WO2001021836A2 - Molecules pour le diagnostic et la therapeutique - Google Patents

Molecules pour le diagnostic et la therapeutique Download PDF

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Publication number
WO2001021836A2
WO2001021836A2 PCT/US2000/025643 US0025643W WO0121836A2 WO 2001021836 A2 WO2001021836 A2 WO 2001021836A2 US 0025643 W US0025643 W US 0025643W WO 0121836 A2 WO0121836 A2 WO 0121836A2
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cell
proteins
polynucleotide
protein
cells
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PCT/US2000/025643
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English (en)
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WO2001021836A3 (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
Purvi Shah
Michael S. Chalup
Jennifer L. Hillman
Anissa Lee Jones
Jimmy Y. Yu
Lila B. Greenawalt
Scott R. Panzer
Ann M. Roseberry
Rachel J. Wright
Wensheng Chen
Tommy F. Liu
Pierre E. Yap
Theresa K. Stockdreher
Stefan Amshey
Willy T. Fong
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Incyte Genomics, Inc.
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Priority to EP00963614A priority Critical patent/EP1224275A2/fr
Priority to CA002385496A priority patent/CA2385496A1/fr
Priority to AU40182/01A priority patent/AU4018201A/en
Publication of WO2001021836A2 publication Critical patent/WO2001021836A2/fr
Publication of WO2001021836A3 publication Critical patent/WO2001021836A3/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • 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
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00—Genetically modified animals
    • A01K2217/05—Animals comprising random inserted nucleic acids (transgenic)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • 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
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • the present invention relates to human molecules and to the use of these sequences in the 5 diagnosis, study, prevention, and treatment of diseases associated with, as well as effects of exogenous compounds on, the expression of human molecules.
  • 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 proliferative 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.
  • 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.
  • cancer represents a type of cell proliferative disorder that affects nearly every tissue in the body.
  • 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.
  • 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, and cell-cycle control proteins.
  • 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.
  • 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 of specific mutations that could result in increased drug metabolism, 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.
  • the interactions may be expected, such as when the genes are part of the same signaling pathway. In other cases, such as when the genes participate in separate signaling 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.
  • SEQ ID NO:l encode, for example, human enzyme molecules.
  • oxidoreductases transferases, hydrolases, lyases, isomerases, and ligases.
  • These 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.
  • Oxidoreductases Oxidoreductases
  • oxidoreductase dehydrogenase or reductase activity
  • 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. 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 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.
  • oxidoreductases oxidases
  • reductases dehydrogenases
  • family members often have distinct cellular localizations, including the cytosol, the plasma membrane, mitochondrial inner or outer membrane, and peroxisomes.
  • Short-chain alcohol dehydrogenases 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.
  • SCADs 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.
  • retinol dehydrogenase is a SCAD-family member (Simon, A. et al. (1995) J. Biol. Chem.
  • 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 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.
  • neurotransmitter degradation pathways that utilize NADVNADH-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 o 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 o the inflammatory response
  • taurine an inhibitory neurotransmitter of the brain stem, spinal cord and retina
  • Epigenetic or genetic defects in neurotransmitter 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. Hu
  • 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, 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. o
  • tetrahydrofolate dehydrogenase plays an important role in generating building blocks for nucleic and amino acids, crucial to proliferating cells.
  • 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 5 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 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.
  • a ⁇ amyloid- ⁇
  • APP amyloid precursor protein
  • 3HACD has been shown to bind the A ⁇ peptide, and is overexpressed in neurons affected in Alzheimer's disease.
  • an antibody against 3HACD can block the toxic effects of A ⁇ in a 5 cell culture model of Alzheimer's disease (Yan, S. et al. (1997) Nature 389:689-695; OMIM, #602057).
  • 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 5 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- ⁇ -steroid dehydrogenase (OASD), a microsomal membrane protein highly expressed in prostate and other androgen-responsive tissues.
  • OASD 3-oxo-5- ⁇ -steroid dehydrogenase
  • 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 o 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 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).
  • OASD plays a central role in sexual 5 differentiation and androgen physiology.
  • 17 ⁇ -hydroxysteroid dehydrogenase plays an important role in the regulation of the male reproductive hormone, dihydrotestosterone (DHTT).
  • 17 ⁇ HSD6 acts to reduce levels of DHTT by oxidizing a precursor of DHTT, 3 ⁇ -diol, to androsterone which is readily glucuronidated and removed from tissues.
  • 17 ⁇ HSD6 is active with both androgen and estrogen substrates when 0 expressed in embryonic kidney 293 cells. At least five other isozymes of 17 ⁇ HSD have been identified that catalyze oxidation and/or reduction reactions in various tissues with preferences for different steroid substrates (Biswas, M.G. and D.W. Russell (1997) J. Biol. Chem.
  • 17 ⁇ HSDl preferentially reduces estradiol and is abundant in the ovary and placenta.
  • 17 ⁇ HSD2 catalyzes oxidation of androgens and is present in the endometrium and placenta.
  • 5 17 ⁇ HSD3 is exclusively a reductive enzyme in the testis (Geissler, W.M. et al. (1994) Nat. Genet.
  • 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, o 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 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.
  • 2,4-dienoyl-CoA reductase is located in both mitochondria and peroxisomes. Inherited deficiencies in mitochondrial and peroxisomal beta-oxidation enzymes are 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, 5 and bifunctional protein deficiency (Suzuki, Y. et al. (1994) Am. J. Hum.
  • 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. 0 166:27-35).
  • 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 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 5 either NAD or NADP dependent, and is found in the cytosol, mitochondria, and peroxisomes. Activity of isocitrate dehydrogenase is regulated developmentally, and by hormones, neurotransmitters, and growth factors.
  • HPR Hydroxypyruvate reductase
  • a peroxisomal 2-hydroxyacid dehydrogenase in the glycolate pathway catalyzes the conversion of hydroxypyruvate to glycerate with the oxidation of o 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 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 5 of serine and cellular serine levels available for protein synthesis.
  • the mitochondrial electron transport (or respiratory) chain is a series of oxidoreductase-type 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 o 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 oxidoreductase (complex II), cytochrome c r 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 5 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).
  • Q membrane bound ubiquinone
  • Transcriptional regulation of these nuclear-encoded genes appears to be the predominant means for controlling the 5 biogenesis of respiratory enzymes. Defects and altered expression of enzymes in the respiratory chain are associated with a variety of disease conditions.
  • 3-hydroxyisobutyrate dehydrogenase important in valine catabolism, catalyzes the NAD-dependent oxidation of 3-hydroxyisobutyrate to methylmalonate semialdehyde within o mitochondria. Elevated levels of 3-hydroxyisobutyrate have been reported in a number of disease states, including ketoacidosis, methylmalonic acidemia, and other disorders associated with deficiencies in methylmalonate semialdehyde dehydrogenase (Rougraff, P.M. et al. (1989) J. Biol. Chem. 264:5899-5903).
  • IVD isovaleryl-CoA-dehydrogenase
  • IVD is involved in leucine metabolism and catalyzes the oxidation of isovaleryl-CoA to 3-methylcrotonyl-CoA.
  • Human IVD is a tetrameric flavoprotein that 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 0 import and processing of the IVD precursor (Vockley, J. et al. (1992) J. Biol. Chem. 267:2494-2501). Transferases
  • 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 5 functions as synthesis and degradation of cell components, regulation of cell functions including cell signaling, cell proliferation, inflamation, apoptosis, secretion and excretion. Transferases are involved in key steps in disease processes involving these functions. Transferases are frequently classified according to the type of group transferred.
  • methyl transferases transfer one- carbon methyl groups
  • amino transferases transfer nitrogenous amino groups
  • similarly o 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 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 5 fatty acid metabolism and transport. Choline O-acetyl transferase catalyzes the biosynthesis of the neurotransmitter acetylcholine.
  • Amino transferases play key roles in protein synthesis and degradation, and they contribute to other processes as well.
  • the amino transferase 5-aminolevulinic acid synthase catalyzes the addition of succinyl-CoA to glycine, the first step in heme biosynthesis.
  • Other amino transferases 5 participate in pathways important for neurological function and metabolism.
  • glutamine- phenylpyruvate amino transferase also known as glutamine transaminase K (GTK) catalyzes several reactions with a pyridoxal phosphate cofactor.
  • GTK glutamine transaminase K
  • 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 o 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. 5
  • 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/ ⁇ -aminoadipate amino transferase (AadAT).
  • AadAT catalyzes the reversible conversion of ⁇ -aminoadipate and ⁇ -ketoglutarate to ⁇ -ketoadipate o 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 5 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 o 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. 5 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- 5 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 0 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 5 reversible phosphate transfer between creatine/creatine phosphate and ATP/ADP.
  • Glycocyamine kinase catalyzes phosphate transfer from ATP to guanidoacetate
  • arginine kinase catalyzes phosphate transfer from ATP to arginine.
  • 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 0 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. 5 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 (Co A) transferase catalyzes the transfer of Co A between two carboxylic acids.
  • Succinyl CoA:3-oxoacid CoA transferase for example, transfers CoA from succinyl-CoA to a o 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 5 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 may 5 be grouped by substrate specificity into classes including phosphatases, peptidases, lysophospholipases, phosphodiesterases, glycosidases, and glyoxalases.
  • LPLs l o Lysophospholipases
  • 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
  • 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,
  • Peptidases function in bacterial, parasitic, and viral invasion and replication within a host.
  • 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
  • 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
  • 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 5 with a gangliosidosis known as Morquio disease type B.
  • the glyoxylase system is involved in gluconeogenesis, the production of glucose from o 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 glyoxylase II, which hydrolyzes S-D-lactoylglutathione to D-lactic acid and reduced glutathione. Glyoxylases are involved in hyperglycemia, non-insuUn-dependent diabetes mellitus, the detoxification of bacterial toxins, and in the control of cell proliferation and microtubule assembly. 5 Lvases
  • Lyases are a class of enzymes that catalyze the cleavage of C-C, C-O, C-N, C-S, C-(halide), P-0 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 0 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-O lyase group includes hydro-lyases, lyases acting on polysaccharides and other lyases.
  • the C-N lyase group includes ammonia-lyases, amidine-lyases, 5 amine-lyases (deaminases) and other lyases.
  • 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-Unked 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 o 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- 5 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 5 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 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 l o interconversion of UDP-galactose and UDP-glucose is catalyzed by UDP-galactose-4' -epimerase.
  • Oxidoreductases can be isomerases as well. Oxidoreductases catalyze the reversible transfer
  • This class of enzymes includes dehydrogenases, hydroxylases, oxidases, oxygenases, peroxidases, and reductases.
  • oxidases 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 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 (phosphotransferases or phosphomutases), and others.
  • the transferase carnitine palmitoyltransferase is an important component of fatty acid metabolism. Genetically-Unked deficiencies in this
  • 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
  • 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
  • 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 Unkage with the appropriate tRNA. The 5 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 ⁇ -sheet 0 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 5 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.
  • ILD interstitial 5 lung disease
  • Ligases forming carbon-sulfur bonds 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 o 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.
  • a carbon substrate is derived from a small molecule containing at least two 5 carbon atoms.
  • the carbon substrate is often covalently bound to a larger molecule which acts as a carbon substrate carrier molecule within the cell.
  • 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 o acts as the site for carbon substrate bond formation.
  • the predominant carbon substrates which utilizes to 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 o
  • 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 5 synthesized in the cell by acyl-CoA synthetase and acetyl-CoA synthetase, respectively.
  • 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; u) medium-chain acyl-CoA synthetase, which activates fatty acids containing between four and eleven carbon atoms 5 (predominantly from dietary sources), and is present only in liver mitochondria; and in) acyl CoA synthetase, which is specific for long chain fatty acids with between six and twenty carbon atoms, and is found in microsomes and the mitochondria.
  • acyl-CoA synthetase activity has 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 o cAMP-dependent protein kinase.
  • Ligases forming carbon-nitrogen bonds include amide synthases such as glutamine synthetase (glutamate-ammonia ligase) that catalyzes the animation of glutamic acid to glutamine by ammonia using the energy of ATP hydrolysis.
  • glutamine synthetase glutamine synthetase
  • 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 5 pyrimidine ribonucleotide interconversions.
  • Overexpression of glutamine synthetase has been observed in primary liver cancer (Christa, L. et al. (1994) Gastroent. 106:1312-1320).
  • Acid-amino-acid ligases 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.
  • UCS ubiquitin conjugation system
  • the UCS mediates the elimination of o abnormal proteins and regulates the half -lives of important regulatory proteins that control cellular processes such as gene transcription and cell cycle progression.
  • proteins 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 5 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 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 o (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 gene is consistently elevated in small cell tumors and adenocarcinomas of the lung (Gray, D.A. (1995) Oncogene 10:2179-2183).
  • Purine biosynthesis occurs de novo from the amino acids glycine and glutamine, and other 5 small molecules.
  • Three of the key reactions in this process are catalyzed by a trifunctional enzyme composed of glycinamide-ribonucleotide synthetase (GARS), aminoimidazole ribonucleotide synthetase (AIRS), and glycinamide ribonucleotide transformylase (GART).
  • GART glycinamide ribonucleotide transformylase
  • Adenylosuccinate synthetase catalyzes a later step in purine biosynthesis that converts inosinic acid to 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 orotidylate derived from orotate and phosphoribosyl pyrophosphate (PPRP).
  • PPRP phosphoribosyl pyrophosphate
  • ATCase aspartate transcarbamylase
  • carbamyl phosphate synthetase II carbamyl phosphate synthetase II
  • DHOase dihydroorotase o
  • Ligases forming carbon-carbon bonds include the carboxylases acetyl-CoA carboxylase and pyruvate carboxylase.
  • Acetyl-CoA carboxylase catalyzes the carboxylation of acetyl-CoA from C0 2 o and H 2 0 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.
  • 5 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 Ugation 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).
  • SEQ ID NO:69, SEQ ID NO:70, and SEQ ID NO:71 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.
  • 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 proUferation, apoptosis, and aging.
  • 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, repUcation 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 cycUns, tumor suppressor binding proteins, chaperones, transcription factors, translation factors, and RNA-binding proteins (Edwards, M.C et al.(1997) Genetics 147:1063-1076).
  • Cdks cycUn-dependent kinases
  • the Cdks are composed of a kinase subunit, Cdk, and an activating subunit, cycUn, in a complex that is subject to many levels of regulation.
  • Cdk a kinase subunit
  • cycUn an activating subunit
  • CycUns act by binding to and activating cycUn-dependent protein kinases which then phosphorylate and activate selected proteins involved in the mitotic process.
  • the Cdk-cycUn complex is both positively and negatively regulated by phosphorylation, and by targeted degradation involving molecules such as CDC4 and CDC53.
  • Cdks are further regulated by binding to inhibitors and other proteins such as Sucl that modify their specificity or accessibiUty to regulators (Patra, D. and W.G. Dunphy (1996) Genes Dev. 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 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 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 masculine characteristics of the male body. Three other male sex hormones, gonadotropin- releasing hormone (GnRH), luteinizing hormone (LH), and follicle-stimulating hormone (FSH) control sexual function.
  • gonadotropin- releasing hormone GnRH
  • LH luteinizing hormone
  • FSH follicle-stimulating hormone
  • 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 reproductive capabiUty during a female' s Ufetime.
  • the primary role of the breasts is lactation. 5
  • 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 Ufetime. Similarly, the sensitivity of reproductive organs to these endocrine signals varies during the female's lifetime.
  • a combination of positive and negative feedback to the ovaries, pituitary and hypothalamus o glands controls physiologic changes during the monthly ovulation and endometrial cycles.
  • the anterior pituitary secretes two major gonadotropin hormones, folUcle-stimulating hormone (FSH) and luteinizing hormone (LH), regulated by negative feedback of steroids, most notably by ovarian estradiol. If fertiUzation does not occur, estrogen and progesterone levels decrease. This sudden reduction of the ovarian hormones leads to menstruation, the desquamation of the endometrium. 5 Hormones further govern all the steps of pregnancy, parturition, lactation, and menopause.
  • hCG human chorionic gonadotropin
  • hCS human chorionic somatomammotropin
  • 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.
  • Parturition involves several hormonal changes that increase uterine contractility toward the end 5 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 produces less estradiol, reducing the negative feedback on the pituitary and hypothalamus glands.
  • o 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 capabiUty ends.
  • 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 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).
  • G-proteins such as Ras, Rab, and Rho
  • GAPs GTPase activating proteins
  • GNRPs guanine nucleotide releasing proteins
  • 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.
  • small signaUng peptides and hormones also influence cell proUferation.
  • GPCR G-protein coupled receptor
  • TGF- ⁇ transforming growth factor beta
  • Some growth factors 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 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 proUferation, survival, differentiation, migration, or function of cells depending on the circumstance.
  • the tumor necrosis factor/nerve growth factor (TNF/NGF) family can activate or inhibit cell death, as well as regulate proUferation and differentiation.
  • the cell response depends on the type of cell, its stage of differentiation and transformation status, which surface receptors are stimulated, and the types of stimuU acting on the cell (Smith, A. et al. (1994) Cell 76:959-962; and Nocentini, G. et al. (1997) Proc. Natl. Acad. Sci. USA 94:6216-6221).
  • ECM extracellular matrix
  • ECM molecules such as laminin or fibronectin
  • 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 maUgnant cells. Some oncoproteins are mutant isoforms of the normal protein, and other oncoproteins are abnormally expressed with respect to location or amount of expression.
  • oncoprotein causes cancer by altering transcriptional control of cell proUferation.
  • 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.
  • oncogenes have been identified and characterized. These include sis, erbA, erbB, her-2, mutated G s , 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 proUferation. Mutations which cause reduced or loss of function in tumor-suppressor genes result in uncontrolled cell proUferation.
  • the retinoblastoma gene product RB
  • RB retinoblastoma gene product
  • 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 eUmination of cells is as important for morphogenesis and tissue 5 remodeUng as is cell proliferation and differentiation. Lack of apoptosis may result in hyperplasia and other disorders associated with increased cell proUferation. 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 eUminated by apoptosis to avoid an o autoimmune response.
  • SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, and SEQ ID NO:68 encode, for example, biochemical pathway molecules.
  • Biochemical pathways are responsible for regulating metaboUsm, growth and development, protein secretion and trafficking, environmental responses, and ecological interactions including immune response and response to parasites.
  • DNA Deoxyribonucleic acid
  • the bulk of human DNA is nuclear, in the form of Unear chromosomes, while mitochondrial DNA is circular.
  • DNA repUcation begins at specific sites called origins of repUcation. Bidirectional synthesis occurs from the origin via two growing forks that move in opposite directions. Replication is semi-conservative, with each daughter duplex containing one old strand and its newly synthesized complementary partner. Proteins involved in DNA repUcation include DNA polymerases, DNA primase, telomerase, DNA heUcase, topoisomerases, DNA Ugases, repUcation factors, and DNA-binding proteins.
  • DNA Recombination and Repair Cells are constantly faced with repUcation 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 Unk repair proteins, recombination and repair proteins, RAD51 proteins, and BLN and WRN proteins that are homologs of RecQ heUcase.
  • DNA polymerase DNA polymerase
  • excision repair proteins excision and cross Unk repair proteins
  • recombination and repair proteins RAD51 proteins
  • BLN and WRN proteins that are homologs of RecQ heUcase.
  • 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. Natl. Acad. Sci. USA 95:8733-8738), ataxia telangiectasia, Cockayne's syndrome, and Fanconi
  • Recombination is the process whereby new DNA sequences are generated by the movements of large pieces of DNA.
  • homologous recombination which occurs during meiosis and DNA repair, parent DNA duplexes aUgn at regions of sequence similarity, and new DNA molecules form by the breakage and joining of homologous segments.
  • Proteins involved include RAD51 recombinase.
  • site-specific recombination two specific but not necessarily homologous DNA sequences are exchanged.
  • 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 5 severe combined immunodeficiency disease in mice.
  • RNA Ribonucleic acid
  • ATP ATP
  • CTP CTP
  • UTP UTP
  • GTP GTP
  • RNA Ribonucleic acid
  • ATP ATP
  • CTP CTP
  • UTP UTP
  • GTP GTP
  • RNA Ribonucleic acid
  • RNA is transcribed as a copy of DNA, the genetic material of the organism.
  • RNA rather than DNA serves as the genetic material.
  • RNA copies of the o genetic material encode proteins or serve various structural, catalytic, or regulatory roles in organisms.
  • RNA is classified according to its cellular locaUzation and function.
  • Messenger 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 5 mRNA codon and the amino acid that matches that codon.
  • hnRNAs include mRNA precursors and other nuclear RNAs of various sizes.
  • RNA Transcription o The transcription process synthesizes an RNA copy of DNA. Proteins involved include multi- subunit RNA polymerases, transcription factors IIA, IIB, IID, HE, IIF, IIH, and ILL Many transcription factors incorporate 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- helix, zinc finger, leucine zipper, and helix-loop-helix. 5 RNA Processing
  • RNA 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.
  • snRNPs small nuclear ribonucleoprotein particles
  • Ul small nuclear ribonucleoprotein particles
  • 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) CUn. Exp. Rheumatol. 16:317-326).
  • hnRNPs include the yeast proteins Hrplp, involved in cleavage and polyadenylation at the 3' end of the RNA; Cbp80p, involved in 5 capping the 5 ' end of the RNA; and Npl3p, a homolog of mammaUan 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).
  • RNA recognition motif (Reviewed in Birney, E. et al. (1993) Nucleic Acids Res. 21 :5803- 0 5816.)
  • the RRM is about 80 amino acids in length and forms four ⁇ -strands and two ⁇ -helices arranged in an ⁇ / ⁇ sandwich.
  • the RRM contains a core RNP-1 octapeptide motif along with surrounding conserved sequences.
  • RNA heUcases alter and regulate RNA conformation and secondary structure by using energy 5 derived from ATP hydrolysis to destabiUze 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 heUcases function in diverse processes such as translation initiation, spUcing, ribosome o assembly, and RNA editing, transport, and stabiUty.
  • Some DEAD-box heUcases 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 neuroblastoma (Nb) and retinoblastoma (Rb) tumors.
  • DEAD-box heUcases have been implicated 5 either directly or indirectly in ultraviolet Ught-induced tumors, B cell lymphoma, and myeloid maUgnancies. (Reviewed in Godbout, R. et al. (1998) J. Biol. Chem. 273:21161-21168.)
  • RNases Ribonucleases catalyze the hydrolysis of phosphodiester bonds in RNA chains, thus cleaving the RNA.
  • 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 o hybrid. Such hybrids occur in cells invaded by retroviruses, and RNase H is an important enzyme in the retroviral repUcation 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 repUcation, 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.
  • the ribosome 5 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).
  • 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 o bind prior to their release from the ribosome.
  • Protein biosynthesis depends on each amino acid forming a linkage with the appropriate tRNA. 5
  • 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 o coxsackie virus has been used to induce experimental viral myositis in animals.
  • ILD interstitial lung disease
  • Initiation of translation 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 5 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).
  • 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.
  • 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-tRNA f , elFl A, eIF3, and 40S ribosomal subunit together make up the 43 S preinitiation complex (Pain, supra).
  • eIF4F is a complex consisting of three proteins: eIF4E, eIF4A, and eIF4G.
  • eIF4E recognizes and binds to the mRNA 5 -terminal m 7 GTP cap
  • eIF4A is a bidirectional RNA-dependent heUcase
  • eIF4G is a scaffolding polypeptide.
  • eIF4G has three binding domains.
  • eIF4G acts as a bridge between the 40S ribosomal subunit and the mRNA (Hentze, M.W. (1997) Science 275:500-501).
  • the abiUty 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.
  • UTR untranslated region
  • eIF4A The heUcase activity of eIF4A is thought to function in removing this secondary structure to faciUtate binding of the 43S preinitiation complex (Pain, supra).
  • Elongation is the process whereby additional amino acids are joined to the initiator methionine to form the complete polypeptide chain.
  • the elongation factors EFl ⁇ , EFl ⁇ ⁇ , and EF2 are involved in elongating the polypeptide chain following initiation.
  • EF 1 ⁇ is a GTP-binding protein. In EF 1 ⁇ ' s GTP-bound form, it brings an aminoacyl-tRNA to the ribosome' s A site. The amino acid attached to the newly arrived aminoacyl-tRNA forms a peptide bond with the initiator methionine.
  • the GTP on EFl ⁇ is hydrolyzed to GDP, and EFl ⁇ -GDP dissociates from the ribosome.
  • EFl ⁇ ⁇ binds EFl ⁇ -GDP and induces the dissociation of GDP from EFl ⁇ , allowing EFl ⁇ to bind GTP and a new cycle to begin.
  • 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 ribosome. This allows the processivity of translation. 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.
  • 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 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.
  • proteases include serine proteases, cysteine proteases, aspartic proteases, and metalloproteases.
  • Signal peptidase in the endoplasmic reticulum (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-Uves of important regulatory proteins that control cellular processes such as gene transcription and cell cycle progression.
  • UCS ubiquitin conjugation system
  • 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.
  • Lipids are water-insoluble, oily or greasy substances that are soluble in nonpolar solvents such as chloroform or ether.
  • Neutral fats triacylglycerols serve as major fuels and energy stores.
  • Upids such as phosphoUpids, sphingoUpids, glycoUpids, and cholesterol, are key structural components of cell membranes.
  • Lipid metabolism is involved in human diseases and disorders.
  • atherosclerosis fatty lesions form on the inside of the arterial wall. These lesions promote the loss of arterial flexibiUty and the formation of blood clots (Guyton, A.C. Textbook of Medical Physiology
  • Niemann-Pick diseases types A and B are caused by accumulation of sphingomyelin (a sphingoUpid) and other Upids in the central nervous system due to a defect in the enzyme sphingomyeUnase, leading to neurodegeneration 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.
  • 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 glycoUpids, 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 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.
  • CoA acetyl-Coenzyme A
  • ACC carboxylase
  • FAS fatty acid synthase
  • FAS catalyzes the synthesis of palmitate from acetyl-CoA and malonyl-CoA.
  • FAS contains acetyl transferase, malonyl transferase, ⁇ -ketoacetyl synthase, acyl carrier protein, ⁇ -ketoacyl reductase, dehydratase, enoyl reductase, and thioesterase activities.
  • the final product of the FAS reaction is the 16-carbon fatty acid palmitate.
  • Triacylglycerols also known as triglycerides and neutral fats, are major energy stores in animals. Triacylglycerols are esters of glycerol with three fatty acid chains. Glyce ⁇ ol-3-phosphate is produced from dihydroxyacetone phosphate by the enzyme glycerol phosphate dehydrogenase or from 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 acyltransferase to give phosphatidate.
  • Phosphatidate phosphatase converts phosphatidate to diacylglycerol, which is subsequently acylated to a triacylglyercol by the enzyme diglyceride acyltransferase.
  • Phosphatidate phosphatase and diglyceride acyltransferase form a triacylglyerol synthetase complex bound to the ER membrane.
  • a major class of phospholipids 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 choUne, 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 PubUshers Inc., New York NY, pp. 494-501). Phosphatidate is converted to CDP-diacylglycerol by the enzyme phosphatidate cytidylyltransferase (ExPASy ENZYME EC 2.7.7.41).
  • 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 choUne is formed using diet-derived choUne by the reaction of CDP-choUne with 1 ,2- 5 diacylglycerol, catalyzed by diacylglycerol choUnephosphotransferase (ExPASy ENZYME 2.7.8.2).
  • 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.
  • Bile salts derived from o cholesterol facilitate the digestion of Upids.
  • 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-translationally 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.
  • HMG-CoA hydroxymethylglutaryl-CoA
  • the rate-Umiting 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.
  • 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.
  • cholesterol is converted to pregnenolone by cholesterol monooxygenases.
  • the other steroid hormones are synthesized from pregnenolone by a series of 5 enzyme-catalyzed reactions including oxidations, isomerizations, hydroxylations, reductions, and demethylations. Examples of these enzymes include steroid ⁇ -isomerase, 3 ⁇ -hydroxy- ⁇ 5 -steroid dehydrogenase, steroid 21 -monooxygenase, steroid 19-hydroxylase, and 3 ⁇ -hydroxysteroid dehydrogenase. Cholesterol is also the precursor to vitamin D.
  • Isoprenoid groups are found in vitamin K, ubiquinone, retinal, doUchol phosphate (a carrier of oUgosaccharides needed for N-linked glycosylation), and farnesyl and geranylgeranyl groups that modify proteins. Enzymes involved include farnesyl transferase, polyprenyl transferases, doUchyl phosphatase, and dolichyl kinase.
  • SphingoUpid MetaboUsm 5 Sphingohpids are an important class of membrane lipids that contain sphingosine, a long chain amino alcohol.
  • sphingolipids 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 gangUosides.
  • SphingomyeUns which contain phosphochoUne or phosphoethanolamine as their head group, are abundant in the myeUn sheath surrounding nerve cells.
  • o Galactocerebrosides which contain a glucose or galactose head group, are characteristic of the brain.
  • Other cerebrosides are found in nonneural tissues.
  • GangUosides whose head groups contain multiple sugar units, are abundant in the brain, but are also found in nonneural tissues.
  • Sphingolipids are built on a sphingosine backbone.
  • Sphingosine is acylated to ceramide by the enzyme sphingosine acetyltransferase.
  • Ceramide and phosphatidyl choUne are converted to 5 sphingomyeUn by the enzyme ceramide choUne phosphotransferase.
  • Cerebrosides are synthesized by the Unkage of glucose or galactose to ceramide by a transferase. Sequential addition of sugar residues to ceramide by transferase enzymes yields gangUosides. Eicosanoid MetaboUsm
  • Eicosanoids including prostaglandins, prostacycUn, thromboxanes, and leukotrienes, are 20- o carbon molecules derived from fatty acids. Eicosanoids are signaling molecules which have roles in pain, fever, and inflammation. The precursor of all eicosanoids is arachidonate, which is generated from phospholipids by phosphoUpase A 2 and from diacylglycerols by diacylglycerol Upase. Leukotrienes are produced from arachidonate by the action of Upoxygenases. Prostaglandin synthase, reductases, and isomerases are responsible for the synthesis of the prostaglandins.
  • Prostaglandins have roles in inflammation, blood flow, ion transport, synaptic transmission, and sleep.
  • ProstacycUn and the thromboxanes are derived from a precursor prostaglandin by the action of prostacycUn synthase and thromboxane synthases, respectively.
  • Ketone Body MetaboUsm 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. 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, ketone bodies produced from stored triacylglyerols 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 MobiUzation
  • Diazepam binding inhibitor also known as endozepine and acyl CoA-binding protein, is an endogenous ⁇ -aminobutyric acid (GABA) receptor Ugand 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; DBI; PROSITE PDOC00686 Acyl-CoA-binding protein signature).
  • Fat stored in Uver 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 Upoprotein particles.
  • the particles consist of a core of hydrophobic lipids surrounded by a shell of polar Upids and apoUpoproteins.
  • the protein components serve in the solubilization of hydrophobic Upids and also contain cell-targeting signals.
  • Lipoproteins include chylomicrons, chylomicron remnants, very-low-density Upoproteins (VLDL), intermediate- density Upoproteins (IDL), low-density Upoproteins (LDL), and high-density Upoproteins (HDL).
  • VLDL very-low-density Upoproteins
  • IDL intermediate- density Upoproteins
  • LDL low-density Upoproteins
  • HDL high-density Upoproteins
  • Triacylglycerols in chylomicrons and VLDL are hydrolyzed by Upoprotein 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 famiUal hypercholesterolemia, leads to increased plasma cholesterol levels and ultimately to atherosclerosis.
  • Plasma cholesteryl ester transfer protein mediates the transfer of cholesteryl esters from HDL to apoUpoprotein B-containing Upoproteins. 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.
  • Macrophage scavenger receptors which bind and internaUze modified Upoproteins, play a role in lipid transport and may contribute to atherosclerosis (Greaves, D.R. et al. (1998) Curr. Opin. Lipidol. 9:425-432).
  • SREBP sterol regulatory element binding protein
  • OSBP oxysterol- binding protein
  • 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 liver, 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, dicarboxyUc fatty acids, branched fatty acids, prostaglandins, xenobiotics, and bile acid intermediates.
  • the chief roles of peroxisomal beta-oxidation are to shorten toxic UpophiUc carboxylic acids to faciUtate 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 acyltransferase, acyl CoA dehydrogenases, enoyl CoA hydratases, L-3-hydroxyacyl CoA dehydrogenase, ⁇ -ketothiolase, 2,4-dienoyl CoA reductase, and isomerase.
  • LPLs LysophosphoUpases 5
  • a particular substrate for LPLs lysophosphatidylchoUne, causes lysis of cell membranes when it is formed or imported into a cell.
  • LPLs are regulated by Upid factors including acylcarnitine, arachidonic acid, and phosphatidic acid.
  • the secretory phosphoUpase A 2 (PLA2) superfamily comprises a number of heterogeneous enzymes whose common feature is to hydrolyze the sn-2 fatty acid acyl ester bond of
  • PLA2 activity generates precursors for the biosynthesis of biologically active Upids, 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 lysophosphoUpids.
  • 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 increased glucose release from cells, respectively. Carbohydrates have three important roles in
  • 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 Upids as they traverse the secretory pathway. Cell surface carbohydrate-containing macromolecules,
  • glycoproteins including glycoproteins, glycoUpids, and transmembrane proteoglycans, mediate adhesion with other cells and with components of the extracellular matrix.
  • the extracellular matrix 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.
  • GAGs glycosaminoglycans
  • carbohydrate-binding proteins which are secreted from the cell and assembled into an organized meshwork in close association with the cell surface.
  • the interaction of the cell with the surrounding matrix profoundly influences cell shape, strength, flexibility, motiUty, and adhesion.
  • Carbohydrate metaboUsm is altered in several disorders including diabetes melUtus, 5 hyperglycemia, hypoglycemia, galactosemia, galactokinase deficiency, and UDP-galactose-4-epimerase deficiency (Fauci, AS. et al. (1998) Harrison's Principles of Internal Medicine. McGraw-Hill, New York NY, pp. 2208-2209).
  • Altered carbohydrate metaboUsm 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 0 frequently expressed on human cancer cells (Kannagi, R. (1997) Glycoconj. J. 14:577-584).
  • Enzymes of the glycolytic pathway convert the sugar glucose to pyruvate while simultaneously o 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.
  • phosphofructokinase, hexokinase, and pyruvate kinase are important in regulating the rate of glycolysis.
  • 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-5 -phosphate. Ribose-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- 5 phosphate and NADP + to ribulose-6-phosphate and NADPH.
  • non-oxidative branch steps which are catalyzed by the enzymes phosphopentose isomerase, phosphopentose epimerase, transketolase, and transaldolase, allow the interconversion of three-, four-, five-, six-, and seven-carbon sugars.
  • Glucouronate MetaboUsm isomerase, phosphopentose epimerase, transketolase, and transaldolase
  • Glucuronate is a monosaccharide which, in the form of D-glucuronic acid, is found in the o GAGs chondroitin and dermatan. D-glucuronic acid is also important in the detoxification and excretion of foreign organic compounds such as phenol. Enzymes involved in glucuronate metaboUsm include UDP-glucose dehydrogenase and glucuronate reductase. Disaccharide MetaboUsm
  • Disaccharides must be hydrolyzed to monosaccharides to be digested. Lactose, a disaccharide 5 found in milk, is hydrolyzed to galactose and glucose by the enzyme lactase. Maltose is derived from 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 o bound to mucosal cells lining the small intestine, where they participate in the digestion of dietary disaccharides.
  • the enzyme lactose synthetase composed of the catalytic subunit galactosyltransferase and the modifier subunit ⁇ -lactalbumin, converts UDP-galactose and glucose to lactose in the mammary glands.
  • Glycogen is the storage form of carbohydrates in mammals. MobiUzation of glycogen 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, ⁇ - 0 1 ,6-glucosidase, and phosphoglucomutase.
  • Enzymes that catalyze the synthesis of glycogen include 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 ⁇ -dextrin by ⁇ -amylase, an enzyme secreted by the saUvary glands and pancreas.
  • Chitin is a polysaccharide found in insects and Crustacea.
  • GAGs Glycosaminoglycans
  • GAGs are anionic Unear unbranched polysaccharides composed of repetitive disaccharide units. These repetitive units contain a derivative of an amino sugar, either 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 matrix. Changes in GAG levels are associated with several autoimmune diseases o including autoimmune thyroid disease, autoimmune diabetes melUtus, and systemic lupus erythematosus (Hansen, C et al. (1996) CUn. Exp. Rheum. 14 (Suppl. 15):S59-S67). GAGs include chondroitin sulfate, keratan sulfate, heparin, heparan sulfate, dermatan sulfate, and hyaluronan.
  • HA GAG hyaluronan
  • GAG 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 (PitsilUdes, AA. et al. (1993) Int. J. Exp. Pathol. 5 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 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 o 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 cell-surface proteoglycans bind growth factors, facilitating their binding to cell-surface receptors and subsequent triggering of signal transduction pathways.
  • Amino Acid and Nitrogen Metabolism 5 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. 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 o amino acid biosynthesis include glutamate kinase dehydrogenase, pyrroline carboxylate reductase, asparagine synthetase, phenylalanine oxygenase, methionine adenosyltransferase, adenosylhomocysteinase, cystathionine ⁇ -synthase, cystathionine ⁇ -lyase, phosphoglycerate dehydrogenase, phosphoserine transaminase, 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 aminotransferases (transaminases), for example, alanine aminotransferase.
  • the amino group is transferred to ⁇ -ketoglutarate to form glutamate.
  • Glutamate dehydrogenase converts glutamate to NH 4 + and ⁇ -ketoglutarate.
  • NH 4 + is converted to urea by the urea cycle which is 5 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 ⁇ -keto dehydrogenase complex, isovaleryl CoA dehydrogenase, ⁇ -methylcrotonyl CoA carboxylase, o phenylalanine hydroxylase, p-hydroxylphenylpyruvate hydroxylase, and homogentisate oxidase.
  • Polyamines which include spermidine, putrescine, and spermine, bind tightly to nucleic acids and are abundant in rapidly proliferating cells. Enzymes involved in polyamine synthesis include ornithine decarboxylase.
  • MetaboUsm proceeds along separate reaction pathways connected by key intermediates such as acetyl coenzyme A (acetyl-CoA). MetaboUc pathways feature anaerobic and aerobic degradation, coupled with the energy-requiring reactions such as phosphorylation of adenosine diphosphate (ADP) to the triphosphate (ATP) or analogous phosphorylations of guanosine (GDP/GTP), uridine (UDP/UTP), or cytidine (CDP/CTP). Subsequent dephosphorylation of the 5 triphosphate drives reactions needed for cell maintenance, growth, and proliferation.
  • ADP adenosine diphosphate
  • ATP triphosphate
  • UDP/UTP uridine
  • CDP/CTP cytidine
  • Digestive enzymes convert carbohydrates and sugars to glucose; fructose and galactose are converted in the liver to glucose. Enzymes involved in these conversions include galactose- 1- phosphate uridyl transferase and UDP-galactose-4 epimerase.
  • glycolysis converts glucose to pyruvate in a series of reactions coupled to ATP synthesis.
  • o Pyruvate is transported into the mitochondria and converted to acetyl-CoA for oxidation via the citric acid cycle, involving pyruvate dehydrogenase components, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase.
  • Enzymes involved in the citric acid cycle include: citrate synthetase, aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including transsuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate 5 dehydrogenase.
  • Acetyl CoA is oxidized to C0 2 with concomitant formation of NADH, FADH 2 , and GTP.
  • Enzyme complexes responsible for electron transport and ATP synthesis include the F ⁇ ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone 5 reductase, cytochrome b, cytochrome C j , 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, and degraded by the glycolysis. Fatty acids are transported into the mitochondria as fatty acyl- carnitine esters and undergo oxidative degradation. 0 In addition to metaboUc 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.
  • Cofactors are small molecular weight inorganic 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 5 mononucleotide, nicotinamide adenine dinucleotide, pyridoxal phosphate, coenzyme A, tetrahydrofolate, Upoamide, and heme. The vitamins biotin and cobalamin are associated with enzymes as well. Heme, a prosthetic group found in myoglobin and hemoglobin, consists of protopo ⁇ hyrin group bound to iron.
  • Po ⁇ hyrin groups contain four substituted pyrroles covalently joined in a ring, often with a bound metal atom. Enzymes involved in po ⁇ hyrin synthesis include ⁇ - o aminolevulinate synthase, ⁇ -aminolevulinate dehydrase, po ⁇ hobilinogen deaminase, and cosynthase.
  • heme formation causes po ⁇ hyrias. Heme is broken down as a part of erythrocyte turnover. Enzymes involved in heme degradation include heme oxygenase and biliverdin reductase. 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 5 reductase. Iron is transported in the blood by the protein transferrin. Binding of transferrin to the transferrin receptor on cell surfaces allows uptake by receptor mediated endocytosis. Cytosolic iron is bound to ferritin protein.
  • a molybdenum-containing cofactor (molybdopterin) is found in enzymes including sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. Molybdopterin biosynthesis is performed by 5 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. Secretion and Trafficking
  • Eukaryotic cells are bound by a Upid bilayer membrane and subdivided into functionally o distinct, membrane bound compartments.
  • the membranes maintain the essential differences between the cytosol, the extracellular environment, and the lumenal space of each intracellular organelle.
  • Upid membranes are highly impermeable to most polar molecules, transport of essential nutrients, metaboUc waste products, cell signaUng molecules, macromolecules and proteins across lipid membranes and between organelles must be mediated by a variety of transport-associated molecules. 5 Protein Trafficking
  • ER-bound ribosomes In eukaryotes, some proteins are synthesized on ER-bound ribosomes, co-translationally imported into the ER, deUvered from the ER to the Golgi complex for post-translational processing and sorting, and transported from the Golgi to specific intracellular and extracellular destinations. All cells possess a constitutive transport process which maintains homeostasis between the cell and its o environment. In many differentiated cell types, the basic machinery is modified to carry out specific transport functions. For example, in endocrine glands, hormones and other secreted proteins are packaged into secretory granules for regulated exocytosis to the cell exterior.
  • 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-translational 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.
  • 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, neurotransmitters, and digestive 5 enzymes.
  • Secretory vesicles eventually fuse with the plasma membrane (GUck, B.S. and V. Malhotra (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 neurons, vesicle o 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 wherein cells internaUze material from the extracellular environment, is essential for transmission of neuronal, metabolic, and proUferative signals; uptake of many essential nutrients; 5 and defense against invading organisms. Most cells exhibit two forms of endocytosis. The first, phagocytosis, is an actin-driven process exempUfied 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 0 the Fc receptors initiates a signal cascade involving src-family cytosoUc 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.
  • pinocytosis The second form of endocytosis, pinocytosis, is a more generaUzed uptake of material from the 5 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-Ugand 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 o 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 Ugands 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 recycUng vesicles (RV).
  • RV recycUng vesicles
  • This selective removal of recycled components produces a carrier vesicle containing Ugand 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 Ugands and other material. As digestion takes place, the LE fuses with the lysosome where digestion is completed (MeUman, I. (1996) Annu. Rev. Cell Dev. Biol. 5 12:575-625).
  • RecycUng vesicles may return directly to the plasma membrane.
  • Receptors internaUzed 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 0 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).
  • vesicles form at the transitional endoplasmic reticulum 5 (tER), the rim of Golgi cisternae, the face of the Trans-Golgi Network (TGN), the plasma membrane (PM), and tubular extensions of the endosomes.
  • tER transitional endoplasmic reticulum 5
  • TGN Trans-Golgi Network
  • PM plasma membrane
  • tubular extensions of the endosomes begins with the budding of a vesicle out of the donor membrane.
  • the membrane-bound vesicle contains proteins to be transported 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 cytosotic ras-Uke GTP-binding protein, ADP- o ribosylating factor (Arf), and adapter proteins (AP).
  • a cytosotic ras-Uke GTP-binding protein ADP- o ribosylating factor (Arf)
  • AP adapter proteins
  • 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 accompUsh 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 5 vesicle (West, M.A. et al.
  • 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 o 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. Natl. Acad. Sci. USA 95:11649-11654.) Membrane Fusion
  • Transport vesicles undergo homotypic or heterotypic fusion in the secretory and endocytotic 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 cytosoUc prenylated GTP-binding protein, Rab a member of the Ras superfamily
  • GTP-bound Rab proteins are directed into nascent transport vesicles where they interact with VAMP. Following vesicle transport, GTPase activating proteins (GAPs) in the target membrane convert Rab proteins to the GDP-bound form.
  • 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 repUcation of HIV-1, the virus responsible for AIDS (Flavell, R.A. et al. (1996) Proc. Natl. Acad. Sci. USA 93:4421-4424).
  • N-ethylmaleimide sensitive factor (NSF) and soluble NSF-attacbment protein ( ⁇ -SNAP and ⁇ -SNAP) are two such o proteins that are conserved from yeast to man and function in most intracellular membrane fusion reactions.
  • Seel represents a family of yeast proteins that function at many different stages in the secretory pathway including membrane fusion. Recently, mammaUan 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). 5
  • the SNARE complex involves three SNARE molecules, one in the vesicular membrane and 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 phosphoUpids, which allows the cytosoUc SNAP protein to displace synaptotagmin from syntaxin and fusion to occur. Thus, synaptotagmin is a negative regulator of o fusion in the neuron (Littleton, J.T. et al. (1993) Cell 74:1125-1134). The most abundant membrane protein of synaptic vesicles appears to be the glycoprotein synaptophysin, a 38 kDa protein with four transmembrane domains.
  • v-SNARE v-SNARE
  • t-SNAREs t-SNAREs
  • associated proteins v-SNARE
  • Different isoforms of SNAREs and Rabs show distinct cellular and subcellular distributions.
  • VAMP-1/synaptobrevin, membrane-anchored synaptosome-associated protein of 25 kDa (SNAP- 25), syntaxin-1 , Rab3A, Rabl5, and Rab23 are predominantly expressed in the brain and nervous system.
  • syntaxin, VAMP, and Rab proteins are associated with distinct subcellular compartments and their vesicular carriers. 5 Nuclear Transport
  • NPCs nuclear 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.
  • o 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 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 inco ⁇ oration with RNA into ribosomal subunits, and export back to the cytoplasm. (Gorlich, D. and I.W. Mattaj (1996) Science 271:1513- 5 1518.)
  • NLS nuclear locaUzation signals
  • NLS nuclear locaUzation signals
  • NLS are found on proteins that are targeted to the nucleus, such as the glucocorticoid receptor. The NLS is o recognized by the NLS receptor, importin, which then interacts with the monomeric GTP-binding protein Raa
  • This NLS protein/receptor/Ran complex navigates the nuclear pore with the help of the 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.
  • abnormal hormonal secretion is Unked to disorders such as diabetes insipidus (vasopressin), hyper- and hypoglycemia (insuUn, glucagon), Grave's disease 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.
  • Disorders related to excessive secretion of biologically active peptides by tumor cells include fasting hypoglycemia due to increased insuUn secretion from insuUnoma-islet cell tumors; hypertension due to increased epinephrine and norepinephrine secreted from pheochromocytomas of the adrenal medulla and sympathetic paragangUa; 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.
  • 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 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 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 G.R. Faloona (1975) N. Engl. J. Med. 293:155-160).
  • Defective nuclear transport may play a role in cancer.
  • the BRCAl protein contains three potential NLSs which interact with importin alpha, and is transported into the nucleus by the importin/NPC pathway.
  • the BRCAl protein is aberrantly locahzed in the cytoplasm.
  • the mislocation of the BRCAl protein in breast cancer cells may be due to a defect in the NPC nuclear import pathway (Chen, CF. et al. (1996) J. Biol. Chem. 271:32863-32868).
  • 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 are channels that transport water and, in some cases, nonionic small solutes such as urea and glycerol. Water movement is important for a number of physiological processes 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; Ishibashi, 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 metaboUsm 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).
  • 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
  • the cellular components of the humoral immune system include six different types of leukocytes: monocytes, lymphocytes, polymo ⁇ honuclear granulocytes (consisting of neutrophils, eosinophils, and basophils) 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.
  • Lymphoid cells travel to the thymus, spleen and lymph nodes, where they mature and differentiate into lymphocytes.
  • Leukocytes are responsible for defending the body against invading pathogens. Neutrophils 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 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. Lymphocytes and plasma cells are produced in various lymphogenous organs, including the lymph nodes, spleen, thymus, and tonsils.
  • 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 basophilic secretion is that the contents of granules go directly into the extracellular environment, not into vacuoles as occurs with 0 neutrophils, eosinophils and monocytes.
  • Basophils have receptors for the Fc fragment of immunoglobulin E (IgE) that are not present on other leukocytes. CrossUnking of membrane IgE with anti-IgE or other ligands triggers degranulation.
  • IgE immunoglobulin E
  • Eosinophils are bi- or multi-nucleated white blood cells which contain eosinophiUc granules. Their plasma membrane is characterized by Ig receptors, particularly IgG and IgE. Generally, 5 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 o 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 5 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 o 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 immunoglobulin proteins produced by B-lymphocytes which bind to specific antigens and cause inactivation or promote destruction of the 5 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 5 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 o 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.
  • 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 5 an "immunological memory” that can provide immunity for years.
  • T cells 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.
  • helper T cells activates macrophages to destroy ingested microorganisms, while another, T H 2, stimulates the production of antibodies by B cells.
  • T H 1 activates macrophages to destroy ingested microorganisms
  • T H 2 stimulates the production of antibodies by B cells.
  • Cytotoxic T cells directly attack the infected target cell.
  • 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. Cresswell (1998) Annu. Rev. Immunol. 16:323-358).
  • TEP antigen processing
  • 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 5 antigen presented on cell surface MHC molecules.
  • T cells secrete ⁇ -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 o 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.
  • Helper T cells are required for most B cells to respond to antigen.
  • an activated helper cell contacts a B cell, its centrosome and Golgi apparatus become oriented toward the B cell, aiding 5 the directing of signal molecules, such as transmembrane-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 produce antibodies which react with specific antigenic proteins presented by pathogens. Once activated, B cells become filled with extensive rough endoplasmic 5 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.
  • Antibodies or immunoglobulins (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 5 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 a, ⁇ , e, ⁇ , and ⁇ H-chain types.
  • IgG the most o common class of antibody found in the circulation, is tetrameric, 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 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. In addition, H chains such as ⁇ 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 o 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 neutrophils. 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.
  • an antigen such as a bacterium
  • 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.
  • AIDS 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 metaboUc resources 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. 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.
  • Eosinophilia is an excess of eosinophils commonly observed in patients with allergies (hay fever, asthma), allergic reactions to drugs, rheumatoid arthritis, and cancers (Hodgkin's disease, lung, and liver cancer) (Isselbacher, KJ. et al. (1994) Harrison's Principles of Internal Medicine, McGraw-Hill, Inc., New York NY).
  • the complement system serves as an effector system and is involved in infectious agent recognition. It can function as an 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 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 serve to define the target and initiate the complement system cascade, culminating in the destruction of the infectious agent.
  • 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 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).
  • Inflammatory responses are divided into four categories on the basis of pathology and include allergic 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.
  • Acute inflammation is observed in individuals wherein specific antigens stimulate IgE antibody production.
  • Mast cells and basophils are subsequently activated by the attachment of 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. 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.
  • immune complexes bind to neutrophils and macrophages they activate the respiratory burst to form protein- and vessel- damaging agents such as hydrogen peroxide, hydroxyl radical, hypochlorous acid, and chloramines.
  • Clinical manifestations include rheumatoid arthritis and systemic lupus erythematosus.
  • SEQ ID NO:9 encodes, for example, an extracellular information transmission molecule.
  • 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 5 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, o 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 5 secreted in diurnal, pulsatile, and cyclic patterns.
  • Hormone secretion is regulated by perturbations in blood biochemistry, by other upstream-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. o 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 5 to respond to the hormone.
  • Hormones can be classified biochemically as polypeptides, steroids, eicosanoids, or amines.
  • Polypeptides which include diverse hormones such as insuUn and growth hormone, vary in size and function and are often synthesized as inactive precursors that are processed intracellularly into mature, active forms.
  • Amines which include epinephrine and dopamine, are amino acid derivatives that o 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 prostacycUns, are fatty acid derivatives that function in a variety of processes.
  • polypeptides and some amines are soluble in the circulation where they are highly susceptible to proteolytic degradation within seconds after their secretion. Steroids and Upids are insoluble and must be transported in the circulation by carrier proteins. The following discussion will focus primarily on polypeptide hormones.
  • Hypothalamic hormones include thyrotropin-releasing hormone, gonadotropin-releasing hormone, somatostatin, growth-hormone releasing factor, corticotropin-releasing hormone, substance P, 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 adrenocorticotropic hormone (ACTH), melanocyte-stimulating hormone, somatotropic hormones such as growth hormone and prolactin, glycoprotein hormones such as thyroid-stimulating hormone, luteinizing hormone (LH), and folUcle-stimulating hormone (FSH), ⁇ -Upotropin, and ⁇ -endo ⁇ hins.
  • ACTH adrenocorticotropic hormone
  • melanocyte-stimulating hormone such as growth hormone and prolactin
  • glycoprotein hormones such as thyroid-stimulating hormone, luteinizing hormone (LH), and folUcle-stimulating hormone (FSH), ⁇ -Upotropin, and ⁇ -endo ⁇ hins.
  • FSH folUcle-stimulating hormone
  • ⁇ -Upotropin ⁇ -Upotropin
  • disorders of the hypothalamus and pituitary often result from lesions such as primary brain tumors, adenomas, infarction associated with pregnancy, hypophysectomy, aneurysms, vascular malformations, thrombosis, infections, immunological disorders, and compUcations due to head trauma. 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-Schuller-Christian disease, Letterer-Siwe disease, sarcoidosis, empty sella syndrome, and dwarfism.
  • Disorders associated with hype ⁇ ituitarism include acromegaly, giantism, and syndrome of inappropriate ADH secretion (SIADH), often caused by benign adenomas.
  • SIADH inappropriate ADH secretion
  • 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, 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 hype ⁇ arathyroidism include Conn disease (chronic hypercalemia) leading to bone reso ⁇ tion and parathyroid hype ⁇ lasia.
  • Pancreatic hormones secreted by the pancreas regulate blood glucose levels by modulating the rates of carbohydrate, fat, and protein metaboUsm.
  • Pancreatic hormones include insuUn, glucagon, amyUn, ⁇ - aminobutyric acid, gastrin, somatostatin, and pancreatic polypeptide.
  • the principal disorder associated with pancreatic dysfunction is diabetes melUtus caused by insufficient insuUn activity. Diabetes melUtus is generally classified as either Type I (insulin-dependent, juvenile diabetes) or Type II (non- insuUn-dependent, adult diabetes). The treatment of both forms by insuUn replacement therapy is well known.
  • Diabetes melUtus often leads to acute complications such as hypoglycemia (insulin shock), 5 coma, diabetic ketoacidosis, lactic acidosis, and chronic compUcations leading to disorders of the eye, kidney, skin, bone, joint, cardiovascular system, nervous system, and to decreased resistance to infection.
  • hypoglycemia insulin shock
  • 5 coma diabetic ketoacidosis
  • lactic acidosis and chronic compUcations leading to disorders of the eye, kidney, skin, bone, joint, cardiovascular system, nervous system, and to decreased resistance to infection.
  • Growth factors are secreted proteins that mediate intercellular communication. UnUke hormones, which travel great distances via the circulatory system, most growth factors are primarily 5 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-translational modifications within the secretory pathway. These modifications can include proteolysis, glycosylation, phosphorylation, and intramolecular disulfide bond formation. Once secreted, growth factors bind to specific receptors on the surfaces of neighboring o 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, and cell motility.
  • the broadest class 5 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- ⁇ (TGF- ⁇ ), insulin-like growth factor (IGF), nerve growth factor (NGF), and platelet-derived growth factor (PDGF), each defining a family of numerous related factors.
  • EGF epidermal growth factor
  • FGF fibroblast growth factor
  • TGF- ⁇ transforming growth factor- ⁇
  • IGF insulin-like growth factor
  • NGF nerve growth factor
  • PDGF platelet-derived growth factor
  • the large polypeptide growth factors act as mitogens on diverse cell types to stimulate wound healing, o bone synthesis and remodeling, extracellular matrix synthesis, and proliferation of epithelial, epidermal, and connective tissues.
  • TGF- ⁇ , EGF, and FGF famines also function as inductive signals in the differentiation of embryonic tissue.
  • NGF functions specifically as a neurotrophic factor, promoting neuron
  • 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, neutrophils, macrophages, and their stem cell precursors. These factors include the colony-stimulating factors (G- CSF, M-CSF, GM-CSF, and CSF1-3), erythropoietin, 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 contribute 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 transcriptional 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).
  • NP/VM Small Peptide Factors - Neuropeptides and Vasomediators
  • 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 signaUng molecules such as angiotensin, complement, calcitonin, endotheUns, formyl-methionyl peptides, glucagon, cholecystokinin, gastrin, and many of the peptide hormones discussed above.
  • 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
  • NP/VMs can transduce signals directly, modulate the activity or release of other neurotransmitters 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, CR. et al. (1985) Endocrine Physiology, Oxford University Press, New York NY, pp. 57-62.)
  • 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 o 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- ⁇ , - ⁇ , and - 5 ⁇ ), the interleukins (ILl-ILl 3), 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 may not reflect the full scope of that cytokine' s o 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 5 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 0 are small proteins which range from about 6-15 kilodaltons in molecular weight. Chemokines are further classified as C, CC, CXC, or CX 3 C 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.
  • 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.
  • chemokines include lymphotactin (C chemokine); macrophage chemotactic and activating factor (MCAF/MCP-1; CC chemokine); platelet factor 4 and IL-8 (CXC chemokines); and fractalkine and neurofractin (CX 3 C chemokines).
  • SEQ ID NO:10 and SEQ ID NO:l 1 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 extracellular ligands and produce cellular responses in the areas of growth, differentiation, endocytosis, and immune response.
  • Other receptors faciUtate the selective transport of proteins out of the endoplasmic reticulum and locaUze enzymes to particular locations in the cell.
  • the term may also be apphed to proteins which act as receptors for Ugands 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.
  • Regulatory proteins such as growth factors coordinately control these cellular processes and act as mediators in cell-cell signaUng 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.
  • 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 signaUng molecules.
  • Cell surface receptors on immune system cells recognize antigens, antibodies, and major histocompatibiUty complex (MHC)-bound peptides. Other cell surface receptors bind ligands to be internaUzed by the cell.
  • MHC major histocompatibiUty complex
  • LDL low density Upoproteins
  • transferrin glucose- or mannose-terminal glycoproteins, galactose-terminal glycoproteins, immunoglobulins, phosphovitellogenins, fibrin, proteinase-inhibitor complexes, plasminogen activators, and thrombospondin
  • phosphovitellogenins fibrin
  • proteinase-inhibitor complexes proteinase-inhibitor complexes
  • plasminogen activators and thrombospondin
  • growth factor receptors including receptors for epidermal growth factor, 5 platelet-derived growth factor, fibroblast growth factor, as well as the growth modulator ⁇ -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 signaUng pathways that eventually link the initial receptor activation at the cell surface to 0 the activation of a specific intracellular target molecule.
  • SH2 domains and SH3 domains are found in phosphoUpase C- ⁇ , PI-3-K p85 regulatory subunit, Ras-GTPase activating protein, and pp ⁇ O 0 (Lowenstein, E.J. et al. (1992) Cell 70:431-442).
  • the cytokine family of receptors share a different common binding domain and include transmembrane 5 receptors for growth hormone (GH), interleukins, erythropoietin, and prolactia
  • receptors and second messenger-binding proteins have intrinsic serine/threonine protein kinase activity. These include activin/TGF- ⁇ /BMP-superfamily receptors, calcium- and diacylglycerol- activated/phosphoUpid-dependant protein kinase (PK-C), and RNA-dependant protein kinase (PK-R).
  • PKI activin/TGF- ⁇ /BMP-superfamily receptors
  • PK-C calcium- and diacylglycerol- activated/phosphoUpid-dependant protein kinase
  • PK-R RNA-dependant protein kinase
  • serine/threonine protein kinases including nematode Twitchin, have fibronectin-Uke, o immunoglobuUn C2-Uke domains.
  • G-protein coupled receptors 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 ( ⁇ ) heUces. These proteins range in size from under 400 to over 1000 5 amino acids (Strosberg, AD. (1991) Eur. J. Biochem. 196:1-10; CoughUn, 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. Extracellular loops of the GPCR alternate with intracellular loops and Unk the transmembrane domains.
  • the most conserved domains of GPCRs are the transmembrane domains and the first two cytoplasmic loops.
  • the o transmembrane domains account for structural and functional features of the receptor.
  • the bundle of ⁇ heUces forms a binding pocket.
  • the extracellular N-terminal segment or one or more of the three extracellular loops may also participate in Ugand binding.
  • Ligand binding activates the receptor by inducing a conformational change in intracellular portions of the receptor.
  • the activated receptor 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 cycUc AMP (cAMP), phosphoUpase C, inositol triphosphate, or interactions with ion channel proteins (Baldwin, J.M. (1994) Curr. Opin. Cell Biol. 6:180-190).
  • G guanine nucleotide binding
  • GPCRs include those for acetylchoUne, adenosine, epinephrine and norepinephrine, bombesin, 5 bradykinin, chemokines, dopamine, endotheUn, ⁇ -aminobutyric acid (GABA), folUcle-stimulating hormone (FSH), glutamate, gonadotropin-releasing hormone (GnRH), hepatocyte growth factor, histamine, leukotrienes, melanocortins, neuropeptide Y, opioid peptides, opsins, prostanoids, serotonin, somatostatin, tachykinins, thrombin, thyrotropin-releasing hormone (TRH), vasoactive intestinal polypeptide family, vasopressin and oxytocin, and o ⁇ han receptors.
  • GABA ⁇ -aminobutyric acid
  • FSH folUcle-stimulating hormone
  • retinitis pigmentosa may arise from mutations in the rhodopsin gene.
  • Rhodopsin is the retinal photoreceptor which is located within the discs of the eye rod cell.
  • Parma, J. et al. (1993, Nature 365:649-651) report that somatic activating mutations in the thyrotropin receptor cause hyperfunctioning thyroid adenomas and suggest 5 that certain GPCRs susceptible to constitutive activation may behave as protooncogenes.
  • Nuclear receptors bind small molecules such as hormones or second messengers, leading to 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 o 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
  • Ligand-gated receptor ion channels fall into two categories.
  • the first category extracellular Ugand-gated receptor ion channels (ELGs), rapidly transduce neurotransmitter-binding events into 5 electrical signals, such as fast synaptic neurotransmission. ELG function is regulated by post- translational modification.
  • the second category intracellular ligand-gated receptor ion channels (ILGs), are activated by many intracellular second messengers and do not require post-translational modifications) to effect a channel-opening response.
  • ELGs depolarize excitable cells to the threshold of action potential generation. In non-excitable o cells, ELGs permit a Umited calcium ion-influx during the presence of agonist.
  • ELGs include channels directly gated by neurotransmitters such as acetylchoUne, L-glutamate, glycine, ATP, serotonin, GABA, and histamine.
  • ELG genes encode proteins having strong structural and functional similarities. ILGs are encoded by distinct and unrelated gene famiUes and include receptors for cAMP, cGMP, calcium ions, ATP, and metaboUtes of arachidonic acid. Macrophage Scavenger Receptors
  • Macrophage scavenger receptors with broad ligand specificity may participate in the binding of low density Upoproteins (LDL) and foreign antigens.
  • Scavenger receptors types I and II are trimeric membrane proteins with each subunit containing a small N-terminal intracellular domain, a 5 transmembrane domain, a large extracellular domain, and a C-terminal cysteine-rich domain.
  • the extracellular domain contains a short spacer domain, an ⁇ -heUcal coiled-coil domain, and a triple heUcal collagenous domain.
  • T cells play a dual role in the immune system as effectors and regulators, coupUng antigen 5 recognition with the transmission of signals that induce cell death in infected cells and stimulate proUferation of other immune cells.
  • TCR T cell receptor
  • MHC major histocompatibiUty molecule
  • Both TCR subunits have an extracellular 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 somatic rearrangement of different gene segments. Interaction of antigen in the proper MHC context 5 with the TCR initiates signaling cascades that induce the proUferation, maturation, and function of cellular components of the immune system (Weiss, A. (1991) Annu. Rev. Genet. 25:487-510).
  • SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO: 17, and SEQ ID NO: 18 encode, for example, intracellular signaling molecules.
  • Intracellular signaling is the general process by which cells respond to extracellular signals (hormones, neurotransmitters, 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 signaling 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, o inositol, and various mitogens, that regulate protein phosphorylation.
  • second messenger molecules such as cyclic nucleotides, calcium-calmodulin, o inositol, and various mitogens, that regulate 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 triphosphate molecule (ATP) to 5 a particular protein by a protein kinase and removed from that protein by a protein phosphatase.
  • ATP adenosine triphosphate molecule
  • 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 o containing specific residues and sequence motifs characteristic of the kinase family (Hardie, G. and S.
  • 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 5 contraction, glycogen breakdown, and neurofransmission; and the mitogen-activated protein kinases
  • PKA cyclic- AMP dependent protein kinases
  • CaM calcium-calmodulin dependent protein kinases
  • MAP 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, KJ. et al. (1994) Harrison's Principles of Internal Medicine McGraw-Hill, New York NY, pp. 416-431, 1887).
  • o PTKs are divided into transmembrane, receptor PTKs and nontransmembrane, non-receptor
  • 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. 5 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.
  • HPK histidine protein kinase family
  • 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 0 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).
  • the two principal categories of protein phosphatases 5 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).
  • 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). 5 Phospholipid and Inositol-Phosphate Signaling
  • Inositol phospholipids 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 (PIP j ) by inositol kinases. Simultaneously, the G- o protein Unked receptor binding stimulates a trimeric G-protein which in turn activates a phosphoinositide-specific phospholipase C- ⁇ .
  • PI phosphatidylinositol
  • IP 3 inositol triphosphate
  • diacylglycerol acts as mediators for separate signaling events.
  • IP 3 diffuses through the plasma membrane to induce calcium release from the endoplasmic reticulum (ER), while diacylglycerol remains in the membrane and helps activate 5 protein kinase C, an STK that phosphorylates selected proteins in the target cell.
  • the calcium response initiated by IP 3 is terminated by the dephosphorylation of IP 3 by specific inositol phosphatases.
  • Cyclic nucleotides function as intracellular second messengers to transduce a variety of extracellular signals including hormones, light, and neurotransmitters.
  • cyclic- AMP dependent protein kinases PKA
  • PKA cyclic- AMP dependent protein kinases
  • adenylyl cyclase which synthesizes cAMP from AMP, is activated to increase cAMP levels in muscle by binding of adrenaUne to ⁇ -andrenergic receptors, while activation 5 of guanylate cyclase and increased cGMP levels in photoreceptors leads to reopening of the
  • PDEs cAMP and cGMP-specific phosphodiesterases
  • PDE inhibitors have been found to be particularly useful in treating various clinical disorders.
  • Rolipram a specific inhibitor of PDE4
  • TheophyUine is a nonspecific PDE inhibitor used in the treatment of bronchial asthma and other respiratory diseases (Banner, K.H. and CP. Page (1995) Eur. Respir. J. 8:996-1000).
  • G-proteins are critical mediators of signal transduction between a particular class of extracellular receptors, the G-protein coupled receptors (GPCR), and 0 intracellular second messengers such as cAMP and Ca 2+ .
  • G-proteins are linked to the cytosoUc 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 Ca 2+ into the cytosol from the ER, which, in turn, regulate phosphorylation and activation of other intracellular 5 proteins.
  • the ⁇ and ⁇ subunits form a tight complex that anchors the protein to the inner side of the plasma membrane.
  • the ⁇ subunits also known as G- ⁇ proteins or ⁇ transducins, contain seven tandem repeats of the WD-repeat sequence motif, a motif found in many proteins with regulatory functions. Mutations and variant expression of ⁇ fransducin proteins are o linked with various disorders (Neer, E. J. et al. (1994) Nature 371 :297-300; Margottin, F. et al. (1998)
  • LMW GTP-proteins are GTPases which regulate cell growth, cell cycle control, protein secretion, and intracellular vesicle interaction. They consist of single polypeptides which, Uke the ⁇ subunit of the heterotrimeric G-proteins, are able to bind and hydrolyze GTP, thus cycling between an 5 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 o 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
  • GTP-ras binds to GTP-ras and induces it to hydrolyze GTP to GDP.
  • GNRP guanine nucleotide releasing protein
  • RGS G-protein signaling
  • RGS family members are related structurally through similarities in an approximately 120 amino acid region termed the RGS domain and functionally by their abiUty to inhibit the interleukin (cytokine) induction of MAP kinase 0 in cultured mammalian 293T cells (Druey, supra).
  • cytokine interleukin
  • Ca +2 is another second messenger molecule that is even more widely used as an intracellular mediator than cAMP.
  • Ca 2+ directly activates regulatory enzymes, such as protein kinase C, which trigger signal transduction pathways.
  • Ca 2+ also binds to specific Ca 2+ -binding proteins (CBPs) 5 such as calmoduUn (CaM) which then activate multiple target proteins in the cell including enzymes, membrane transport pumps, and ion channels.
  • CBPs Ca 2+ -binding proteins
  • 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 0 Calcium-binding Proteins, Oxford University Press, Oxford, UK, pp. 15-20).
  • CBPs can serve as a storage depot for Ca 2+ 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 Ca 2+ in a rapidly exchangeable state that is released during Ca 2+ -signaling conditions (Celio, M.R. et al. (1996) Guidebook to Calcium-binding Proteins, Oxford University Press, New York NY, pp. 222- 5 224).
  • Cell division is the fundamental process by which all Uving things grow and reproduce. In most organisms, the cell cycle consists of three principle steps; inte ⁇ hase, mitosis, and cytokinesis. Inte ⁇ hase, involves preparations for cell division, replication of the DNA and production of essential o proteins. In mitosis, the nuclear material is divided and separates to opposite sides of the cell.
  • Cytokinesis is the final division and fission of the cell cytoplasm to produce the daughter cells.
  • Cyclins act by binding to and activating a group of cycUn-dependent protein kinases (Cdks) which then phosphorylate and activate selected proteins 5 involved in the mitotic process.
  • Cdks cycUn-dependent protein kinases
  • Two principle types are mitotic cycUn, or cyclin B, which controls entry of the cell into mitosis, and Gl cyclin, which controls events that drive the cell out of mitosis.
  • cyclin B which controls entry of the cell into mitosis
  • Gl cyclin which controls events that drive the cell out of mitosis.
  • Ceretain proteins in intracellular signaling pathways serve to link or cluster other proteins o involved in the signaling cascade.
  • a conserved protein domain called the PDZ domain has been 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 cytosoUc face of the plasma membrane. (For a review of PDZ domain-containing proteins, see Ponting, CP. et al.
  • PDZ domains are found in the eukaryotic MAGUK (membrane-associated guanylate kinase) protein family, members of which bind to the intracellular domains of receptors and channels.
  • MAGUK membrane-associated guanylate kinase
  • 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 5 such as syntrophins and neuronal nitric oxide synthase (nNOS).
  • nNOS neuronal nitric oxide synthase
  • Membrane Transport Molecules o
  • the plasma membrane acts as a barrier to most molecules. Transport between the cytoplasm and the extracellular environment, and between the cytoplasm and lumenal spaces of cellular 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 transport protein. For 5 example, cystinuria is an inherited disease that results from the inability to transport cystine, the disulfide-linked dimer of cysteine, from the urine into the blood. Accumulation of cystine in the 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 transport involves o directional pumping of a solute across the membrane, usually against an electrochemical gradient.
  • Active transport is tightly coupled to a source of metabolic energy, such as ATP hydrolysis or an 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 transport, bind to a specific 5 solute to be transported and undergo a conf ormational change which transfers the bound solute across the membrane.
  • Channel proteins which only function in passive transport, form hydrophilic pores 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 0 are called uniporters.
  • coupled transporters link the transfer of one solute with simultaneous or sequential transfer of a second solute, either in the same direction (symport) or in the opposite direction (antiport).
  • 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 5 sodium gradient that provides the driving force for solute uptake is maintained by the ubiquitous Na7K + ATPase.
  • Sodium-coupled transporters include the mammaUan glucose transporter (SGLT1), iodide transporter (NIS), and multivitamin transporter (SMVT). Al 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 5 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. Natl. Acad. Sci. 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).
  • o Transporters play a major role in the regulation of pH, excretion of drugs, and the cellular
  • Monocarboxylate anion transporters are proton-coupled symporters with a broad 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) heUcal domains with a large intracellular loop between TM6 and 5 TM7, and play a critical role in maintaining intracellular pH by removing the protons that are produced stoichiometrically with lactate during glycolysis.
  • TM transmembrane
  • H(+)-monocarboxylate transporter is that of the erythrocyte membrane, which transports L-lactate and a wide range of other aUphatic monocarboxylates.
  • Other cells possess H(+)-Unked monocarboxylate transporters with differing substrate and inhibitor selectivities.
  • cardiac muscle and tumor cells have o transporters that differ in their K m values for certain substrates, including stereoselectivity for L- over
  • D-lactate D-lactate, and in their sensitivity to inhibitors.
  • Na(+)-monocarboxylate cotransporters on the luminal surface of intestinal and kidney epitheUa, which allow the uptake of lactate, pyruvate, and ketone bodies in these tissues.
  • transporters for organic cations and organic anions in organs including the kidney, intestine and liver 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 drugs and endogenous metaboUtes, and contribute to the maintenance of intercellular pH.
  • Am. J. Physiol. 264:C761-C782 mediate the secretion of a variety of drugs and endogenous metaboUtes, and contribute to the maintenance of intercellular pH.
  • 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. Haggstrom (1993) J. Biotechnol. 30: 339-350.
  • ATP-binding cassette The largest and most diverse family of transport proteins known is the ATP-binding cassette
  • ABC transporters can transport substances that differ markedly in chemical structure and size, ranging from small molecules such as ions, sugars, amino acids, peptides, and phosphoUpids, to Upopeptides, 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 transport, 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 for the cystic fibrosis transmembrane regulator (CFTR), or by separate genes.
  • NBD nucleotide-binding domains
  • MSD membrane-spanning domains
  • each gene product contains a single NBD and MSD. These "half-molecules" form 5 homo- and heterodimers, such as Tapl and Tap2, the endoplasmic reticulum-based major histocompatibiUty (MHC) peptide transport system.
  • MHC major histocompatibiUty
  • CFTR cystic fibrosis
  • ALDP adrenoleukodystrophy
  • ALDP adrenoleukodysfrophy protein
  • Zellweger syndrome peroxisomal membrane protein-70, PMP70
  • hyperinsuUnemic hypoglycemia 0 sulfonylurea receptor, SUR.
  • MDR multidrug resistance
  • ABC transporter in human cancer cells makes the cells resistant to a variety of cytotoxic drugs used in chemotherapy (TagUght, D. and S. MichaeUs (1998) Meth. Enzymol. 292:131-163).
  • Fatty acid transport protein 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. o Biol. Chem. 273 :27420-27429). Ion Channels
  • the electrical potential of a cell is generated and maintained by controlUng the movement of ions across the plasma membrane.
  • the movement of ions requires ion channels, which form an ion- selective pore within the membrane.
  • ion channels There are two basic types of ion channels, ion transporters and 5 gated ion channels.
  • Ion transporters utilize the energy obtained from ATP hydrolysis to actively transport 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.
  • these types of ion channels generate, maintain, and utitize an electrochemical gradient that is used in 1) electrical impulse conduction down the axon of a nerve cell, 2) transport of molecules into cells against concentration o gradients, 3) initiation of muscle contraction, and 4) endocrine cell secretion.
  • Ion transporters generate and maintain the resting electrical potential of a cell. UtiUzing the energy derived from ATP hydrolysis, they transport ions against the ion's concentration gradient. These transmembrane ATPases are divided into three famiUes.
  • the phosphorylated (P) class ion transporters including Na + -K + ATPase, Ca 2+ -ATPase, and H + -ATPase, are activated by a phosphorylation event.
  • P-class ion transporters are responsible for maintaining resting potential distributions such that cytosoUc concentrations of Na + and Ca 2+ are low and cytosoUc concentration of K + is high.
  • the vacuolar (V) class of ion transporters includes H + pumps on intracellular organelles, such as lysosomes and Golgi. V-class ion transporters are responsible for generating the low pH within 5 the lumen of these organelles that is required for function.
  • the coupUng factor (F) class consists of H + pumps in the mitochondria. F-class ion transporters utiUze a proton gradient to generate ATP from ADP and inorganic phosphate (PJ.
  • the resting potential of the cell is utiUzed in many processes involving carrier proteins and gated ion channels.
  • Carrier proteins utilize the resting potential to transport molecules into and out of 0 the cell.
  • Amino acid and glucose transport into many cells is Unked to sodium ion co-transport
  • Ion channels share common structural and mechanistic themes.
  • the channel consists of four or 5 five subunits or protein monomers that are arranged like a barrel in the plasma membrane. Each subunit typically consists of six potential transmembrane segments (SI, S2, S3, S4, S5, and S6).
  • the center of the barrel forms a pore lined by ⁇ -helices or ⁇ -strands.
  • the side chains of the amino acid residues comprising the ⁇ -heUces or ⁇ -strands e stabUsh the charge (cation or anion) selectivity of the channel.
  • the degree of selectivity, or what specific ions are allowed to pass through the channel o 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 changes in membrane potential, and Ugand-gated channels open pores in the presence of a specific ion, 5 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 contraction, arise from large, transient changes in the permeabiUty of the membrane to Na + and K + ions. Depolarization of the membrane beyond the threshold level opens voltage-gated Na + channels. Sodium o 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 transmembrane 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.
  • Voltage-gated Na + channels are heterotrimeric complexes composed of a 260 kDa pore forming ⁇ subunit that associates with two smaller auxiliary subunits, ⁇ l and ⁇ 2.
  • the ⁇ 2 subunit is an integral membrane glycoprotein that contains an extracellular Ig domain, and its association with ⁇ and ⁇ l 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.
  • Voltage-gated Ca 2+ channels are involved in presynaptic neurotransmitter release, and heart and skeletal muscle contraction.
  • the voltage-gated Ca 2+ 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 a ⁇ subunit forms the membrane pore and voltage sensor, while the ⁇ 2 ⁇ and ⁇ subunits modulate the voltage-dependence, gating properties, and the current amplitude of the channel.
  • These subunits are encoded by at least six ⁇ 1( one 0 2 8, and four ⁇ genes.
  • a fourth subunit, ⁇ has been identified in skeletal muscle. (Walker, D. et al.
  • Chloride channels are necessary in endocrine secretion and in regulation of cytosoUc and organelle pH.
  • Cl " enters the cell across a basolateral membrane through an Na + , K7C1 " cotransporter, 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 transmembrane conductance regulator is a chloride channel encoded by the gene for cystic fibrosis, a common fatal genetic disorder in humans. Loss of CFTR function decreases transepitheUal water secretion and, as a result, the layers of mucus that coat the respiratory tree, 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” (A-Awqati, Q. et al. (1992) J. Exp. Biol. 172:245-266).
  • H + - ATPase pumps that generate transmembrane pH and electrochemical 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 electrochemical 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, 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 (A-Awqati, supra).
  • Ligand-gated channels open their pores when an extracellular or intracellular mediator binds to 5 the channel.
  • Neurotransmitter-gated channels are channels that open when a neurotransmitter binds to their extracellular domain. These channels exist in the postsynaptic membrane of nerve or muscle cells.
  • Chloride channels open in response to inhibitory neurotransmitters, such as ⁇ -aminobutyric acid (GABA) and glycine, leading to hype ⁇ olarization of the membrane and the subsequent generation of an action potential.
  • GABA ⁇ -aminobutyric acid
  • Ligand-gated channels can be regulated by intracellular second messengers. Calcium-activated K + channels are gated by internal calcium ions. In nerve cells, an influx of calcium during 5 depolarization opens K + channels to modulate the magnitude of the action potential (Ishi, T.M. et al. (1997) Proc. Nail. Acad. Sci. USA 94:11651-11656). Cyclic micleotide-gated (CNG) channels are gated by cytosoUc cyclic 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 ligand-mediated activation of a G-protein coupled receptor which then alters the level of cyclic o nucleotide within the cell.
  • Ion channels are expressed in a number of tissues where they are impUcated in a variety of processes.
  • CNG channels while abundantly expressed in photoreceptor and olfactory sensory cells, are also found in kidney, lung, pineal, retinal gangUon cells, testis, aorta, and brain.
  • Calcium-activated K + channels may be responsible for the vasodilatory effects of bradykinin in the kidney and for shunting 5 excess K + from brain capillary endotheUal cells into the blood. They are also impUcated in repolarizing granulocytes after agonist-stimulated depolarization (Ishi, supra). Ion channels have been the target for many drug therapies.
  • Neurotransmitter-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 trauma, and neurodegenerative disease (Taylor, CP. o and L.S. Narasimhan (1997) Adv. Pharmacol. 39:47-98).
  • SEQ ID NO:34 encodes, for example, a protein modification and maintenance molecule.
  • the cellular processes regulating modification and maintenance of protein molecules o 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 cleave proteins and peptides at the peptide bond that forms the backbone of the 5 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 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 o 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 Press, New York NY, pp. 1-5).
  • SPs serine proteases
  • the serine proteases have a serine residue, usually within a conserved sequence, in an 5 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 control extracellular protein degradation.
  • the main SP sub-families are 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 o 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. Natl. Acad. Sci. USA 91:7588-7592).
  • Prolylcarboxypeptidase a lysosomal serine peptidase that cleaves peptides such as angiotensin II and III and [des- Ag9] 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 catalysis proceeds via an intermediate thiol ester and is facilitated by adjacent histidine and aspartic 5 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 cytosoUc 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 tissue repair. Overabundance of these repair molecules plays a role in certain disorders. In o 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 matrix of bones.
  • Aspartic proteases are members of the cathepsin family of lysosomal proteases and include pepsin A, gastricsin, chymosin, renin, and cathepsins D and E. Aspartic proteases have a pair of 5 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.
  • the mRNA for stromelysin, cytokines, TIMP-1, cathepsin, gelatinase, o 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 contribute to the influx of mononuclear cells which exacerbates the destruction of the rheumatoid synovium. (Keyszer, G.M. (1995) Arthritis Rheum.
  • 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 metalloproteases. Both are exoproteases of similar structure and active sites.
  • Carboxypeptidase A o like chymotrypsin, 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 0-sialoglycoproteins such as glycophorin A.
  • P-LAP placental leucine aminopeptidase
  • 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.
  • 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 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 homolog of this gene is consistently elevated in small cell tumors and adenocarcinomas of the lung (Gray, D. A. (1995) Oncogene 10:2179-2183).
  • the mechanism for the translocation process into the endoplasmic reticulum involves the recognition of an N-terminal signal peptide on the elongating protein.
  • the signal peptide directs 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 Protease inhibitors and other regulators of protease activity control the activity and effects of proteases.
  • Protease inhibitors have been shown to control pathogenesis in animal models of proteolytic disorders (Mu ⁇ hy, 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). Se ⁇ ins are inhibitors of mammalian plasma serine proteases. Many se ⁇ ins 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 matrix (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 domains" containing a series of cysteine residues that are regularly spaced over approximately 50 amino acid residues and form three intrachain disulfide bonds.
  • TFPI-1 and TFPI-2 tissue factor pathway inhibitor
  • bikunin aprotinin
  • TFPI-1 and TFPI-2 tissue factor pathway inhibitor
  • inter- ⁇ -trypsin inhibitor inter- ⁇ -trypsin inhibitor
  • bikunin bikunin.
  • kalUkrein and plasmin serine proteases
  • Aprotinin 5 has cUnical utiUty in reduction of perioperative blood loss.
  • 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 intramolecular disulfide bonds in proteins.
  • PDI protein disulfide isomerase
  • PPI peptidyl-prolyl isomerase
  • cyclophilins represent a major class of PPI that was originally identified as the major receptor for the immunosuppressive drug cyclosporin A (Handschumacher, RE. et al. (1984) Science 226: 544-547). 0 Protein Glvcosylation
  • 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 o 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, pp.700-708). 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-Unked 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 5 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.
  • Chaperones o 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 transport 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 5 that have become denatured by the high temperatures.
  • hsp heat-shock proteins
  • Chaperones may be divided into several classes according to their location, function, and molecular weight, and include hsp60, TCP1, hsp70, hsp40 (also called DnaJ), and hsp90.
  • hsp90 binds to steroid hormone receptors, represses transcription in the absence of the Ugand, 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 0 Biochem. 29:125-136).
  • Hsp60 and hsp70 chaperones aid in the transport and folding of newly 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.
  • Al chaperones share an affinity for hydrophobic patches on incompletely folded 5 proteins and the ability to hydrolyze ATP. The energy of ATP hydrolysis is used to release the hsp- bound protein in its properly folded state (Aberts, supra, pp 214, 571-572).
  • SEQ ID NO:35 and SEQ ID NO:36 encode, for example, nucleic acid synthesis and o modification molecules .
  • 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 5 complementary base-pairing into a complementary nucleic acid sequence of either DNA or RNA.
  • templating the process in which the nucleotide sequence of a DNA or RNA strand is copied by 5 complementary base-pairing into a complementary nucleic acid sequence of either DNA or RNA.
  • 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 5 of the Cell, Garland Publishing Inc., New York NY, pp. 251-254).
  • the substrates for the polymerization 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.
  • 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 0 therefore inherits a new DNA double helix containing one old and one new strand.
  • DNA is said to be replicated "semiconservatively" by DNA polymerase.
  • DNA polymerase is also involved in the repair of damaged DNA as discussed below under “Ligases.”
  • RNA polymerase uses a DNA template strand to "transcribe" 5 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' -OH end of a growing RNA chain. DNA transcription 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 o different types of RNA (Aberts, supra, pp. 367-368).
  • mRNA messenger RNAs
  • RNA polymerase I makes the large ribosomal RNAs
  • RNA polymerase II makes the mRNAs that will be translated into proteins
  • RNA polymerase III makes a variety of small, stable RNAs, including 5S ribosomal RNA and the transfer RNAs (tRNA).
  • 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 5 completed at a broad, general stop or termination region in the DNA where both the polymerase and the completed RNA chain are released.
  • 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 o replication or transcription 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. 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 5 break left between the inserted nucleotide(s) and the existing DNA strand by DNA ligase.
  • DNA ligase uses the energy from ATP hydrolysis to activate the 5 ' end of the broken phosphodiester bond before forming the new bond with the 3'-OH of the DNA strand.
  • 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). 5 Nucleases
  • Nucleases comprise both enzymes that hydrolyze DNA (DNase) and RNA (RNase). They serve different pu ⁇ oses in nucleic acid metaboUsm. 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, o 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 endonuclease activity is involved in the excision step of the DNA repair process.
  • 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 5 the RNA strand of an RN A/DNA hybrid. Such hybrids occur in cells invaded by retroviruses, and RNase H is an important enzyme in the retroviral replication cycle.
  • Pancreatic RNase secreted by the pancreas into 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 o tumor angiogenesis, allergic reactions, viral infection and replication, and fungal infections.
  • 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- 5 helix. 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-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).
  • 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 codons by specific tRNAs.
  • the primary methylation pattern is the dimethylation of guanine residues to form N,N-dimethyl guanine.
  • HeUcases and Single-Stranded Binding Proteins 5 HeUcases are enzymes that destabiUze 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 first separate to generate a replication "fork” for DNA polymerase to act on.
  • DNA heUcases hydrolyze ATP and use the energy of hydrolysis to separate the DNA strands.
  • Single- 5 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).
  • RNA helicases 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 l o 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, 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.
  • 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. 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.
  • DNA topoisomerase effectively acts as a reversible nuclease that hydrolyzes a phosphodiesterase bond in a DNA strand, permitting the two strands to
  • 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 heUces 35 cross over one another. This type of topoisomerase can efficiently separate two interlocked DNA circles (Aberts, supra, pp.260-262).
  • 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 Aberts, 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.
  • 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.
  • 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.
  • this form of recombination can alter the relative positions of nucleotide sequences in chromosomes.
  • RNA processing steps include capping at the 5' end with methylguanosine, polyadenylating the 3' end, and splicing 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 sphceosome.
  • the spUceosomal complex is composed of five small nuclear ribonucleoprotein particles (snRNPs) designated Ul, U2, U4, U5, and U6, and a number of additional proteins.
  • snRNP small nuclear ribonucleoprotein particles
  • Ul small nuclear ribonucleoprotein particles
  • U2, U4, U5, and U6 small nuclear ribonucleoprotein particles
  • U6 small nuclear ribonucleoprotein particles
  • RNA components of some snRNPs recognize and base pair with intron consensus sequences.
  • the protein components mediate sphceosome 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 Company, New York NY, p. 863).
  • Adhesion Molecules The surface of a cell is rich in transmembrane proteoglycans, glycoproteins, glycoUpids, and receptors. These macromolecules mediate adhesion with other cells and with components of the extracellular matrix (ECM). The interaction of the cell with its surroundings profoundly influences cell shape, strength, flexibility, motiUty, and adhesion. These dynamic properties are intimately 5 associated with signal transduction pathways controlUng cell proliferation and differentiation, tissue construction, and embryonic development. Cadherins
  • Cadherins comprise a family of calcium-dependent glycoproteins that function in mediating cell-cell adhesion in virtually all soUd tissues of multicellular organisms. These proteins share o multiple repeats of a cadherin-specific motif, and the repeats form the folding units of the cadherin extracellular domain. Cadherin molecules cooperate to form focal contacts, or adhesion plaques, between adjacent 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 epithelial cells and is especially important for embryonic 5 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 a variety of cell-cell interactions (Suzuki, S.T. (1996) J. Cell Sci. 109:2609-2611).
  • the intracellular anchorage of cadherins is regulated by their dynamic association with catenins, a family of cytoplasmic signal transduction proteins associated with the actin o cytoskeleton.
  • cadherins The anchorage of cadherins to the actin cytoskeleton appears to be regulated by protein tyrosine phosphorylation, and the cadherins are the target of phosphorylation-induced junctional disassembly (Aberle, H. et al. (1996) J. Cell. Biochem. 61:514-523).
  • Integrins are ubiquitous transmembrane adhesion molecules that link the ECM to the internal 5 cytoskeleton. Integrins are composed of two noncovalently associated transmembrane glycoprotein subunits called and ⁇ . Integrins function as receptors that play a role in signal transduction. For example, binding of integrin to its extracellular ligand may stimulate changes in intracellular 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, o which is involved in many different biological processes including cell migration and embryogenesis
  • Lectins comprise a ubiquitous family of extracellular glycoproteins which bind cell surface carbohydrates specifically and reversibly, resulting in the agglutination of cells (reviewed in 5 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 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 subfamiUes based on carbohydrate-binding specificity and 5 other criteria.
  • the galectin subfamily includes lectins that bind ⁇ -galactoside carbohydrate moieties in a thiol-dependent manner (reviewed in Hadari, Y.R. et al. (1998) J. Biol. Chem. 270:3447-3453). Galectins are widely expressed and developmentally 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 0 and oUgomerization properties. Small galectins form homodimers and are about 14 to 16 kilodaltons in mass, while large galectins are monomeric and about 29-37 kilodaltons.
  • 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 5 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 predictions indicate that the CRD forms several ⁇ -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 o 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 and mice. Moreover, anti-galectin antibodies inhibit processes associated with cell transformation, such as cell aggregation and anchorage-independent growth (See, for example, Su, Z.-Z. et al. (1996) Proc. Natl. Acad. Sci. USA 93:7252-7257). 5 Selectins
  • Selectins comprise a specialized lectin subfamily involved primarily in 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 o leukocyte cell membrane and enable the leukocyte to adhere to and migrate along the endothelial surface. Binding of selectin to its ligand leads to polarized rearrangement of the actin cytoskeleton and stimulates signal transduction within the leukocyte (Brenner, B. et al. (1997) Biochem. Biophys. Res.
  • selectins include lymphocyte 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).
  • SEQ ID NO:37 encodes, for example, an antigen recognition molecule.
  • Al 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 transmembrane proteins expressed by leukocytes (white blood cells) such as lymphocytes, granulocytes, and monocytes. Most of these proteins belong to the immunoglobulin (Ig) superfamily, members of which contain one or more repeats of a conserved structural domain. This Ig domain is comprised of antiparallel ⁇ sheets joined by a disulfide bond in an arrangement called the Ig fold.
  • Members of the Ig superfamily include T-cell receptors, major histocompatibiUty (MHC) proteins, antibodies, and immune cell-specific surface markers such as CD4, CD8, and CD28.
  • 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 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.
  • MHC molecules also play an important role in organ rejection following transplantation. 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 Aberts, B. et al. (1994) Molecular Biology of the Cell. Garland PubUshing, New York NY, pp. 1229-1246.)
  • Aitibodies, or immunoglobulins are either expressed on the surface of B-cells or secreted by B-cells into the circulation. Aitibodies bind and neutralize foreign antigens in the blood and other extracellular fluids.
  • 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 ⁇ , ⁇ , e, ⁇ , and ⁇ H-chain types.
  • L- chains There are two types of L- chains, K and ⁇ , either of which may associate as a pair with any H-chain pair.
  • IgG the most 5 common class of antibody found in the circulation, is tetrameric, 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.
  • 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 0 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 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. 5 (Reviewed in Aberts, supra, pp. 1206-1213 and 1216-1217.)
  • 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 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 o 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 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- 5 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 rate of somatic mutation within these segments further contribute to the generation of a diverse antibody population.
  • o T-cell receptors are both structurally and functionally related to antibodies. (Reviewed in
  • 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 of two disulfide-Unked 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 5 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.
  • T-cell receptors recognize small peptide antigens that are 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 histocompatibiUty proteins which provide the 5 proper context for antigen recognition.
  • SEQ ID NO:38 and SEQ ID NO:39 encode, for example, secreted/extracellular matrix molecules.
  • 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 pathway or remain in any of the secretory organelles such as theER, Golgi apparatus, or lysosomes. 5 Proteins that transit through the secretory pathway are either secreted into the extracellular space or retained in the plasma membrane.
  • Secreted proteins are often synthesized as inactive precursors that are activated by post-translational processing events during transit through the secretory pathway. Such events include glycosylation, proteolysis, and removal of the signal peptide by a signal peptidase. Other events that may occur during protein transport include chaperone-dependent unfolding and o 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, extracellular matrix molecules, cytokines, hormones, growth and differentiation factors, neuropeptides, vasomediators, ion channels, transporters/pumps, and proteases. (Reviewed in Aberts, B. et al.
  • the extracellular matrix is a complex network of glycoproteins, polysaccharides, proteoglycans, and other macromolecules that are secreted from the cell into the extracellular 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 cell to its surrounding matrix is required for cell survival except in the case of metastatic tumor cells, o which have overcome the need for cell-ECM anchorage.
  • 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 triple helix stabihzed by interchain disulfide bonds. Bundles of these triple heUces then associate to form fibrils.
  • Collagen primary structure 5 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 triple 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, 0 hypermobile joints, and susceptibiUty to aortic and intestinal rupture. Chondrodysplasia patients have short stature and ocular disorders. Aport syndrome patients have hematuria, sensorineural deafness, and eye lens deformation. (Isselbacher, KJ. et al.
  • Elastin is a highly hydrophobic protein of about 750 amino acids that is rich in proUne and glycine residues. Elastin molecules are highly cross-Unked, 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 fibrilUn. Mutations in the gene encoding fibrilUn are responsible for o 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 Aberts, 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-Uke structure containing multiple domains. The domains each contain multiple repeated modules, the most common 5 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.
  • some type III fibronectin repeats contain a characteristic tripeptide consisting of Aginine-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.
  • Laminin is a major glycoprotein component of the basal lamina which underlies and supports epitheUal 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 Aberts, supra, pp. 990-991.)
  • proteoglycans are composed of unbranched polysaccharide chains
  • proteoglycans 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 signaUng molecules, such as fibroblast growth factor and transforming growth factor ⁇ , suggesting a role for proteoglycans in cell-cell communication and cell 0 growth.
  • 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.)
  • SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, and SEQ ID NO:45 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 o 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 5 structure or activity of the fibers while cytoskeletal membrane anchors connect the fibers to the cell membrane.
  • Tubulins include myosin, dynein, and kinesin.
  • 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 o 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 5 heterodimer of ⁇ - and ⁇ - tubulin, multiple isoforms of which exist.
  • the hydrolysis of GTP is linked to the addition of tubuUn 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 ⁇ -tubulin and the other with ⁇ -tubulin, and the two ends differ in their rates of assembly.
  • each microtubule is composed of 13 protofilaments although 11 or 15 0 protofilament-microtubules are sometimes found.
  • Cilia and flagella contain doublet microtubules.
  • Microtubules grow from speciaUzed 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 5 polymerization of ⁇ - and ⁇ - tubulin heterodimers but does not polymerize into microtubules.
  • Microtubule- Associated Proteins are important for nucleating the 5 polymerization of ⁇ - and ⁇ - tubulin heterodimers but does not polymerize into microtubules.
  • Microtubule-associated proteins have roles in the assembly and stabilization of microtubules.
  • assembly MAPs can be identified in neurons as well as non-neuronal cells. Assembly MAPs are responsible for cross-Unking microtubules in the cytosol. o 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 MAP1B, are large, filamentous molecules that co-purify with microtubules and are abundantly expressed in brain and testes.
  • Type I 5 MAPs contain several repeats of a positively-charged amino acid sequence motif that binds and neutralizes negatively charged tubulin, leading to stabiUzation of microtubules.
  • MAPI A and MAP1B are each derived from a single precursor polypeptide that is subsequently proteolytically processed to generate one heavy chain and one Ught chain.
  • LC3 Another Ught chain, LC 3, is a 16.4 kDa molecule that binds MAPI A, MAP1B, and o microtubules. It is suggested that LC3 is synthesized from a source other than the MAPI A or MAPI B transcripts, and that the expression of LC3 may be important in regulating the microtubule binding activity of MAPI A and MAP1B during cell proUferation (Mann, S.S. et al. (1994) J. Biol. Chem. 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
  • Tau is found in axons and dendrites of nerve cells. Ater native spUcing of the Tau mRNA leads to the existence of multiple forms of Tau protein.
  • Tau phosphorylation is altered in neurodegenerative disorders such as Azheimer' 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).
  • the protein pericentrin is found in the MTOC and has a role in microtubule assembly. Actins
  • Microfilaments are vital to cell locomotion, cell shape, cell adhesion, cell division, and muscle contraction. Assembly and disassembly of the microfilaments allow cells to change their mo ⁇ hology. Microfilaments are the polymerized form of actin, the most abundant intracellular protein in the eukaryotic cell. Human cells contain six isoforms of actin. The three ⁇ -actins are found in different kinds of muscle, nonmuscle ⁇ - actin and nonmuscle ⁇ -actin are found in nonmuscle cells, and another ⁇ -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 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.
  • Actin-associated proteins have roles in cross-linking, severing, and stabilization of actin filaments and in sequestering actin monomers.
  • 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 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-Unking proteins have pairs of a 26,000-MW actin-binding domain and include fimbrin, spectrin, dystrophin, 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 vilUn.
  • Capping proteins can cap the ends of actin filaments, but cannot break filaments. Capping proteins include CapZ and tropomodulin.
  • Intermediate filaments are cytoskeletal fibers with a diameter of about 10 nm, 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 I and Type II proteins are the acidic and basic keratins, respectively.
  • Heterodimer s 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 epitheUa such as nails and hair, and in epitheUa that Une internal body cavities.
  • Type III IF proteins include desmin, gUal fibrillary acidic protein, vimentin, and peripherin.
  • Desmin filaments in muscle cells link myofibrils into bundles and stabiUze sarcomeres in contracting muscle.
  • GUal fibrillary acidic protein filaments are found in the gUal 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 amyotrophic lateral sclerosis, Parkinson's disease, and Azheimer '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 ⁇ -heUcal rod region interrupted by short nonheUcal Unker segments.
  • the rod region is bracketed, in most cases, by non-heUcal 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, unUke that of 5 microfilaments and microtubules.
  • IF-associated proteins 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-Unk IFs to the microfilament and microtubule cytoskeleton. Microtubules and IFs are in particular closely associated.
  • IFAPs include BPAG1, plakoglobin, desmoplakin I, desmoplakin II, o plectin, ankyrin, filaggrin, and lamin B receptor.
  • Cytoskeletal fibers are attached to the plasma membrane by specific proteins. These attachments are important for maintaining cell shape and for muscle contraction.
  • the spectrin- actin cytoskeleton is attached to cell membrane by three proteins, band 4.1, ankyrin, and 5 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 dystrophin links actin filaments to the plasma membrane; mutations in the dystrophin gene lead to Duchenne muscular dystrophy.
  • adherens junctions and adhesion plaques o 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 5 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 Unk 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 o Myosins are actin-activated ATPases, found in eukaryotic cells, that couple hydrolysis of
  • Myosin provides the motor function for muscle contraction 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 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 5 binding, and a carboxy-terminal tail domain.
  • the tail domains may associate to form an ⁇ -helical 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 intracellular motion, may contain either one or two heavy chains and associated light chains. There is evidence for o about 25 myosin heavy chain genes in vertebrates, more than half of them unconventional.
  • Dyneins are (-) end-directed motor proteins which act on microtubules. Two classes of dyneins, cytosoUc and axonemal, have been identified. CytosoUc dyneins are responsible for translocation of materials along cytoplasmic microtubules, for example, transport from the nerve 5 terminal to the cell body and transport of endocytic vesicles to lysosomes. Cytoplasmic dyneins are 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.
  • Dyneins have a native mass between 1000 and 2000 kDa and contain either two or three force-producing heads driven by the o hydrolysis of ATP. The heads are Unked via stalks to a basal domain which is composed of a highly variable number of accessory intermediate and Ught chains.
  • 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 5 is particularly important for axonal transport in neurons.
  • Kinesin is also important in all cell types for the transport of vesicles from the Golgi complex to the endoplasmic reticulum. This role is critical for maintaining the identity and functionaUty 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 0 cellular function. (Reviewed in Moore, J.D. and S.A. Endow (1996) Bioessays 18:207-219; and Hoyt,
  • the prototypical kinesin molecule is a heterotetramer comprised of two heavy polypeptide chains (KHCs) and two light polypeptide chains (KLCs).
  • KHCs heavy polypeptide chains
  • KLCs light polypeptide chains
  • 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 ⁇ -hehcal coiled-coil region which mediates dimerization.
  • a fan-shaped tail that associates with 5 molecular cargo. The tail is formed by the interaction of the KHC C-termini with the two KLCs.
  • KRPs kinesin-related 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.
  • dynamin' s self-assembly into spirals that may act to constrict a flat membrane surface into a tubule.
  • GTP hydrolysis induces a change in o 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 transported to another region of the cell.
  • Three homologous dynamin genes have been discovered, in addition to several dynamin-related proteins.
  • 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 0 (1997) Cell. Signal. 9:395-401.)
  • the cytoskeleton is reviewed in Lodish, H. et al. (1995) Molecular Cell Biology, Scientific American Books, New York NY.
  • Ribosomal Molecules SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, and SEQ ID NO:53 encode, for example, ribosomal molecules.
  • Ribosomal RNAs are assembled, along with ribosomal proteins, into ribosomes, which are cytoplasmic particles that translate 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.
  • 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 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 where the initiator tRNA binds.
  • the exit 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.)
  • 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 transcription. Chromatin packing thus serves to regulate protein expression in eukaryotes. Bacteria lack chromatin and the chromatin-packing level of gene regulation.
  • 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 Unked by another class of histones, HI .
  • HMG high mobiUty group
  • Chromodomain proteins function in compaction of chromatin into its transcriptionally silent heterochromatin form. During mitosis, all DNA is compacted into heterochromatin and transcription ceases.
  • Patterns of chromatin structure can be stably inherited, producing heritable patterns of gene expression.
  • one of the two X chromosomes in each female cell is inactivated by 5 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 control region (LCR) required for decondensation of the o globin gene locus.
  • LCR locus control region
  • Glucose is initially converted to pyruvate in the cytoplasm.
  • Fatty acids and pyruvate are transported to the mitochondria for complete oxidation to C0 2 coupled by enzymes to the transport of electrons from NADH and FADH 2 5 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 dihydrolipoyl dehydrogenase.
  • Enzymes involved in the citric acid cycle include: citrate synthetase, aconitases, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex including o transsuccinylases, succinyl CoA synthetase, succinate dehydrogenase, fumarases, and malate dehydrogenase.
  • Acetyl CoA is oxidized to C0 2 with concomitant formation of NADH, FADH 2 , and GTP.
  • oxidative phosphorylation the transfer 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 the mitochondrial inner membrane.
  • Enzyme complexes responsible for electron transport and ATP synthesis include the F Q F J ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone reductase, cytochrome b, cytochrome c 1; FeS protein, and cytochrome c oxidase.
  • ATP synthesis requires membrane transport enzymes including the phosphate transporter and the ATP- ADP antiport protein.
  • the ATP-binding casette (ABC) superfamily has also been suggested 5 as belonging to the mitochondrial transport 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 trauma (Cannon, B. et al. (1998) Ann. NY Acad. Sci. 856:171-187).
  • 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 o 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 transport proteins that transfer only selected molecules.
  • Mitochondria are the primary sites of energy production in cells.
  • Mitochondria contain a small amount of DNA.
  • Human mitochondrial DNA encodes 13 5 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.
  • Cytochrome b5 is a central electron donor for various reductive reactions occurring on the cytoplasmic surface of liver o endoplasmic reticulum. Cytochrome b5 has been found in Golgi, plasma, endoplasmic reticulum
  • 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 o 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).
  • TOM translocase of outer 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 5 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. 12:2211-22
  • 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. Natl. Acad. Sci. USA 90:5355-5358).
  • MPP mitochondrial processing peptidase
  • 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 intracellular and extracellular 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 amyotrophic 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 promotes cell proliferation by stabilizing mitochondrial membranes so that apoptosis signals are not released (Susin, S.A. (1998) Biochim. Biophys. Acta 1366:151-165).
  • SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, and SEQ ID NO:33 encode, for example, transcription 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.
  • gene expression is regulated in response to extracellular 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 functions are required at a given time.
  • Transcriptional regulatory proteins are essential for the control of gene expression. Some of these proteins function as transcription 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) 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 transcription factors. These features are hydrogen bond donor and acceptor groups, hydrophobic patches, major and minor grooves, and regular, repeated stretches of sequence which induce distinct bends in the helix.
  • transcription factors recognize specific DNA sequence motifs of about 20 nucleotides in length. Multiple, adjacent transcription factor-binding motifs may be required for gene regulation.
  • DNA-binding structural motifs which comprise either ⁇ heUces or ⁇ sheets that bind to the major groove of DNA.
  • 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 ⁇ 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 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 ⁇ heUx and an antiparallel ⁇ sheet whose proximity and conformation are maintained by the zinc ion. Contact with DNA is made by the arginine prece ding the ⁇ heUx and by the second, third, and sixth residues of the ⁇ heUx. 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 amphipafhic ⁇ helix. 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 transcription factors.
  • the helix-loop-heUx motif (HLH) consists of a short ⁇ heUx connected by a loop to a longer 5 cc heUx.
  • 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.
  • 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 translocations 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 Ukely results in 5 inappropriate gene transcription, potentially contributing to malignancy.
  • the immune system responds to infection or trauma 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 o 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, stroke, and infections (Isselbacher, KJ. et al. (1996) Harrison's Principles of Internal Medicine, 13/e, McGraw Hill, Inc. and Teton Data Systems Software).
  • SEQ ID NO:46, SEQ ID NO:47, and SEQ ID NO:48 encode, for example, cell membrane molecules.
  • Eukaryotic cells are surrounded by plasma membranes which enclose the cell and maintain an 5 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 organeUes and vesicles are composed of phosphoglycerides, fatty acids, cholesterol, phosphoUpids, glycolipids, 0 proteoglycans, and proteins. These components confer identity and functionaUty to the membranes with which they associate. Integral Membrane Proteins
  • TM proteins transmembrane proteins
  • TM domains are 5 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, transporters of ions or metabolites, ion channels, o cell anchoring proteins, and cell type-specific surface antigens.
  • MPs membrane proteins
  • PDZ domains KDEL, RGD, NGR, and GSL sequence motifs
  • vWFA von Willebrand factor A
  • EGF-like domains EGF-like domains.
  • RGD, NGR, and GSL motif-containing peptides have been used as drug delivery agents in targeted cancer 5 treatment of tumor vasculature (Aap, 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 extracellular or intracellular 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 transmembrane regions, an extracellular N-terminus, and a cytoplasmic C-terminus. Three extracellular loops alternate with three intracellular loops to link the seven transmembrane regions. Cysteine disulfide bridges connect the second and 5 third extracellular loops.
  • the most conserved regions of GPCRs are the transmembrane regions and the first two cytoplasmic loops.
  • GPCR-encoding genes A conserved, acidic- g-aromatic residue triplet present in the second cytoplasmic loop may interact with G proteins.
  • a GPCR consensus pattern is characteristic of most proteins belonging to this superfamily (ExPASy PROSITE document PS00237; and Watson, S. and S. Akinstall (1994) The G-protein Linked Receptor Facts Book. Academic Press, San Diego CA, pp. 2-6). Mutations and changes in transcriptional activation of GPCR-encoding genes have been associated with neurological disorders such as schizophrenia, Parkinson's disease, Azheimer' s disease, drug addiction, and feeding disorders. Scavenger Receptors
  • Macrophage scavenger receptors with broad ligand specificity may participate in the binding of low density Upoproteins (LDL) and foreign antigens.
  • Scavenger receptors types I and II are trimeric 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 region, an ⁇ -helical coiled-coil region, and a triple helical collagen-like region.
  • the transmembrane 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. 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 with one another.
  • TM4SF members have been implicated in signal transduction, control of ceU 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.
  • 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).
  • Leukocyte Antigens are cell surface molecules that are differentially expressed in tumor cells relative to normal cells. Tumor 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 “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 transmembrane 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
  • Ion channels are found in the plasma membranes of virtually every cell in the body.
  • 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).
  • Electrophysiological and pharmacological properties of chloride 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.
  • 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 channel activity in cells. Inappropriate phosphorylation of proteins in cells has been Unked 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
  • 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 within various organelles involved in the processes of endocytosis and exocytosis (Mellman, I. et al. (1986) Annu. Rev. Biochem. 55:663-700).
  • TAP transporter Another type of peptide transporter, the TAP transporter, is a heterodimer consisting of TAP 1 and TAP 2 and is associated with antigen processing. Peptide antigens are transported across the membrane of the endoplasmic reticulum by l o TAP so they can be expressed on the cell surface in association with MHC molecules.
  • TAP protein consists of multiple hydrophobic membrane spanning segments and a highly conserved ATP-binding cassette (Boll, M. et al. (1996) Proc. Natl.
  • Pathogenic microorganisms such as he ⁇ es 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.
  • ABSC ATP-binding cassette
  • the ATP-binding cassette (ABC) transporters also called the "traffic ATPases”, comprise a superfamily of membrane proteins that mediate transport and channel functions in prokaryotes and eukaryotes (Higgins, CF. (1992) Annu. Rev. Cell Biol. 8:67-113). ABC proteins share a similar
  • ABC transporter genes are associated with various disorders, such as hyperbilirubinemia II/Dubin- Johnson syndrome, recessive Stargardt's disease, X-linked adrenoleukodystrophy, multidrug resistance, celiac disease, and cystic fibrosis.
  • Membrane anchors are covalently joined to a protein post-ttanslationally and include such moieties as prenyl, myristyl, and glycosylphosphatidyl inositol groups.
  • 3 o 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.
  • 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 extracellular signaling molecules with plasma membrane receptors results in the formation of plasma membrane-derived vesicles that enclose and ttansport the molecules into the cytosol. These transport vesicles fuse with and mature into endosomal and lysosomal (digestive) 5 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.
  • vesicles form at the transitional endoplasmic reticulum o (tER), the rim of Golgi cisternae, the face of the Trans-Golgi Network (TGN), the plasma membrane
  • vesicle formation occurs when a region of membrane buds off from the donor organelle.
  • the membrane-bound vesicle contains proteins to be transported 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 5 vesicles derived from the TGN and PM, whereas coatomer (COP) coats form on vesicles derived from the ER and Golgi.
  • COPI involved in retrograde traffic through the Golgi and from the Golgi to the ER
  • COPII involved in anterograde traffic from the ER to the Golgi
  • adapter proteins bring vesicle cargo and coat proteins o together at the surface of the budding membrane.
  • Adapter protein- 1 and -2 select cargo from the
  • TGN and plasma membrane are based on molecular information encoded on the cytoplasmic tail of integral membrane cargo proteins.
  • Adapter proteins also recruit clathrin to the bud site.
  • Clathrin is a protein complex consisting of three large and three small polypeptide chains arranged in a three-legged structure called a triskelion. Multiple triskelions and other coat proteins 5 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 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. o 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).
  • the coat protein is assembled from cytosoUc precursor molecules at specific budding regions on the organelle.
  • the COP coat consists of two 5 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 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. Natl. Acad. Sci. USA 95:11649-11654).
  • SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:62, and SEQ ID NO:63 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 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 transport processes. Important cell organelles include the nucleus, the Golgi apparatus, the endoplasmic reticulum, mitochondria, peroxisomes, lysosomes, endosomes, and secretory vesicles. Nucleus
  • 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 transcription of DNA into RNA.
  • DNA is organized into compact structures in the nucleus by interactions with various DNA-binding proteins such as histones and non-histone chromosomal proteins.
  • DNA-specific nucleases, DNAses partially degrade these compacted structures prior to DNA replication or transcription.
  • 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 these proteins function as transcription 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) Genes IV, Oxford University Press, New York NY, and Cell Press, Cambridge MA, pp. 554-570.) Many transcription factors inco ⁇ orate DNA-binding structural motifs which comprise either ⁇ helices or ⁇ sheets that bind to the major groove of DNA.
  • helix-turn-heUx helix-turn-heUx
  • zinc finger helix-turn-heUx
  • leucine zipper helix-loop-helix. Proteins containing these motifs may act alone as monomers, or they may form homo- or heterodimers that interact with DNA.
  • 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, MX. (1992) Cancer Surv. 15:89-104).
  • Chromosomal translocations 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 Ukely results in inappropriate gene transcription, potentially contributing to malignancy.
  • the immune system responds to infection or trauma 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, stroke, 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 II transcribes genes that will be translated into proteins.
  • the primary transcript of RNA polymerase II is called heterogenous nuclear RNA (nnRNA), and must be further processed by splicing to remove non-coding sequences called introns.
  • nnRNA heterogenous nuclear RNA
  • RNA splicing is mediated by small nuclear ribonucleoprotein complexes, or snRNPs, producing mature messenger RNA (mRNA) which is then transported out of the nucleus for translation into proteins.
  • the nucleolus is a highly organized subcompartment in the nucleus that contains high concentrations of RNA and proteins and functions mainly in ribosomal RNA synthesis and assembly (Alberts, et al. supra, pp. 379-382).
  • 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.
  • Ribosomes are assembled in the nucleolus initially from a large, 45S rRNA combined with a 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
  • proteins are synthesized within the endoplasmic reticulum (ER), deUvered from the ER to the Golgi apparatus for post-translational processing and sorting, and transported from the 5 Golgi to specific intracellular and extracellular 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.
  • Protein destined for the ER actually begins in the cytosol with the synthesis of a specific signal 0 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 across the ER membrane but remain anchored in the lipid bilayer of the membrane by one or more 5 membrane-spanning ⁇ -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- prolyl isomerase (PPI).
  • PDI protein disulfide isomerase
  • PPI peptidyl- prolyl isomerase
  • PPI peptidyl- prolyl isomerase
  • 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 immunosuppressive drug cyclosporin A (Handschumacher, R.E. et al. (1984) Science 226:544-547).
  • 5 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 (Aberts, et al. supra, pp. 600-610). Additional posttranslational 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 oUgosaccharides, 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 oUgosaccharides 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.
  • TGN Trans-Golgi Network
  • Other transport 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, neurotransmitters, and digestive enzymes.
  • 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, o endosomes, and secretory vesicles. Endocytosis is the process in cells of internaUzing nutrients, solutes or small particles (pinocytosis) or large particles such as internaUzed receptors, viruses, bacteria, or bacterial toxins (phagocytosis). Exocytosis is the process of transporting molecules to the cell surface. It faciUtates placement or localization of membrane-bound receptors or other membrane proteins and secretion of hormones, neurotransmitters, digestive enzymes, wastes, etc.
  • vacuoles 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 electrochemical 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 proteoUpid component of vp-
  • Lysosomes 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, phosphoUpases, phosphatases, and sulfatases, all of which are acid hydrolases that function at a pH of about 5. Lysosomes are surrounded by a unique 5 membrane containing ttansport proteins that allow the final products of macromolecule degradation, such as sugars, amino acids, and nucleotides, to be transported 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 (Aberts, supra, pp. 610-611).
  • Endosomes o Endosomes are another type of acidic vacuole that is used to transport substances from the 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. 61 -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 5 function primarily in the recycling of intemaUzed receptors back to the cell surface.
  • Late endosomes 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 o cytosoUc prenylated GTP-binding protein, Rab is one such protein.
  • Rabs 4, 5, and 11 are associated with the early endosome, whereas Rabs 7 and 9 associate with the late endosome.
  • 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 5 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 transport proteins that transfer only selected molecules. Mitochondria are the primary sites of energy production in cells.
  • Glucose is initially converted 0 to pyruvate in the cytoplasm.
  • Fatty acids and pyruvate are transported to the mitochondria for complete oxidation to C0 2 coupled by enzymes to the transport 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 transacetylase, and dihydrolipoyl dehydrogenase.
  • Enzymes involved in the citric 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 C0 2 with concomitant formation of NADH, FADH 2 , and GTP.
  • oxidative phosphorylation the transfer 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 ⁇ F ⁇ ATPase complex in the mitochondrial inner membrane.
  • Enzyme complexes responsible for electron transport and ATP synthesis include the FJ ⁇ ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone reductase, cytochrome b, cytochrome c 1( FeS protein, and cytochrome c oxidase.
  • Peroxisomes include the FJ ⁇ ATPase complex, ubiquinone(CoQ)-cytochrome c reductase, ubiquinone reductase, cytochrome b, cytochrome c
  • Peroxisomes like mitochondria, are a major site of oxygen utilization. They contain one or 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 (Aberts, 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.
  • 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 (Aberts, 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
  • peroxisome assembly factor- 1 Another major function of oxidative reactions in peroxisomes is the breakdown of fatty acids in a process called ⁇ oxidation, ⁇ 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 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.
  • peroxisome assembly factor- 1 Another major function of oxidative reactions in peroxisomes is the breakdown of fatty acids in a process called ⁇ oxidation, ⁇ oxidation results in shortening of the alkyl chain of fatty acids
  • 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 SEQ ID NO: 1-71 ; 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: 1-71 ; 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 NO: 1-71.
  • 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 NO: 1 -71 ; 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: 1-71 ; 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: 1-71 ; 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: 1-71 ; 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.
  • 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 polyn
  • 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: 1-71; 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: 1-71 ; 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 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:l- 71 ; 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: 1-71 ; c) a polynucleotide 5 sequence complementary to a); d) a polynucleotide sequence complementary to b); and e) an RNA equivalent of a) through d).
  • 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 for producing a human diagnostic and therapeutic polypeptide, the method comprising a) culturing a o 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) encoded by at least one polynucleotide comprising a polynucleotide sequence selected from the group 5 consisting of SEQ ID NO:l-71. 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 the human diagnostic and therapeutic polypeptide with the test compound for a sufficient time and o 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 an isolated polynucleotide comprising at least 60 contiguous nucleotides of a polynucleotide comprising 5 a polynucleotide sequence selected from the group consisting of a) a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 -71 ; 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:l-71 ; 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 also provides a method o 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 NO: 1-71 ; 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 NO:l-71 ; 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 assessing toxicity of a test compound, said method 0 comprising a) treating a biological sample containing nucleic acids with the test compound; b) hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide comprising a polynucleotide sequence selected from the group consisting of i) a polynucleotide sequence selected from the group consisting of SEQ ID NO:l- 71 ; U) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a 5 polynucleotide sequence selected from the group consisting of SEQ ID NO : 1 -71 ; Ui) a polynucleotide sequence complementary to i), iv) a polynucleotide sequence complementary to u), and v) an RNA equivalent of i)-iv).
  • Hybridization occurs under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide comprising a polynucleotide sequence selected from the group consisting of i) a o polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 -71 ; ii) a naturally occurring polynucleotide sequence having at least 90% sequence identity to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-71; iii) a polynucleotide sequence complementary to i), iv) a polynucleotide sequence complementary to ii), and v) an RNA equivalent of i)-iv), and alternatively, the target polynucleotide comprises a fragment of a polynucleotide sequence 5 selected from the group consisting of i-v above; c) quantifying the amount of hybridization complex
  • 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), probabiUty 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 5 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” o 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 transmembrane (TM) domains, as indicated.
  • SP signal peptide
  • TM transmembrane
  • 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 shows the tissue distribution profiles for the templates of the invention.
  • Table 6 summarizes the bioinformatics tools which are useful for analysis of the o polynucleotides of the present invention.
  • the first column of Table 6 Usts analytical tools, programs, 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 appUcable, the scores, probabiUty values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score, the greater the homology between 5 two sequences).
  • dithp refers to a nucleic acid sequence
  • DITHP amino acid sequence encoded by dithp
  • a “full-length” dithp refers to a nucleic o 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 surface active substances (lysolecitbin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinifrophenol) which may be administered to increase a host's immunological response.
  • Alele refers to an alternative form of a nucleic acid sequence. Aleles result from a
  • Mutation a change or an alternative reading of the genetic code.
  • a y 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 alleUc dithp. 0
  • Amino acid sequence refers to a peptide, a polypeptide, or a protein of either natural or synthetic origin. The amino acid sequence is not Umited 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.
  • PCR polymerase chain reaction
  • Aitibody 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.
  • Aitibodies 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 o mouse, a rat, or a rabbit
  • an animal e.g., a o mouse, a rat, or a rabbit
  • Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobulin, and keyhole Umpet 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); oUgonucleotides having modified backbone Unkages such as phosphorothioates, methylphosphonates, or benzylphosphonates; oUgonucleotides 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 reUes 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 spUce 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).
  • 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.
  • 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 hetical 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.
  • array element refers to a polynucleotide, polypeptide, or other chemical compound having a unique and defined position on a microarray.
  • a "fragment” is a unique portion of dithp or DITHP which is identical in sequence to but 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 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.
  • 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.
  • 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.
  • 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 5 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 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 0 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 fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended pu ⁇ ose for the fragment. 5
  • 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.
  • “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 o 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 5 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 o conditions include the anneahng 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 anneahng 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.
  • TJ thermal melting point
  • 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 0.1 % SDS, for 1 hour. Aternatively, 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 5 are used to block non-specific hybridizatioa 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. o 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 lines.
  • “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.
  • Mcroarray is any arrangement of nucleic acids, amino acids, antibodies, etc., on a substrate.
  • the substrate may be a sohd support such as beads, glass, paper, nitrocellulose, nylon, or an appropriate membrane.
  • Linkers are short stretches of nucleotide sequence which may be added to a vector or a dithp to create restriction endonuclease sites to faciUtate cloning.
  • PolyUnkers are engineered to inco ⁇ orate multiple restriction 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).
  • 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 oUgomer, 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 either double-stranded or single-stranded, and can represent either the sense or antisense 0 (complementary) strand.
  • OUgomer 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 ampUfication technologies. OUgomers may be used as, e.g., primers for PCR, and are usually chemically synthesized. 5 "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 Unked to a coding sequence if the promoter affects the transcription or expression of the coding sequence.
  • operably Unked DNA sequences may be in close proximity or contiguous and, where necessary to join two protein coding regions, in the same reading frame.
  • PNA protein nucleic acid
  • PNA refers to a DNA mimic in which nucleotide bases are attached to a pseudopeptide backbone to increase stability.
  • PNA also designated antigene agents, can prevent gene expression by targeting complementary messenger RNA.
  • percent identity and % identity refer to the percentage of residue matches between at least two polynucleotide sequences aUgned using a 5 standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize aUgnment 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 parameters of the CLUSTAL V algorithm as inco ⁇ orated into the MEGALIGN version 3.12e sequence o aUgnment 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 Sha ⁇ , P.M. (1989) CABIOS 5:151-153 and in Higgins, D.G. et al. (1992) CABIOS 8:189-191.
  • BLAST Basic Local AUgnment Search 5 Tool
  • 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 5 2.0.9 (May-07-1999) set at default parameters.
  • Such default parameters may be, for example:
  • 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 proteia
  • the phrases "percent identity” and "% identity", as appUed to polypeptide sequences refer to the percentage of residue matches between at least two polypeptide sequences aUgned using a standardized algorithm. Methods of polypeptide sequence aUgnment are well-known. Some aUgnment 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 residue, thus preserving the structure (and therefore function) of the folded polypeptide.
  • NCBI BLAST software suite may be used.
  • BLAST 2 Sequences Version 2.0.9 (May-07-1999) with blastp set at default parameters.
  • Such default parameters may be, for example:
  • 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, 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.
  • Probe refers to dithp or fragments thereof, which are used to detect identical, alletic or related nucleic acid sequences. Probes are isolated oUgonucleotides or polynucleotides attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, Ugands, chemiluminescent agents, and enzymes.
  • Primer pairs are short nucleic acids, usually DNA oUgonucleotides, which may be 5 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 ampUfication (and identification) of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR).
  • PCR polymerase chain reaction
  • 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 0 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 specification, including the figures and Sequence Listing, may be used.
  • PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that pu ⁇ ose such as Primer o (Version 0.5, 1991 , Whitehead Institute for Biomedical Research, Cambridge MA).
  • OUgonucleotides for use as primers are selected using software known in the art for such pu ⁇ ose. For example, OLIGO 4.06 software is useful for the selection of PCR primer pairs of up to 100 nucleotides each, and for the analysis of oUgonucleotides and larger polynucleotides of up to 5,000 nucleotides from an input polynucleotide sequence of up to 32 kilobases. Similar primer selection 5 programs have inco ⁇ orated additional features for expanded capabiUties.
  • the PrimOU primer selection program (available to the pubUc from the Genome Center at University of Texas South West Medical Center, Dallas TX) is capable of choosing specific primers from megabase sequences and is thus useful for designing primers on a genome-wide scope.
  • the Primer3 primer selection program (available to the pubUc from the Whitehead Institute/MIT Center for Genome Research, o Cambridge MA) allows the user to input a "mispriming Ubrary," in which sequences to avoid as primer binding sites are user-specified. Primer3 is useful, in particular, for the selection of oUgonucleotides for microarrays.
  • the source code for the latter two primer selection programs may also be obtained from 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 aUgned nucleic acid sequences.
  • this program is useful for identification of both unique and conserved oligonucleotides and polynucleotide fragments.
  • the oUgonucleotides 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 oUgonucleotide selection are not Umited to those described above.
  • “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.
  • This artificial combination is often accompUshed 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.
  • a recombinant nucleic acid may include a nucleic acid sequence operably Unked to a promoter sequence.
  • Such a recombinant nucleic acid may be part of a vector that is used, for example, to transform a cell.
  • 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, and includes enhancers, promoters, introns, and 3' untranslated regions, which interact with host proteins to carry out or regulate transcription or translation.
  • RNA equivalent in reference to a DNA sequence, is composed of the same Unear 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.
  • 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, saUva, blood, and urine; chromosome(s), organelles, or membranes isolated from a cell; genomic DNA, RNA, or cDNA in solution or bound to a substrate; and cleared cells or tissues or blots 5 or imprints from such cells or tissues).
  • bodily fluids including, but not Umited to, saUva, blood, and urine
  • chromosome(s), organelles, or membranes isolated from a cell genomic DNA, RNA, or cDNA in solution or bound to a substrate
  • cleared cells or tissues or blots 5 or imprints from such cells or tissues e.g., bodily fluids including, but not Umited to, saUva, blood, and urine; chromosome(s), organelles, or membranes isolated from a cell; genomic DNA, RNA, or
  • 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 o presence of a polypeptide containing epitope A, or the presence of free unlabeled A, in a reaction 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.
  • Substrate refers to any suitable rigid or semi-rigid support including, e.g., membranes, filters, chips, sUdes, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles or capillaries.
  • the substrate 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 o cell type under given conditions at a given time.
  • 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 5 transformed.
  • Transformants include stably transformed cells in which the inserted DNA is capable of replication either as an autonomously repUcating 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 Umited to animals o and plants, in which one or more of the cells of the organism contains heterologous nucleic acid 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 deUberate 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 fertiUzation, but rather is directed to the introduction of a recombinant DNA molecule.
  • the transgenic organisms 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, transformation or transconjugatioa 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.
  • 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 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 “polymo ⁇ hic” variant.
  • a spUce variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate spUcing of exons during mRNA processing.
  • the 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 polymo ⁇ hic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species.
  • Polymo ⁇ hic variants also may encompass "single nucleotide polymorphisms" (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.
  • variants of the polynucleotides of the present invention may be generated through recombinant methods.
  • One possible method is a DNA shuffling technique such as MOLECULARBREEDING (Maxygen Inc., Santa Clara CA; described in U.S.
  • DNA shuffling is a process by which a Ubrary of gene variants is produced using PCR-mediated recombination of gene fragments.
  • the Ubrary 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.
  • 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. Aternatively, 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.
  • cDNA sequences derived from human tissues and cell Unes were aUgned 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 probabiUty score in column 4, and the functional annotation corresponding to each GenBank hit is Usted in column 5.
  • the invention inco ⁇ orates 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 utiUzes these sequences in hybridization and ampUfication 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.
  • cDNA was isolated from Ubraries constructed using RNA derived from normal and diseased human tissues and cell Unes.
  • the human tissues and cell Unes used for cDNA Ubrary construction were selected from a broad range of sources to provide a diverse population of cDNA representative of gene transcription throughout the human body. Descriptions of the human tissues and cell Unes used for cDNA Ubrary construction are provided in the LEFESEQ database (Incyte Genomics, Inc. (Incyte), Palo Ato CA).
  • Human tissues were broadly selected from, for example, cardiovascular, dermatologic, endocrine, gastrointestinal, hematopoietic/immune system, musculoskeletal, neural, reproductive, and urologic sources.
  • Cell Unes used for cDNA library construction were derived from, for example, leukemic cells, teratocarcinomas, neuroepitheUomas, cervical carcinoma, lung fibroblasts, and endotheUal cells.
  • Such cell lines include, for example, THP-1, Jurkat, HUVEC, hNT2, WI38, HeLa, and other cell Unes commonly used and available from pubUc depositories (American Type Culture Collection, Manassas VA).
  • cell Unes 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 Upopolysaccharide in the case of leukocytic cell Unes, or, in the case of endotheUal cell lines, subjected to shear stress.
  • a pharmaceutical agent such as 5 -aza-2'-deoxycytidine
  • an activating agent such as Upopolysaccharide in the case of leukocytic cell Unes, or, in the case of endotheUal cell lines, subjected to shear stress.
  • Sequencing of the cDNA 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 Co ⁇ oration, 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 ampUfication system (Life Technologies Inc. (Life Technologies), Gaithersburg MD), to extend the nucleic acid sequence from an oUgonucleotide primer annealed to the DNA template of interest.
  • SEQUENASE DNA polymerase U.S. Biochemical Co ⁇ oration, Cleveland OH
  • Taq polymerase PE Biosystems, Foster City CA
  • thermostable T7 polymerase Amersham Pharmacia Biotech, Inc. (Amersham Pharma
  • Chain termination reaction products may be electrophoresed on urea-polyacrylamide 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 cDNA 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.
  • 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 5 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.)
  • Human polynucleotide sequences may be assembled using programs or algorithms well known 0 in the art. Sequences to be assembled are related, wholly or in part, and may be derived from a single or many different transcripts. Asembly of the sequences can be performed using such programs as PHRAP (Phils Revised Asembly Program) and the GEL VIEW fragment assembly system (GCG), or other methods known in the art.
  • PHRAP Phils Revised Asembly Program
  • GCG GEL VIEW fragment assembly system
  • cDNA sequences are used as "component" sequences that are assembled into 5 "template” or “consensus” sequences as follows. Sequence chromatograms are processed, verified, and quaUty scores are obtained using PHRED. Raw sequences are edited using an editing pathway known as Block 1 (See, e.g., theLIFESEQ Asembled User Guide, Incyte Genomics, Palo Ato, CA). A series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucleotide repeats, Au repeats, etc.) are replaced by "n's", or masked, to prevent spurious matches.
  • Block 1 See, e.g., theLIFESEQ Asembled User Guide, Incyte Genomics, Palo Ato, CA).
  • a series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucleotide repeats, Au repeats, etc.) are replaced by "n's
  • 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.
  • RDMS relational database management system
  • 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.
  • the templates can be merged into bins. If multiple templates exist in one bin, the bin can be spUt and the templates reannotated.
  • 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 o 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 cDNA of many genes are several hundred, and sometimes several thousand, bases in length. With current technology, cDNA comprising the coding regions of large genes cannot be cloned because of vector Umitations, incomplete reverse transcription 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.
  • 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 6.) These analyses o 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 5 AUgnment Search Tool
  • BLAST is especially useful in determining exact matches and comparing two sequence fragments of arbitrary but equal lengths, whose aUgnment is locally maximal and for which the alignment score meets or exceeds a threshold or cutoff score set by the user (KarUn, S. et al. (1988) Proc. Natl. Acad. Sci.
  • GenBank e.g., 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.
  • search tool e.g., o BLAST or HMM
  • GenBank e.g., 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.
  • 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 o "Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data,"
  • SEQ ID NO:l SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, and SEQ ID NO:8 encode, for example, human enzyme molecules.
  • SEQ ID NO:9 encodes, for example, an extracellular information transmission molecule.
  • SEQ ID NO: 10 and SEQ ID NO: 11 encode, for example, receptor molecules.
  • SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, and SEQ ID NO:18 encode, for example, intracellular signaling molecules.
  • SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, and SEQ ID NO:33 encode, for example, ttanscription factor molecules.
  • SEQ ID NO:34 encodes, for example, a protein modification and maintenance molecule.
  • SEQ ID NO:35 and SEQ ID NO:36 encode, for example, nucleic acid synthesis and modification molecules.
  • SEQ ID NO:37 encodes, for example, an antigen recognition molecule.
  • SEQ ID NO:38 and SEQ ID NO:39 encode, for example, secreted/extracellular matrix molecules.
  • SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, and SEQ ID NO:45 encode, for example, cytoskeletal molecules.
  • SEQ ID NO:46, SEQ ID NO:47, and SEQ ID NO:48 encode, for example, cell membrane molecules.
  • SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ ID NO:52, and SEQ ID NO:53 encode, for example, ribosomal molecules.
  • SEQ ID NO:54, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:57, SEQ ID NO:58, SEQ ID NO:59, SEQ ID NO:60, SEQ ID NO:61, SEQ ID NO:62, and SEQ ID NO:63 encode, for example, organelle associated molecules.
  • SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:66, SEQ ID NO:67, and SEQ ID NO:68 encode, for example, biochemical pathway molecules.
  • SEQ ID NO:69, SEQ ID NO:70, and SEQ ID NO:71 encode, for example, molecules associated with growth and development.
  • the dithp of the present invention may be used for a variety of diagnostic and therapeutic pu ⁇ oses.
  • 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 Umited 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,
  • 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 from appropriate reference samples, and a diagnosis is estabUshed. Aternatively, a polynucleotide complementary to a given dithp can inhibit or inactivate a therapeutically relevant gene related to the dithp.
  • 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.
  • 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 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 ampUfication technologies and include membrane- based procedures such as northern blot analysis, high-throughput procedures that utitize, for example, microarrays, and PCR-based procedures.
  • the dithp, their fragments, or complementary sequences may be used to identify the presence 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 concentrations.
  • 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 selected from non-conserved or unique regions of at least one of the polynucleotides of SEQ ID NO:l- 71 and tested for their abiUty to identify or ampUfy the target nucleic acid sequence using standard protocols.
  • Polynucleotide sequences that are capable of hybridizing, in particular, to those shown in SEQ ID NO: 1-71 and fragments thereof, can be identified using various conditions of stringency. (See, e.g. , Wahl, G.M. and S.L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, AR. (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 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 5 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 tink polynucleotides to the surface of a substrate 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.,
  • 5 Probes may be labeled by either PCR or enzymatic techniques using a variety of commercially available reporter molecules.
  • commercial kits are available for radioactive and chemiluminescent labeling (Amersham Pharmacia Biotech) and for alkaline phosphatase labeUng (Life Technologies).
  • 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 o nucleotide (e.g. , 32 P-ATP, Amersham Pharmacia Biotech).
  • polynucleotides of SEQ ID NO: 1-71 or suitable fragments thereof can be used to isolate full length cDNA sequences utihzing hybridization and/or ampUfication procedures well known in the art, e.g., cDNA Ubrary screening, PCR ampUfication, etc.
  • the molecular cloning of such full length cDNA sequences may employ the method of cDNA library screening with probes using the 5 hybridization, stringency, washing, and probing strategies described above and in Ausubel, supra.
  • a genetic tinkage map traces parts of chromosomes that are inherited in the same pattern as the conditioa Statistics Unk the inheritance of particular conditions to particular regions of chromosomes, as defined by RFLP or other markers. 0 (See, for example, Lander, E. S. and Botstein, D. (1986) Proc. Natl. 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 tinkage maps can be found in various scientific journals or at the Onhne Mendelian Inheritance in Man (OMIM) World Wide Web site.
  • OMIM Onhne Mendelian Inheritance in Man
  • 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 o 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 cDNA Ubraries.
  • HACs human artificial chromosomes
  • YACs yeast artificial chromosomes
  • BACs bacterial artificial chromosomes
  • PI constructions or single chromosome cDNA Ubraries.
  • 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. o The dithp sequences may also be used to detect polymo ⁇ hisms that are genetically Unked to the inheritance of a particular condition, disease, or disorder.
  • In situ hybridization of chromosomal preparations and genetic mapping techniques 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.
  • 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., ttanslocations 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 5 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 5 from dithp sequences are added to a sample under hybridizing conditions of desired sttingency. In some instances, dithp, or fragments or oUgonucleotides derived from dithp, may be used as primers in ampUfication 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.
  • QuaUtative or o 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-Unked immunosorbent assay (ELISA)-Uke, pin, or chip-based assays.
  • PCR enzyme-Unked 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, precUnical tests, cUnical trials, or in monitoring the treatment of an individual patient.
  • standard expression is estabUshed by methods well known in 5 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 o 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 5 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.
  • oUgonucleotide 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 Umited to, single-stranded conformation polymorphism (SSCP) and fluorescent SSCP (fSSCP) methods.
  • SSCP single-stranded conformation polymorphism
  • fSSCP fluorescent SSCP
  • oligonucleotide primers derived from dithp are used to 5 ampUfy 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 electrophoresis in non-denaturing gels.
  • the oUgonucleotide primers are fluorescently labeled, which allows detection of the ampUmers in high- o throughput equipment such as DNA sequencing machines.
  • sequence database analysis methods termed in siUco 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 spectrometry 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, 5 semen, etc., can be ampUfied 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 0 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 subtracted cDNA Ubraries which aid in the discovery of novel polynucleotides, in selection and synthesis of oUgomers for attachment to an array or other support, and as an antigen to elicit an immune response.
  • the dithp of the invention or their mammaUan 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.
  • mouse ES cells such as the mouse 129/SvJ cell Une, are derived from the early mouse embryo and grown in culture.
  • the ES 5 cells are transformed with a vector containing the gene of interest disrupted by a marker gene, e.g., the neomycin phosphotransferase gene (neo; Capecchi, M.R. (1989) Science 244:1288-1292).
  • the vector integrates into the corresponding region of the host genome by homologous recombination. Aternatively, 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- o 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.
  • 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 Uneages including endoderm, mesoderm, and ectodermal cell types. These cell Uneages differentiate into, for example, neural cells, hematopoietic Uneages, and cardiomyocytes (Thomson, J.A. et al. (1998) Science 5 282:1145-1147).
  • 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.
  • 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 obtain information on treatment of a human disease.
  • 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. Ainu. 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, oUgonucleotides, 0 proteins (e.g., receptors), or small molecules.
  • the molecule is closely related to the natural Ugand of the polypeptide, e.g., a Ugand or fragment thereof, a natural substrate, 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, 5 e.g., the active site. In either case, the molecule can be rationally designed using known techniques.
  • 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, o stimulation, or inhibition of activity of either the polypeptide or the molecule is analyzed.
  • Ai 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. Aternatively, 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 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 5 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 indirectly, to the polypeptide or by competing with the polypeptide for a substrate.
  • Al of the above assays can be used in a diagnostic or prognostic context.
  • the molecules o 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.
  • the assays can discover agents which may inhibit or enhance the production of the polypeptide from suitably manipulated cells or tissues.
  • Aiother embodiment relates to the use of dithp to develop a transcript image of a tissue or cell type.
  • a transcript image represents the global pattern of gene expression by a particular tissue or cell type. Global gene expression patterns are analyzed by quantifying the number of expressed genes and their relative abundance under given conditions and at a given time. (See Seilhamer et al., o "Comparative Gene Transcript Analysis," U.S. Patent Number 5,840,484, expressly inco ⁇ orated by reference herein.)
  • a transcript image may be generated by hybridizing the polynucleotides of the present invention or their complements to the totaUty of transcripts or reverse transcripts of a particular tissue or cell type.
  • the hybridization takes place in high-throughput format, wherein the polynucleotides of the present invention or their complements comprise a subset of a 5 plurality of elements on a microarray.
  • the resultant transcript image would provide a profile of gene activity pertaining to human molecules for diagnostics and therapeutics.
  • Transcript images which profile dithp expression may be generated using transcripts isolated from tissues, cell Unes, 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 0 Une.
  • Transcript images which profile dithp expression may also be used in conjunction with in vitro model systems and preclinical evaluation of pharmaceuticals, as well as toxicological testing of industrial and naturally-occurring environmental compounds.
  • Al compounds induce characteristic gene expression patterns, frequently termed molecular finge ⁇ rints or toxicant signatures, which are indicative of mechanisms of action and toxicity (Nuwaysir, E. F. et al. (1999) Mol. Carcinog. 24:153- 159; Steiner, S. and Aiderson, N. L. (2000) Toxicol. Lett. 112-113:467-71, expressly inco ⁇ orated by reference herein). If a test compound has a signature similar to that of a compound with known toxicity, it is Ukely to share those toxic properties.
  • finge ⁇ rints or signatures are most useful and 5 refined when they contain expression information from a large number of genes and gene famiUes. Ideally, a genome-wide measurement of expression provides the highest quality signature. Even genes whose expression is not altered by any tested compounds are important as well, as the levels of expression of these genes are used to normatize the rest of the expression data. The normatization procedure is useful for comparison of expression data after treatment with different compounds. While 0 the assignment of gene function to elements of a toxicant signature aids in inte ⁇ retation of toxicity mechanisms, knowledge of gene function is not necessary for the statistical matching of signatures which leads to prediction of toxicity.
  • the toxicity of a test compound is assessed by treating a biological sample containing nucleic acids with the test compound.
  • Nucleic acids that are expressed in the treated biological sample are hybridized with one or more probes specific to the polynucleotides of the present invention, so that transcript levels corresponding to the polynucleotides of the present o invention may be quantified.
  • the transcript levels in the treated biological sample are compared with levels in an untreated biological sample. Differences in the transcript levels between the two samples are indicative of a toxic response caused by the test compound in the treated sample.
  • Aiother particular embodiment relates to the use of DITHP encoded by polynucleotides of the present invention to analyze the proteome of a tissue or cell type.
  • proteome refers to the 5 global pattern of protein expression in a particular tissue or cell type. Each protein component of a proteome can be subjected individually to further analysis. Proteome expression patterns, or profiles, are analyzed by quantifying the number of expressed proteins and their relative abundance under given conditions and at a given time. A profile of a cell's proteome may thus be generated by separating and analyzing the polypeptides of a particular tissue or cell type.
  • the separation is o achieved using two-dimensional gel electtophoresis, in which proteins from a sample are separated by isoelectric focusing in the first dimension, and then according to molecular weight by sodium dodecyl sulfate slab gel electrophoresis in the second dimension (Steiner and Anderson, supra).
  • the proteins are visuahzed in the gel as discrete and uniquely positioned spots, typically by staining the gel with an agent such as Coomassie Blue or silver or fluorescent stains.
  • the optical density of each protein spot is generally proportional to the level of the protein in the sample.
  • the optical densities of equivalently positioned protein spots from different samples are compared to identify any changes in protein spot density related to the treatment.
  • the proteins in the spots are partially sequenced using, for example, standard methods employing chemical or enzymatic cleavage followed by mass spectiOmetry.
  • the identity of the protein in a spot may be determined by comparing its partial sequence, preferably of at least 5 contiguous amino acid residues, to the polypeptide sequences of the present invention. In some cases, further sequence data may be obtained for definitive protein identification.
  • a proteomic profile may also be generated using antibodies specific for DITHP to quantify the levels of DITHP expression.
  • the antibodies are used as elements on a microarray, and protein expression levels are quantified by exposing the microarray to the sample and detecting the levels of protein bound to each array element (Lueking, A. et al. (1999) Anal. Biochem. 270:103-11; Mendoze, L. G. et al. (1999) Biotechniques 27:778-88). Detection may be performed by a variety of methods known in the art, for example, by reacting the proteins in the sample with a thiol- or amino- reactive fluorescent compound and detecting the amount of fluorescence bound at each array element.
  • Toxicant signatures at the proteome level are also useful for toxicological screening, and should be analyzed in parallel with toxicant signatures at the transcript level.
  • There is a poor correlation between transcript and protein abundances for some proteins in some tissues (Anderson, N. L. and Seilhamer, J. (1997) Electrophoresis 18:533-537), so proteome toxicant signatures may be useful in the analysis of compounds which do not significantly affect the transcript image, but which alter the proteomic profile.
  • the analysis of transcripts in body fluids is difficult, due to rapid degradation of mRNA, so proteomic profiling may be more reUable and informative in such cases.
  • the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound.
  • Proteins that are expressed in the treated biological sample are separated so that the amount of each protein can be quantified.
  • the amount of each protein is compared to the amount of the corresponding protein in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample.
  • Individual proteins are identified by sequencing the amino acid residues of the individual proteins and comparing these partial sequences to the DITHP encoded by polynucleotides of the present invention.
  • the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins from the biological sample are incubated with antibodies specific to the DITHP encoded by polynucleotides of the present invention. The amount of protein recognized by the antibodies is quantified. The amount of protein in the treated biological sample is compared with the amount in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample.
  • Transcript images may be used to profile dithp expression in distinct tissue types. This process 5 can be used to determine human molecule activity in a particular 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 molecules. o Transcript images of cell Unes can be used to assess human molecule activity and/or to identify cell lines that lack or misregulate this activity. Such cell Unes may then be treated with pharmaceutical agents, and a transcript image following treatment may indicate the efficacy of these agents in restoring desired levels of this activity. A similar approach may be used to assess the toxicity of pharmaceutical agents as reflected by undesirable changes in human molecule activity. Candidate pharmaceutical 5 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 o technology or therapy reUes 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; Aa a, A. et al. (1997) Pharmacol. Res. 36(3):171-178; Crooke, S.T. (1997) Adv. Pharmacol. 40:1-49; Sharma, H.W. and R.
  • 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 transcription. Antisense 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.
  • the binding which results in modulation of expression occurs through hybridization or binding of complementary base pairs.
  • Antisense sequences can also 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.
  • 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, such as by transforming an appropriate host cell with an expression vector containing the sequence of interest. (See, e.g., Agrawal, supra.)
  • Antisense sequences can be delivered inttacellularly in the form of an expression plasmid which, upon transcription, produces a sequence complementary to at least a portion of the cellular sequence encoding the target protein.
  • Aitisense sequences can also be introduced inttacellularly through the use of viral vectors, such as retrovirus and adeno-associated virus vectors.
  • viral vectors such as retrovirus and adeno-associated virus vectors.
  • retrovirus 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, 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.
  • 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 transcriptional and translational control of the inserted coding sequence in a suitable host.
  • an appropriate expression vector i.e., a vector which contains the necessary elements for transcriptional and translational 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 expression vectors containing sequences encoding DITHP and appropriate transcriptional and translational 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 utiUzed to contain and express sequences encoding DITHP. These include, but are not Umited to, microorganisms such as bacteria ttansformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast ttansformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems transformed with viral expression vectors (e.g., cauliflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal (mammalian) cell systems.
  • microorganisms such as bacteria ttansformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors
  • yeast ttansformed with yeast expression vectors e.g., baculovirus
  • Expression vectors derived from rettoviruses, adenoviruses, 0 or he ⁇ es or vaccinia viruses, or from various bacterial plasmids may be used for deUvery of nucleotide sequences to the targeted organ, tissue, or cell population.
  • the invention is not 5 Umited by the host cell employed.
  • sequences encoding DITHP can be ttansformed into cell Unes using expression vectors which may contain viral origins of repUcation and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Any number of o selection systems may be used to recover transformed cell Unes. (See, e.g., Wigler, M. et al. (1977)
  • the dithp of the invention may be used for somatic or germUne 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-Unked inheritance (Cavazzana-Calvo, M. et o al. (2000) Science 288 :669-672), severe combined immunodeficiency syndrome associated with an inherited adenosine deaminase (ADA) deficiency (Blaese, R.M. et al. (1995) Science 270:475-480; Bordignon, C et al.
  • SCID severe combined immunodeficiency
  • ADA adenosine deaminase
  • hepatitis B or C virus HBV, HCV
  • fungal parasites such as Candida albicans and Paracoccidioides brasihensis
  • protozoan parasites such as Plasmodium falciparum and Trvpanosoma cruzi.
  • the expression of dithp from an appropriate population of o transduced cells may alleviate the clinical manifestations caused by the genetic deficiency.
  • diseases or disorders caused by deficiencies in dithp are treated by constructing mammaUan expression vectors comprising dithp and introducing these vectors by mechanical means into dithp-deficient cells.
  • Mechanical transfer technologies for use with cells in vivo or ex vitro include (i) direct DNA microinjection into individual cells, (u) balUstic gold 5 particle delivery, (ui) Uposome-mediated transfection, (iv) receptor-mediated gene transfer, and (v) the use of DNA transposons (Morgan, R.A. and Anderson, W.F. (1993) Annu. Rev. Biochem. 62:191-217; Ivies, Z. (1997) Cell 91:501-510; Boulay, J-L. and R ⁇ cipon, H. (1998) Curr. Opin. Biotechnol. 9:445- 450).
  • Expression vectors that may be effective for the expression of dithp include, but are not Umited o to, the PCDNA 3.1, EPITAG, PRCCMV2, PREP, PVAX vectors (Invitrogen, Carlsbad C A),
  • 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), (n) an inducible promoter 5 (e.g., the tetracycUne-regulated promoter (Gossen, M. and Bujard, H.
  • a constitutively active promoter e.g., from cytomegalovirus (CMV), Rous sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or ⁇ -actin genes
  • an inducible promoter 5 e.g., the tetracycUne-regulated promoter (Gossen, M. and Bujard, H.
  • Uposome transformation kits e.g., the PERFECT LIPID TRANSFECTION KIT, available from Invitrogen
  • Uposome transformation allows one with ordinary skill in the art to deliver polynucleotides to target cells in culture and require minimal effort to optimize experimental parameters.
  • transformation is performed using the calcium phosphate method (Graham, F.L. andEb, AJ. (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.
  • diseases or disorders caused by genetic defects with respect to dithp expression are treated by constructing a rettovirus vector consisting of (i) dithp under the control of an independent promoter or the rettovirus long terminal repeat (LTR) promoter, (U) appropriate RNA packaging signals, and (iti) a Rev-responsive element (RRE) along with additional rettovirus cis-acting RNA sequences and coding sequences required for efficient vector propagation.
  • a rettovirus vector consisting of (i) dithp under the control of an independent promoter or the rettovirus long terminal repeat (LTR) promoter, (U) appropriate RNA packaging signals, and (iti) a Rev-responsive element (RRE) along with additional rettovirus cis-acting RNA sequences and coding sequences required for efficient vector propagation.
  • RRE Rev-responsive element
  • the vector is propagated in an appropriate vector producing cell Une (VPCL) that expresses an envelope gene with a tropism for receptors on the target cells or a promiscuous envelope protein such as VSVg (Amentano, D. et al. (1987) J. Virol. 61:1647-1650; Bender, M.A. et al. (1987) 5 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.
  • VPCL vector producing cell Une
  • U.S. Patent Number 5,910,434 to Rigg discloses a method for obtaining retrovirus packaging cell Unes and is hereby inco ⁇ orated by reference. Propagation of retrovirus vectors, transduction of a population of o cells (e.g., CD4 + T-cells), and the return of ttansduced 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.
  • an adenovirus-based gene therapy delivery system is used to deUver dithp to cells which have one or more genetic abnormaUties 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) o Transplantation 27:263-268). Potentially useful adenoviral vectors are described in U.S. Patent
  • Adenovirus vectors for gene therapy hereby inco ⁇ orated by reference.
  • adenoviral vectors see also Antinozzi, P.A et al. (1999) Ainu. Rev. Nutr. 19:511-544 and Verma, I.M. and Somia, N. (1997) Nature 18:389:239-242, both inco ⁇ orated by reference herein.
  • a herpes-based, gene therapy deUvery system is used to deliver dithp to target cells which have one or more genetic abnormatities with respect to the expression of dithp.
  • HSV he ⁇ es simplex virus
  • the construction and packaging of 5 he ⁇ es-based vectors are well known to those with ordinary skill in the art.
  • a repUcation-competent he ⁇ es simplex virus (HSV) type 1 -based vector has been used to deUver a reporter gene to the eyes of primates (Liu, X. et al. (1999) Exp. Eye Res.l69:385-395).
  • the construction of a HSV-1 virus vector has also been disclosed in detail in U.S.
  • Patent Number 5,804,413 to DeLuca (“He ⁇ es simplex virus strains for gene transfer"), which is hereby inco ⁇ orated by reference.
  • U.S. Patent Number 5,804,413 o 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 control of the appropriate promoter for pu ⁇ oses including human gene therapy.
  • Aso taught by this patent are the construction and use of recombinant HSV strains deleted for ICP4, ICP27 and ICP22.
  • an alphavirus (positive, single-stranded RNA virus) vector is used to o deUver dithp to target cells.
  • SFV SemUki Forest Virus
  • alphavirus RNA repUcation a subgenomic RNA is generated that normally encodes the viral capsid proteins.
  • This subgenomic RNA repUcates to higher levels than the full-length genomic RNA, resulting in the overproduction of capsid proteins 5 relative to the viral proteins with enzymatic activity (e.g., protease and polymerase).
  • enzymatic activity e.g., protease and polymerase.
  • inserting dithp into the alphavirus genome in place of the capsid-coding region results in the production of a large number of dithp RNA and the synthesis of high levels of DITHP in vector transduced cells.
  • alphavirus infection is typically associated with cell lysis within a few days
  • the abiUty to estabUsh a persistent infection in hamster normal kidney cells (BHK-21) with a variant of Sindbis virus o (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 and RNA ttansfections, and performing alphavirus infections, are well known to those with ordinary skill in the art.
  • Anti-DITHP antibodies may be used to analyze protein expression levels. Such antibodies 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.
  • amino acid sequence encoded by the dithp of the Sequence Listing may be analyzed by o appropriate software (e.g. , LASERGENE NAVIGATOR software, DNASTAR) to determine regions of high immunogenicity.
  • the optimal sequences for immunization are selected from the C-terminus, the N-terminus, and those intervening, hydrophiUc 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 5 antibody induction do not need to have biological activity; however, they must be antigenic.
  • Peptides 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 Umpet cyanin (KLH; Sigma, St. Louis MO) for antibody production.
  • KLH keyhole Umpet cyanin
  • a peptide encompassing an antigenic o region may be expressed from a dithp, synthesized as described above, or purified from human cells.
  • mice, goats, and rabbits may be immunized by injection with a peptide.
  • various adjuvants may be used to increase immunological response.
  • peptides about 15 residues in length may be synthesized using an ABI 431 A 5 peptide synthesizer (PE Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction 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.
  • BSA bovine serum albumin
  • Antisera with antipeptide activity are tested for anti-DITHP activity using protocols well known in the art, including ELISA, radioimmunoassay (RIA), and immunoblotting.
  • isolated and purified peptide may be used to immunize mice (about 100 ⁇ g 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 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.
  • wells of a multi-well plate (FAST, Becton-Dickinson, Palo Ato, CA) 5 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 supematants from 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 o injected into pristane-tteated mice to produce ascites, and monoclonal antibody is purified from the ascitic fluid by affinity chromatography on protein A (Amersham Pharmacia Biotech). Several 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.
  • Aitibody fragments containing specific binding sites for an epitope may also be generated.
  • such fragments include, but are not Umited to, the F(ab')2 fragments produced by pepsin digestion of the antibody molecule, and the Fab fragments generated by reducing the disulfide bridges of the F(ab')2 fragments.
  • construction of Fab expression libraries in filamentous bacteriophage allows rapid and easy identification of monoclonal fragments with desired specificity 0 (Pound, supra. Chaps. 45-47).
  • Aitibodies generated against polypeptide encoded by dithp can be used to purify and characterize full-length DITHP protein and its activity, binding partners, etc.
  • Aiti-DITHP antibodies may be used in assays to quantify the amount of DITHP found in a 5 particular human cell. Such assays include methods utiUzing the antibody and a label to detect expression level under normal or disease conditions.
  • the peptides and antibodies of the invention may be used with or without modification or labeled by joining them, either covalently or noncovalently, with a reporter molecule.
  • Protocols for detecting and measuring protein expression using either polyclonal or monoclonal o 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 and its specific antibody and the measurement of such complexes. These and other assays are described in Pound (supra). Without further elaboration, it is beUeved that one skilled in the art can, using the preceding description, utiUze the present invention to its fullest extent. The following preferred specific embodiments are, therefore, to be construed as merely illusttative, and not Umitative of the remainder of the disclosure in any way whatsoever.
  • 60/167,945, U.S. Ser. No. 60/167,520, U.S. Ser. No. 60/168,468, U.S. Ser. No. 60/168,599, U.S. Ser. No. 60/167,410, U.S. Ser. No. 60/168,265, U.S. Ser. No. 60/168,429, U.S. Ser. No. 60/168,432, U.S. Ser. No. 60/167,521, U.S. Ser. No. 60/168,857, U.S. Ser. No. 60/168,197, U.S. Ser. No. 60/168,611, and U.S. Ser. No. 60/168,613 are hereby expressly inco ⁇ orated by reference.
  • RNA was purchased from CLONTECH Laboratories, Inc. (Palo Ato 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 Technologies), a monophasic solution of phenol and guanidine isothiocyanate. The resulting lysates were centrifuged over CsCl cushions or extracted with chloroform. RNA was precipitated with either isopropanol or sodium acetate and ethanol, or by other routine methods.
  • RNA was provided with RNA and constructed the corresponding cDNA Ubraries. Otherwise, cDNA was synthesized and cDNA Ubraries were constructed with the UNLZAP vector system (Stratagene Cloning Systems, Inc. (Stratagene), 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 5.1 through 6.6.) Reverse transcription was initiated using oligo d(T) or random primers. Synthetic oligonucleotide adapters were Ugated to double stranded cDNA, and the cDNA was digested with the appropriate restriction enzyme or enzymes.
  • cDNA was size-selected (300-1000 bp) using SEPHACRYL S1000, SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (Amersham Pharmacia Biotech) or preparative agarose gel electtophoresis.
  • cDN A were Ugated into compatible restriction enzyme sites of the polylinker of a suitable plasmid, e.g., PBLUESCRIPT plasmid (Stratagene), pSPORTl plasmid 5 (Life Technologies), or pINCY (Incyte).
  • Recombinant plasmids were transformed into competent E. coU cells including XLl-Blue, XLl-BlueMRF, or SOLR from Stratagene or DH5 ⁇ , DH10B, or ElectroMAX DH10B from Life Technologies.
  • 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 0.1 ml of distilled water and stored, with or without lyophiUzation, at 4°C
  • plasmid DNA was amplified from host cell lysates using direct Unk PCR in a high-throughput format. (Rao, V.B. (1994) Anal. Biochem. 216:1-14.) Host cell lysis and thermal cycling steps were carried out in a single reaction mixture. Samples were processed and stored in 384- o well plates, and the concentration of ampUfied plasmid DNA was quantified fluorometticaUy using
  • PICOGREEN dye (Molecular Probes, Inc. (Molecular Probes), Eugene OR) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy, Helsinki, Finland).
  • 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 Co ⁇ ., Sunnyvale CA) or the MICROLAB 2200 Uquid transfer system (Hamilton).
  • cDNA sequencing reactions were prepared using reagents provided by Amersham Pharmacia Biotech or suppUed in ABI o sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (PE
  • Component sequences from chromatograms were subject to PHRED analysis and assigned a quaUty score.
  • the sequences having at least a required quatity score were subject to various preprocessing editing pathways to eUminate, e.g., low quaUty 3' ends, vector and linker sequences, polyA tails, Au repeats, mitochondrial and ribosomal sequences, bacterial contamination sequences, and sequences smaller than 50 base pairs.
  • low-information sequences and repetitive elements e.g., dinucleotide repeats, Au repeats, etc.
  • 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 existing bins using BLASTn (v.1.4 WashU) and CROSSMATCH. Candidate pairs were identified as all BLAST hits having a quaUty score greater than or equal to 150. Aignments 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.
  • each assembled template was determined based on the number and orientation of its component sequences. Template sequences as disclosed in the sequence Usting 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 listed in Table 4, along with their positions along the template nucleotide sequences.
  • 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. Asembled templates were also subject to analysis by STITCHER/EXON MAPPER algorithms which analyze the probabilities of the presence of spUce variants, alternatively spUced exons, spUce junctions, differential expression of alternative spliced genes across tissue types or disease states, etc. These resulting bins were subject to several rounds of the above assembly procedures.
  • bins were clone joined based upon clone informatioa 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 Ukely that the two bins actually belonged together in a single bin. The resulting combined bins underwent assembly procedures to regenerate the consensus sequences.
  • the template sequences were further analyzed by translating each template in all three forward reading frames and searching each translation against the Pfam database of hidden Markov model- based protein famiUes and domains using the HMMER software package (available to the pubUc from Washington University School of Medicine, St. Louis MO). Regions of templates which, when 5 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 IO "3 are reported. (See also World Wide Web site http://pfarawustl.edu/ for detailed descriptions of Pfam protein domains and famiUes.)
  • 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 6, 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 pubUc databases such as the GenBank rodent, mammaUan, vertebrate, prokaryote, and eukaryote databases.
  • 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 RN from a particular cell type or tissue have been bound. (See, e.g., Sambrook, supra, ch. 7; Ausubel, 1995, supra, ch. 4 and 16.)
  • 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 normaUzed value between 0 and 100, and is calculated as follows: the BLAST score is multipUed 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 aUgnment. 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.
  • 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 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; genitaUa, 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 sequences, and cDNA library/tissue information are found in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto C A).
  • Table 5 shows the tissue distribution profile for the templates of the invention. For each template, the three most frequently observed tissue categories are shown in column 3, along with the percentage of component sequences belonging to each category. Only tissue categories with percentage values of > 10% are shown. A tissue distribution of "widely distributed" in column 3 indicates percentage values of ⁇ 10% in aU tissue categories.
  • Transcript images are generated as described in Seilhamer et al., "Comparative Gene Transcript Analysis," U.S. Patent Number 5,840,484, inco ⁇ orated herein by reference.
  • 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 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 hai ⁇ in structures and primer-primer dimerizations are avoided.
  • Selected human 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.
  • PCR is performed in 96-well plates using the PTC-200 thermal cycler (MJ Research).
  • the reaction mix 5 contains DNA template, 200 nmol of each primer, reaction buffer containing Mg 2+ , (NH 4 ) 2 S0 4 , and ⁇ - mercaptoethanol, Taq DNA polymerase (Amersham Pharmacia Biotech), ELONGASE enzyme (Life Technologies), and Pfu DNA polymerase (Stratagene), 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 0 alternative, the parameters for primer pair T7 and SK+ are as follows: Step 1 : 94°C, 3 min;
  • the concentration of DNA in each well is determined by dispensing 100 ⁇ l PICOGREEN quantitation reagent (0.25% (v/v); Molecular Probes) dissolved in IX Tris-EDTA (TE) and 0.5 ⁇ l of 5 undiluted PCR product into each well of an opaque fluorimeter plate (Corning Inco ⁇ orated (Corning), 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
  • FLUOROSKAN II (Labsystems Oy) to measure the fluorescence of the sample and to quantify the concentration of DNA
  • a 5 ⁇ l to 10 ⁇ l ahquot 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, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison WI), and sonicated or sheared prior to reUgation into pUC 18 vector (Amersham Pharmacia Biotech).
  • the digested nucleotides are separated on low concentration (0.6 to 0.8%) agarose gels, fragments are excised, and agar digested with AGAR ACE (Promega). Extended clones are 5 religated using T4 Ugase (New England Biolabs, Inc., Beverly MA) into pUC 18 vector (Amersham Pharmacia Biotech), treated with Pfu DNA polymerase (Sttatagene) to fill-in restriction site overhangs, and transfected into competent E. coh 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 carbenicilUn Uquid media. o The cells are lysed, and DNA is ampUfied by PCR using Taq DNA polymerase (Amersham
  • 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 reampUfied using the same conditions as described above.
  • Samples are diluted with 20% dimethysulfoxide (1 :2, v/v), and sequenced using DYENAMIC energy transfer sequencing primers and the DYENAMIC DIRECT kit (Amersham Pharmacia Biotech) or the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (PE Biosystems). 5
  • the dithp is used to obtain regulatory sequences (promoters, introns, and enhancers) using the procedure above, oUgonucleotides designed for such extension, and an appropriate genomic Ubrary.
  • Hybridization probes derived from the dithp of the Sequence Listing are employed for screening cDN , mRNA, or genomic DNA.
  • the labehng of probe nucleotides between 100 and 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, ⁇ P-ATP, and 0.5X One-Phor-Al Plus (Amersham Pharmacia Biotech) 5 buffer and purified using a ProbeQuant G-50 Microcolumn (Amersham Pharmacia Biotech). The probe mixture is diluted to IO 7 dpm/ ⁇ g/ml hybridization buffer and used in a typical membrane-based hybridization analysis.
  • the DNA is digested with a restriction endonuclease such as Eco RV and is electrophoresed through a 0.7% agarose gel.
  • the DNA fragments are transferred from the agarose to nylon membrane o (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
  • blots are sequentially washed at room temperature under increasingly stringent conditions, up to 0. lx saUne sodium citrate (SSC) and 0.5% sodium dodecyl sulfate. After the blots are placed in a PHOSPHORIMAGER cassette 5 (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
  • the cDNA sequences which were used to assemble SEQ ID NO: 1-71 are compared with o sequences from the Incyte LIFESEQ database and pubUc domain databases using BLAST and other implementations of the Smith- Waterman algorithm. Sequences from these databases that match SEQ ID NO: 1-71 are assembled into clusters of contiguous and overlapping sequences using assembly algorithms such as PHRAP (Table 6). 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 G ⁇ nethon are used to determine if any of the clustered sequences have been previously mapped.
  • SHGC Stanford Human Genome Center
  • WIGR Whitehead Institute for Genome Research
  • G ⁇ nethon are used to determine if any of the clustered sequences have been previously mapped.
  • 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: 1-71 are described as ranges, or intervals, of human chromosomes.
  • the map 5 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.
  • 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.
  • Mb megabase
  • the cM distances are based on genetic markers mapped by Gen ⁇ thon which provide boundaries for radiation hybrid o markers whose sequences were included in each of the clusters.
  • RNA is isolated from tissue samples using the guanidinium thiocyanate method and 5 polyA + RNA is purified using the oligo (dT) cellulose method.
  • Each polyA + RNA sample is reverse transcribed using MMLV reverse-transcriptase, 0.05 pg/ ⁇ l oUgo-dT primer (21mer), IX first sfrand buffer, 0.03 units/ ⁇ l RNase inhibitor, 500 ⁇ M dATP, 500 ⁇ M dGTP, 500 ⁇ M dTTP, 40 ⁇ M dCTP, 40 ⁇ M 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 GEMB RIGHT kits o (Incyte).
  • Specific control polyA + RNA are synthesized by in vitro transcription from non-coding yeast genomic DNA (W. Lei, unpubhshed).
  • a quantitative controls, the control mRNA at 0.002 ng, 0.02 ng, 0.2 ng, and 2 ng are diluted into reverse ttanscription reaction at ratios of 1 :100,000, 1 :10,000, 1 : 1000, 1 :100 (w/w) to sample mRNA respectively.
  • control mRNA are diluted into reverse transcription reaction at ratios of 1:3, 3:1, 1:10, 10:1, 1:25, 25:1 (w/w) to sample mRNA differential 5 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 filtration spin columns (CLONTECH Laboratories, Inc.
  • reaction samples are ethanol precipitated using 1 ml of glycogen (1 o 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 ⁇ l 5X SSC/0.2% SDS.
  • Microarray Preparation Sequences of the present invention are used to generate array elements.
  • Each array element is ampUfied from bacterial cells containing vectors with cloned cDNA inserts.
  • PCR ampUfication uses primers complementary to the vector sequences flanking the cDNA insert.
  • Array elements are ampUfied in thirty cycles of PCR from an initial quantity of 1-2 ng to a final quantity greater than 5 ⁇ g.
  • AmpUfied array elements are then purified using SEPHACRYL-400 (Amersham Pharmacia Biotech). Purified array elements are immobiUzed on polymer-coated glass sUdes.
  • Glass microscope sUdes are cleaned by ultrasound in 0.1% SDS and acetone, with extensive distilled water washes between and after treatments. Glass slides are etched in 4% hydrofluoric acid (VWR Scientific Products Corporation (VWR), West Chester, PA), washed extensively in distilled water, and coated with 0.05% aminopropyl silane (Sigma) in 95% ethanol. Coated sUdes are cured in a 110°C oven. Array elements are appUed to the coated glass substrate using a procedure described in US Patent No. 5,807,522, inco ⁇ orated herein by reference.
  • Microarrays are UV-crosslinked using a STRATALINKER UV-crossUnker (Stratagene).
  • 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.
  • PBS phosphate buffered saUne
  • Hybridization reactions contain 9 ⁇ l of probe mixture consisting of 0.2 ⁇ g 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 cm 2 coversUp.
  • the arrays are ttansferred to a wate ⁇ roof chamber having a cavity just sUghtly larger than a microscope sUde.
  • the chamber is kept at 100% humidity internally by the addition of 140 ⁇ l 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 (0. IX SSC), and dried.
  • Reporter-labeled hybridization complexes are detected with a microscope equipped with an Lnnova 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 Ught is focused on the array using a 20X microscope objective (Nikon, Inc., Melville NY).
  • the sUde 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. 5 In two separate scans, a mixed gas multiline laser excites the two fluorophores sequentially.
  • Emitted light is spUt, based on wavelength, into two photomultipUer tube detectors (PMT R1477, Hamamatsu Photonics Systems, Bridgewater NJ) corresponding to the two fluorophores.
  • Appropriate filters positioned between the array and the photomultipUer 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 o 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 caUbrated 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 5 be correlated with a weight ratio of hybridizing species of 1 : 100,000.
  • the calibration is done by labehng samples of the calibrating cDNA with the two fluorophores and adding identical amounts of each to the hybridization mixture. o
  • the output of the photomultipUer tube is digitized using a 12-bit RTI-835H analog-to-digital
  • A/D conversion board Analog Devices, Inc., Norwood, MA
  • the digitized data are displayed as an image where the signal intensity is mapped using a Unear 20-color transformation 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 5 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 o signal analysis is the GEMTOOLS gene expression analysis program (Incyte).
  • 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 oUgonucleotides 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 oUgonucleotide is designed from the 5 most unique 5 ' sequence and used to prevent transcription factor binding to the promoter sequence.
  • To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding and processing of the transcript.
  • DITHP expression and purification of DITHP is accomplished using bacterial or virus-based expression systems.
  • cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA ttanscription.
  • promoters include, but are not Umited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator 5 regulatory element.
  • Recombinant vectors are transformed into suitable bacterial hosts, e.g.,
  • DITHP upon induction with isopropyl beta-D- thiogalactopyranoside (IPTG).
  • IPTG isopropyl beta-D- thiogalactopyranoside
  • Expression of DITHP in eukaryotic cells is achieved by infecting insect or mammaUan cell Unes with recombinant Autographica caUfornica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus.
  • AcMNPV Autographica caUfornica nuclear polyhedrosis virus
  • the nonessential polyhedrin gene of baculovirus is o replaced with cDNA encoding DITHP by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA ttanscription.
  • baculovirus 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, 5 supra; and Sandig, supra.)
  • 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 o glutathione under conditions that maintain protein activity and antigenicity (Amersham Pharmacia).
  • the GST moiety can be proteolytically cleaved from DITHP at specifically engineered sites.
  • FLAG an 8-amino acid peptide
  • 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.
  • DITHP activity is demonstrated through a variety of specific assays, some of which are outUned 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 l o coefficient of NAD(P)H coenzyme at 340 nmfor the measurement of reduction activity (Dalziel, K.

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Abstract

L'invention concerne des polynucléotides humains purifiés pour le diagnostic et la thérapeutique (dithp). Elle porte encore sur les polypeptides (DITHP) codés par dithp, ainsi que sur l'utilisation de dithp, de compléments, d'oligonucléotides ou de fragments de ceux-ci dans des analyses diagnostiques. L'invention se rapporte encore à des vecteurs et à des cellules hôtes contenant dithp, pour l'expression de DITHP, ainsi qu'à l'utilisation de DITHP isolés et purifiés pour l'induction d'anticorps et pour le criblage de banques de composés, et à l'utilisation d'anticorps anti-DITHP dans des analyses diagnostiques. Des jeux ordonnés de microéchantillons contenant dithp et leurs procédés d'utilisation sont également décrits.
PCT/US2000/025643 1999-09-23 2000-09-19 Molecules pour le diagnostic et la therapeutique WO2001021836A2 (fr)

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WO2001072777A2 (fr) * 2000-03-13 2001-10-04 Incyte Genomics, Inc. Facteurs de transcription
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WO2001072777A2 (fr) * 2000-03-13 2001-10-04 Incyte Genomics, Inc. Facteurs de transcription
WO2001072777A3 (fr) * 2000-03-13 2002-04-18 Incyte Genomics Inc Facteurs de transcription
US11142570B2 (en) 2017-02-17 2021-10-12 Bristol-Myers Squibb Company Antibodies to alpha-synuclein and uses thereof
US11827695B2 (en) 2017-02-17 2023-11-28 Bristol-Myers Squibb Company Antibodies to alpha-synuclein and uses thereof

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