 2 aminotran_5 Aminotransferases class-V 3.20E-32
50 441779. l .j 76 498 forward 1 globin Globin 4.20E-53
TABLE 3
SEQ ID NO: Template ID Start Stop Frame Domain Type
2 404508.3.J 468 548 reverse 3 TM
2 404508.3.J 549 626 forward 3 SP
2 404508.3.J 348 428 reverse 3 TM
2 404508.3J 430 513 reverse 1 SP
2 404508.3.J 459 539 forward 3 TM
3 441227.2 523 606 forward 1 SP
6 13039.2 1507 1581 forward 1 TM
7 238005.4 887 973 forward 2 SP
7 238005.4 1691 1783 forward 2 SP
7 238005.4 1583 1678 forward 2 SP
7 238005.4 566 643 forward 2 TM
9 348094.6.J 1994 2077 forward 2 TM
9 348094.6.J 1871 1948 reverse 2 TM
9 348094.6.J 2046 21 17 forward 3 TM
9 348094.6 21 12 2195 reverse 3 TM
9 348094.6.J 2035 21 15 forward 1 TM
9 348094.6.J 2920 3000 forward 1 TM
10 233678.1 2412 2495 forward 3 SP
1 1 312243.1 528 614 forward 3 SP
16 346078.5 1406 1492 forward 2 TM
17 394637. l .j 36 122 forward 3 TM
18 222429.3 646 726 forward 1 SP
19 366739.2 791 880 forward 2 SP
19 366739.2 1 1 15 1207 forward 2 SP
20 474635.6 1293 1370 forward 3 TM
22 407090.5.J 2955 3038 reverse 3 SP
24 41 1449.2 283 366 forward 1 SP
27 445433.2 123 203 forward 3 TM
29 257121.2 3656 3736 forward 2 TM
29 257121.2 851 934 forward 2 TM
46 338992.1 1601 1690 forward 2 SP
46 338992.1 1478 1561 forward 2 SP
TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
4 277927.2 2706884H1 1 199
4 277927.2 4317170F6 1 384
4 277927.2 2706884F6 1 320
4 277927.2 g1062337 36 388
4 277927.2 gl064195 39 230
4 277927.2 2862653H1 42 117
4 277927.2 494376H1 53 305
4 277927.2 494376R7 53 383
4 277927.2 494376R6 53 492
4 277927.2 g1275473 57 586
4 277927.2 g2055898 59 543
4 277927.2 2707487H1 64 162
4 277927.2 491071H1 74 319
4 277927.2 g1975146 80 403
4 277927.2 g1142488 84 471
4 277927.2 g1839772 84 214
4 277927.2 gl012520 84 292
4 277927.2 3396290H1 86 344
4 277927.2 5896091 HI 246 523
4 277927.2 g946240 246 551
4 277927.2 g943428 247 449
5 475311.1 1948746H1 1 233
5 475311.1 go14088 12 271
5 475311.1 5644994H1 32 287
5 475311.1 g645077 37 260
5 475311.1 g668814 40 366
5 475311.1 g645713 42 263
5 475311.1 g645045 42 359
5 475311.1 4297187H1 46 315
5 475311.1 3486028H1 53 385
5 475311.1 g683448 54 438
5 475311.1 g645139 54 252
5 475311.1 g645138 54 316
5 475311.1 g670408 54 433
5 475311.1 g646240 56 444
5 475311.1 g562499 56 444
5 475311.1 g4113162 56 511
5 475311.1 g2003099 59 473
5 475311.1 g815985 71 481
5 475311.1 g674342 77 421
5 475311.1 4151149H1 88 355
5 475311.1 3843963H1 88 393
5 475311.1 5029373H1 92 346
5 475311.1 3584334H1 98 435
5 475311.1 g3015753 105 441
5 475311.1 g831378 105 457
5 475311.1 g900504 105 401
5 475311.1 g817737 105 402
5 475311.1 g817003 105 418
5 475311.1 gδ12268 105 397 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
5 475311. 1 g2052991 105 462
5 475311. 1 g3922575 105 509
5 475311. 1 g2884797 105 548
5 475311. 1 g2354824 105 375
5 475311. 1 g2788503 105 214
5 475311. 1 g797560 105 342
5 475311. 1 g820611 105 346
5 475311. 1 g821223 105 347
5 475311. 1 g1678742 138 543
5 475311. 1 5590296H1 150 396
5 475311. 1 2446939H1 155 407
5 475311. 1 4178404H1 164 434
5 475311. 1 4970343H1 179 455
5 475311. 1 g1720508 218 502
5 475311. 4816085H1 242 326
5 475311. g1296172 248 789
5 475311. 5778021 HI 256 544
5 475311. 1579546F6 263 712
5 475311. 1227469H1 263 535
5 475311. 1951396H1 287 527
5 475311. g19807 1 307 631
5 475311. 3369048H1 322 455
5 475311. 261669H1 325 559
5 475311. 1005556H1 344 651
5 475311. g1987083 364 686
5 475311.1 3153327H1 364 683
5 475311.1 5086472H1 372 552
5 475311.1 g2038507 365 782
5 475311.1 3791124H1 366 623
5 475311.1 3342191 HI 383 665
5 475311.1 2727001 HI 403 658
5 475311.1 5691335H1 421 697
5 475311.1 2246168H1 434 702
5 475311.1 4186012H1 582 933
5 475311.1 2630947H1 653 899
5 475311.1 g1444007 793 1005
6 13039.2 4189083H1 3573 3883
6 13039.2 g3802900 3582 3888
6 13039.2 2881380H1 3588 3897
6 13039.2 g864431 3590 3852
6 13039.2 g1481926 3594 3881
6 13039.2 g667472 3600 3883
6 13039.2 g3154327 3607 3891
6 13039.2 4583956H1 3611 3880
6 13039.2 g776778 3615 3887
6 13039.2 2381092H1 3622 3854
6 13039.2 3810284H1 3623 3895
6 13039.2 4906362H2 3624 3904
6 13039.2 2202368H1 3632 3875
6 13039.2 g4072852 3636 4070 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
6 13039.2 2561132H1 3646 3748
6 13039.2 1294323F1 3648 3884
6 13039.2 1294323H1 3648 3780
6 13039.2 446234H1 3649 3871
6 13039.2 4774923H1 3650 3935
6 13039.2 g789650 3651 3882
6 13039.2 g1220073 3652 3888
6 13039.2 g776622 3658 3886
6 13039.2 g1522080 3663 3883
6 13039.2 449477H1 3667 3875
6 13039.2 2293709H1 3669 3884
6 13039.2 gl 114992 3695 3885
6 13039.2 g667182 3700 3883
6 13039.2 gl 162269 3703 4063
6 13039.2 g1773892 3703 4081
6 13039.2 g3887238 3705 4083
6 13039.2 3542520H1 3707 3870
6 13039.2 4633040H1 3727 4003
6 13039.2 gl!28515 3763 4081
6 13039.2 2804481 HI 3793 3899
6 13039.2 556467R6 3816 3871
6 13039.2 556467H1 3816 3871
6 13039.2 g683155 3819 4075
6 13039.2 g878104 3824 4075
6 13039.2 2945643H1 3841 4076
6 13039.2 g821501 3869 4087
6 13039.2 g782508 3869 4083
6 13039.2 2590326H2 4016 4075
6 13039.2 4535971T6 1081 1596
6 13039.2 2887511 HI 1137 1386
6 13039.2 5060591 HI 1078 1278
6 13039.2 2261086H1 1154 1385
6 13039.2 3535673H1 1214 1493
6 13039.2 1951291H1 1264 1453
6 13039.2 488798H1 1330 1587
6 13039.2 2634402H1 1381 1594
6 13039.2 2135368H1 1421 1684
6 13039.2 2135368F6 1421 1863
6 13039.2 2837860T6 3920 4029
6 13039.2 2837860F6 3927 4069
6 13039.2 2837860H1 3927 4069
6 13039.2 3536266H1 3936 4027
6 13039.2 3536268H1 3937 4038
6 13039.2 g776777 3055 3279
6 13039.2 g1856268 3100 3505
6 13039.2 2604507H1 3110 3384
6 13039.2 5065865H1 3071 3344
6 13039.2 3472443H1 3077 3330
6 13039.2 5017370H1 3114 3384
6 13039.2 2767212H1 3090 3334 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
6 13039.2 790129R1 3121 3597
6 13039.2 2690375H1 3094 3357
6 13039.2 2411049H1 3099 3334
6 13039.2 g1976982 1594 1956
6 13039.2 2642416H1 1599 1728
6 13039.2 g1476955 1606 2005
6 13039.2 g1062967 1606 1901
6 13039.2 gl481925 1606 1784
6 13039.2 3136852H1 1738 2037
6 13039.2 2500241 HI 1778 2029
6 13039.2 2788782H1 1863 2121
6 13039.2 874642H1 1862 2024
6 13039.2 g1200951 1869 2062
6 13039.2 4535987H1 1879 2008
6 13039.2 4536041 HI 1884 2151
6 13039.2 1921318T6 3558 4028
6 13039.2 g2458968 3562 3880
6 13039.2 3434402H1 1 237
6 13039.2 g1774870 25 371
6 13039.2 5090377H1 28 270
6 13039.2 5090377F6 28 341
6 13039.2 g2243533 71 456
6 13039.2 4535971 HI 377 641
6 13039.2 4535971F6 377 900
6 13039.2 2738090H1 634 871
6 13039.2 2738090F6 634 1152
6 13039.2 4032617H1 652 788
6 13039.2 3247382H1 687 986
6 13039.2 2886124H1 2974 3263
6 13039.2 2886134H1 2974 3255
6 13039.2 2882975H1 2974 3267
6 13039.2 731806R1 2984 3499
6 13039.2 3715202H1 2984 3092
6 13039.2 g1993687 2985 3312
6 13039.2 731806H1 2984 3258
6 13039.2 2468144H1 2990 3229
6 13039.2 1907815H1 2991 3218
6 13039.2 4148570H1 3006 3269
6 13039.2 g778804 3015 3330
6 13039.2 3256396H1 3017 3269
6 13039.2 g789649 3021 3255
6 13039.2 4983180H1 3028 3311
6 13039.2 g865926 3030 3351
6 13039.2 4983190H1 3028 3302
6 13039.2 998221 Rl 3039 3594
6 13039.2 998221 HI 3039 3328
6 13039.2 4650828H1 3041 3328
6 13039.2 g776667 3055 3330
6 13039.2 3699551 HI 759 1043
6 13039.2 2784137H1 768 999 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
6 13039.2 5092174H1 863 1136
6 13039.2 2736123H1 901 1143
6 13039.2 2736123F6 901 1374 ό 13039.2 2841123H2 964 1052
6 13039.2 g!801914 984 1330
6 13039.2 3627415H1 990 1242
6 13039.2 2049675H1 1064 1318
6 13039.2 2783785F6 1067 1509
6 13039.2 2783785H1 1067 1319
6 13039.2 4764557H1 2700 2895
6 13039.2 g862228 2711 2935
6 13039.2 4977405H1 2718 2987
6 13039.2 4324144H1 2725 3007
6 13039.2 5195156H1 2730 2831
6 13039.2 4625438H1 2738 2992
6 13039.2 2881531H1 2740 3023
6 13039.2 1545834H1 2740 2953
6 13039.2 3214807H1 2740 2990
6 13039.2 1312356H1 2750 2954
6 13039.2 1312307H1 2750 2979
6 13039.2 g1238200 3569 3881
6 13039.2 g792128 3570 3881
6 13039.2 g3109745 3571 3878
6 13039.2 g789837 2241 2520
6 13039.2 g666844 2248 2506
6 13039.2 g793332 2260 2481
6 13039.2 g862227 2260 2522
6 13039.2 3321110H1 2293 2570
6 13039.2 g1636044 2306 2530
6 13039.2 3738558H1 2316 2611
6 13039.2 5700029H1 2317 2575
6 13039.2 5030623H1 2361 2636
6 13039.2 3321569H2 2364 2614
6 13039.2 3484339H1 2365 2701
6 13039.2 g317338 2375 2655
6 13039.2 4922854H1 2377 2683
6 13039.2 1382370H1 2377 2615
6 13039.2 3364673H1 2393 2653
6 13039.2 4014451H1 2393 2645
6 13039.2 4296168H1 2429 2676
6 13039.2 4296144H1 2429 2683
6 13039.2 4295505H1 2429 2696
6 13039.2 4775793H1 2466 2741
6 13039.2 5190065H1 1477 1620
6 13039.2 g2013579 1518 1807
6 13039.2 3201887H1 1570 1835
6 13039.2 g708914 1436 1737
6 13039.2 g691657 1479 1801
6 13039.2 489678H1 1579 1818
6 13039.2 044642H1 2172 2328 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
6 13039.2 3129828H1 2163 2472
6 13039.2 5702193H1 2183 2423
6 13039.2 g866587 2185 2551
6 13039.2 4968731 HI 2217 2474
6 13039.2 4969450H1 2217 2498
6 13039.2 g434208 2221 2510
6 13039.2 g666222 3533 3878
6 13039.2 1861085T6 3554 3841
6 13039.2 g1476956 3554 3883
6 13039.2 2472134H1 1917 2158
6 13039.2 2460193H1 1973 2223
6 13039.2 5544753H1 1977 2125
6 13039.2 1894461 HI 1994 2224
6 13039.2 4989013H1 2004 2267
6 13039.2 2504842H1 2018 2250
6 13039.2 3817686H1 2039 2289
6 13039.2 1709583F6 2086 2637
6 13039.2 1709583H1 2086 2292
6 13039.2 5496588H1 2117 2221
6 13039.2 go18254 2133 2456
6 13039.2 2302357H2 2134 2358
6 13039.2 3076667H1 2142 2408
6 13039.2 g4096030 3440 3883
6 13039.2 g4394182 3444 3889
6 13039.2 g3298631 3450 3883
6 13039.2 g4152977 3452 3888
6 13039.2 4150667H1 3456 3752
6 13039.2 5036313H1 3454 3744
6 13039.2 g4110089 3455 3887
6 13039.2 g3110528 3467 3881
6 13039.2 g3884368 3468 3883
6 13039.2 g2631703 3472 3882
6 13039.2 g4329108 3483 3871
6 13039.2 g4307404 3484 3891
6 13039.2 g3887724 3487 3890
6 13039.2 5679544H1 3488 3784
6 13039.2 4643394H1 3488 3741
6 13039.2 231550R1 3496 3891
6 13039.2 231550H1 3496 3719
6 13039.2 g2659034 3504 3678
6 13039.2 3635404H1 3504 3814
6 13039.2 2736123T6 3515 3839
6 13039.2 231550F1 3523 3882
6 13039.2 g3596402 3524 3881
6 13039.2 2736217H1 3526 3796
6 13039.2 2368391 H2 3323 3556
6 13039.2 4761918H1 3324 3582
6 13039.2 3162730H1 3331 3637
6 13039.2 2911248H1 3338 3625
6 13039.2 780353H1 3345 3665 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
6 13039.2 1233680H1 3349 3681
6 13039.2 1233680F1 3349 3971
6 13039.2 3792837H1 3351 3635
6 13039.2 g2357493 3351 3602
6 13039.2 2005695H1 3354 3432
6 13039.2 g3087116 3355 3891
6 13039.2 3038679H1 3359 3631
6 13039.2 731806F1 3361 3882
6 13039.2 g3070256 3362 3878
6 13039.2 g3049253 3364 3885
6 13039.2 g3049251 3366 3885
6 13039.2 g3070255 3369 3878
6 13039.2 g3076969 3370 3878
6 13039.2 g4292218 3374 3875
6 13039.2 2379289H1 3376 3605
6 13039.2 6026190H1 3375 3685
6 13039.2 2887871 HI 3378 3685
6 13039.2 g3841328 3384 3878
6 13039.2 g4073143 3385 3881
6 13039.2 602339H1 3386 3668
6 13039.2 g2901329 3390 3885
6 13039.2 g4153184 3401 3882
6 13039.2 1862447T6 3417 3836
6 13039.2 2738090T6 3429 3840
6 13039.2 1709583T6 3431 3837
6 13039.2 2870017H1 3229 3528
6 13039.2 2859049H1 3229 3512
6 13039.2 1822377H1 3237 3499
6 13039.2 3601353H1 3245 3577
6 13039.2 2760117H1 3247 3543
6 13039.2 2751935H1 3247 3520
6 13039.2 1921318H1 3255 3535
6 13039.2 1921318R6 3255 3696
6 13039.2 4797434H1 3262 3539
6 13039.2 g778894 3266 3611
6 13039.2 g855990 3266 3591
6 13039.2 2135368T6 3266 3840
6 13039.2 3975369H1 3275 3387
6 13039.2 3442784H1 3283 3547
6 13039.2 1832656H1 3299 3596
6 13039.2 2219316H1 3317 3573
6 13039.2 4761911H1 3323 3598
6 13039.2 g1238488 3188 3379
6 13039.2 g877900 3195 3513
6 13039.2 g2148718 3196 3847
6 13039.2 1736290H1 3199 3439
6 13039.2 1734801 HI 3199 3448
6 13039.2 1734817H1 3199 3447
6 13039.2 3812780H1 3201 3506
6 13039.2 3814117H1 3202 3367 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
6 13039.2 2404648H1 3213 3450
6 13039.2 1736463H1 3215 3509
6 13039.2 5019558H1 3217 3470
6 13039.2 5559285H1 3217 3498
6 13039.2 793056H1 3123 3357
6 13039.2 790129H1 3134 3376
6 13039.2 2671569H1 3169 3272
6 13039.2 4255130H1 3176 3267
6 13039.2 4164759H1 3170 3434
6 13039.2 4255178H1 3175 3459
6 13039.2 1861085F6 3562 3882
6 13039.2 g1203064 3563 3884
6 13039.2 1861177H1 3563 3888
6 13039.2 2803220H1 2525 2792
6 13039.2 4879807H1 2476 2740
6 13039.2 1627449H1 2527 2661
6 13039.2 2660611 HI 2481 2734
6 13039.2 3449673H1 2502 2757
6 13039.2 5039738H2 2535 2749
6 13039.2 4595615H1 2538 2813
6 13039.2 1862447F6 2566 3056
6 13039.2 1862447H1 2566 2831
6 13039.2 4251362H1 2587 2852
6 13039.2 g864534 2601 2918
6 13039.2 g1949105 2608 2883
6 13039.2 4831252H1 2612 2740
6 13039.2 4830165H1 2612 2824
6 13039.2 gl522198 2629 2917
6 13039.2 2962002H1 2642 2938
6 13039.2 4111 mm 2668 2941
6 13039.2 4581818H1 2674 2970
6 13039.2 3480168H1 2674 2966
6 13039.2 059851 HI 2688 2875
6 13039.2 3463785H1 2827 3087
6 13039.2 1379162H1 2833 3074
6 13039.2 827278H1 2833 3141
6 13039.2 1379162F1 2833 3380
6 13039.2 827278R1 2833 3428
6 13039.2 4970664H1 2852 3138
6 13039.2 3765903H1 2856 3173
6 13039.2 g828803 2876 3107
6 13039.2 2912660H1 2876 3139
6 13039.2 2945011 HI 2929 3231
6 13039.2 1900343H1 2930 3184
6 13039.2 4177622H1 2939 3215
6 13039.2 2714979H1 2941 3205
6 13039.2 5098921 HI 2946 3241
6 13039.2 4589878H1 2963 3194
6 13039.2 1350496H1 2966 3227
6 13039.2 1350496F1 2966 3639 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
6 13039.2 g793050 2751 2936
6 13039.2 2396484H1 2751 2985
6 13039.2 3677377H1 2764 2931
6 13039.2 1613610H1 2765 2976
6 13039.2 3677367H1 2765 3072
6 13039.2 3813522H1 2772 3037
6 13039.2 4688970H1 2782 3032
6 13039.2 4889047H1 2811 3096
6 13039.2 4550845H1 2811 2992
6 13039.2 g1986776 2811 3068
6 13039.2 2943108H1 2816 3136
6 13039.2 919863H1 2816 3094
6 13039.2 2220586H1 2818 3075
7 238005.4 3494842H1 1 146
7 238005.4 1513955H1 19 211
7 238005.4 1513931 HI 19 189
7 238005.4 1895354H1 24 255
7 238005.4 3216547H1 53 287
7 238005.4 2492948H1 210 525
7 238005.4 3393775H1 226 487
7 238005.4 3110735H1 237 520
7 238005.4 2114053H1 238 500
7 238005.4 2639154H1 229 480
7 238005.4 2639154F6 229 615
7 238005.4 3489530H1 251 540
7 238005.4 2452873H1 253 499
7 238005.4 2452873F6 253 419
7 238005.4 3149681 HI 258 499
7 238005.4 2952379H1 265 542
7 238005.4 2466034H1 291 507
7 238005.4 3074678H1 330 611
7 238005.4 g2003143 378 830
7 238005.4 2310518R6 454 935
7 238005.4 2310518H1 454 735
7 238005.4 2466818H1 500 732
7 238005.4 3243701 HI 503 764
7 238005.4 3108380H1 506 773
7 238005.4 4250192H1 506 710
7 238005.4 3688838H1 527 810
7 238005.4 2312916H1 543 816
7 238005.4 4087821 HI 570 878
7 238005.4 g3173776 593 909
7 238005.4 3960672H2 599 874
7 238005.4 1830753H1 644 897
7 238005.4 3936919H1 690 871
7 238005.4 3183381H1 691 942
7 238005.4 3165765H1 714 1037
7 238005.4 3231218H1 762 1012
7 238005.4 5273755H1 763 1032
7 238005.4 4710712H1 876 997 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
7 238005.4 g847384 989 1313
7 238005.4 5810260H1 999 1303
7 238005.4 2046234F6 1017 1417
7 238005.4 4547319H1 1024 1320
7 238005.4 5302724H1 1041 1284
7 238005.4 5267284H1 1053 1283
7 238005.4 4862949H1 1072 1245
7 238005.4 2893053H1 1078 1355
7 238005.4 2893053F6 1078 1449
7 238005.4 3408366H1 1120 1378
7 238005.4 5427753H1 1132 1350
7 238005.4 2046234H1 1135 1417
7 238005.4 g846587 1153 1408
7 238005.4 1978835H1 1173 1431
7 238005.4 5187046H1 1212 1303
7 238005.4 5049433F6 1212 1740
7 238005.4 5069619H1 1213 1457
7 238005.4 079996H1 1221 1447
7 238005.4 2755107H1 1244 1546
7 238005.4 2994580H1 1250 1546
7 238005.4 1357968H1 1253 1465
7 238005.4 2486058H1 1290 1528
7 238005.4 3155023H1 1308 1607
7 238005.4 1405122H1 1358 1634
7 238005.4 074212H1 1360 1547
7 238005.4 g1775652 1362 1565
7 238005.4 5426560H1 1368 1643
7 238005.4 2452873T6 1376 1902
7 238005.4 5597619H1 1385 1634
7 238005.4 2640268T6 1394 1890
7 238005.4 2971688H1 1399 1715
7 238005.4 2310518T6 1425 1902
7 238005.4 522334H1 1421 1673
7 238005.4 4787913H1 1436 1716
7 238005.4 6093903H1 1439 1775
7 238005.4 3716621 H1 1449 1751
7 238005.4 3435261 HI 1451 1718
7 238005.4 3256708H1 1454 1740
7 238005.4 769094H1 1454 1685
7 238005.4 g2526289 1458 1946
7 238005.4 4974673H1 1461 1728
7 238005.4 3870931 HI 1471 1787
7 238005.4 4701192H1 1471 1746
7 238005.4 g4113880 1481 1936
7 238005.4 5703513H1 1508 1795
7 238005.4 5867713H1 1510 1740
7 238005.4 g3430405 1520 1936
7 238005.4 g4304488 1527 1925
7 238005.4 g3446639 1532 1952
7 238005.4 g3843850 1534 1956 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
7 238005.4 5049433T6 1538 1924
7 238005.4 g3895204 1538 1945
7 238005.4 3343709T6 1541 1905
7 238005.4 g4267940 1548 1946
7 238005.4 2269156H1 1556 1832
7 238005.4 3211050H1 1556 1795
7 238005.4 3858314H1 1561 1865
7 238005.4 3858359H1 1561 1845
7 238005.4 3861114H1 1561 1868
7 238005.4 4215258H1 1567 1843
7 238005.4 g1647982 1573 1944
7 238005.4 6106957H1 1583 1903
7 238005.4 4974030H1 1586 1853
7 238005.4 g518289 1588 1946
7 238005.4 g2526290 1592 1945
7 238005.4 4562130H1 1603 1871
7 238005.4 6093354H1 1607 1891
7 238005.4 2611577H1 1612 1852
7 238005.4 g2003142 1617 1950
7 238005.4 g2213309 1628 1935
7 238005.4 g1893696 1633 1950
7 238005.4 2759732H1 1636 1924
7 238005.4 g4243121 1640 1944
7 238005.4 g4108171 1645 1945
7 238005.4 g3765581 1650 1946
7 238005.4 3027260T6 1677 1899
7 238005.4 1213283H1 1736 1875
7 238005.4 g846910 1739 1936
7 238005.4 2753427H1 1746 1944
7 238005.4 2150089H1 1756 1944
7 238005.4 g1775754 1824 1936
7 238005.4 5288457H1 1860 1978
7 238005.4 g4285357 1863 1946
10 233678.1 1803848F6 1839 2351
10 233678.1 2355751 HI 1855 1998
10 233678.1 1923122H1 1895 2186
10 233678.1 1858559H1 1896 2188
10 233678.1 2949425H1 1896 2193
10 233678.1 1858559F6 1896 2326
10 233678.1 4542183H1 1896 2166
10 233678.1 3786222H1 1898 2215
10 233678.1 6091924H1 1943 2212
10 233678.1 4584888H1 1958 2251
10 233678.1 1651475H1 1991 2242
10 233678.1 3967280H1 2006 2242
10 233678.1 5623384H1 2022 2351
10 233678.1 5623284H1 2022 2314
10 233678.1 4948649H1 2031 2325
10 233678.1 1521957H1 2030 2222
10 233678.1 1726538H1 2034 2236 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
10 233678.1 1723946H1 2034 2252
10 233678.1 1605814H1 2037 2174
10 233678.1 5554120H1 2037 2321
10 233678.1 1874743F6 2056 2410
10 233678.1 1874743H1 2057 2352
10 233678.1 4857286H1 2097 2352
10 233678.1 1509348H1 2102 2301
10 233678.1 2242767H1 2114 2370
10 233678.1 2848660H1 2126 2428
10 233678.1 2686671 HI 2129 2380
10 233678.1 1576284H1 2142 2375
10 233678.1 887052R1 2142 2769
10 233678.1 887052H1 2142 2447
10 233678.1 3785578H1 2149 2345
10 233678.1 3111926H1 2149 2473
10 233678.1 766862H1 2158 2406
10 233678.1 2227686H1 2171 2407
10 233678.1 2013238H1 2171 2277
10 233678.1 823920R1 2176 2721
10 233678.1 1583169H1 2176 2393
10 233678.1 823920H1 2176 2328
10 233678.1 1583137H1 2176 2390
10 233678.1 g1426492 2182 2682
10 233678.1 2275987H1 2225 2478
10 233678.1 4730301 HI 2231 2455
10 233678.1 176909H1 2231 2495
10 233678.1 170271OH1 2230 2441
10 233678.1 2845122H1 2231 2466
10 233678.1 5895659H1 2245 2544
10 233678.1 4703091 HI 2244 2507
10 233678.1 4214988H1 2256 2569
10 233678.1 1622006H1 2271 2508
10 233678.1 1250975T6 2285 2941
10 233678.1 5874967H1 2299 2566
10 233678.1 3291543H1 2301 2556
10 233678.1 5874909H1 2300 2556
10 233678.1 3291543F6 2301 2749
10 233678.1 4588984H1 2318 2524
10 233678.1 4564713H1 2321 2549
10 233678.1 1607223F6 2329 2631
10 233678.1 1607223H1 2329 2561
10 233678.1 777428R1 2329 2946
10 233678.1 4196029H1 2328 2638
10 233678.1 777428H1 2329 2573
10 233678.1 3098571T6 2334 2942
10 233678.1 2008649H1 2355 2571
10 233678.1 1607223T6 2360 2927
10 233678.1 1803848T6 2373 2929
10 233678.1 2210370T6 2375 2928
10 233678.1 1701603H1 2387 2602 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
10 233678.1 5286984H1 2406 2602
10 233678.1 2355751T6 2414 2928
10 233678.1 285554H1 2419 2806
10 233678.1 285554R6 2420 2891
10 233678.1 3289542T6 2435 2926
10 233678.1 2518190T6 2436 2916
10 233678.1 285554T6 2452 2926
10 233678.1 4949921 HI 2453 2734
10 233678.1 2814466T6 2451 2932
10 233678.1 3291543T6 2464 2930
10 233678.1 4197595H1 2466 2785
10 233678.1 5105034H1 2468 2740
10 233678.1 g2963989 2472 2972
10 233678.1 g2063675 2474 2971
10 233678.1 g517590 2474 2968
10 233678.1 4950109H1 2484 2768
10 233678.1 1874743T6 2498 2928
10 233678.1 g4107810 2500 2968
10 233678.1 g4175509 2507 2977
10 233678.1 g3411743 2509 2973
10 233678.1 1858559T6 2509 2930
10 233678.1 5848668H1 2517 2804
10 233678.1 g4269824 2519 2968
10 233678.1 3578266T6 2525 2934
10 233678.1 2623196H1 2526 2783
10 233678.1 g3770184 2541 2971
10 233678.1 g3923313 2548 2973
10 233678.1 3274147T6 2551 2910
10 233678.1 g2356198 2568 2897
10 233678.1 1684804T6 2577 2928
10 233678.1 g2784196 2581 2968
10 233678.1 3236618H1 2583 2844
10 233678.1 g2241760 2584 2968
10 233678.1 g316793 2586 2979
10 233678.1 g2816392 2588 2977
10 233678.1 g1954535 2588 2782
10 233678.1 g3700690 2586 2968
10 233678.1 g1887793 2590 2968
10 233678.1 3643238H1 2593 2897
10 233678.1 3650438H1 2594 2894
10 233678.1 2466533H1 2612 2850
10 233678.1 2210370F6 1632 2079
10 233678.1 2210367H1 1632 1886
10 233678.1 4795285H1 1659 1948
10 233678.1 g761628 1670 2092
10 233678.1 3803218H1 1669 1902
10 233678.1 4379275H1 1672 1949
10 233678.1 1606564H1 1682 1912
10 233678.1 5657623H1 1337 1607
10 233678.1 2312430H1 1358 1602 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
10 233678.1 3390808H1 1274 1553
10 233678.1 4171822H1 1390 1671
10 233678.1 4508866H1 1437 1711
10 233678.1 4505362H1 1437 1676
10 233678.1 632775H1 1451 1683
10 233678.1 2326782H1 1451 1677
10 233678.1 1684804H1 1281 1507
10 233678.1 1684804F6 1281 1743
10 233678.1 3948184H1 1457 1585
10 233678.1 3804480H1 1487 1706
10 233678.1 5546966H1 1486 1671
10 233678.1 5545829H1 1487 1700
10 233678.1 3088194H1 1498 1735
10 233678.1 3288867H1 1285 1546
10 233678.1 1250975F1 1577 2054
10 233678.1 1250975F6 1577 2051
10 233678.1 5812225H1 1317 1607
10 233678.1 5897556H1 1330 1555
10 233678.1 5893318H1 1330 1640
10 233678.1 5900195H1 1330 1548
10 233678.1 5897434H1 1330 1411
10 233678.1 5898715H1 1330 1634
10 233678.1 1250975H1 1577 1826
10 233678.1 5396479H1 1593 1852
10 233678.1 3797732H1 1604 1709
10 233678.1 5542957H1 1604 1815
10 233678.1 5558368H1 1609 1869
10 233678.1 1002256H1 1 246
10 233678.1 1002256R1 1 482
10 233678.1 1399306H1 74 326
10 233678.1 1399306F6 74 632
10 233678.1 1894055H1 182 422
10 233678.1 1270831 FI 393 979
10 233678.1 1270831 HI 393 667
10 233678.1 1003419R1 414 915
10 233678.1 1003419H1 414 608
10 233678.1 2518190F6 454 973
10 233678.1 2518190H1 454 706
10 233678.1 5659236H1 474 628
10 233678.1 3288389H1 1161 1413
10 233678.1 5005539H1 1189 1264
10 233678.1 5546782H1 1192 1398
10 233678.1 2809270H1 1239 1456
10 233678.1 2814466H1 762 1073
10 233678.1 5594064H1 496 757
10 233678.1 g764169 598 923
10 233678.1 5546549H1 626 827
10 233678.1 3289542F6 652 1084
10 233678.1 3289542H1 652 893
10 233678.1 5544312H1 687 896 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
10 233678.1 2814466F6 762 1334
10 233678.1 2466560H1 766 1014
10 233678.1 2661506H1 769 1035
10 233678.1 2441878H1 884 988
10 233678.1 2437941 HI 893 1114
10 233678.1 4785794H1 905 1166
10 233678.1 5574111 HI 940 1157
10 233678.1 3964034H1 1006 1286
10 233678.1 4786766H1 1010 1266
10 233678.1 650941 HI 1026 1285
10 233678.1 4601334H1 1061 1307
10 233678.1 3275906H1 1100 1352
10 233678.1 3274147F6 1101 1655
10 233678.1 3274147H1 1101 1348
10 233678.1 g3163775 1145 1490
10 233678.1 g4244100 2615 2969
10 233678.1 g4329102 2618 2969
10 233678.1 g4451360 2615 2971
10 233678.1 g3802177 2627 2971
10 233678.1 g3092982 2628 2969
10 233678.1 g3921970 2626 2972
10 233678.1 3516016H1 2646 2918
10 233678.1 1377689H1 2654 2926
10 233678.1 4986111 HI 2666 2956
10 233678.1 g845966 2675 2968
10 233678.1 g3777917 2683 2968
10 233678.1 g761629 2702 2962
10 233678.1 g3086793 2719 2968
10 233678.1 5273307H1 2727 2976
10 233678.1 g1139236 2748 2972
10 233678.1 4987591 HI 2793 2957
10 233678.1 4987593H1 2794 2968
10 233678.1 2424047H1 2804 2968
10 233678.1 6094676H1 2807 2968
10 233678.1 3083086H1 2842 2968
10 233678.1 3787162H1 2863 2968
10 233678.1 4901030H1 2902 2968
10 233678.1 5103514H1 2904 2974
10 233678.1 5060557H1 1720 2021
10 233678.1 5193174H1 1731 1877
10 233678.1 5003089H1 1750 2052
10 233678.1 3937103H1 1754 2052
10 233678.1 2210665H1 1754 1986
10 233678.1 4951636H2 1754 2033
10 233678.1 4589805H1 1754 1970
10 233678.1 2738891 HI 1754 1967
10 233678.1 4793896H1 1754 2005
10 233678.1 1651922H1 1754 1961
10 233678.1 3121552H1 1754 2049
10 233678.1 1236003H1 1754 1975 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
10 233678.1 3361752H1 1754 2001
10 233678.1 3282866H1 1754 2003
10 233678.1 3114487H1 1754 2013
10 233678.1 1652026H1 1754 1943
10 233678.1 3804172H1 1809 2145
10 233678.1 g2063923 1820 2231
10 233678.1 5191775H1 1834 1987
10 233678.1 1508970H1 1833 2054
10 233678.1 763920H1 1833 2139
10 233678.1 1803848H1 1839 1940
10 233678.1 2674708H1 1839 2112
11 312243.1 4605386H1 1343 1593
11 312243.1 4605386F7 1343 1784
11 312243.1 1483834H1 1462 1744
11 312243.1 4696494H1 1721 1986
11 312243.1 1823519H1 1734 1955
11 312243.1 1823519F6 1734 2013
11 312243.1 1696230H1 1749 1855
11 312243.1 1695671 HI 1757 1986
11 312243.1 1696055H1 1757 1969
11 312243.1 1460083H1 1773 2007
11 312243.1 1823519T6 1787 2427
11 312243.1 3845858H1 1787 1988
11 312243.1 386870H1 1792 2067
11 312243.1 gl515884 1886 2193
11 312243.1 2581154F6 21 197
11 312243.1 2581154H1 21 289
11 312243.1 694181 HI 26 222
11 312243.1 3383640H1 33 277
11 312243.1 878997H1 250 387
11 312243.1 881475H1 252 495
11 312243.1 878997R1 252 816
11 312243.1 881475R6 252 705
11 312243.1 641653R6 480 1033
11 312243.1 641653H1 480 729
11 312243.1 g2055007 674 772
11 312243.1 g2063527 684 806
11 312243.1 1316282H1 912 1148
11 312243.1 2120964F6 1099 1478
11 312243.1 2120964H1 1099 1353
11 312243.1 g4186493 1088 1442
11 312243.1 g4451005 1162 1479
11 312243.1 g2273834 1273 1458
11 312243.1 4605366H1 1343 1599
11 312243.1 4605386T7 1923 2422
11 312243.1 641653T6 1947 2441
11 312243.1 2120964T6 1957 2429
11 312243.1 g4305745 2052 2366
11 312243.1 881475T6 2069 2428
11 312243.1 g2138940 2087 2472 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
11 312243.1 4601955H1 2114 2269
11 312243.1 g3897513 2313 2467
11 312243.1 g3281088 1 220
11 312243.1 g4189325 1 177
11 312243.1 g3419223 1 219
11 312243.1 3460792H1 1 206
12 425487.3 g4187652 25 467
12 425487.3 g3804148 48 413
12 425487.3 g4265777 50 441
12 425487.3 gl810525 25 243
12 425487.3 g3075563 51 536
12 425487.3 g1576978 582 740
12 425487.3 g2276774 236
12 425487.3 g1576933 386
12 425487.3 g1860480 247
12 425487.3 g3835346 498
12 425487.3 g3839178 474
12 425487.3 g3839255 504
12 425487.3 g1920365 417
12 425487.3 g4113340 25 317
12 425487.3 4845742H1 69 296
12 425487.3 g2816806 66 402
12 425487.3 g2881811 75 519
12 425487.3 g2901201 84 461
12 425487.3 g2819800 80 494
12 425487.3 g2899484 91 540
12 425487.3 g2240223 266 660
12 425487.3 5639438H1 531 769
18 222429.3 3135386H1 322 523
18 222429.3 4193895H1 745 1038
18 222429.3 g3917627 750 967
18 222429.3 4773983H1 750 1030
18 222429.3 3110313H1 767 1070
18 222429.3 3818019H1 322 637
18 222429.3 5270075H1 770 1008
18 222429.3 228521OH1 324 583
18 222429.3 3451580H1 783 1039
18 222429.3 5690354H1 788 1045
18 222429.3 3368856H1 323 607
18 222429.3 5692143H1 796 1012
18 222429.3 1695061 HI 796 886
18 222429.3 622658H1 803 1062
18 222429.3 4264839H1 814 968
18 222429.3 4382955H1 324 595
18 222429.3 2513281H1 325 584
18 222429.3 g1395660 816 1293
18 222429.3 3182679H1 325 653
18 222429.3 g2881072 817 1302
18 222429.3 1852753H1 328 622
18 222429.3 1852753F6 329 803 TABLE 4
ID NO: Template ID Component ID Start Stop
18 222429.3 g4073351 823 1300
18 222429.3 3619548H1 332 599
18 222429.3 1772964H1 829 1110
18 222429.3 5016650H1 835 1123
18 222429.3 891033R1 835 967
18 222429.3 2782761 HI 341 620
18 222429.3 4855161 HI 347 487
18 222429.3 2802335H1 380 661
18 222429.3 4616684H1 380 653
18 222429.3 g1395574 387 641
18 222429.3 g2032347 393 677
18 222429.3 3553107H1 395 615
18 222429.3 4309262H1 423 747
18 222429.3 4721466T6 428 934
18 222429.3 3466526H1 435 706
18 222429.3 2316414H1 439 697
18 222429.3 g3087119 484 970
18 222429.3 2859627H1 491 779
18 222429.3 g3888504 540 971
18 222429.3 1266732H1 540 774
18 222429.3 g3887405 551 869
18 222429.3 g3801166 560 970
18 222429.3 759622R1 567 804
18 222429.3 759622H1 567 920
18 222429.3 g1496653 586 967
18 222429.3 053812H1 589 802
18 222429.3 1822941 HI 602 829
18 222429.3 g3871758 609 967
18 222429.3 g3888431 624 972
18 222429.3 5274484H1 626 878
18 222429.3 g3802660 651 970
18 222429.3 1852753T6 655 1252
18 222429.3 6015049H1 672 969
18 222429.3 1430609H1 686 919
18 222429.3 798615H1 694 975
18 222429.3 3113611T6 698 1224
18 222429.3 1685142H1 742 976
18 222429.3 5900905H1 743 1032
18 222429.3 2078759H1 849 1127
18 222429.3 2043774H1 851 1124
18 222429.3 g2985157 859 1298
18 222429.3 1402308H1 861 1118
18 222429.3 g717242 882 971
18 222429.3 g4109637 883 1293
18 222429.3 g4110383 891 1293
18 222429.3 g3178557 926 1301
18 222429.3 1463294H1 928 1142
18 222429.3 1463335H1 928 1120
18 222429.3 1463294T1 928 1248
18 222429.3 g3871712 929 1292 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
18 222429.3 g4307952 950 1295
18 222429.3 1940845T6 953 1251
18 222429.3 1940845R6 953 1294
18 222429.3 1940845H1 953 1181
18 222429.3 3730073H1 957 1278
18 222429.3 gl218940 968 1293
18 222429.3 g2575322 974 1293
18 222429.3 3726214H1 989 1294
18 222429.3 2872559H1 994 1288
18 222429.3 2875466H1 994 1134
18 222429.3 4247311 HI 996 1144
18 222429.3 6007354H1 1016 1290
18 222429.3 2154383H1 1040 1293
18 222429.3 5680928H1 1043 1293
18 222429.3 214245H1 1081 1279
18 222429.3 g1069690 1091 1208
18 222429.3 g2212472 1098 1350
18 222429.3 839255H1 1103 1312
18 222429.3 839255R1 1103 1293
18 222429.3 3235786H1 1143 1252
18 222429.3 891762R1 1164 1300
18 222429.3 891762H1 1164 1300
18 222429.3 1849630H1 1184 1293
18 222429.3 1849630F6 1184 1284
18 222429.3 1849630T6 1192 1252
18 222429.3 4865293H1 1210 1293
18 222429.3 4721466F6 1 466
18 222429.3 4721466H1 1 271
18 222429.3 5638504H1 65 317
18 222429.3 5638852H1 65 316
18 222429.3 3076642H1 228 498
18 222429.3 3076642F6 228 487
18 222429.3 4940608H1 247 533
18 222429.3 5388153H1 267 412
18 222429.3 3750219H1 253 506
18 222429.3 3937336H1 253 527
18 222429.3 4122661 HI 253 500
18 222429.3 3680329H1 253 572
18 222429.3 4943143H1 253 516
18 222429.3 4585314H1 254 510
18 222429.3 2732104H1 254 510
18 222429.3 2537505H1 257 492
18 222429.3 g2015403 274 591
18 222429.3 4786776H1 274 526
18 222429.3 4045742H1 274 579
18 222429.3 3567962H1 274 529
18 222429.3 1386440H1 276 413
18 222429.3 5187636H1 275 560
18 222429.3 5197384H1 277 547
18 222429.3 1572627H1 277 491
192 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
18 222429.3 1572748H1 277 502
18 222429.3 2372113H1 279 527
18 222429.3 5187033H1 279 420
18 222429.3 2785651 HI 279 563
18 222429.3 2727323H1 280 534
18 222429.3 3134034H1 280 554
18 222429.3 927455H1 280 558
18 222429.3 927455R1 280 894
18 222429.3 2596333H1 280 528
18 222429.3 2372113F6 280 797
18 222429.3 5847736H1 281 565
18 222429.3 2853635H1 281 538
18 222429.3 2854289H1 281 561
18 222429.3 2730059H1 281 540
18 222429.3 1268178F1 282 704
18 222429.3 2492274H1 282 517
18 222429.3 4124267H1 282 513
18 222429.3 2459370H1 282 511
18 222429.3 1268178H1 282 556
18 222429.3 6013641 HI 282 518
18 222429.3 5378585H1 283 535
18 222429.3 3985882H1 274 384
18 222429.3 3870288H1 285 576
18 222429.3 4608143H1 283 534
18 222429.3 3983482H1 286 464
18 222429.3 5843644H1 286 511
18 222429.3 2605545H1 288 536
18 222429.3 3088525H1 288 577
18 222429.3 3218430H1 290 587
18 222429.3 g1496652 291 538
18 222429.3 4248167H1 294 568
18 222429.3 4767534H1 294 424
18 222429.3 4174335H1 294 613
18 222429.3 3695889H1 295 582
18 222429.3 5592876H1 294 443
18 222429.3 2658509H1 296 546
18 222429.3 730756H1 296 565
18 222429.3 4613408H1 297 505
18 222429.3 264145H1 297 616
18 222429.3 5810372H1 299 665
18 222429.3 3319788H1 300 476
18 222429.3 4202422H1 301 596
18 222429.3 4613487H1 306 507
18 222429.3 g712550 306 583
18 222429.3 5090055H1 307 567
18 222429.3 2823320H1 309 631
18 222429.3 2529472H1 311 578
18 222429.3 4850016H1 312 590
18 222429.3 4606729H1 313 569
18 222429.3 4608174H1 313 567 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
18 222429.3 4334782H1 314 584
18 222429.3 3508043H1 314 609
18 222429.3 4638791 HI 316 578
18 222429.3 2941851 HI 316 594
18 222429.3 2533245H1 317 556
18 222429.3 033345H1 317 444
18 222429.3 2888083H1 317 573
18 222429.3 2766782H1 318 591
18 222429.3 g1069689 321 669
18 222429.3 2514805H1 321 656
19 366739.2 3793584H1 1 276
19 366739.2 3093259F6 1 396
19 366739.2 3093259H1 1 272
19 366739.2 5586972H1 28 288
19 366739.2 1562228H1 28 244
19 366739.2 g1976820 31 385
19 366739.2 5472436H1 30 254
19 366739.2 g1974601 38 290
19 366739.2 3536311 HI 63 278
19 366739.2 gl301142 203 492
19 366739.2 2996019H1 226 495
19 366739.2 1291844F6 265 754
19 366739.2 1291844F1 265 757
19 366739.2 1291844H1 265 495
19 366739.2 5107426H1 323 395
19 366739.2 6077830H1 331 653
19 366739.2 2690675H1 335 549
19 366739.2 3673120H1 341 654
19 366739.2 4626753H1 343 626
19 366739.2 2814563H1 344 559
19 366739.2 5019593H1 348 607
19 366739.2 5591354H1 350 602
19 366739.2 4337887H1 348 533
19 366739.2 2830045H1 350 618
19 366739.2 3614922H1 351 637
19 366739.2 3034106H1 352 640
19 366739.2 4765938H1 352 635
19 366739.2 3375151H1 354 621
19 366739.2 804576H1 357 612
19 366739.2 2188984H1 360 622
19 366739.2 157111H1 361 569
19 366739.2 5391316H1 370 647
19 366739.2 808513H1 372 654
19 366739.2 1966930H1 381 617
19 366739.2 1966930R6 381 755
19 366739.2 5194739H1 431 658
19 366739.2 4946548H1 431 604
19 366739.2 4768533F6 455 865
19 366739.2 4768533H1 455 739
19 366739.2 g778805 457 743 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
19 366739.2 gl921131 463 977
19 366739.2 4353206H2 492 757
19 366739.2 5325529H1 501 794
19 366739.2 5322285H1 501 774
19 366739.2 5322857H1 502 752
19 366739.2 869959H1 564 808
19 366739.2 875716R6 564 1081
19 366739.2 875716H1 564 855
19 366739.2 875716R1 564 1203
19 366739.2 3221359H1 601 939
19 366739.2 3869036H1 630 910
19 366739.2 3353207H1 645 955
19 366739.2 g2016781 644 916
19 366739.2 4587185H1 645 907
19 366739.2 5406614H1 653 850
19 366739.2 g1300754 650 1123
19 366739.2 370417H1 713 1027
19 366739.2 1265285H1 720 861
19 366739.2 1265285R1 720 1186
19 366739.2 1265102H1 720 891
19 366739.2 3946741 HI 742 1024
19 366739.2 3603130H1 771 1093
19 366739.2 5472209H1 846 1043
19 366739.2 3717241 HI 870 1172
19 366739.2 1291844T6 871 1416
19 366739.2 2608544H1 898 1103
19 366739.2 g922177 903 1148
19 366739.2 251965H1 925 1273
19 366739.2 3470188H1 935 1210
19 366739.2 g2838122 936 1451
19 366739.2 1636138F6 963 1441
19 366739.2 1636138H1 963 1184
19 366739.2 923492H1 968 1270
19 366739.2 3811371H1 977 1294
19 366739.2 g3430481 978 1454
19 366739.2 g4282887 982 1458
19 366739.2 g4372283 986 1454
19 366739.2 5138130H1 1015 1307
19 366739.2 g2958044 1019 1453
19 366739.2 1636138T6 1035 1416
19 366739.2 g2397938 1039 1452
19 366739.2 1415729H1 1048 1289
19 366739.2 676581 HI 1055 1273
19 366739.2 3093259T6 1056 1412
19 366739.2 gl921132 1059 1465
19 366739.2 337785H1 1075 1288
19 366739.2 3773169H1 1088 1367
19 366739.2 g2820846 1095 1453
19 366739.2 g23229όl 1109 1457
19 366739.2 g3923575 1124 1453 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
19 366739.2 5399095H1 1135 1273
19 366739.2 g1266798 1140 1459
19 366739.2 g2883870 1143 1434
19 366739.2 g4325983 1152 1458
19 366739.2 g4325893 1154 1458
19 366739.2 1223335T1 1154 1414
19 366739.2 1223335H1 1154 1434
19 366739.2 g3959938 1177 1453
19 366739.2 g1970868 1179 1468
19 366739.2 2228180H1 1185 1460
19 366739.2 g2574692 1223 1462
19 366739.2 2505795H1 1237 1456
19 366739.2 g2877025 1242 1453
19 366739.2 g4268440 1259 1453
19 366739.2 g2575341 1264 1453
19 366739.2 g778806 1268 1452
19 366739.2 1772854R6 1273 1453
19 366739.2 1772849H1 1273 1453
19 366739.2 g1264282 1343 1473
20 474635.6 340786H1 2181 2422
20 474635.6 2242239H1 2179 2347
20 474635.6 g991123 2179 2514
20 474635.6 2234442H1 2179 2397
20 474635.6 g1056895 2180 2498
20 474635.6 g959046 2182 2471
20 474635.6 gl004715 2183 2527
20 474635.6 4996329T6 2189 2625
20 474635.6 4746496H1 2192 2451
20 474635.6 g3737429 2197 2728
20 474635.6 g1039999 2210 2512
20 474635.6 gl081479 2210 2391
20 474635.6 2204795T6 2217 2671
20 474635.6 g3736649 2220 2704
20 474635.6 2242239T6 2220 2816
20 474635.6 3733918T6 2230 2786
20 474635.6 g3742588 2229 2728
20 474635.6 gl014336 2235 2566
20 474635.6 3638137H1 2230 2511
20 474635.6 g835640 2232 2567
20 474635.6 1666516H1 2236 2449
20 474635.6 2083270H1 2262 2567
20 474635.6 1761002H1 2284 2581
20 474635.6 612373H1 2291 2581
20 474635.6 665014H1 2291 2558
20 474635.6 g867547 2291 2662
20 474635.6 g1986029 2312 2772
20 474635.6 3000193H1 2318 2627
20 474635.6 461079H1 2328 2588
20 474635.6 g1274411 2332 2863
20 474635.6 2237019H1 2332 2557 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
20 474635.6 g856812 2334 2693
20 474635.6 5275784H1 2343 2627
20 474635.6 4085512H1 2393 2714
20 474635.6 g1240371 2407 2873
20 474635.6 g848488 2408 2767
20 474635.6 g897948 2408 2722
20 474635.6 g848512 2408 2850
20 474635.6 g1444420 2410 2880
20 474635.6 665169H1 2419 2677
20 474635.6 2090332H1 2439 2728
20 474635.6 gl004911 2454 2877
20 474635.6 g2900276 2464 2950
20 474635.6 g3848664 2464 2910
20 474635.6 5432669H1 2472 2741
20 474635.6 3134278H1 2486 2792
20 474635.6 g4174578 2487 2999
20 474635.6 g3433111 2489 2991
20 474635.6 g3419207 2491 3017
20 474635.6 4087752H1 2502 2814
20 474635.6 5327883H1 2520 2806
20 474635.6 5326114H1 2523 2818
20 474635.6 5326214H1 2524 2806
20 474635.6 g3229542 2527 3017
20 474635.6 2757338F6 2528 3008
20 474635.6 g3405868 938 1282
20 474635.6 572947H1 944 1190
20 474635.6 3002964H1 961 1013
20 474635.6 g982216 976 1338
20 474635.6 2309094H1 1029 1217
20 474635.6 4638158H1 1036 1287
20 474635.6 1912857H1 1042 1285
20 474635.6 g916500 1047 1247
20 474635.6 3633880H1 1055 1354
20 474635.6 3634680H1 1055 1325
20 474635.6 4546165H1 1074 1351
20 474635.6 g1276377 1073 1325
20 474635.6 5677925H1 1154 1382
20 474635.6 4663039H1 1163 1425
20 474635.6 3511926H1 1174 1426
20 474635.6 4996329H1 1324 1605
20 474635.6 4996329F6 1324 1683
20 474635.6 4740909H1 1330 1603
20 474635.6 64791OH1 1344 1623
20 474635.6 1715955F6 1431 1896
20 474635.6 3281456H1 1463 1723
20 474635.6 2204795F6 1494 2015
20 474635.6 2204795H1 1494 1739
20 474635.6 4546440H1 1504 1781
20 474635.6 1669175H1 1524 1751
20 474635.6 1443714F6 1644 2033 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
20 474635.6 1443714H1 1644 1900
20 474635.6 1715955H1 1680 1896
20 474635.6 4088721 HI 1699 1960
20 474635.6 4049359H1 1718 1989
20 474635.6 3322874H1 1720 1987
20 474635.6 3733918F6 1806 2215
20 474635.6 4411044H1 1832 2038
20 474635.6 5173224H1 1866 2144
20 474635.6 5098372H1 1930 2150
20 474635.6 4412048H1 1933 2137
20 474635.6 1265323R1 1935 2488
20 474635.6 1265323H1 1935 2151
20 474635.6 376565H1 1961 2151
20 474635.6 1630741 HI 1961 2147
20 474635.6 1631939H1 1961 2151
20 474635.6 6102550H1 1966 2151
20 474635.6 6102850H1 1966 2154
20 474635.6 g958816 2172 2378
20 474635.6 g1047675 2173 2505
20 474635.6 g965279 2173 2563
20 474635.6 g3098969 2173 2510
20 474635.6 gl202194 2174 2528
20 474635.6 g1099631 2174 2567
20 474635.6 g1047662 2174 2514
20 474635.6 g1228299 2176 2306
20 474635.6 gl 193583 2176 2464
20 474635.6 g2912515 2176 2667
20 474635.6 2242239F6 2176 2646
20 474635.6 gl211570 2176 2487
20 474635.6 g1225734 2176 2491
20 474635.6 g1226785 2176 2462
20 474635.6 g1043793 2176 2392
20 474635.6 gl 162551 2176 2505
20 474635.6 1725002H1 1 207
20 474635.6 1726247H1 1 216
20 474635.6 3495066H1 1 301
20 474635.6 1727369F6 1 387
20 474635.6 1727369H1 1 249
20 474635.6 3109953H1 10 305
20 474635.6 2362517H1 16 279
20 474635.6 2361835H1 16 270
20 474635.6 3617437H1 58 382
20 474635.6 2659652H1 91 348
20 474635.6 3734189H1 92 393
20 474635.6 2679260H1 96 409
20 474635.6 1466462H1 96 295
20 474635.6 3563056H1 96 415
20 474635.6 2235355H1 100 364
20 474635.6 2202076H1 99 367
20 474635.6 3129502H1 101 436 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
20 474635.6 2051824H1 118 293
20 474635.6 3633032H1 122 294
20 474635.6 3150266H1 126 379
20 474635.6 2051825H1 132 414
20 474635.6 g1227685 128 482
20 474635.6 4288817H1 146 437
20 474635.6 4860794H1 155 246
20 474635.6 174879H1 161 364
20 474635.6 5700836H1 163 471
20 474635.6 5539631 H2 182 413
20 474635.6 5206045H1 220 491
20 474635.6 375911R6 244 566
20 474635.6 375911 HI 244 536
20 474635.6 g657023 255 500
20 474635.6 3939757H1 275 433
20 474635.6 3939749H1 276 433
20 474635.6 g704964 290 589
20 474635.6 gl013184 290 695
20 474635.6 g1472478 326 795
20 474635.6 1220725H1 355 600
20 474635.6 4980839H1 358 659
20 474635.6 375911T6 370 902
20 474635.6 3675542H1 371 682
20 474635.6 3669542H1 371 695
20 474635.6 3671542H1 371 558
20 474635.6 g1447913 383 835
20 474635.6 1282181H1 391 534
20 474635.6 g2020599 418 783
20 474635.6 4133026H2 447 725
20 474635.6 2236848H1 450 698
20 474635.6 gl 278197 473 1017
20 474635.6 g1941907 514 972
20 474635.6 g2695124 514 1013
20 474635.6 1470350F6 554 998
20 474635.6 578500H1 557 758
20 474635.6 g4371917 558 1013
20 474635.6 gl447816 558 1013
20 474635.6 g2702599 559 1013
20 474635.6 505476H1 560 793
20 474635.6 2086083H1 579 884
20 474635.6 g3430549 602 1020
20 474635.6 gl671099 609 1029
20 474635.6 g1472421 658 1013
20 474635.6 g656857 700 1013
20 474635.6 3381660H1 715 902
20 474635.6 4270822H1 742 1016
20 474635.6 g1977606 753 1013
20 474635.6 4594512H1 755 1013
20 474635.6 g944107 761 1016
20 474635.6 1470350H1 802 998 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
20 474635.6 2362517T6 802 970
20 474635.6 gl011912 812 1004
20 474635.6 g1201979 871 1013
20 474635.6 4412657H1 883 969
20 474635.6 g916501 928 1234
20 474635.6 g1238628 931 1126
20 474635.6 g2057226 934 1034
20 474635.6 3450474H1 938 1128
20 474635.6 g2022938 938 1147
20 474635.6 g982171 939 1266
20 474635.6 2757338H1 2528 2825
20 474635.6 2757338R6 2528 2995
20 474635.6 5425690H1 2531 2796
20 474635.6 g1046524 2535 2900
20 474635.6 g3134715 2534 2985
20 474635.6 380176H1 2537 2654
20 474635.6 gl 186355 2560 2772
20 474635.6 g856701 2582 2772
20 474635.6 1795930H1 2583 2701
20 474635.6 g651862 2589 2849
20 474635.6 g651879 2589 2896
20 474635.6 g3076096 2594 2992
20 474635.6 g4078849 2605 2999
20 474635.6 g835594 2606 2985
20 474635.6 gl081771 2618 2893
20 474635.6 g1266372 2625 2900
20 474635.6 971739H1 2631 2952
20 474635.6 1808492H1 2639 2869
20 474635.6 649261 HI 2645 2940
20 474635.6 g867525 2652 2949
20 474635.6 1352072H1 2682 2960
20 474635.6 g848398 2688 2993
20 474635.6 g3754493 2700 2999
20 474635.6 g2839098 2719 3187
20 474635.6 g848419 2728 3010
20 474635.6 g1524564 2740 3015
20 474635.6 g806064 2765 2972
20 474635.6 1402667H1 2791 3002
20 474635.6 g2752910 2841 2938
20 474635.6 g715956 2849 2968
20 474635.6 g3428030 2948 2997
24 411449.2 3292975H1 654 917
24 411449.2 g1277242 663 1052
24 411449.2 1355750H1 662 944
24 411449.2 1355750F6 662 1150
24 411449.2 g1443735 707 1043
24 411449.2 198401OH1 722 990
24 411449.2 gl243124 747 1012
24 411449.2 gl243130 747 939
24 411449.2 gl 243104 748 938 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
24 411449.2 gl243131 773 923
24 411449.2 g841841 823 1176
24 411449.2 g1635822 830 1026
24 411449.2 677686H1 890 1140
24 411449.2 2896619H1 891 1077
24 411449.2 g3933055 644 1016
24 411449.2 1689376H1 898 1105
24 411449.2 3783111 HI 908 1221
24 411449.2 4796764H1 515 795
24 411449.2 4796772H1 515 795
24 411449.2 g2037311 533 814
24 411449.2 g2819773 551 815
24 411449.2 057539H1 507 708
24 411449.2 g3098856 560 922
24 411449.2 gl 125331 560 950
24 411449.2 g1386245 583 970
24 411449.2 3323088H1 586 854
24 411449.2 g2816548 607 1022
24 411449.2 3660962H1 612 867
24 411449.2 g1887649 615 946
24 411449.2 g1489541 618 866
24 411449.2 g1489523 619 965
24 411449.2 g4327095 909 1337
24 411449.2 5275975H1 911 1077
24 411449.2 2682468H1 941 1157
24 411449.2 2682429H1 943 1218
24 411449.2 3448516T6 966 1496
24 411449.2 5517642H1 966 1232
24 411449.2 3723582H1 970 1267
24 411449.2 589712H1 978 1222
24 411449.2 589712R1 978 1519
24 411449.2 2613128H1 1015 1252
24 411449.2 1355750T6 1052 1482
24 411449.2 3820979H1 1057 1340
24 411449.2 1811236H1 1068 1326
24 411449.2 1811236F6 1068 1562
24 411449.2 1811236T6 1083 1726
24 411449.2 g4033830 1106 1519
24 411449.2 g3917075 1106 1519
24 411449.2 g3917072 1108 1519
24 411449.2 3297093H1 1117 1204
24 411449.2 4513565H1 1174 1440
24 411449.2 4798512H1 1190 1460
24 411449.2 264511OH1 1195 1450
24 411449.2 2096680R6 1216 1644
24 411449.2 2096680H1 1216 1462
24 411449.2 321613H1 1233 1492
24 411449.2 2995437H1 1251 1538
24 411449.2 g4371719 1378 1775
24 411449.2 2096680T6 1380 1715 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
24 411449.2 4653462H1 1411 1685
24 411449.2 g1489542 1416 1765
24 411449.2 4144044H1 1422 1709
24 411449.2 g1224160 1425 1770
24 411449.2 g1224144 1433 1770
24 411449.2 g1489524 1473 1766
24 411449.2 g769281 1485 1823
24 411449.2 g2955239 1501 1777
24 411449.2 g4078417 1503 1770
24 411449.2 g1224166 1517 1770
24 411449.2 g1224143 1529 1770
24 411449.2 1972386H1 1531 1804
24 411449.2 g4084798 1534 1954
24 411449.2 g1224165 1560 1770
24 411449.2 g784201 1564 1798
24 411449.2 g2657184 1564 1868
24 411449.2 5919979H1 1256 1559
24 411449.2 008248H1 1258 1569
24 411449.2 g889333 1271 1666
24 411449.2 gl 139751 1287 1746
24 411449.2 589712F1 1305 1770
24 411449.2 3659604H1 1316 1588
24 411449.2 2598057H1 1327 1458
24 411449.2 g3178153 1345 1772
24 411449.2 g4187548 1373 1774
24 411449.2 g574838 1617 1824
24 411449.2 3778628H1 1645 1948
24 411449.2 g3785651 1656 1770
24 411449.2 763788H1 1696 1765
24 411449.2 1490003H1 1788 2054
24 411449.2 g2000780 1844 2185
24 411449.2 4704775H1 1862 2105
24 411449.2 g3921575 1873 2274
24 411449.2 g3231159 1901 2276
24 411449.2 g2222962 1902 2260
24 411449.2 g2222973 1902 2258
24 411449.2 638241 HI 1908 2160
24 411449.2 001302H1 1908 2236
24 411449.2 1625423F6 1911 2197
24 411449.2 1625423H1 1911 2113
24 411449.2 491356H1 1923 2185
24 411449.2 g1964447 1927 2193
24 411449.2 g1963729 1927 2263
24 411449.2 g1379590 1936 2272
24 411449.2 g1472323 1948 2197
24 411449.2 2399751 HI 1951 2192
24 411449.2 4856606H1 1973 2197
24 411449.2 995171 HI 1978 2209
24 411449.2 gl472316 1979 2197
24 411449.2 5194364H2 1982 2194 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
24 411449.2 3451002H1 2043 2168
24 411449.2 g4524789 2083 2553
24 411449.2 g2159625 2209 2405
24 411449.2 g2154000 2210 2639
24 411449.2 g3739242 2216 2561
24 411449.2 5276078H1 2220 2494
24 411449.2 g889241 2223 2564
24 411449.2 g1148058 2235 2554
24 411449.2 g3077322 2268 2561
24 411449.2 g784419 2295 2555
24 411449.2 2758260H1 2312 2541
24 411449.2 g4109094 2349 2619
24 411449.2 gl 785173 2442 2554
24 411449.2 350471OH1 2444 2554
24 411449.2 g3678027 2544 2899
24 411449.2 g3412805 2545 2944
24 411449.2 g3214749 2546 2950
24 411449.2 g4149617 2546 2995
24 411449.2 g2969810 2546 2703
24 411449.2 g746614 2551 2916
24 411449.2 g3756632 2550 2615
24 411449.2 g2969693 2551 2970
24 411449.2 g3770455 2552 2832
24 411449.2 g2538262 2552 2618
24 411449.2 g2882695 2552 2871
24 411449.2 3073355H1 3031 3337
24 411449.2 2502022H1 3034 3299
24 411449.2 2203860H1 3035 3321
24 411449.2 2415335H1 3040 3241
24 411449.2 4068029H1 3043 3337
24 411449.2 3633303H1 3044 3319
24 411449.2 1972353H1 3039 3301
24 411449.2 g746725 3044 3326
24 411449.2 3737404H1 3044 3324
24 411449.2 3557887H1 3044 3317
24 411449.2 3295556H1 3046 3325
24 411449.2 4114476H1 3047 3337
24 411449.2 4795315H1 3048 3337
24 411449.2 577995H1 3047 3307
24 411449.2 3167827H1 3051 3339
24 411449.2 5686358H1 3055 3339
24 411449.2 2781948H1 3066 3331
24 411449.2 2561784H2 3068 3340
24 411449.2 4712882H1 3077 3339
24 411449.2 5374882H1 3086 3335
24 411449.2 g2153894 3087 3334
24 411449.2 3596863H1 3133 3337
24 411449.2 4675071 HI 3155 3312
24 411449.2 5285819H1 3161 3337
24 411449.2 3638749H1 3186 3301 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
24 411449.2 2707450H1 3198 3319
24 411449.2 5695240H1 3208 3337
24 411449.2 5059716H1 3251 3316
24 411449.2 gl781709 1 493
24 411449.2 g1775656 1 432
24 411449.2 2472307F6 18 397
24 411449.2 2472307H1 18 265
24 411449.2 g822142 36 381
24 411449.2 g2000779 51 258
24 411449.2 2782774H1 79 356
24 411449.2 g1295851 138 810
24 411449.2 gl312393 138 614
24 411449.2 3448516R6 142 624
24 411449.2 g1010505 2552 2714
24 411449.2 g1692011 2553 2956
24 411449.2 1274760F1 2555 2848
24 411449.2 g2658624 2554 2974
24 411449.2 gl921464 2554 2863
24 411449.2 gl 153184 2554 2764
24 411449.2 g2768980 2555 2668
24 411449.2 g2153787 2555 2972
24 411449.2 g3117405 2555 2850
24 411449.2 g2933847 2554 2995
24 411449.2 g2934183 2555 3034
24 411449.2 g2568950 2556 2868
24 411449.2 2018010H1 2562 2849
24 411449.2 g1636435 2656 2796
24 411449.2 2050014H1 2689 2969
24 411449.2 2910217H1 2694 2967
24 411449.2 g2153999 2709 3188
24 411449.2 g2204848 2778 3188
24 411449.2 2476089H1 2798 3037
24 411449.2 g1925326 2847 3323
24 411449.2 g1678125 2913 3317
24 411449.2 g2558304 2937 3101
24 411449.2 g2100182 2951 3334
24 411449.2 506236H1 2971 3182
24 411449.2 3518329H1 2976 3311
24 411449.2 3473456H1 2979 3337
24 411449.2 1698871 HI 2986 3230
24 411449.2 4512967H1 2987 3259
24 411449.2 gl692106 2999 3198
24 411449.2 3081295H1 3009 3317
24 411449.2 4819058H1 3020 3324
24 411449.2 3492756H1 3028 3337
24 411449.2 3448616H1 142 413
24 411449.2 6138342H1 150 451
24 411449.2 1957671 HI 154 438
24 411449.2 g3888550 166 634
24 411449.2 239023H1 199 433 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
24 411449.2 463172H1 205 453
24 411449.2 gl471862 257 732
24 411449.2 gl471855 257 691
24 411449.2 5153884H1 352 608
24 411449.2 593640H1 385 596
24 411449.2 g2037867 408 741
24 411449.2 g2946071 438 791
25 18549.2 2666675H1 1 256
25 18549.2 2666675F6 1 447
25 18549.2 2872055H1 35 324
25 18549.2 3674803H1 45 340
25 18549.2 g4393247 48 393
26 236043.3 4854788H1 57 322
26 236043.3 2637174H1 57 313
26 236043.3 4154039H1 57 326
26 236043.3 4154437H1 66 332
26 236043.3 g1784274 72 327
26 236043.3 g1782229 74 421
26 236043.3 5167751H1 1 259
26 236043.3 4154654H1 31 288
26 236043.3 2637174F6 57 407
26 236043.3 5856494H1 52 322
26 236043.3 753667H1 57 311
26 236043.3 2638855F6 615 912
26 236043.3 2638855T6 624 1270
26 236043.3 4000427H1 750 952
26 236043.3 118534H1 826 1086
26 236043.3 gl782014 858 1286
26 236043.3 g2553565 891 1313
26 236043.3 g707651 915 1263
26 236043.3 506959H1 946 1251
26 236043.3 gl 792156 953 1283
26 236043.3 g2616478 957 1266
26 236043.3 g1792664 975 1281
26 236043.3 g3754889 1007 1313
26 236043.3 g707650 1011 1322
26 236043.3 g1784007 1062 1313
26 236043.3 g1782018 1086 1313
26 236043.3 1209542H1 1096 1326
26 236043.3 2433413H1 1134 1379
26 236043.3 g1792600 1184 1283
26 236043.3 4401019T6 1210 1699
26 236043.3 2637174T6 1202 1260
26 236043.3 g2342125 1329 1530
26 236043.3 118858H1 75 275
26 236043.3 g1760400 77 392
26 236043.3 g1664195 79 448
26 236043.3 g1784031 82 542
26 236043.3 529811 OH1 93 360
26 236043.3 5280294H1 110 358 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
26 236043.3 3516062H1 113 391
26 236043.3 4012792H1 114 402
26 236043.3 5856458H1 176 453
26 236043.3 5856757H1 176 310
26 236043.3 g1784279 204 475
26 236043.3 g707758 277 621
26 236043.3 4150892H1 309 572
26 236043.3 g1792258 414 803
26 236043.3 3420770H1 432 622
26 236043.3 2638855H1 615 846
26 236043.3 121222H1 615 730
27 445433.2 3287379H1 1 244
27 445433.2 2275475H1 193 424
27 445433.2 3967290T6 308 705
27 445433.2 3967290F6 315 723
27 445433.2 4133307H1 315 574
27 445433.2 3967290H1 315 558
27 445433.2 1343762F6 681 1042
29 257121.2 2808987H1 805 1039
29 257121.2 4021166H1 831 1064
29 257121.2 g1720349 2858 3353
29 257121.2 g1522235 2858 3196
29 257121.2 3517880H1 2876 3155
29 257121.2 4459330H1 2876 3127
29 257121.2 3917168H1 2886 3150
29 257121.2 3160987H1 2897 3193
29 257121.2 4506429H1 2901 2981
29 257121.2 4624935H1 2909 3181
29 257121.2 879657H1 3382 3640
29 257121.2 434236H1 3388 3610
29 257121.2 2078370H1 2935 3207
29 257121.2 5058836H1 2958 3241
29 257121.2 1955941 HI 2984 3250
29 257121.2 3993470H1 3015 3322
29 257121.2 2693754H1 3017 3296
29 257121.2 3528783H1 3020 3325
29 257121.2 2945721 HI 3030 3196
29 257121.2 2947643H1 3028 3355
29 257121.2 5271360H1 3029 3276
29 257121.2 g3840958 3443 3849
29 257121.2 406453H1 3445 3689
29 257121.2 865275H1 3451 3684
29 257121.2 2373951 HI 3455 3695
29 257121.2 g2329311 3465 3849
29 257121.2 5201726T6 3463 3823
29 257121.2 3929807H1 3466 3775
29 257121.2 4466537H1 3466 3723
29 257121.2 2071630H1 2781 3036
29 257121.2 2714703H1 2800 3056
29 257121.2 630218H1 2804 3049 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
29 257121.2 g2219708 2818 3192
29 257121.2 5435973H1 2403 2648
29 257121.2 g2189770 2409 2575
29 257121.2 3091740F6 2434 2892
29 257121.2 3091740H1 2435 2721
29 257121.2 4931375H1 2450 2729
29 257121.2 5086828H1 2466 2717
29 257121.2 4706266H1 2474 2701
29 257121.2 4623814H1 2489 2746
29 257121.2 1711729H1 2493 2682
29 257121.2 3808352H1 2493 2707
29 257121.2 g1999011 2496 2841
29 257121.2 2080982H1 2500 2772
29 257121.2 4936350H1 2507 2800
29 257121.2 2473816H1 2534 2761
29 257121.2 2473816F6 2534 3077
29 257121.2 2228396H1 2540 2791
29 257121.2 4021166F6 831 1284
29 257121.2 2051255H1 838 1128
29 257121.2 3001820F6 870 1041
29 257121.2 3001820H1 871 1152
29 257121.2 5395159H1 935 1013
29 257121.2 492727H1 1100 1333
29 257121.2 2738108H1 1122 1378
29 257121.2 3344641 HI 1132 1370
29 257121.2 526778H1 1241 1504
29 257121.2 310738H1 1296 1527
29 257121.2 2754594H1 1296 1556
29 257121.2 4055308H1 3034 3328
29 257121.2 4021166T6 3036 3558
29 257121.2 4465912H1 3059 3327
29 257121.2 5586546H1 3067 3312
29 257121.2 g1239705 3068 3332
29 257121.2 552938H1 3096 3365
29 257121.2 3730966H1 3111 3436
29 257121.2 g1444147 3121 3612
29 257121.2 5550566H1 3172 3413
29 257121.2 5507424H1 1840 2028
29 257121.2 5508405H1 1840 2087
29 257121.2 3000303H1 1849 2065
29 257121.2 g1975045 1853 2120
29 257121.2 5662088H1 1854 2082
29 257121.2 g3770956 1868 2224
29 257121.2 g3802745 1899 2216
29 257121.2 4892961 HI 1903 2189
29 257121.2 3479021 HI 1924 2149
29 257121.2 1690528H1 1938 2158
29 257121.2 4467223H1 1953 2159
29 257121.2 5270694H1 3395 3651
29 257121.2 gl719483 3568 3855 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
29 257121.2 g4531585 3586 3849
29 257121.2 3720345H1 3594 3759
29 257121.2 2569980H1 3601 3849
29 257121.2 g1203034 3610 3783
29 257121.2 g4450994 3614 3849
29 257121.2 4901641 HI 3614 3822
29 257121.2 4960977H1 2828 3096
29 257121.2 g2728590 2834 3223
29 257121.2 3162492H1 2842 3125
29 257121.2 gl719482 2858 3289
29 257121.2 g2211339 3417 3848
29 257121.2 g2659436 3422 3854
29 257121.2 g4296041 3428 3849
29 257121.2 5921004H1 3429 3679
29 257121.2 2962704H1 3431 3741
29 257121.2 5922274H1 3431 3715
29 257121.2 g2329245 3433 3703
29 257121.2 g4328182 3435 3849
29 257121.2 1994936R6 3438 3848
29 257121.2 1994936T6 3438 3808
29 257121.2 1994936H1 3438 3705
29 257121.2 865275T1 3439 3794
29 257121.2 453069H1 1980 2189
29 257121.2 5982875H1 2023 2298
29 257121.2 g2457731 2054 2450
29 257121.2 2883663H1 2077 2328
29 257121.2 1786163H1 2091 2273
29 257121.2 3433528H1 2097 2303
29 257121.2 2588747H2 2117 2375
29 257121.2 4715351H1 2157 2241
29 257121.2 4691328H1 2198 2462
29 257121.2 2904069H1 2226 2537
29 257121.2 4300967H1 2236 2508
29 257121.2 4624918H1 2909 3183
29 257121.2 2374252H1 2910 3120
29 257121.2 4909794H1 2922 3203
29 257121.2 1741105H1 2925 3159
29 257121.2 1741564H1 2925 3086
29 257121.2 1741564R6 2925 3384
29 257121.2 g531805 3303 3701
29 257121.2 3091740T6 3306 3809
29 257121.2 2697055H1 3308 3597
29 257121.2 1672059T6 3344 3809
29 257121.2 g2818402 3359 3858
29 257121.2 2423136H1 3377 3613
29 257121.2 879657T1 3382 3809
29 257121.2 g4329746 3472 3849
29 257121.2 g4243717 3477 3856
29 257121.2 3929886H1 3478 3759
29 257121.2 g2619701 3487 3892 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
29 257121.2 g2835679 3490 3849
29 257121.2 g2216408 3495 3849
29 257121.2 3040078H1 3500 3780
29 257121.2 g2261946 3498 3849
29 257121.2 gl 522116 3502 3855
29 257121.2 g3190675 3510 3848
29 257121.2 g3281587 3517 3852
29 257121.2 gl 186385 3517 3849
29 257121.2 g3069539 3519 3856
29 257121.2 g3229168 3523 3849
29 257121.2 g2278678 3527 3855
29 257121.2 g2595803 3528 3819
29 257121.2 g1994549 3533 3860
29 257121.2 g613905 3177 3513
29 257121.2 5905841 HI 3186 3500
29 257121.2 1444396H1 3186 3461
29 257121.2 g4187265 3195 3670
29 257121.2 2473816T6 3190 3808
29 257121.2 g4186245 3195 3664
29 257121.2 g3278632 3196 3616
29 257121.2 g1506304 3213 3436
29 257121.2 1658291 HI 3211 3453
29 257121.2 g1994550 2249 2499
29 257121.2 3053733H1 2279 2581
29 257121.2 5641114H1 2298 2545
29 257121.2 995725R1 2300 2819
29 257121.2 995725H1 2300 2596
29 257121.2 2173193F6 2302 2653
29 257121.2 2173193H1 2302 2536
29 257121.2 3474978H1 2324 2601
29 257121.2 2106564H1 2329 2585
29 257121.2 5171463H1 2343 2629
29 257121.2 3449591 HI 2355 2601
29 257121.2 2824470T6 2356 2941
29 257121.2 5546639H1 2387 2525
29 257121.2 5658068H1 2396 2642
29 257121.2 3771054H1 1386 1692
29 257121.2 2714558T6 1407 1749
29 257121.2 g2037431 1419 1693
29 257121.2 2436316H1 1459 1650
29 257121.2 g953893 1502 1633
29 257121.2 6075654H1 1487 1796
29 257121.2 g1055687 1504 1601
29 257121.2 g2034372 1557 1818
29 257121.2 1235661 HI 1567 1836
29 257121.2 2824470F6 1573 1997
29 257121.2 2824470H1 1573 1809
29 257121.2 g4509712 1585 1995
29 257121.2 g3700825 1587 1927
29 257121.2 4876427H1 1618 1807 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
29 257121.2 3297894H1 1657 1904
29 257121.2 g3764184 1663 1795
29 257121.2 4306167H1 1689 1809
29 257121.2 446319T6 1703 2175
29 257121.2 5984668H1 1802 2091
29 257121.2 5594456H1 1805 1931
29 257121.2 3202943H1 1818 2073
29 257121.2 309745H1 3396 3648
29 257121.2 4652103H1 3402 3556
29 257121.2 g3058761 3407 3849
29 257121.2 g3961167 3409 3844
29 257121.2 g3178632 3413 3849
29 257121.2 5645258H1 190 462
29 257121.2 g751765 209 449
29 257121.2 g751766 344 636
29 257121.2 2478708H1 363 607
29 257121.2 5544313H1 370 582
29 257121.2 1911275H1 460 725
29 257121.2 1437425F1 511 985
29 257121.2 1437426H1 511 734
29 257121.2 1437425H1 511 736
29 257121.2 3697654H1 541 823
29 257121.2 3333937H1 589 769
29 257121.2 2639996H1 706 952
29 257121.2 446319R6 788 1254
29 257121.2 446319H1 788 1039
29 257121.2 3068429F7 1 419
29 257121.2 3068429H1 1 291
29 257121.2 2821269H1 126 301
29 257121.2 3160523H1 3217 3501
29 257121.2 5024976H1 3222 3513
29 257121.2 3894771 HI 3241 3546
29 257121.2 3360915H1 3240 3354
29 257121.2 1427954T6 3250 3809
29 257121.2 1741564T6 3251 3811
29 257121.2 1892219H1 3250 3516
29 257121.2 2173193T6 3255 3819
29 257121.2 1861145H1 3261 3586
29 257121.2 1531024H1 3769 3849
29 257121.2 2608136H1 3540 3797
29 257121.2 2608136T6 3533 3805
29 257121.2 2608136F6 3540 3853
29 257121.2 gl210010 3540 3850
29 257121.2 g2805071 3540 3827
29 257121.2 g2218792 3542 3849
29 257121.2 2721666H1 3563 3814
29 257121.2 4901093H1 3614 3850
29 257121.2 g3092920 3617 3818
29 257121.2 4347921 HI 3623 3877
29 257121.2 3109370H1 3625 3723 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
29 257121.2 g1757345 3644 3855
29 257121.2 gl211126 3645 3857
29 257121.2 g1505472 3647 3864
29 257121.2 5565971 HI 3650 3853
29 257121.2 4613032H1 3668 3856
29 257121.2 892266H1 3672 3830
29 257121.2 3729288H1 3676 3853
29 257121.2 gl813011 3677 3855
29 257121.2 g2063050 3680 3849
29 257121.2 3729209T1 3681 3810
29 257121.2 g2063735 3707 3849
29 257121.2 g2882056 3741 3849
29 257121.2 1547677H1 3769 3844
29 257121.2 6024576H1 2558 2843
29 257121.2 4909221 HI 2607 2901
29 257121.2 1427954H1 2634 2884
29 257121.2 5170995H1 2648 2874
29 257121.2 1427954F6 2665 3120
29 257121.2 946401 HI 2666 2926
29 257121.2 1374579H1 2670 2923
29 257121.2 2261955H1 2684 2948
29 257121.2 3094766H1 2691 2994
29 257121.2 2741005H1 2693 2978
29 257121.2 4635067H1 2704 2978
29 257121.2 1007503H1 2718 3048
29 257121.2 5284328H1 2720 2957
29 257121.2 5064384H1 2731 2941
29 257121.2 1672059H1 2742 2924
29 257121.2 1672008H1 2742 2975
29 257121.2 1672059F6 2742 3123
29 257121.2 2410045H1 2774 3011
37 84399.1 2520472H1 1 226
37 84399.1 g4148125 155 499
38 350044.1 3110061 F7 1 276
38 350044.1 3110061H1 3 289
38 350044.1 4308349H1 158 426
38 350044.1 4308349F6 158 587
38 350044.1 5333549H1 185 413
38 350044.1 3399811 HI 405 650
38 350044.1 2288313H1 496 629
38 350044.1 4637040H1 583 844
38 350044.1 4637040F6 582 916
38 350044.1 4308349T6 662 1020
38 350044.1 308559H1 664 884
38 350044.1 g1803082 832 926
38 350044.1 3977826H1 852 968
39 441329.2 g3751157 1 412
39 441329.2 g1470664 342 578
39 441329.2 g1395945 342 644
39 441329.2 4327736H1 355 622 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
39 441329.2 132848H1 360 540
39 441329.2 132849R6 360 805
39 441329.2 131890H1 360 563
39 441329.2 131890R6 360 802
39 441329.2 gl 165579 361 542
39 441329.2 gl928191 371 650
39 441329.2 4204432F6 374 765
39 441329.2 g1734964 378 763
39 441329.2 3357071 HI 701 979
39 441329.2 3357071F6 701 1118
39 441329.2 131890T6 1077 1235
39 441329.2 g1733361 1084 1235
39 441329.2 132849T6 1123 1235
39 441329.2 4204432T6 1128 1235
40 442401.2 3349655H1 1 327
40 442401.2 4309840H1 10 304
40 442401.2 4349106H1 25 238
40 442401.2 5043378H1 42 296
40 442401.2 4789236H1 44 123
40 442401.2 5320882H1 45 180
40 442401.2 2551237H1 64 319
40 442401.2 4664370H1 71 322
40 442401.2 3510753H1 75 389
40 442401.2 693783H1 80 286
40 442401.2 693783R6 83 554
40 442401.2 3865603H1 88 388
40 442401.2 2289862H1 86 326
40 442401.2 3681694H1 92 386
40 442401.2 693783T6 128 736
40 442401.2 519767H1 511 741
41 444933.2 3492265H1 7 310
41 444933.2 gl 501708 7 263
41 444933.2 3155609H1 7 99
41 444933.2 g1474433 9 386
41 444933.2 3118539H1 9 310
41 444933.2 3295816H1 15 277
41 444933.2 1592931 HI 29 229
41 444933.2 1592931F6 29 395
41 444933.2 1592931T6 43 579
41 444933.2 3436778H1 1 229
42 481129.4 999203H1 234 552
42 481129.4 999203T1 234 708
42 481129.4 g3278054 236 751
42 481129.4 3868296H1 240 560
42 481129.4 g4522433 240 752
42 481129.4 3137701H1 240 575
42 481129.4 g3417930 241 746
42 481129.4 3868754H1 240 570
42 481129.4 g4070375 243 752
42 481129.4 715742H1 248 618 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
42 481129.4 4950629H1 245 592
42 481129.4 g3644668 250 755
42 481129.4 1577433H1 250 516
42 4811294 g3446453 265 747
42 481129.4 2055077H1 267 589
42 481129.4 g2288119 272 746
42 4811294 3358220H1 293 617
42 481129.4 g3797800 295 747
42 481129.4 g2113046 296 749
42 4811294 g2740428 301 747
42 481129.4 g2268545 312 747
42 481129.4 g4087282 314 750
42 4811294 g2017050 320 622
42 481129.4 g1924476 320 647
42 481129.4 g3735602 323 748
42 4811294 g4532931 324 747
42 4811294 g3734942 324 751
42 481129.4 g273 174 325 747
42 4811294 g3960674 330 751
42 4811294 g2252043 328 746
42 4811294 g3330470 342 747
42 4811294 g3960381 342 755
42 481129.4 g4452123 351 746
42 4811294 g3678389 352 747
42 4811294 1632555H1 353 564
42 4811294 1632539H1 353 571
42 481129.4 4228443H1 353 686
42 4811294 g3108753 369 749
42 4811294 g2319165 368 747
42 4811294 g3755458 374 754
42 481129.4 g4086634 397 747
42 4811294 g2322475 404 746
42 4811294 g3750698 406 748
42 481129.4 g2021853 411 746
42 4811294 3099690H1 423 747
42 4811294 4125491 HI 425 735
42 481129.4 5107680H1 443 746
42 4811294 1253080F1 454 746
42 4811294 2741014H1 456 747
42 4811294 g4086632 472 747
42 4811294 3381102H1 195 363
42 481129.4 3136744H1 132 344
42 481129.4 2485548H1 37 110
42 4811294 3238530H1 36 320
42 481129.4 5332434H1 132 262
42 481129.4 1743373H1 37 342
42 481129.4 2398059H1 30 282
42 481129.4 5299970H1 36 291
42 481129.4 4857940H1 132 351
42 481129.4 982689H1 28 284 TABLE 4
HDNO: Template ID Component ID Start Stop
42 4811294 1684768H1 34 296
42 4811294 4901916H1 29 347
42 4811294 4340959H1 25 317
42 481129.4 1275760H1 195 375
42 481129.4 gl975121 132 336
42 4811294 534025H1 30 348
42 4811294 3555252H1 24 317
42 4811294 1504151 HI 30 329
42 481129.4 4652858H1 195 379
42 4811294 4638612H1 132 320
42 4811294 4801179H1 30 310
42 4811294 1970489H1 35 306
42 481129.4 2497883H1 30 272
42 481129.4 2557615H1 132 324
42 4811294 4079990H1 195 386
42 4811294 3555091 HI 31 350
42 481129.4 g1635875 160 388
42 481129.4 3010470H1 132 368
42 4811294 g1685660 488 846
42 481129.4 2716085H1 492 747
42 4811294 g2669356 508 750
42 481129.4 g2035379 508 768
42 4811294 g4330124 517 749
42 4811294 gl 125228 503 768
42 4811294 g1237906 515 746
42 481129.4 1253080H1 547 746
42 4811294 1924052H1 559 747
42 4811294 1444584H1 557 747
42 4811294 3089459H1 563 755
42 481129.4 1952233H1 596 746
42 481129.4 g2269237 609 746
42 4811294 2058183R6 620 747
42 481129.4 2058183H1 620 747
42 4811294 g3321468 627 746
42 4811294 g2277314 629 747
42 481129.4 4363320H1 652 742
42 481129.4 g2752791 670 746
42 481129.4 3221190H1 49 104
42 4811294 529956H1 197 303
42 4811294 1781280H1 202 315
42 4811294 586079H1 35 104
42 4811294 644429H1 37 104
42 4811294 4713384H1 32 97
42 481129.4 1434389H1 30 104
42 4811294 2286414H1 30 104
42 4811294 1648951 HI 34 111
42 481129.4 3589355H1 36 111
42 4811294 1916331H1 195 338
42 4811294 880829H1 28 97
42 481129.4 2475170H1 195 350 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
42 4811294 gl 301383 263 352
42 481129.4 4612347H1 169 315
42 4811294 116571H1 25 83
42 481129.4 gl023181 141 205
42 4811294 835155H1 37 333
42 4811294 4153116H1 132 329
42 4811294 4300976H1 132 343
42 4811294 962735H1 132 324
42 481129.4 4904613H2 132 339
42 481129.4 4904321 HI 195 362
42 481129.4 4130260H1 132 334
42 4811294 534025F1 1 184
42 4811294 5165213H2 4 265
42 4811294 g3085628 187
42 4811294 g2836097 184
42 481129.4 g2397633 179
42 481129.4 g2669712 181
42 4811294 811971T1 191
42 4811294 811971H1 67
42 481129.4 gl 578417 184
42 4811294 g3016145 253
42 4811294 g1425361 232
42 4811294 g2237584 231
42 4811294 g4072976 234
42 481129.4 g3076557 252
42 4811294 3716227H1 125
42 481129.4 g2350483 232
42 4811294 g1289724 184
42 4811294 4830687H1 14 227
42 4811294 1270745H1 82
42 4811294 g3423624 187
42 4811294 g1685572 232
42 481129.4 g2907402 79
42 4811294 g2987865 235
42 481129.4 4664951 HI 115
42 4811294 gl 114304 162
42 481129.4 1694416H1 78
42 481129.4 g4076242 234
42 4811294 g2806310 181
42 4811294 g3110520 231
42 481129.4 g3178699 235
42 481129.4 5691870H1 56
42 481129.4 g2408708 232
42 481129.4 g3070820 231
42 481129.4 gll94184 183
42 481129.4 g3400227 296
42 481129.4 g1080367 151
42 4811294 g2768589 231
42 481129.4 g3804766 184
42 481129.4 g3190855 232 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
42 481129.4 g1087452 267
42 4811294 4065091 HI 169
42 481129.4 g2838959 236
42 4811294 3091849H1 226
42 4811294 g2263870 183
42 481129.4 g2279285 239
42 481129.4 2755370H1 184
42 4811294 2757311 HI 184
42 4811294 863475H1 192
42 4811294 g1689421 183
42 4811294 5528923H1 19 211
42 4811294 g1506021 1 184
42 481129.4 2467514H1 10 261
42 481129.4 2943819H1 15 312
42 4811294 g1043884 16 196
42 481129.4 4461552H1 5 231
42 4811294 gl 281569 1 531
42 481129.4 g727471 1 234
42 4811294 4889929H1 29 314
42 4811294 4985113H1 29 354
42 481129.4 1488272H1 5 319
42 4811294 2450834F6 6 558
42 4811294 2450834H1 6 287
42 481129.4 g2027943 7 201
42 4811294 2394311H2 8 123
42 4811294 3372442H1 1 258
42 481129.4 g3307272 28 238
42 4811294 3773060H1 38 366
42 481129.4 4125777H1 10 329
42 481129.4 5159564H1 12 302
42 4811294 3233460H1 12 297
42 4811294 5552762H1 12 315
42 481129.4 593632H1 12 123
42 4811294 4513470H1 13 313
42 4811294 5115162H1 44 356
42 481129.4 5039159H2 15 286
42 4811294 2134140H1 15 328
42 481129.4 5943202H1 44 374
42 481129.4 027622R6 17 589
42 4811294 027622H1 17 197
42 481129.4 3115953H1 46 372
42 481129.4 3489959H1 46 382
42 4811294 5166761 HI 44 322
42 481129.4 3626341 HI 18 386
42 481129.4 3645933H1 48 327
42 4811294 3159541 HI 19 348
42 481129.4 2741058H1 52 282
42 481129.4 1475821 HI 50 252
42 481129.4 4567661 HI 22 350
42 481129.4 3601462H1 22 394 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
42 481129.4 4595577H1 53 283
42 4811294 3819717H1 22 426
42 4811294 4975524H1 22 359
42 4811294 2084168H1 50 348
42 4811294 5529123H1 18 212
42 4811294 5700770H1 52 344
42 481129.4 5701471H1 52 355
42 4811294 g3134982 45 234
42 4811294 4979603H1 52 355
42 4811294 3202264H1 23 321
42 481129.4 4938763H1 16 130
42 481129.4 4202906H1 8 274
42 481129.4 526404H1 22 322
42 481129.4 2665708H1 21 280
42 481129.4 2941705H1 22 327
42 4811294 gl321143 11 346
42 4811294 g2021854 22 337
42 481129.4 1833977H1 22 134
42 4811294 2100632H1 12 285
42 4811294 3675543H1 12 320
42 4811294 3186510H1 13 400
42 4811294 3229333H1 14 321
42 4811294 4885571 HI 19 306
42 4811294 3074685H1 16 321
42 4811294 3663968H1 16 329
42 4811294 g2154555 1 29
42 4811294 863475R1 1 192
42 4811294 4230048H1 1 176
42 4811294 3693558H1 18 328
42 4811294 g1648658 1 23
42 481129.4 584205H1 18 309
42 481129.4 4227248H1 21 324
42 4811294 g1043979 28 415
42 4811294 g2142101 1 24
42 4811294 4203722H1 22 321
42 4811294 4174825H1 22 337
42 481129.4 5115519H1 23 321
42 481129.4 3133373H1 25 334
42 481129.4 1275760F6 1 147
42 481129.4 1275760F1 1 76
42 4811294 2051350H1 27 350
42 4811294 4341005H1 27 398
42 4811294 3134845H1 1 260
42 481129.4 3484150H1 1 316
42 481129.4 4584348H1 1 279
42 481129.4 g2004902 1 283
42 481129.4 4374817H1 1 288
42 481129.4 g1967486 1 183
42 481129.4 4147580H1 1 267
42 481129.4 g1425470 1 78 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
42 4811294 4276424H1 1 301
42 4811294 082654H1 15 171
42 481129.4 g3003216 1 306
42 4811294 g1648659 1 183
42 4811294 4563261 HI 1 255
42 481129.4 4563351 HI 12 136
42 481129.4 116571F1 1 233
42 481129.4 g4372584 1 234
42 481129.4 3994691 HI 23 288
42 481129.4 g2437312 1 188
42 4811294 136145F1 1 184
42 4811294 2768229H1 1 256
42 4811294 5852546H1 1 272
42 4811294 5844492H1 6 279
42 4811294 1727158H1 8 249
42 4811294 1950091 HI 8 264
42 481129.4 3204976H1 10 290
42 481129.4 4554858H1 10 275
42 4811294 5840991 H2 11 303
42 481129.4 5840890H2 11 314
42 481129.4 4559105H1 12 298
42 4811294 871105H1 12 123
42 4811294 4998348H1 12 293
42 4811294 871105R1 12 123
42 4811294 4770486H1 13 287
42 4811294 3426271HI 14 295
42 4811294 3273645H1 14 298
42 4811294 4502129H1 14 202
42 481129.4 3403224H1 15 221
42 4811294 1511018H1 15 89
42 4811294 4502229H1 15 288
42 4811294 4042436H1 8 283
42 4811294 3845464H1 10 357
42 4811294 3720453H1 12 340
42 481129.4 1998071 HI 22 123
42 4811294 5835243H1 22 290
42 4811294 3801167H1 22 236
42 4811294 746353H1 12 243
42 4811294 g1685558 13 441
42 481129.4 2537659H1 15 303
42 481129.4 1728205H1 13 209
42 481129.4 2674637H1 15 271
42 4811294 4855434H1 14 293
42 4811294 2943583H2 15 322
42 4811294 116571 Rl 1 182
42 481129.4 g1320320 1 363
42 481129.4 2801342H1 5 264
42 481129.4 5528955H1 21 208
42 481129.4 3618142H1 24 377
42 481129.4 122118H1 17 164 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
42 4811294 3580438H1 69 320
42 481129.4 g1638276 25 435
42 4811294 833841Tl 40 708
42 4811294 3997421 HI 26 345
42 4811294 4110340H1 56 374
42 4811294 2403135H1 58 320
42 4811294 g1969685 58 472
42 4811294 3026745H1 57 366
42 481129.4 833841 HI 40 406
42 4811294 5681519H1 42 198
42 4811294 3987429H1 58 376
42 4811294 51 7261H2 70 330
42 4811294 880829R1 29 768
42 4811294 g1954123 46 346
42 481129.4 755972H1 59 323
42 481129.4 755972R1 59 709
42 481129.4 3944829H1 77 366
42 4811294 1546083H1 58 262
42 481129.4 g1496701 1 184
42 481129.4 962735R2 78 716
42 481129.4 2561965H1 32 359
42 481129.4 g2008330 80 340
42 481129.4 881179T1 30 687
42 481129.4 534025R1 32 572
42 481129.4 871105T1 54 123
42 481129.4 g1956736 64 347
42 4811294 4800988H1 83 224
42 4811294 g1685765 83 403
42 4811294 1230023H1 32 172
42 4811294 1805729H1 27 189
42 4811294 1320892H1 38 321
42 481129.4 1599902H1 38 290
42 4811294 4588734H1 85 374
42 481129.4 g1955622 70 445
42 481129.4 3517903H1 40 255
42 481129.4 136145R1 69 590
42 4811294 4979660H1 40 354
42 4811294 1741320H1 42 338
42 4811294 5117019H1 88 386
42 4811294 g1924567 88 536
42 4811294 2343536H1 89 355
42 481129.4 4536803H1 90 398
42 481129.4 g2158823 96 655
42 481129.4 g1958858 97 676
42 481129.4 g828123 93 501
42 481129.4 g3988556 97 621
42 481129.4 g3096874 99 539
42 481129.4 g3178165 107 566
42 481129.4 g4079967 no 541
42 481129.4 465693H1 66 199 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
42 4811294 g3003210 111 467
42 481129.4 5265746H1 120 374
42 481129.4 966316H1 118 374
42 4811294 1458085H1 122 396
42 4811294 1457484H1 122 305
42 4811294 2109149H1 122 442
42 481129.4 2109149R6 123 704
42 4811294 g1243536 77 215
42 4811294 958148H1 122 431
42 4811294 5020591Tl 124 705
42 481129.4 g1087561 133 459
42 481129.4 g1958920 135 700
42 4811294 gl 147415 139 444
42 4811294 g3890878 103 203
42 4811294 2401220H1 144 390
42 481129.4 3223013H1 149 494
42 4811294 1680890H1 149 361
42 4811294 gl 298313 155 667
42 481129.4 828345H1 143 226
42 481129.4 3441046H1 159 442
42 481129.4 2109149T6 163 707
42 4811294 2004957H1 176 484
42 4811294 6063286H1 180 511
42 481129.4 5020591 HI 179 501
42 4811294 2450834T6 182 707
42 4811294 027622T6 183 830
42 481129.4 5597771 HI 189 470
42 4811294 821831T6 192 705
42 4811294 821831 Rl 192 746
42 4811294 821831 R6 192 746
42 4811294 821831F1 192 757
42 481129.4 g2252207 199 748
42 481129.4 1457484R1 199 746
42 481129.4 g3736470 203 746
42 4811294 g1295465 204 757
42 4811294 5185783H1 205 496
42 4811294 g2115256 211 352
42 4811294 4085165H1 215 541
42 481129.4 g1577977 221 716
42 4811294 g3593921 222 750
42 481129.4 g3429019 222 747
42 4811294 5221813H2 225 517
42 481129.4 5863560H1 232 539
42 481129.4 999208H1 234 544
42 481129.4 999203R1 234 750
42 481129.4 g3649202 235 753
42 4811294 g2265393 234 751
42 481129.4 4049323H1 235 584
43 481999.1 1255239H1 838 1104
43 481999.1 4913234H1 397 512 TABLE 4
- ID NO: Template ID Component ID Start Stop
43 481999.1 1724376H1 864 932
43 481999.1 1509213H1 819 1012
43 481999.1 1849705H1 281 501
43 481999.1 1509213F6 819 1104
43 481999.1 1476972F6 260 574
43 481999.1 g2195301 866 1104
43 481999.1 g985997 864 941
43 481999.1 880602R1 397 512
43 481999.1 g1980533 1 283
43 481999.1 g2195281 987 1104
43 481999.1 5526658H1 780 991
43 481999.1 880602H1 394 457
43 481999.1 1255206H1 838 1104
43 481999.1 1509479F6 819 1104
43 481999.1 3457008H1 397 481
43 481999.1 3641330H1 723 1014
43 481999.1 4181741H1 717 799
43 481999.1 3384087F6 604 857
43 481999.1 4760678H1 1 286
43 481999.1 1509221 HI 819 1006
43 481999.1 1509455H1 819 997
43 481999.1 2603491 HI 880 1104
43 481999.1 170070H1 797 982
43 481999.1 3427420F6 521 604
43 481999.1 4760678F6 1 499
43 481999.1 4913234F6 235 670
43 481999.1 4072789H1 237 499
43 481999.1 1524891F6 269 890
43 481999.1 398973R1 305 830
43 481999.1 4972169H1 420 695
43 481999.1 4357304H1 435 710
43 481999.1 4181741 F6 718 1107
43 481999.1 3123901F6 380 434
43 481999.1 5585642H1 650 868
43 481999.1 1724376F6 864 941
43 481999.1 2938884H1 864 941
43 481999.1 3369038H1 429 706
43 481999.1 g1148977 1 387
43 481999.1 gl971119 842 1104
43 481999.1 gl 761297 704 1005
43 481999.1 1476972H1 260 455
43 481999.1 4211180H1 642 873
43 481999.1 g3665013 371 434
43 481999.1 5153580H1 813 1066
43 481999.1 g2141617 440 513
43 481999.1 1509479H1 819 997
46 338992.1 5510632H1 1 202
46 338992.1 4782751 F6 127 187
46 338992.1 4782751 HI 127 372
46 338992.1 2987413H1 192 478 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
46 338992.1 6064208H1 204 465
46 338992.1 g1984325 272 505
46 338992.1 g3239921 294 653
46 338992.1 g2026718 300 591
46 338992.1 g2816869 321 569
46 338992.1 4760384H1 492 580
46 338992.1 4760384F6 492 965
46 338992.1 1305496F6 802 1270
46 338992.1 1305496H1 802 945
46 338992.1 3617505H1 823 1024
46 338992.1 g875546 878 1132
46 338992.1 g669800 877 1199
46 338992.1 g874649 878 1180
46 338992.1 g771213 1011 1062
46 338992.1 3211592H1 1056 1292
46 338992.1 093259H1 1081 1322
46 338992.1 926880H1 1123 1363
46 338992.1 1366443H1 1137 1385
46 338992.1 1366443R6 1137 1466
46 338992.1 4960778H1 1160 1431
46 338992.1 4625867H1 1224 1487
46 338992.1 3383444H1 1259 1504
46 338992.1 5640688H1 1417 1657
46 338992.1 4030718H1 1568 1830
46 338992.1 4030718F6 1568 1945
46 338992.1 2742284H1 1620 1870
51 206603.1 g3278540 1 465
51 206603.1 g4390504 25 492
51 206603.1 g3870096 41 504
51 206603.1 gl 109407 277 604
51 206603.1 5631413H1 367 608
51 206603.1 5631413F6 367 812
51 206603.1 1992082H1 531 726
51 206603.1 6092061 HI 626 906
52 435694.2 4936540H1 1112 1364
52 435694.2 5021371 HI 1139 1417
52 435694.2 3726226H1 1155 1450
52 435694.2 g2015121 1170 1366
52 435694.2 456419H1 1185 1425
52 435694.2 461227R6 1185 1685
52 435694.2 456301 HI 1185 1433
52 435694.2 461227H1 1185 1446
52 435694.2 460920H1 1185 1432
52 435694.2 461106H1 1185 1440
52 435694.2 457987H1 1185 1424
52 435694.2 458221 HI 1185 1435
52 435694.2 454834R1 1185 1705
52 435694.2 461049H1 1185 1425
52 435694.2 454834H1 1185 1424
52 435694.2 4957324H1 266 486 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
52 435694.2 3390485H1 267 486
52 435694.2 1437407H1 243 486
52 435694.2 5902323H1 243 486
52 435694.2 3676724H1 271 486
52 435694.2 1437407F6 243 486
52 435694.2 1436837H1 243 480
52 435694.2 5900454H1 243 486
52 435694.2 2706491 HI 270 566
52 435694.2 2837043H1 244 486
52 435694.2 3165547H1 246 486
52 435694.2 5903233H1 247 568
52 435694.2 3687630H1 251 565
52 435694.2 4268779H1 252 486
52 435694.2 3460048H1 251 487
52 435694.2 3077826H1 253 501
52 435694.2 4121058H1 271 486
52 435694.2 4900932H1 273 562
52 435694.2 3615215F6 280 731
52 435694.2 832322H1 252 486
52 435694.2 3615215H1 280 588
52 435694.2 2406515H1 254 486
52 435694.2 3141771H1 327 608
52 435694.2 3615215T6 351 720
52 435694.2 g1774842 351 728
52 435694.2 3932194H1 351 486
52 435694.2 4003539H1 351 589
52 435694.2 g587196 351 593
52 435694.2 1285417F6 400 708
52 435694.2 1285417H1 400 637
52 435694.2 2763950H1 502 762
52 435694.2 2415062H1 512 710
52 435694.2 2415070H1 512 702
52 435694.2 3860483H1 517 813
52 435694.2 g1766458 520 850
52 435694.2 g3076400 519 940
52 435694.2 823127H1 556 831
52 435694.2 g3190613 562 745
52 435694.2 2926224H2 688 999
52 435694.2 2708490H1 690 942
52 435694.2 g4311248 702 1175
52 435694.2 g4389608 707 1164
52 435694.2 g3700432 738 1174
52 435694.2 g1773867 738 1172
52 435694.2 1285417T6 758 904
52 435694.2 g4111706 797 1172
52 435694.2 774013H1 825 1036
52 435694.2 1454843H1 899 1163
52 435694.2 1450887FI 899 1172
52 435694.2 3742523H1 896 1163
52 435694.2 1450887H1 899 1152 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
52 435694.2 3742566H1 899 1163
52 435694.2 1454843T6 913 1128
52 435694.2 4710458H1 961 1249
52 435694.2 4977443H1 1005 1268
52 435694.2 3237593H1 1060 1304
52 435694.2 4705379T6 1071 1144
52 435694.2 4853112H1 1100 1295
52 435694.2 2666646T6 1628 2175
52 435694.2 2959842H1 1635 1861
52 435694.2 2963934T6 1633 2162
52 435694.2 3639070H1 1655 1967
52 435694.2 4322530H1 1660 1782
52 435694.2 5062716H1 1673 1795
52 435694.2 1710033H1 1703 1959
52 435694.2 5021371T1 1715 2162
52 435694.2 3894718H1 1752 1968
52 435694.2 2151922H1 1765 2018
52 435694.2 gl645818 1810 2162
52 435694.2 2323908H1 1816 1878
52 435694.2 g4070415 1817 2162
52 435694.2 g4175351 1821 2162
52 435694.2 g3595864 1824 2162
52 435694.2 g3434496 1843 2162
52 435694.2 g1775010 1845 2162
52 435694.2 gl645819 1872 2162
52 435694.2 gl 164565 1885 2262
52 435694.2 4701327H1 1906 2173
52 435694.2 g1766363 1910 2162
52 435694.2 2253564R6 1939 2171
52 435694.2 2253564H1 1939 2195
52 435694.2 4540530H1 1951 2181
52 435694.2 4540144H1 1953 2199
52 435694.2 1833058H1 1959 2171
52 435694.2 g3003709 1979 2171
52 435694.2 g3959558 1980 2162
52 435694.2 g2358889 2057 2171
52 435694.2 g4264824 2059 2162
52 435694.2 474448H1 2096 2171
52 435694.2 4615243H1 1 250
52 435694.2 2533844H1 21 246
52 435694.2 g3154852 56 491
52 435694.2 4270549H1 86 338
52 435694.2 3330903H1 114 331
52 435694.2 4315068H1 219 423
52 435694.2 4315053H1 221 486
52 435694.2 4706408H1 242 486
52 435694.2 1436837F1 243 695
52 435694.2 5900458H1 243 486
52 435694.2 5903501 HI 242 486
52 435694.2 5903201 HI 243 486 TABLE 4
SEQ ID NO: Template ID Component ID Start Stop
52 435694.2 5426328H1 1199 1361
52 435694.2 g1989927 1223 1525
52 435694.2 gl989319 1223 1632
52 435694.2 g572779 1276 1621
52 435694.2 4611420H1 1351 1610
52 435694.2 4243682H1 1370 1625
52 435694.2 5868132H1 1375 1642
52 435694.2 792533H1 1412 1646
52 435694.2 g1775555 1428 1811
52 435694.2 1469570H1 1472 1684
52 435694.2 1469570F6 1472 1787
52 435694.2 2461531 HI 1485 1710
52 435694.2 g2220895 1488 1893
52 435694.2 gl 196070 1498 1783
52 435694.2 3561975H1 1527 1843
52 435694.2 1830391 HI 1583 1847
Table 5
Program Description Reference Parameter Threshold
ABI FACTURA A program that removes vector sequences and PE Biosystems, Foster City, CA masks ambiguous bases in nucleic acid sequences
ABI/PARACEL FDF A Fast Data Finder useful in comparing and PE Biosystems, Foster City, CA, Mismatch <50% annotating amino acid or nucleic acid sequences Paracel Inc , Pasadena, CA
ABI AutoAssembler A program that assembles nucleic acid sequences PE Biosystems, Foster City, CA
BLAST A Basic Local Alignment Search Tool useful in Altschul, S F et al (1990) J Mol Biol ESTs Probability value= 1 0E-8 sequence similarity search for amino acid and 215 403-410, Altschul, S F et al (1997) or less nucleic acid sequences BLAST includes five Nucleic Acids Res 25 3389-3402 Full Length sequences Probabili functions blastp, blastn, blastx, tblastn, and tblastx value= 1 OE-10 or less
FASTA A Pearson and Lipman algorithm that searches for Pearson, W R and D J Lipman (1988) Proc ESTs fasta E value=l 06E-6 similarity between a query sequence and a group of Nati Acad Sci USA 85 2444-2448, Pearson, Assembled ESTs fasta Identιty= sequences of the same type FASTA comprises as W R (1990) Methods Enzymol 183 63-98, 95% or greater and least five functions fasta, tfasta, fastx, tfastx, and and Smith, T F and M S Waterman (1981) Match length=200 bases or great ssearch Adv Appl Math 2 482-489 fastx E value=l 0E-8 or less
Full Length sequences fastx score=100 or greater
BLIMPS A BLocks IMProved Searcher that matches a Henikoff, S and J G Henikoff (1991) Nucleic Score=1000 or greater, sequence against those in BLOCKS, PRINTS, Acids Res 19 6565-6572, Henikoff, J G and Ratio of Score/Strength = 0 75 o DOMO, PRODOM, and PFAM databases to search S Henikoff (1996) Methods Enzymol larger, and, if applicable, for gene families, sequence homology, and structural 266 88-105, and Attwood, T K et al (1997) J Probability value= 1 0E-3 or less fingerpi int regions Chem Inf Comput Sci 37 417-424
HMMER An algorithm for searching a query sequence against Krogh, A et al (1994) J Mol Biol Score=10-50 bits for PFAM hits hidden Markov model (HMM)-based databases of 235 1501-1531, Sonnhammer, E L L et al depending on individual protein protein family consensus sequences, such as PFAM (1988) Nucleic Acids Res 26 320-322 families
Table 5 (cont.)
Program Description Reference Parameter Threshold
PiofileScan An algorithm that searches for structural and Gπbskov, M et al (1988) CABIOS 4 61-66, Normalized quality score≥GCG- sequence motifs in protein sequences that match Gπbskov, M et al (1989) Methods Enzymol specified "HIGH" value for that sequence patterns defined in Prosite 183 146-159, Bairoch, A et al (1997) particular Prosite motif Nucleic Acids Res 25 217-221 Generally, score=l 4-2 1
Phied A base-calling algorithm that examines automated Ewing, B et al (1998) Genome Res sequencer traces with high sensitivity and 8 175-185, Ewing, B and P Green probability (1998) Genome Res 8 186-194
Phiap A Phils Revised Assembly Program including Smith, T F and M S Waterman (1981) Adv Score= 120 or greater, SWAT and CrossMatch, programs based on Appl Math 2 482-489, Smith, T F and M S Match length= 56 or greater efficient implementation of the Smith- Waterman Waterman (1981) J Mol Biol 147 195-197, algorithm, useful in searching sequence homology and Green, P , University of Washington, and assembling DNA sequences Seattle, WA
Consed A graphical tool for viewing and editing Phrap Gordon, D et al (1998) Genome assemblies Res 8 195-202
SPScan A weight matrix analysis program that scans protein Nielson, H et al (1997) Protein Engineering Score=3 5 or greater sequences for the presence of secretory signal 10 1-6, Claveπe. J M and S Audic (1997) peptides CABIOS 12 431-439
Motifs A program that searches amino acid sequences for Bairoch, A et al (1997) Nucleic Acids Res patterns that matched those defined in Prosite 25 217-221 , Wisconsin Package Program Manual, version 9, page M51-59, Genetics Computer Group, Madison, WI

Claims

CLAIMS What is claimed is:
1. An isolated polynucleotide comprising a polynucleotide sequence selected from the group 5 consisting of: a) a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52, b) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52, c) a polynucleotide sequence complementary to a), 0 d) a polynucleotide sequence complementary to b), and e) an RNA equivalent of a) through d).
2. An isolated polynucleotide of claim 1 , comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOJ-52. 5
3. An isolated polynucleotide comprising at least 60 contiguous nucleotides of a polynucleotide of claim 1.
4. A composition for the detection of expression of diagnostic and therapeutic polynucleotides o comprising at least one of the polynucleotides of claim 1 and a detectable label.
5. A method for detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide of claim 1 , the method comprising: a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction 5 amplification, and b) detecting the presence or absence of said amplified target polynucleotide or fragment thereof, and, optionally, if present, the amount thereof.
6. A method for detecting a target polynucleotide in a sample, said target polynucleotide o comprising a sequence of a polynucleotide of claim 1 , the method comprising: a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide, and 5 b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof.
7. A method of claim 5, wherein the probe comprises at least 30 contiguous nucleotides.
5 8. A method of claim 5, wherein the probe comprises at least 60 contiguous nucleotides.
9. A recombinant polynucleotide comprising a promoter sequence operably linked to a polynucleotide of claim 1.
0 10. A cell transformed with a recombinant polynucleotide of claim 9.
11. A transgenic organism comprising a recombinant polynucleotide of claim 9.
12. A method for producing a diagnostic and therapeutic polypeptide, the method comprising: 5 a) culturing a cell under conditions suitable for expression of the diagnostic and therapeutic polypeptide, wherein said cell is transformed with a recombinant polynucleotide of claim 9, and b) recovering the diagnostic and therapeutic polypeptide so expressed.
13. A purified diagnostic and therapeutic polypeptide (DITHP) encoded by at least one of the o polynucleotides of claim 2.
14. An isolated antibody which specifically binds to a diagnostic and therapeutic polypeptide of claim 13.
5 15. A method of identifying a test compound which specifically binds to the diagnostic and therapeutic polypeptide of claim 13, the method comprising the steps of: a) providing a test compound; b) combining the diagnostic and therapeutic polypeptide with the test compound for a sufficient time and under suitable conditions for binding; and 0 c) detecting binding of the diagnostic and therapeutic polypeptide to the test compound, thereby identifying the test compound which specifically binds the diagnostic and therapeutic polypeptide.
16. A microarray wherein at least one element of the microarray is a polynucleotide of claim 3.
17. A method for generating a transcript image of a sample which contains polynucleotides, the method comprising the steps of: a) labeling the polynucleotides of the sample, b) contacting the elements of the microarray of claim 16 with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample.
18. A method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide sequence of claim 1, the method comprising: a) exposing a sample comprising the target polynucleotide to a compound, and b) detecting altered expression of the target polynucleotide.
19. A method of claim 6 for toxicity testing of a compound, further comprising: c) comparing the presence, absence or amount of said target polynucleotide in a first biological sample and a second biological sample, wherein said first biological sample has been contacted with said compound, and said second sample is a control, whereby a change in presence, absence or amount of said target polynucleotide in said first sample, as compared with said second sample, is indicative of toxic response to said compound.
EP00938123A 1999-06-01 2000-05-31 Molecules for diagnostics and therapeutics Withdrawn EP1268758A2 (en)

Applications Claiming Priority (49)

Application Number Priority Date Filing Date Title
US13716199P 1999-06-01 1999-06-01
US137161P 1999-06-01
US13725999P 1999-06-02 1999-06-02
US13710999P 1999-06-02 1999-06-02
US13711499P 1999-06-02 1999-06-02
US13725899P 1999-06-02 1999-06-02
US13717399P 1999-06-02 1999-06-02
US13726099P 1999-06-02 1999-06-02
US13711399P 1999-06-02 1999-06-02
US137109P 1999-06-02
US137258P 1999-06-02
US137113P 1999-06-02
US137260P 1999-06-02
US137173P 1999-06-02
US137259P 1999-06-02
US137114P 1999-06-02
US13733799P 1999-06-03 1999-06-03
US13741799P 1999-06-03 1999-06-03
US13739699P 1999-06-03 1999-06-03
US13741199P 1999-06-03 1999-06-03
US137396P 1999-06-03
US137411P 1999-06-03
US137337P 1999-06-03
US137417P 1999-06-03
US14743699P 1999-08-04 1999-08-04
US14737799P 1999-08-04 1999-08-04
US147436P 1999-08-04
US147377P 1999-08-04
US14754999P 1999-08-05 1999-08-05
US14753699P 1999-08-05 1999-08-05
US14782499P 1999-08-05 1999-08-05
US14754299P 1999-08-05 1999-08-05
US14754799P 1999-08-05 1999-08-05
US14752799P 1999-08-05 1999-08-05
US14753099P 1999-08-05 1999-08-05
US14750099P 1999-08-05 1999-08-05
US14754199P 1999-08-05 1999-08-05
US14752099P 1999-08-05 1999-08-05
US147500P 1999-08-05
US147824P 1999-08-05
US147536P 1999-08-05
US147530P 1999-08-05
US147549P 1999-08-05
US147520P 1999-08-05
US147527P 1999-08-05
US147542P 1999-08-05
US147547P 1999-08-05
US147541P 1999-08-05
PCT/US2000/015404 WO2000073509A2 (en) 1999-06-01 2000-05-31 Molecules for diagnostics and therapeutics

Publications (1)

Publication Number Publication Date
EP1268758A2 true EP1268758A2 (en) 2003-01-02

Family

ID=27586737

Family Applications (1)

Application Number Title Priority Date Filing Date
EP00938123A Withdrawn EP1268758A2 (en) 1999-06-01 2000-05-31 Molecules for diagnostics and therapeutics

Country Status (3)

Country Link
EP (1) EP1268758A2 (en)
CA (1) CA2381319A1 (en)
WO (1) WO2000073509A2 (en)

Families Citing this family (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6025191A (en) * 1995-06-07 2000-02-15 Ludwig Institute For Cancer Research Isolated nucleic acid molecules which encode a melanoma specific antigen and uses thereof
WO2001062926A2 (en) * 2000-02-25 2001-08-30 Millennium Pharmaceuticals, Inc. 44576, a novel g-protein coupled receptor and uses therefor
WO2001053836A2 (en) * 2000-01-24 2001-07-26 Millennium Pharmaceuticals, Inc. Identification, assessment, prevention, and therapy of prostate cancer
WO2001066765A2 (en) * 2000-03-07 2001-09-13 Millennium Pharmaceuticals, Inc. 26583, a serine/threonine phosphatase and uses thereof
WO2001072962A2 (en) * 2000-03-24 2001-10-04 Fahri Saatcioglu Novel prostate-specific or testis-specific nucleic acid molecules, polypeptides, and diagnostic and therapeutic methods
US7189565B2 (en) 2001-03-23 2007-03-13 Fahri Saatcioglu Prostate-specific or testis-specific nucleic acid molecules, polypeptides, and diagnostic and therapeutic methods
US7611892B2 (en) 2000-03-24 2009-11-03 President And Fellows Of Harvard College Prostate-specific or testis-specific nucleic acid molecules, polypeptides, and diagnostic and therapeutic methods
US7250279B2 (en) 2000-04-07 2007-07-31 Merck Patent Gmbh Human pyruvate dehydrogenese phosphatase
US20040126759A1 (en) * 2001-01-05 2004-07-01 Baughn Mariah R. Molecules for disease detection and treatment
EP1349935A2 (en) * 2001-01-12 2003-10-08 Incyte Genomics, Inc. Molecules for disease detection and treatment
WO2004016733A2 (en) 2002-08-16 2004-02-26 Agensys, Inc. Nucleic acid and corresponding protein entitled 251p5g2 useful in treatment and detection of cancer
US20040147469A1 (en) * 2002-11-01 2004-07-29 Case Western Reserve University Methods of inhibiting glial scar formation
JP4643450B2 (en) 2003-08-08 2011-03-02 株式会社ペルセウスプロテオミクス Cancer high expression gene
CN111269944A (en) * 2020-02-05 2020-06-12 青岛大学 Mouse cataract animal model and application thereof
CN115725733B (en) * 2022-08-10 2023-11-14 人和未来生物科技（长沙）有限公司 ZNF135 gene methylation detection reagent and application thereof

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6114114A (en) * 1992-07-17 2000-09-05 Incyte Pharmaceuticals, Inc. Comparative gene transcript analysis
US6458939B1 (en) * 1996-03-15 2002-10-01 Millennium Pharmaceuticals, Inc. Compositions and methods for the diagnosis, prevention, and treatment of neoplastic cell growth and proliferation
EP0948531A1 (en) * 1996-12-11 1999-10-13 Chiron Corporation Secreted human proteins
EP0990045A1 (en) * 1997-06-11 2000-04-05 Abbott Laboratories Reagents and methods useful for detecting diseases of the lung
JP3964982B2 (en) * 1997-06-19 2007-08-22 生化学工業株式会社 Heparan sulfate 6-O sulfotransferase polypeptide and DNA encoding the same
WO1999002724A2 (en) * 1997-07-11 1999-01-21 Mount Sinai Hospital Corporation Methods for identifying genes expressed in selected lineages, and a novel genes identified using the methods

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See references of WO0073509A3 *

Also Published As

Publication number Publication date
WO2000073509A3 (en) 2001-04-26
WO2000073509A2 (en) 2000-12-07
CA2381319A1 (en) 2000-12-07

Similar Documents

Publication Publication Date Title
US20040115629A1 (en) Molecules for diagnostics and therapeutics
WO2004023973A2 (en) Molecules for diagnostics and therapeutics
CA2442705A1 (en) Molecules for diagnostics and therapeutics
US20040014087A1 (en) Molecules for diagnostics and therapeutics
JP2004528003A (en) Extracellular matrix and cell adhesion molecules
WO2000073509A2 (en) Molecules for diagnostics and therapeutics
US20040048253A1 (en) Molecules for diagnostics and therapeutics
JP2004516812A (en) Receptor
JP2003529325A (en) Human transport protein
WO2003062376A2 (en) Molecules for diagnostics and therapeutics
WO2001062927A2 (en) Polypeptides and corresponding polynucleotides for diagnostics and therapeutics
JP2003532419A (en) Cytoskeletal binding protein
EP1265998A2 (en) Polypeptides and corresponding polynucleotides for diagnostics and therapeutics
EP1364015A2 (en) Molecules for diagnostics and therapeutics
JP2003517290A (en) Human transcription regulatory protein
WO2001021836A2 (en) Molecules for diagnostics and therapeutics
WO2003062385A2 (en) Secretory molecules
CA2434677A1 (en) Molecules for diagnostics and therapeutics
US20040171012A1 (en) Nucleic acid-associated proteins
JP2004511208A (en) RNA metabolism protein
JP2005508636A (en) Nucleic acid binding protein
US20040101884A1 (en) Molecules for disease detection and treatment
JP2004509610A (en) Nuclear hormone receptor
EP1224275A2 (en) Molecules for diagnostics and therapeutics
WO2002078420A2 (en) Molecules for disease detection and treatment

Legal Events

Date Code Title Description
PUAI Public reference made under article 153(3) epc to a published international application that has entered the european phase

Free format text: ORIGINAL CODE: 0009012

17P Request for examination filed

Effective date: 20011218

AK Designated contracting states

Kind code of ref document: A2

Designated state(s): AT BE CH CY DE DK ES FI FR GB GR IE IT LI LU MC NL PT SE

STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: THE APPLICATION IS DEEMED TO BE WITHDRAWN

18D Application deemed to be withdrawn

Effective date: 20041201

RIN1 Information on inventor provided before grant (corrected)

Inventor name: ROSEBERRY, ANN, M.

Inventor name: JONES, ANISSA, L.

Inventor name: HILLMAN, JENNIFER, L.

Inventor name: BANVILLE, STEVEN, C.

Inventor name: RUSSO, FRANK, D.

Inventor name: PANZER, SCOTT, R.

Inventor name: YU, JIMMY, Y.

Inventor name: SPIRO, PETER A.

Inventor name: DANIELS, SUSAN, E.

Inventor name: DUFOUR, GERARD, E.

Inventor name: CHALUP, MICHAEL, S.

Inventor name: ROSEN, BRUCE, H.

Inventor name: HODGSON, DAVID, M

Inventor name: BRATCHER, SHAWN, R.

Inventor name: LINCOLN, STEPHEN, E.

Inventor name: GREENAWALT, LILA, B.

Inventor name: COHEN, HOWARD, J.

Inventor name: WRIGHT, RACHEL, J.