US20070111230A1 - Corynebacterium glutamicum genes encoding proteins involved in membrane synthesis and membrane transport - Google Patents

Corynebacterium glutamicum genes encoding proteins involved in membrane synthesis and membrane transport Download PDF

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US20070111230A1
US20070111230A1 US11/507,094 US50709406A US2007111230A1 US 20070111230 A1 US20070111230 A1 US 20070111230A1 US 50709406 A US50709406 A US 50709406A US 2007111230 A1 US2007111230 A1 US 2007111230A1
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protein
nucleic acid
mct
acid molecule
amino acid
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Markus Pompejus
Burkhard Kroger
Hartwig Schroder
Oskar Zelder
Gregor Haberhauer
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BASF SE
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    • 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
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/34—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Corynebacterium (G)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/18—Carboxylic ester hydrolases (3.1.1)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56911—Bacteria

Definitions

  • Certain products and by-products of naturally-occurring metabolic processes in cells have utility in a wide array of industries, including the food, feed, cosmetics, and pharmaceutical industries.
  • These molecules collectively termed ‘fine chemicals’, include organic acids, both proteinogenic and non-proteinogenic amino acids, nucleotides and nucleosides, lipids and fatty acids, diols, carbohydrates, aromatic compounds, vitamins and cofactors, and enzymes.
  • Their production is most conveniently performed through the large-scale culture of bacteria developed to produce and secrete large quantities of one or more desired molecules.
  • One particularly useful organism for this purpose is Corynebacterium glutamicum , a gram positive, nonpathogenic bacterium. Through strain selection, a number of mutant strains have been developed which produce an array of desirable compounds. However, selection of strains improved for the production of a particular molecule is a time-consuming and difficult process.
  • the invention provides novel bacterial nucleic acid molecules which have a variety of uses. These uses include the identification of microorganisms which can be used to produce fine chemicals, the modulation of fine chemical production in C. glutamicum or related bacteria, the typing or identification of C. glutamicum or related bacteria, as reference points for mapping the C. glutamicum genome, and as markers for transformation. These novel nucleic acid molecules encode proteins, referred to herein as membrane construction and membrane transport (MCT) proteins.
  • MCT membrane construction and membrane transport
  • C. glutamicum is a gram positive, aerobic bacterium which is commonly used in industry for the large-scale production of a variety of fine chemicals, and also for the degradation of hydrocarbons (such as in petroleum spills) and for the oxidation of terpenoids.
  • the MCT nucleic acid molecules of the invention therefore, can be used to identify microorganisms which can be used to produce fine chemicals, e.g., by fermentation processes.
  • Modulation of the expression of the MCT nucleic acids of the invention, or modification of the sequence of the MCT nucleic acid molecules of the invention, can be used to modulate the production of one or more fine chemicals from a microorganism (e.g., to improve the yield or production of one or more fine chemicals from a Corynebacterium or Brevibacterium species).
  • the MCT nucleic acids of the invention may also be used to identify an organism as being Corynebacterium glutamicum or a close relative thereof, or to identify the presence of C. glutamicum or a relative thereof in a mixed population of microorganisms.
  • the invention provides the nucleic acid sequences of a number of C. glutamicum genes; by probing the extracted genomic DNA of a culture of a unique or mixed population of microorganisms under stringent conditions with a probe spanning a region of a C. glutamicum gene which is unique to this organism, one can ascertain whether this organism is present.
  • Corynebacterium glutamicum itself is nonpathogenic, it is related to species pathogenic in humans, such as Corynebacterium diphtheriae (the causative agent of diphtheria); the detection of such organisms is of significant clinical relevance.
  • the MCT nucleic acid molecules of the invention may also serve as reference points for mapping of the C. glutamicum genome, or of genomes of related organisms. Similarly, these molecules, or variants or portions thereof, may serve as markers for genetically engineered Corynebacterium or Brevibacterium species. e.g.e.g.
  • the MCT proteins encoded by the novel nucleic acid molecules of the invention are capable of, for example, performing a function involved in the metabolism (e.g., the biosynthesis or degradation) of compounds necessary for membrane biosynthesis, or of assisting in the transmembrane transport of one or more compounds either into or out of the cell.
  • the nucleic acid molecules of the invention may be utilized in the genetic engineering of this organism to make it a better or more efficient producer of one or more fine chemicals.
  • This improved production or efficiency of production of a fine chemical may be due to a direct effect of manipulation of a gene of the invention, or it may be due to an indirect effect of such manipulation.
  • an MCT protein of the invention may directly affect the yield, production, and/or efficiency of production of a fine chemical from a C. glutamicum strain incorporating such an altered protein.
  • Those MCT proteins involved in the export of fine chemical molecules from the cell may be increased in number or activity such that greater quantities of these compounds are secreted to the extracellular medium, from which they are more readily recovered.
  • those MCT proteins involved in the import of nutrients necessary for the biosynthesis of one or more fine chemicals e.g., phosphate, sulfate, nitrogen compounds, etc.
  • these precursors, cofactors, or intermediate compounds are increased in concentration within the cell.
  • fatty acids and lipids themselves are desirable fine chemicals; by optimizing the activity or increasing the number of one or more MCT proteins of the invention which participate in the biosynthesis of these compounds, or by impairing the activity of one or more MCT proteins which are involved in the degradation of these compounds, it may be possible to increase the yield, production, and/or efficiency of production of fatty acid and lipid molecules from C. glutamicum.
  • MCT proteins of the invention involved in the export of waste products may be increased in number or activity such that the normal metabolic wastes of the cell (possibly increased in quantity due to the overproduction of the desired fine chemical) are efficiently exported before they are able to damage nucleotides and proteins within the cell (which would decrease the viability of the cell) or to interfere with fine chemical biosynthetic pathways (which would decrease the yield, production, or efficiency of production of the desired fine chemical).
  • the relatively large intracellular quantities of the desired fine chemical may in itself be toxic to the cell, so by increasing the activity or number of transporters able to export this compound from the cell, one may increase the viability of the cell in culture, in turn leading to a greater number of cells in the culture producing the desired fine chemical.
  • the MCT proteins of the invention may also be manipulated such that the relative amounts of different lipid and fatty acid molecules are produced. This may have a profound effect on the lipid composition of the membrane of the cell. Since each type of lipid has different physical properties, an alteration in the lipid composition of a membrane may significantly alter membrane fluidity. Changes in membrane fluidity can impact the transport of molecules across the membrane, as well as the integrity of the cell, both of which have a profound effect on the production of fine chemicals from C. glutamicum in large-scale fermentative culture.
  • the invention provides novel nucleic acid molecules which encode proteins, referred to herein as MCT proteins, which are capable of, for example, participating in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes.
  • MCT proteins proteins
  • Nucleic acid molecules encoding an MCT protein are referred to herein as MCT nucleic acid molecules.
  • the MCT protein participates in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes. Examples of such proteins include those encoded by the genes set forth in Table 1.
  • one aspect of the invention pertains to isolated nucleic acid molecules (e.g., cDNAs, DNAs, or RNAs) comprising a nucleotide sequence encoding an MCT protein or biologically active portions thereof, as well as nucleic acid fragments suitable as primers or hybridization probes for the detection or amplification of MCT-encoding nucleic acid (e.g., DNA or mRNA).
  • the isolated nucleic acid molecule comprises one of the nucleotide sequences set forth in Appendix A or the coding region or a complement thereof of one of these nucleotide sequences.
  • the isolated nucleic acid molecule of the invention comprises a nucleotide sequence which hybridizes to or is at least about 50%, preferably at least about 60%, more preferably at least about 70%, 80% or 90%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more homologous to a nucleotide sequence set forth in Appendix A, or a portion thereof.
  • the isolated nucleic acid molecule encodes one of the amino acid sequences set forth in Appendix B.
  • the preferred MCT proteins of the present invention also preferably possess at least one of the MCT activities described herein.
  • the isolated nucleic acid molecule encodes a protein or portion thereof wherein the protein or portion thereof includes an amino acid sequence which is sufficiently homologous to an amino acid sequence of Appendix B, e.g., sufficiently homologous to an amino acid sequence of Appendix B such that the protein or portion thereof maintains an MCT activity.
  • the protein or portion thereof encoded by the nucleic acid molecule maintains the ability to participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes.
  • the protein encoded by the nucleic acid molecule is at least about 50%, preferably at least about 60%, and more preferably at least about 70%, 80%, or 90% and most preferably at least about 95%, 96%, 97%, 98%, or 99% or more homologous to an amino acid sequence of Appendix B (e.g., an entire amino acid sequence selected from those sequences set forth in Appendix B).
  • the protein is a full length C. glutamicum protein which is substantially homologous to an entire amino acid sequence of Appendix B (encoded by an open reading frame shown in Appendix A).
  • the isolated nucleic acid molecule is derived from C. glutamicum and encodes a protein (e.g., an MCT fusion protein) which includes a biologically active domain which is at least about 50% or more homologous to one of the amino acid sequences of Appendix B and is able to participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes, or has one or more of the activities set forth in Table 1, and which also includes heterologous nucleic acid sequences encoding a heterologous polypeptide or regulatory regions.
  • a protein e.g., an MCT fusion protein
  • the isolated nucleic acid molecule is at least 15 nucleotides in length and hybridizes under stringent conditions to a nucleic acid molecule comprising a nucleotide sequence of Appendix A.
  • the isolated nucleic acid molecule corresponds to a naturally-occurring nucleic acid molecule. More preferably, the isolated nucleic acid encodes a naturally-occurring C. glutamicum MCT protein, or a biologically active portion thereof.
  • vectors e.g., recombinant expression vectors, containing the nucleic acid molecules of the invention, and host cells into which such vectors have been introduced.
  • a host cell is used to produce an MCT protein by culturing the host cell in a suitable medium. The MCT protein can be then isolated from the medium or the host cell.
  • Yet another aspect of the invention pertains to a genetically altered microorganism in which an MCT gene has been introduced or altered.
  • the genome of the microorganism has been altered by introduction of a nucleic acid molecule of the invention encoding wild-type or mutated MCT sequence as a transgene.
  • an endogenous MCT gene within the genome of the microorganism has been altered, e.g., functionally disrupted, by homologous recombination with an altered MCT gene.
  • an endogenous or introduced MCT gene in a microorganism has been altered by one or more point mutations, deletions, or inversions, but still encodes a functional MCT protein.
  • one or more of the regulatory regions (e.g., a promoter, repressor, or inducer) of an MCT gene in a microorganism has been altered (e.g., by deletion, truncation, inversion, or point mutation) such that the expression of the MCT gene is modulated.
  • the microorganism belongs to the genus Corynebacterium or Brevibacterium, with Corynebacterium glutamicum being particularly preferred.
  • the microorganism is also utilized for the production of a desired compound, such as an amino acid, with lysine being particularly preferred.
  • the invention provides a method of identifying the presence or activity of Cornyebacterium diphtheriae in a subject.
  • This method includes detection of one or more of the nucleic acid or amino acid sequences of the invention (e.g., the sequences set forth in Appendix A or Appendix B) in a subject, thereby detecting the presence or activity of Corynebacterium diphtheriae in the subject.
  • Still another aspect of the invention pertains to an isolated MCT protein or a portion, e.g., a biologically active portion, thereof.
  • the isolated MCT protein or portion thereof can participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes.
  • the isolated MCT protein or portion thereof is sufficiently homologous to an amino acid sequence of Appendix B such that the protein or portion thereof maintains the ability to participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes.
  • the invention also provides an isolated preparation of an MCT protein.
  • the MCT protein comprises an amino acid sequence of Appendix B.
  • the invention pertains to an isolated full length protein which is substantially homologous to an entire amino acid sequence of Appendix B (encoded by an open reading frame set forth in Appendix A).
  • the protein is at least about 50%, preferably at least about 60%, and more preferably at least about 70%, 80%, or 90%, and most preferably at least about 95%, 96%, 97%, 98%, or 99% or more homologous to an entire amino acid sequence of Appendix B.
  • the isolated MCT protein comprises an amino acid sequence which is at least about 50% or more homologous to one of the amino acid sequences of Appendix B and is able to participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes, or has one or more of the activities set forth in Table 1.
  • the isolated MCT protein can comprise an amino acid sequence which is encoded by a nucleotide sequence which hybridizes, e.g., hybridizes under stringent conditions, or is at least about 50%, preferably at least about 60%, more preferably at least about 70%, 80%, or 90%, and even more preferably at least about 95%, 96%, 97%, 98,%, or 99% or more homologous, to a nucleotide sequence of Appendix B. It is also preferred that the preferred forms of MCT proteins also have one or more of the MCT bioactivities described herein.
  • the MCT polypeptide, or a biologically active portion thereof, can be operatively linked to a non-MCT polypeptide to form a fusion protein.
  • this fusion protein has an activity which differs from that of the MCT protein alone.
  • this fusion protein participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes.
  • integration of this fusion protein into a host cell modulates production of a desired compound from the cell.
  • the invention provides methods for screening molecules which modulate the activity of an MCT protein, either by interacting with the protein itself or a substrate or binding partner of the MCT protein, or by modulating the transcription or translation of an MCT nucleic acid molecule of the invention.
  • Another aspect of the invention pertains to a method for producing a fine chemical.
  • This method involves the culturing of a cell containing a vector directing the expression of an MCT nucleic acid molecule of the invention, such that a fine chemical is produced.
  • this method further includes the step of obtaining a cell containing such a vector, in which a cell is transfected with a vector directing the expression of an MCT nucleic acid.
  • this method further includes the step of recovering the fine chemical from the culture.
  • the cell is from the genus Corynebacterium or Brevibacterium, or is selected from those strains set forth in Table 3.
  • Another aspect of the invention pertains to methods for modulating production of a molecule from a microorganism.
  • Such methods include contacting the cell with an agent which modulates MCT protein activity or MCT nucleic acid expression such that a cell associated activity is altered relative to this same activity in the absence of the agent.
  • the cell is modulated for one or more C. glutamicum metabolic pathways for cell membrane components or is modulated for the transport of compounds across such membranes, such that the yields or rate of production of a desired fine chemical by this microorganism is improved.
  • the agent which modulates MCT protein activity can be an agent which stimulates MCT protein activity or MCT nucleic acid expression.
  • agents which stimulate MCT protein activity or MCT nucleic acid expression include small molecules, active MCT proteins, and nucleic acids encoding MCT proteins that have been introduced into the cell.
  • agents which inhibit MCT activity or expression include small molecules and antisense MCT nucleic acid molecules.
  • Another aspect of the invention pertains to methods for modulating yields of a desired compound from a cell, involving the introduction of a wild-type or mutant MCT gene into a cell, either maintained on a separate plasmid or integrated into the genome of the host cell. If integrated into the genome, such integration can be random, or it can take place by homologous recombination such that the native gene is replaced by the introduced copy, causing the production of the desired compound from the cell to be modulated.
  • said yields are increased.
  • said chemical is a fine chemical.
  • said fine chemical is an amino acid.
  • said amino acid is L-lysine.
  • the present invention provides MCT nucleic acid and protein molecules which are involved in the metabolism of cellular membrane components in C. glutamicum or in the transport of compounds across such membranes.
  • the molecules of the invention may be utilized in the modulation of production of fine chemicals from microorganisms, such as C. glutamicum , either directly (e.g., where overexpression or optimization of a fatty acid biosynthesis protein has a direct impact on the yield, production, and/or efficiency of production of the fatty acid from modified C.
  • glutamicum may have an indirect impact which nonetheless results in an increase of yield, production, and/or efficiency of production of the desired compound (e.g., where modulation of the metabolism of cell membrane components results in alterations in the yield, production, and/or efficiency of production or the composition of the cell membrane, which in turn may impact the production of one or more fine chemicals). Aspects of the invention are further explicated below.
  • the term ‘fine chemical’ is art-recognized and includes molecules produced by an organism which have applications in various industries, such as, but not limited to, the pharmaceutical, agriculture, and cosmetics industries.
  • Such compounds include organic acids, such as tartaric acid, itaconic acid, and diaminopimelic acid, both proteinogenic and non-proteinogenic amino acids, purine and pyrimidine bases, nucleosides, and nucleotides (as described e.g. in Kuninaka, A. (1996) Nucleotides and related compounds, p. 561-612, in Biotechnology vol. 6, Rehm et al., eds.
  • VCH Weinheim, and references contained therein
  • lipids both saturated and unsaturated fatty acids (e.g., arachidonic acid), diols (e.g., propane diol, and butane diol), carbohydrates (e.g, hyaluronic acid and trehalose), aromatic compounds (e.g, aromatic amines, vanillin, and indigo), vitamins and cofactors (as described in Ullmann's Encyclopedia of Industrial Chemistry, vol. A27, “Vitamins”, p. 443-613 (1996) VCH: Weinheim and references therein; and Ong, A.S., Niki, E. & Packer, L.
  • saturated and unsaturated fatty acids e.g., arachidonic acid
  • diols e.g., propane diol, and butane diol
  • carbohydrates e.g, hyaluronic acid and trehalose
  • aromatic compounds e.g, aromatic amines, vanillin, and
  • Amino acids comprise the basic structural units of all proteins, and as such are essential for normal cellular functioning in all organisms.
  • the term “amino acid” is art-recognized.
  • the proteinogenic amino acids, of which there are 20 species, serve as structural units for proteins, in which they are linked by peptide bonds, while the nonproteinogenic amino acids (hundreds of which are known) are not normally found in proteins (see Ulmann's Encyclopedia of Industrial Chemistry, vol. A2, p. 57-97 VCH: Weinheim (1985)).
  • Amino acids may be in the D- or L-optical configuration, though L-amino acids are generally the only type found in naturally-occurring proteins.
  • the ‘essential’ amino acids histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine
  • they are generally a nutritional requirement due to the complexity of their biosyntheses are readily converted by simple biosynthetic pathways to the remaining 11 ‘nonessential’ amino acids (alanine, arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine).
  • Higher animals do retain the ability to synthesize some of these amino acids, but the essential amino acids must be supplied from the diet in order for normal protein synthesis to occur.
  • Lysine is an important amino acid in the nutrition not only of humans, but also of monogastric animals such as poultry and swine.
  • Glutamate is most commonly used as a flavor additive (mono-sodium glutamate, MSG) and is widely used throughout the food industry, as are aspartate, phenylalanine, glycine, and cysteine. Glycine, L-methionine and tryptophan are all utilized in the pharmaceutical industry.
  • Glutamine, valine, leucine, isoleucine, histidine, arginine, proline, serine and alanine are of use in both the pharmaceutical and cosmetics industries. Threonine, tryptophan, and D/ L-methionine are common feed additives. (Leuchtenberger, W. (1996) Amino aids—technical production and use, p. 466-502 in Rehm et al. (eds.) Biotechnology vol. 6, chapter 14a, VCH: Weinheim).
  • amino acids have been found to be useful as precursors for the synthesis of synthetic amino acids and proteins, such as N-acetylcysteine, S-carboxymethyl-L-cysteine, (S)-5-hydroxytryptophan, and others described in Ulmann's Encyclopedia of Industrial Chemistry, vol. A2, p. 57-97, VCH: Weinheim, 1985.
  • cysteine and glycine are produced from serine; the former by the condensation of homocysteine with serine, and the latter by the transferal of the side-chain ⁇ -carbon atom to tetrahydrofolate, in a reaction catalyzed by serine transhydroxymethylase.
  • Phenylalanine, and tyrosine are synthesized from the glycolytic and pentose phosphate pathway precursors erythrose 4-phosphate and phosphoenolpyruvate in a 9-step biosynthetic pathway that differ only at the final two steps after synthesis of prephenate. Tryptophan is also produced from these two initial molecules, but its synthesis is an 11-step pathway.
  • Tyrosine may also be synthesized from phenylalanine, in a reaction catalyzed by phenylalanine hydroxylase.
  • Alanine, valine, and leucine are all biosynthetic products of pyruvate, the final product of glycolysis.
  • Aspartate is formed from oxaloacetate, an intermediate of the citric acid cycle.
  • Asparagine, methionine, threonine, and lysine are each produced by the conversion of aspartate.
  • Isoleucine is formed from threonine.
  • a complex 9-step pathway results in the production of histidine from 5-phosphoribosyl-1-pyrophosphate, an activated sugar.
  • Amino acids in excess of the protein synthesis needs of the cell cannot be stored, and are instead degraded to provide intermediates for the major metabolic pathways of the cell (for review see Stryer, L. Biochemistry 3 rd ed. Ch. 21 “Amino Acid Degradation and the Urea Cycle” p. 495-516 (1988)).
  • the cell is able to convert unwanted amino acids into useful metabolic intermediates, amino acid production is costly in terms of energy, precursor molecules, and the enzymes necessary to synthesize them.
  • amino acid biosynthesis is regulated by feedback inhibition, in which the presence of a particular amino acid serves to slow or entirely stop its own production (for overview of feedback mechanisms in amino acid biosynthetic pathways, see Stryer, L. Biochemistry, 3 rd ed. Ch. 24: “Biosynthesis of Amino Acids and Heme” p. 575-600 (1988)).
  • the output of any particular amino acid is limited by the amount of that amino acid present in the cell.
  • Vitamins, cofactors, and nutraceuticals comprise another group of molecules which the higher animals have lost the ability to synthesize and so must ingest, although they are readily synthesized by other organisms such as bacteria. These molecules are either bioactive substances themselves, or are precursors of biologically active substances which may serve as electron carriers or intermediates in a variety of metabolic pathways. Aside from their nutritive value, these compounds also have significant industrial value as coloring agents, antioxidants, and catalysts or other processing aids. (For an overview of the structure, activity, and industrial applications of these compounds, see, for example, Ullman's Encyclopedia of Industrial Chemistry, “Vitamins” vol. A27, p.
  • vitamin is art-recognized, and includes nutrients which are required by an organism for normal functioning, but which that organism cannot synthesize by itself.
  • the group of vitamins may encompass cofactors and nutraceutical compounds.
  • cofactor includes nonproteinaceous compounds required for a normal enzymatic activity to occur. Such compounds may be organic or inorganic; the cofactor molecules of the invention are preferably organic.
  • nutraceutical includes dietary supplements having health benefits in plants and animals, particularly humans. Examples of such molecules are vitamins, antioxidants, and also certain lipids (e.g., polyunsaturated fatty acids).
  • Thiamin (vitamin B 1 ) is produced by the chemical coupling of pyrimidine and thiazole moieties.
  • Riboflavin (vitamin B 2 ) is synthesized from guanosine-5′-triphosphate (GTP) and ribose-5′-phosphate. Riboflavin, in turn, is utilized for the synthesis of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).
  • vitamin B 6 The family of compounds collectively termed ‘vitamin B 6 ’ (e.g., pyridoxine, pyridoxamine, pyridoxa-5′-phosphate, and the commercially used pyridoxin hydrochloride) are all derivatives of the common structural unit, 5-hydroxy-6-methylpyridine.
  • Pantothenate pantothenic acid, (R)-(+)-N-(2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)- ⁇ -alanine
  • pantothenate biosynthesis consist of the ATP-driven condensation of ⁇ -alanine and pantoic acid.
  • pantothenate The enzymes responsible for the biosynthesis steps for the conversion to pantoic acid, to ⁇ -alanine and for the condensation to panthotenic acid are known.
  • the metabolically active form of pantothenate is Coenzyme A, for which the biosynthesis proceeds in 5 enzymatic steps.
  • Pantothenate, pyridoxal-5′-phosphate, cysteine and ATP are the precursors of Coenzyme A.
  • These enzymes not only catalyze the formation of panthothante, but also the production of (R)-pantoic acid, (R)-pantolacton, (R)-panthenol (provitamin B 5 ), pantetheine (and its derivatives) and coenzyme A.
  • Biotin biosynthesis from the precursor molecule pimeloyl-CoA in microorganisms has been studied in detail and several of the genes involved have been identified. Many of the corresponding proteins have been found to also be involved in Fe-cluster synthesis and are members of the nifS class of proteins.
  • Lipoic acid is derived from octanoic acid, and serves as a coenzyme in energy metabolism, where it becomes part of the pyruvate dehydrogenase complex and the ⁇ -ketoglutarate dehydrogenase complex.
  • the folates are a group of substances which are all derivatives of folic acid, which is turn is derived from L-glutamic acid, p-amino-benzoic acid and 6-methylpterin.
  • GTP guanosine-5′-triphosphate
  • L-glutamic acid L-glutamic acid
  • p-amino-benzoic acid The biosynthesis of folic acid and its derivatives, starting from the metabolism intermediates guanosine-5′-triphosphate (GTP), L-glutamic acid and p-amino-benzoic acid has been studied in detail in certain microorganisms.
  • Corrinoids such as the cobalamines and particularly vitamin B 12
  • porphyrines belong to a group of chemicals characterized by a tetrapyrole ring system.
  • the biosynthesis of vitamin B 12 is sufficiently complex that it has not yet been completely characterized, but many of the enzymes and substrates involved are now known.
  • Nicotinic acid (nicotinate), and nicotinamide are pyridine derivatives which are also termed ‘niacin’.
  • Niacin is the precursor of the important coenzymes NAD (nicotinamide adenine dinucleotide) and NADP (nicotinamide adenine dinucleotide phosphate) and their reduced forms.
  • purine and pyrimidine metabolism genes and their corresponding proteins are important targets for the therapy of tumor diseases and viral infections.
  • the language “purine” or “pyrimidine” includes the nitrogenous bases which are constituents of nucleic acids, co-enzymes, and nucleotides.
  • the term “nucleotide” includes the basic structural units of nucleic acid molecules, which are comprised of a nitrogenous base, a pentose sugar (in the case of RNA, the sugar is ribose; in the case of DNA, the sugar is D-deoxyribose), and phosphoric acid.
  • the language “nucleoside” includes molecules which serve as precursors to nucleotides, but which are lacking the phosphoric acid moiety that nucleotides possess.
  • nucleic acid molecules By inhibiting the biosynthesis of these molecules, or their mobilization to form nucleic acid molecules, it is possible to inhibit RNA and DNA synthesis; by inhibiting this activity in a fashion targeted to cancerous cells, the ability of tumor cells to divide and replicate may be inhibited. Additionally, there are nucleotides which do not form nucleic acid molecules, but rather serve as energy stores (i.e., AMP) or as coenzymes (i.e., FAD and NAD).
  • energy stores i.e., AMP
  • coenzymes i.e., FAD and NAD
  • purine and pyrimidine bases, nucleosides and nucleotides have other utilities: as intermediates in the biosynthesis of several fine chemicals (e.g., thiamine, S-adenosyl-methionine, folates, or riboflavin), as energy carriers for the cell (e.g., ATP or GTP), and for chemicals themselves, commonly used as flavor enhancers (e.g., IMP or GMP) or for several medicinal applications (see, for example, Kuninaka, A. (1996) Nucleotides and Related Compounds in Biotechnology vol. 6, Rehm et al., eds. VCH: Weinheim, p. 561-612).
  • enzymes involved in purine, pyrimidine, nucleoside, or nucleotide metabolism are increasingly serving as targets against which chemicals for crop protection, including fungicides, herbicides and insecticides, are developed.
  • Purine nucleotides are synthesized from ribose-5-phosphate, in a series of steps through the intermediate compound inosine-5′-phosphate (IMP), resulting in the production of guanosine-5′-monophosphate (GMP) or adenosine-5′-monophosphate (AMP), from which the triphosphate forms utilized as nucleotides are readily formed. These compounds are also utilized as energy stores, so their degradation provides energy for many different biochemical processes in the cell. Pyrimidine biosynthesis proceeds by the formation of uridine-5′-monophosphate (UMP) from ribose-5-phosphate. UMP, in turn, is converted to cytidine-5′-triphosphate (CTP).
  • IMP inosine-5′-phosphate
  • AMP adenosine-5′-monophosphate
  • deoxy- forms of all of these nucleotides are produced in a one step reduction reaction from the diphosphate ribose form of the nucleotide to the diphosphate deoxyribose form of the nucleotide. Upon phosphorylation, these molecules are able to participate in DNA synthesis.
  • Trehalose consists of two glucose molecules, bound in ⁇ , ⁇ -1,1 linkage. It is commonly used in the food industry as a sweetener, an additive for dried or frozen foods, and in beverages. However, it also has applications in the pharmaceutical, cosmetics and biotechnology industries (see, for example, Nishimoto et al., (1998) U.S. Pat. No. 5,759,610; Singer, M. A. and Lindquist, S. (1998) Trends Biotech. 16: 460-467; Paiva, C. L. A. and Panek, A. D. (1996) Biotech. Ann. Rev. 2: 293-314; and Shiosaka, M. (1997) J. Japan 172: 97-102). Trehalose is produced by enzymes from many microorganisms and is naturally released into the surrounding medium, from which it can be collected using methods known in the art.
  • Cellular membranes serve a variety of functions in a cell. First and foremost, a membrane differentiates the contents of a cell from the surrounding environment, thus giving integrity to the cell. Membranes may also serve as barriers to the influx of hazardous or unwanted compounds, and also to the efflux of desired compounds. Cellular membranes are by nature impervious to the unfacilitated diffusion of hydrophilic compounds such as proteins, water molecules and ions due to their structure: a bilayer of lipid molecules in which the polar head groups face outwards (towards the exterior and interior of the cell, respectively) and the nonpolar tails face inwards at the center of the bilayer, forming a hydrophobic core (for a general review of membrane structure and function, see Gennis, R. B.
  • This regulation, or ‘gating’ is generally specific to the molecules to be transported by the pore or channel, rendering these transmembrane constructs selectively permeable to a specific class of substrates; for example, a potassium channel is constructed such that only ions having a like charge and size to that of potassium may pass through.
  • Channel and pore proteins tend to have discrete hydrophobic and hydrophilic domains, such that the hydrophobic face of the protein may associate with the interior of the membrane while the hydrophilic face lines the interior of the channel, thus providing a sheltered hydrophilic environment through which the selected hydrophilic molecule may pass.
  • Many such pores/channels are known in the art, including those for potassium, calcium, sodium, and chloride ions.
  • This pore and channel-mediated system of facilitated diffusion is limited to very small molecules, such as ions, because pores or channels large enough to permit the passage of whole proteins by facilitated diffusion would be unable to prevent the passage of smaller hydrophilic molecules as well. Transport of molecules by this process is sometimes termed ‘facilitated diffusion’ since the driving force of a concentration gradient is required for the transport to occur. Permeases also permit facilitated diffusion of larger molecules, such as glucose or other sugars, into the cell when the concentration of these molecules on one side of the membrane is greater than that on the other (also called ‘uniport’).
  • these integral membrane proteins do not form open channels through the membrane, but rather bind to the target molecule at the surface of the membrane and then undergo a conformational shift such that the target molecule is released on the opposite side of the membrane.
  • symport or antiport couples the movement of two different molecules across the membrane (via permeases having two separate binding sites for the two different molecules); in symport, both molecules are transported in the same direction, while in antiport, one molecule is imported while the other is exported. This is possible energetically because one of the two molecules moves in accordance with a concentration gradient, and this energetically favorable event is permitted only upon concomitant movement of a desired compound against the prevailing concentration gradient.
  • Single molecules may be transported across the membrane against the concentration gradient in an energy-driven process, such as that utilized by the ABC transporters.
  • the transport protein located in the membrane has an ATP-binding cassette; upon binding of the target molecule, the ATP is converted to ADP+Pi, and the resulting release of energy is used to drive the movement of the target molecule to the opposite face of the membrane, facilitated by the transporter.
  • the transport protein located in the membrane has an ATP-binding cassette; upon binding of the target molecule, the ATP is converted to ADP+Pi, and the resulting release of energy is used to drive the movement of the target molecule to the opposite face of the membrane, facilitated by the transporter.
  • lipid molecules The synthesis of membranes is a well-characterized process involving a number of components, the most important of which are lipid molecules. Lipid synthesis may be divided into two parts: the synthesis of fatty acids and their attachment to sn-glycerol-3-phosphate, and the addition or modification of a polar head group. Typical lipids utilized in bacterial membranes include phospholipids, glycolipids, sphingolipids, and phosphoglycerides. Fatty acid synthesis begins with the conversion of acetyl CoA either to malonyl CoA by acetyl CoA carboxylase, or to acetyl-ACP by acetyltransacylase.
  • CFA cyclopropane fatty acids
  • lipid synthesis Another essential step in lipid synthesis is the transfer of fatty acids onto the polar head groups by, for example, glycerol-phosphate-acyltransferases.
  • the combination of various precursor molecules and biosynthetic enzymes results in the production of different fatty acid molecules, which has a profound effect on the composition of the membrane.
  • the present invention is based, at least in part, on the discovery of novel molecules, referred to herein as MCT nucleic acid and protein molecules, which control the production of cellular membranes in C. glutamicum and govern the movement of molecules across such membranes.
  • MCT molecules participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes.
  • the activity of the MCT molecules of the present invention to regulate membrane component production and membrane transport has an impact on the production of a desired fine chemical by this organism.
  • the MCT molecules of the invention are modulated in activity, such that the C.
  • glutamicum metabolic pathways which the MCT proteins of the invention regulate are modulated in yield, production, and/or efficiency of production and the transport of compounds through the membranes is altered in efficiency, which either directly or indirectly modulates the yield, production, and/or efficiency of production of a desired fine chemical by C. glutamicum.
  • MCT protein or “MCT polypeptide” includes proteins which participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes.
  • MCT proteins include those encoded by the MCT genes set forth in Table 1 and Appendix A.
  • MCT gene or “MCT nucleic acid sequence” include nucleic acid sequences encoding an MCT protein, which consist of a coding region and also corresponding untranslated 5′ and 3′ sequence regions. Examples of MCT genes include those set forth in Table 1.
  • production or “productivity” are art-recognized and include the concentration of the fermentation product (for example, the desired fine chemical) formed within a given time and a given fermentation volume (e.g., kg product per hour per liter).
  • efficiency of production includes the time required for a particular level of production to be achieved (for example, how long it takes for the cell to attain a particular rate of output of a fine chemical).
  • yield or “product/carbon yield” is art-recognized and includes the efficiency of the conversion of the carbon source into the product (i.e., fine chemical). This is generally written as, for example, kg product per kg carbon source.
  • biosynthesis or a “biosynthetic pathway” are art-recognized and include the synthesis of a compound, preferably an organic compound, by a cell from intermediate compounds in what may be a multistep and highly regulated process.
  • degradation or a “degradation pathway” are art-recognized and include the breakdown of a compound, preferably an organic compound, by a cell to degradation products (generally speaking, smaller or less complex molecules) in what may be a multistep and highly regulated process.
  • metabolism is art-recognized and includes the totality of the biochemical reactions that take place in an organism.
  • the metabolism of a particular compound e.g., the metabolism of an amino acid such as glycine
  • the MCT molecules of the invention are capable of modulating the production of a desired molecule, such as a fine chemical, in a microorganism such as C. glutamicum .
  • a desired molecule such as a fine chemical
  • C. glutamicum a microorganism
  • MCT proteins involved in the export of fine chemical molecules from the cell may be increased in number or activity such that greater quantities of these compounds are secreted to the extracellular medium, from which they are more readily recovered.
  • those MCT proteins involved in the import of nutrients necessary for the biosynthesis of one or more fine chemicals may be increased in number or activity such that these precursor, cofactor, or intermediate compounds are increased in concentration within the cell.
  • fatty acids and lipids themselves are desirable fine chemicals; by optimizing the activity or increasing the number of one or more MCT proteins of the invention which participate in the biosynthesis of these compounds, or by impairing the activity of one or more MCT proteins which are involved in the degradation of these compounds, it may be possible to increase the yield, production, and/or efficiency of production of fatty acid and lipid molecules from C. glutamicum.
  • MCT proteins of the invention involved in the export of waste products may be increased in number or activity such that the normal metabolic wastes of the cell (possibly increased in quantity due to the overproduction of the desired fine chemical) are efficiently exported before they are able to damage nucleotides and proteins within the cell (which would decrease the viability of the cell) or to interfere with fine chemical biosynthetic pathways (which would decrease the yield, production, or efficiency of production of the desired fine chemical).
  • the relatively large intracellular quantities of the desired fine chemical may in itself be toxic to the cell, so by increasing the activity or number of transporters able to export this compound from the cell, one may increase the viability of the cell in culture, in turn leading to a greater number of cells in the culture producing the desired fine chemical.
  • the MCT proteins of the invention may also be manipulated such that the relative amounts of different lipid and fatty acid molecules are produced. This may have a profound effect on the lipid composition of the membrane of the cell. Since each type of lipid has different physical properties, an alteration in the lipid composition of a membrane may significantly alter membrane fluidity. Changes in membrane fluidity can impact the transport of molecules across the membrane, as well as the integrity of the cell, both of which have a profound effect on the production of fine chemicals from C. glutamicum in large-scale fermentative culture.
  • the isolated nucleic acid sequences of the invention are contained within the genome of a Corynebacterium glutamicum strain available through the American Type Culture Collection, given designation ATCC 13032.
  • the nucleotide sequence of the isolated C. glutamicum MCT DNAs and the predicted amino acid sequences of the C. glutamicum MCT proteins are shown in Appendices A and B, respectively. Computational analyses were performed which classified and/or identified these nucleotide sequences as sequences which encode proteins involved in the metabolism of cellular membrane components or proteins involved in the transport of compounds across such membranes.
  • the present invention also pertains to proteins which have an amino acid sequence which is substantially homologous to an amino acid sequence of Appendix B.
  • a protein which has an amino acid sequence which is substantially homologous to a selected amino acid sequence is least about 50% homologous to the selected amino acid sequence, e.g., the entire selected amino acid sequence.
  • a protein which has an amino acid sequence which is substantially homologous to a selected amino acid sequence can also be least about 50-60%, preferably at least about 60-70%, and more preferably at least about 70-80%, 80-90%, or 90-95%, and most preferably at least about 96%, 97%, 98%, 99% or more homologous to the selected amino acid sequence.
  • the MCT protein or a biologically active portion or fragment thereof of the invention can participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes, or have one or more of the activities set forth in Table 1.
  • nucleic acid molecules that encode MCT polypeptides or biologically active portions thereof, as well as nucleic acid fragments sufficient for use as hybridization probes or primers for the identification or amplification of MCT-encoding nucleic acid (e.g., MCT DNA).
  • nucleic acid molecule is intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs.
  • nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA.
  • isolated nucleic acid molecule is one which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid.
  • an “isolated” nucleic acid is free of sequences which naturally flank the nucleic acid (i.e., sequences located at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived.
  • the isolated MCT nucleic acid molecule can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived (e.g, a C. glutamicum cell).
  • an “isolated” nucleic acid molecule, such as a DNA molecule can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or chemical precursors or other chemicals when chemically synthesized.
  • a nucleic acid molecule of the present invention e.g., a nucleic acid molecule having a nucleotide sequence of Appendix A, or a portion thereof, can be isolated using standard molecular biology techniques and the sequence information provided herein.
  • a C. glutamicum MCT DNA can be isolated from a C. glutamicum library using all or portion of one of the sequences of Appendix A as a hybridization probe and standard hybridization techniques (e.g., as described in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2 nd, ed., Cold Spring Harbor Laboratory , Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989).
  • nucleic acid molecule encompassing all or a portion of one of the sequences of Appendix A can be isolated by the polymerase chain reaction using oligonucleotide primers designed based upon this sequence (e.g., a nucleic acid molecule encompassing all or a portion of one of the sequences of Appendix A can be isolated by the polymerase chain reaction using oligonucleotide primers designed based upon this same sequence of Appendix A).
  • mRNA can be isolated from normal endothelial cells (e.g., by the guanidinium-thiocyanate extraction procedure of Chirgwin et al.
  • DNA can be prepared using reverse transcriptase (e.g., Moloney MLV reverse transcriptase, available from Gibco/BRL, Bethesda, Md.; or AMV reverse transcriptase, available from Seikagaku America, Inc., St. Louis, Fla.).
  • reverse transcriptase e.g., Moloney MLV reverse transcriptase, available from Gibco/BRL, Bethesda, Md.; or AMV reverse transcriptase, available from Seikagaku America, Inc., St. Russia, Fla.
  • Synthetic oligonucleotide primers for polymerase chain reaction amplification can be designed based upon one of the nucleotide sequences shown in Appendix A.
  • a nucleic acid of the invention can be amplified using cDNA or, alternatively, genomic DNA, as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques.
  • oligonucleotides corresponding to an MCT nucleotide sequence can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.
  • an isolated nucleic acid molecule of the invention comprises one of the nucleotide sequences shown in Appendix A.
  • the sequences of Appendix A correspond to the Corynebacterium glutamicum MCT DNAs of the invention.
  • This DNA comprises sequences encoding MCT proteins (i.e., the “coding region”, indicated in each sequence in Appendix A), as well as 5′ untranslated sequences and 3′ untranslated sequences, also indicated in Appendix A.
  • the nucleic acid molecule can comprise only the coding region of any of the sequences in Appendix A.
  • each of the sequences set forth in Appendix A has an identifying RXA, RXN, RXS, or RXC number having the designation “RXA”, “RXN”, “RXS” or “RXC” followed by 5 digits (i.e., RXA02099, RXN03097, RXS00148, or RXC01748).
  • Each of these sequences comprises up to three parts: a 5′ upstream region, a coding region, and a downstream region. Each of these three regions is identified by the same RXA, RXN, RXS, or RXC designation to eliminate confusion.
  • the amino acid sequences in Appendix B designated RXA02099, RXN03097, RXS00148, and RXC01748 are translations of the coding region of the nucleotide sequences of nucleic acid molecules RXA02099, RXN03097, RXS00148, and RXC01748, respectively, in Appendix A.
  • Each of the RXA, RXN, RXS, and RXC nucleotide and amino acid sequences of the invention has also been assigned a SEQ ID NO, as indicated in Table 1.
  • the nucleotide sequence of RXA00104 is SEQ ID NO:5
  • the amino acid sequence of RXA00104 is SEQ ID NO:6.
  • F-designated genes include those genes set forth in Table 1 which have an ‘F’ in front of the RXA, RXN, RXS, or RXC designation.
  • SEQ ID NO:11 designated, as indicated on Table 1, as “F RXA02581”, is an F-designated gene, as are SEQ ID NOs: 31, 33, and 43 (designated on Table 1 as “F RXA02487”, “F RXA02490”, and “F RXA02809”, respectively).
  • the nucleic acid molecules of the present invention are not intended to include those compiled in Table 2.
  • a sequence for this gene was published in Wehrmann, A., et al. (1998) J. Bacteriol. 180(12): 3159-3165.
  • the sequence obtained by the inventors of the present application is significantly longer than the published version. It is believed that the published version relied on an incorrect start codon, and thus represents only a fragment of the actual coding region.
  • an isolated nucleic acid molecule of the invention comprises a nucleic acid molecule which is a complement of one of the nucleotide sequences shown in Appendix A, or a portion thereof.
  • a nucleic acid molecule which is complementary to one of the nucleotide sequences shown in Appendix A is one which is sufficiently complementary to one of the nucleotide sequences shown in Appendix A such that it can hybridize to one of the nucleotide sequences shown in Appendix A, thereby forming a stable duplex.
  • an isolated nucleic acid molecule of the invention comprises a nucleotide sequence which is at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more homologous to a nucleotide sequence shown in Appendix A, or a portion thereof.
  • an isolated nucleic acid molecule of the invention comprises a nucleotide sequence which hybridizes, e.g., hybridizes under stringent conditions, to one of the nucleotide sequences shown in Appendix A, or a portion thereof.
  • the nucleic acid molecule of the invention can comprise only a portion of the coding region of one of the sequences in Appendix A, for example a fragment which can be used as a probe or primer or a fragment encoding a biologically active portion of an MCT protein.
  • the nucleotide sequences determined from the cloning of the MCT genes from C. glutamicum allows for the generation of probes and primers designed for use in identifying and/or cloning MCT homologues in other cell types and organisms, as well as MCT homologues from other Corynebacteria or related species.
  • the probe/primer typically comprises substantially purified oligonucleotide.
  • the oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12, preferably about 25, more preferably about 40, 50 or 75 consecutive nucleotides of a sense strand of one of the sequences set forth in Appendix A, an anti-sense sequence of one of the sequences set forth in Appendix A, or naturally occurring mutants thereof.
  • Primers based on a nucleotide sequence of Appendix A can be used in PCR reactions to clone MCT homologues. Probes based on the MCT nucleotide sequences can be used to detect transcripts or genomic sequences encoding the same or homologous proteins.
  • the probe further comprises a label group attached thereto, e.g. the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor.
  • the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor.
  • Such probes can be used as a part of a diagnostic test kit for identifying cells which misexpress an MCT protein, such as by measuring a level of an MCT-encoding nucleic acid in a sample of cells, e.g., detecting MCT mRNA levels or determining whether a genomic MCT gene has been mutated or deleted.
  • the nucleic acid molecule of the invention encodes a protein or portion thereof which includes an amino acid sequence which is sufficiently homologous to an amino acid sequence of Appendix B such that the protein or portion thereof maintains the ability to participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes.
  • the language “sufficiently homologous” refers to proteins or portions thereof which have amino acid sequences which include a minimum number of identical or equivalent (e.g., an amino acid residue which has a similar side chain as an amino acid residue in one of the sequences of Appendix B) amino acid residues to an amino acid sequence of Appendix B such that the protein or portion thereof is able to participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes. Protein members of such membrane component metabolic pathways or membrane transport systems, as described herein, may play a role in the production and secretion of one or more fine chemicals. Examples of such activities are also described herein. Thus, “the function of an MCT protein” contributes either directly or indirectly to the yield, production, and/or efficiency of production of one or more fine chemicals. Examples of MCT protein activities are set forth in Table 1.
  • the protein is at least about 50-60%, preferably at least about 60-70%, and more preferably at least about 70-80%, 80-90%, 90-95%, and most preferably at least about 96%, 97%, 98%, 99% or more homologous to an entire amino acid sequence of Appendix B.
  • portions of proteins encoded by the MCT nucleic acid molecules of the invention are preferably biologically active portions of one of the MCT proteins.
  • biologically active portion of an MCT protein is intended to include a portion, e.g., a domain/motif, of an MCT protein that participates in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes, or has an activity as set forth in Table 1.
  • an assay of enzymatic activity may be performed. Such assay methods are well known to those of ordinary skill in the art, as detailed in Example 8 of the Exemplification.
  • Additional nucleic acid fragments encoding biologically active portions of an MCT protein can be prepared by isolating a portion of one of the sequences in Appendix B, expressing the encoded portion of the MCT protein or peptide (e.g., by recombinant expression in vitro) and assessing the activity of the encoded portion of the MCT protein or peptide.
  • the invention further encompasses nucleic acid molecules that differ from one of the nucleotide sequences shown in Appendix A (and portions thereof) due to degeneracy of the genetic code and thus encode the same MCT protein as that encoded by the nucleotide sequences shown in Appendix A.
  • an isolated nucleic acid molecule of the invention has a nucleotide sequence encoding a protein having an amino acid sequence shown in Appendix B.
  • the nucleic acid molecule of the invention encodes a full length C. glutamicum protein which is substantially homologous to an amino acid sequence of Appendix B (encoded by an open reading frame shown in Appendix A).
  • sequences of the invention are not meant to include the sequences of the prior art, such as those Genbank sequences set forth in Tables 2 or 4 which were available prior to the present invention.
  • the invention includes nucleotide and amino acid sequences having a percent identity to a nucleotide or amino acid sequence of the invention which is greater than that of a sequence of the prior art (e.g., a Genbank sequence (or the protein encoded by such a sequence) set forth in Tables 2 or 4).
  • the invention includes a nucleotide sequence which is greater than and/or at least 38% identical to the nucleotide sequence designated RXA01420 (SEQ ID NO:7), a nucleotide sequence which is greater than and/or at least 43% identical to the nucleotide sequence designated RXA00104 (SEQ ID NO:5), and a nucleotide sequence which is greater than and/or at least 45% identical to the nucleotide sequence designated RXA02173 (SEQ ID NO:25).
  • nucleic acid and amino acid sequences having percent identities greater than the lower threshold so calculated are also encompassed by the invention.
  • DNA sequence polymorphisms that lead to changes in the amino acid sequences of MCT proteins may exist within a population (e.g., the C. glutamicum population).
  • Such genetic polymorphism in the MCT gene may exist among individuals within a population due to natural variation.
  • the terms “gene” and “recombinant gene” refer to nucleic acid molecules comprising an open reading frame encoding an MCT protein, preferably a C. glutamicum MCT protein.
  • Such natural variations can typically result in 1-5% variance in the nucleotide sequence of the MCT gene. Any and all such nucleotide variations and resulting amino acid polymorphisms in MCT that are the result of natural variation and that do not alter the functional activity of MCT proteins are intended to be within the scope of the invention.
  • Nucleic acid molecules corresponding to natural variants and non- C. glutamicum homologues of the C. glutamicum MCT DNA of the invention can be isolated based on their homology to the C. glutamicum MCT nucleic acid disclosed herein using the C. glutamicum DNA, or a portion thereof, as a hybridization probe according to standard hybridization techniques under stringent hybridization conditions. Accordingly, in another embodiment, an isolated nucleic acid molecule of the invention is at least 15 nucleotides in length and hybridizes under stringent conditions to the nucleic acid molecule comprising a nucleotide sequence of Appendix A. In other embodiments, the nucleic acid is at least 30, 50, 100, 250 or more nucleotides in length.
  • hybridizes under stringent conditions is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 60% homologous to each other typically remain hybridized to each other.
  • the conditions are such that sequences at least about 65%, more preferably at least about 70%, and even more preferably at least about 75% or more homologous to each other typically remain hybridized to each other.
  • stringent conditions are known to those of ordinary skill in the art and can be found in Current Protocols in Molecular Biology , John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.
  • a preferred, non-limiting example of stringent hybridization conditions are hybridization in 6 ⁇ sodium chloride/sodium citrate (SSC) at about 45° C., followed by one or more washes in 0.2 ⁇ SSC, 0.1% SDS at 50-65° C.
  • an isolated nucleic acid molecule of the invention that hybridizes under stringent conditions to a sequence of Appendix A corresponds to a naturally-occurring nucleic acid molecule.
  • a “naturally-occurring” nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural protein).
  • the nucleic acid encodes a natural C. glutamicum MCT protein.
  • nucleotide sequence of Appendix A thereby leading to changes in the amino acid sequence of the encoded MCT protein, without altering the functional ability of the MCT protein.
  • nucleotide substitutions leading to amino acid substitutions at “non-essential” amino acid residues can be made in a sequence of Appendix A.
  • a “non-essential” amino acid residue is a residue that can be altered from the wild-type sequence of one of the MCT proteins (Appendix B) without altering the activity of said MCT protein, whereas an “essential” amino acid residue is required for MCT protein activity.
  • Other amino acid residues, however, may not be essential for activity and thus are likely to be amenable to alteration without altering MCT activity.
  • nucleic acid molecules encoding MCT proteins that contain changes in amino acid residues that are not essential for MCT activity.
  • MCT proteins differ in amino acid sequence from a sequence contained in Appendix B yet retain at least one of the MCT activities described herein.
  • the isolated nucleic acid molecule comprises a nucleotide sequence encoding a protein, wherein the protein comprises an amino acid sequence at least about 50% homologous to an amino acid sequence of Appendix B and is capable of participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes, or has one or more activities set forth in Table 1.
  • the protein encoded by the nucleic acid molecule is at least about 50-60% homologous to one of the sequences in Appendix B, more preferably at least about 60-70% homologous to one of the sequences in Appendix B, even more preferably at least about 70-80%, 80-90%, 90-95% homologous to one of the sequences in Appendix B, and most preferably at least about 96%, 97%, 98%, or 99% homologous to one of the sequences in Appendix B.
  • sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of one protein or nucleic acid for optimal alignment with the other protein or nucleic acid).
  • amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared.
  • a position in one sequence e.g., one of the sequences of Appendix B
  • the molecules are homologous at that position (i.e., as used herein amino acid or nucleic acid “homology” is equivalent to amino acid or nucleic acid “identity”).
  • An isolated nucleic acid molecule encoding an MCT protein homologous to a protein sequence of Appendix B can be created by introducing one or more nucleotide substitutions, additions or deletions into a nucleotide sequence of Appendix A such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced into one of the sequences of Appendix A by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more predicted non-essential amino acid residues. A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain.
  • Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).
  • basic side chains e.g., lysine, arginine, histidine
  • acidic side chains e.g.
  • a predicted nonessential amino acid residue in an MCT protein is preferably replaced with another amino acid residue from the same side chain family.
  • mutations can be introduced randomly along all or part of an MCT coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for an MCT activity described herein to identify mutants that retain MCT activity.
  • the encoded protein can be expressed recombinantly and the activity of the protein can be determined using, for example, assays described herein (see Example 8 of the Exemplification).
  • an antisense nucleic acid comprises a nucleotide sequence which is complementary to a “sense” nucleic acid encoding a protein, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. Accordingly, an antisense nucleic acid can hydrogen bond to a sense nucleic acid.
  • the antisense nucleic acid can be complementary to an entire MCT coding strand, or to only a portion thereof.
  • an antisense nucleic acid molecule is antisense to a “coding region” of the coding strand of a nucleotide sequence encoding an MCT protein.
  • coding region refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues (e.g., the entire coding region of SEQ ID NO:5 (RXA00104 in Appendix A) comprises nucleotides 1 to 756).
  • the antisense nucleic acid molecule is antisense to a “noncoding region” of the coding strand of a nucleotide sequence encoding MCT.
  • noncoding region refers to 5′ and 3′ sequences which flank the coding region that are not translated into amino acids (i.e., also referred to as 5′ and 3′ untranslated regions).
  • antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick base pairing.
  • the antisense nucleic acid molecule can be complementary to the entire coding region of MCT mRNA, but more preferably is an oligonucleotide which is antisense to only a portion of the coding or noncoding region of MCT mRNA.
  • the antisense oligonucleotide can be complementary to the region surrounding the translation start site of MCT mRNA.
  • An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length.
  • An antisense nucleic acid of the invention can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art.
  • an antisense nucleic acid e.g., an antisense oligonucleotide
  • an antisense nucleic acid e.g., an antisense oligonucleotide
  • modified nucleotides which can be used to generate the antisense nucleic acid include 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5′-methoxycar
  • the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).
  • the antisense nucleic acid molecules of the invention are typically administered to a cell or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding an MCT protein to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation.
  • the hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove of the double helix.
  • the antisense molecule can be modified such that it specifically binds to a receptor or an antigen expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecule to a peptide or an antibody which binds to a cell surface receptor or antigen.
  • the antisense nucleic acid molecule can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of the antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong prokaryotic, viral, or eukaryotic promoter are preferred.
  • the antisense nucleic acid molecule of the invention is an ⁇ -anomeric nucleic acid molecule.
  • An ⁇ -anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual ⁇ -units, the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids. Res. 15:6625-6641).
  • the antisense nucleic acid molecule can also comprise a 2′-o-methylribonucleotide (Inoue et al. (1987) Nucleic Acids Res. 15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215:327-330).
  • an antisense nucleic acid of the invention is a ribozyme.
  • Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region.
  • ribozymes e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to catalytically cleave MCT mRNA transcripts to thereby inhibit translation of MCT mRNA.
  • a ribozyme having specificity for an MCT-encoding nucleic acid can be designed based upon the nucleotide sequence of an MCT DNA disclosed herein (i.e., SEQ ID NO. 5 (RXA00104) in Appendix A)).
  • SEQ ID NO. 5 RXA00104
  • a derivative of a Tetrahymena L- 19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in an MCT-encoding mRNA. See, e.g., Cech et al. U.S. Pat. No. 4,987,071 and Cech et al. U.S. Pat. No. 5,116,742.
  • MCT mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel, D. and Szostak, J. W. (1993) Science 261:1411-1418.
  • MCT gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of an MCT nucleotide sequence (e.g., an MCT promoter and/or enhancers) to form triple helical structures that prevent transcription of an MCT gene in target cells.
  • an MCT nucleotide sequence e.g., an MCT promoter and/or enhancers
  • vectors preferably expression vectors, containing a nucleic acid encoding an MCT protein (or a portion thereof).
  • vector refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked.
  • plasmid refers to a circular double stranded DNA loop into which additional DNA segments can be ligated.
  • viral vector Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome.
  • Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors).
  • vectors e.g., non-episomal mammalian vectors
  • Other vectors are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome.
  • certain vectors are capable of directing the expression of genes to which they are operatively linked.
  • Such vectors are referred to herein as “expression vectors”.
  • expression vectors of utility in recombinant DNA techniques are often in the form of plasmids.
  • plasmid and vector can be used interchangeably as the plasmid is the most commonly used form of vector.
  • the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.
  • the recombinant expression vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed.
  • “operably linked” is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell).
  • regulatory sequence is intended to include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cell and those which direct expression of the nucleotide sequence only in certain host cells.
  • Preferred regulatory sequences are, for example, promoters such as cos-, tac-, trp-, tet-, trp-tet-, lpp-, lac-, lpp-lac-, lacI q -, T7-, T5-, T3-, gal-, trc-, ara-, SP6-, amy, SPO2, ⁇ -P R -or ⁇ P L , which are used preferably in bacteria.
  • promoters such as cos-, tac-, trp-, tet-, trp-tet-, lpp-, lac-, lpp-lac-, lacI q -, T7-, T5-, T3-, gal-, trc-, ara-, SP6-, amy, SPO2, ⁇ -P R -or ⁇ P L , which are used preferably in bacteria.
  • Additional regulatory sequences are, for example, promoters from yeasts and fungi, such as ADC1, MF ⁇ , AC, P-60, CYC1, GAPDH, TEF, rp28, ADH, promoters from plants such as CaMV/35S, SSU, OCS, lib4, usp, STLS1, B33, nos or ubiquitin- or phaseolin-promoters. It is also possible to use artificial promoters. It will be appreciated by one of ordinary skill in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc.
  • the expression vectors of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein (e.g., MCT proteins, mutant forms of MCT proteins, fusion proteins, etc.).
  • the recombinant expression vectors of the invention can be designed for expression of MCT proteins in prokaryotic or eukaryotic cells.
  • MCT genes can be expressed in bacterial cells such as C. glutamicum , insect cells (using baculovirus expression vectors), yeast and other fungal cells (see Romanos, M. A. et al. (1992) “Foreign gene expression in yeast: a review”, Yeast 8: 423-488; van den Hondel, C.A.M.J.J. et al. (1991) “Heterologous gene expression in filamentous fungi” in: More Gene Manipulations in Fungi, J. W. Bennet & L. L. Lasure, eds., p.
  • telomeres Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990).
  • the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.
  • Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein but also to the C-terminus or fused within suitable regions in the proteins.
  • Such fusion vectors typically serve three purposes: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification.
  • a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein.
  • enzymes, and their cognate recognition sequences include Factor Xa, thrombin and enterokinase.
  • Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D. B. and Johnson, K. S. (1988) Gene 67:31-40), pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein.
  • GST glutathione S-transferase
  • maltose E binding protein or protein A, respectively
  • the coding sequence of the MCT protein is cloned into a pGEX expression vector to create a vector encoding a fusion protein comprising, from the N-terminus to the C-terminus, GST-thrombin cleavage site-X protein.
  • the fusion protein can be purified by affinity chromatography using glutathione-agarose resin. Recombinant MCT protein unfused to GST can be recovered by cleavage of the fusion protein with thrombin.
  • suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al., (1988) Gene 69:301-315) pLG338, pACYC184, pBR322, pUC18, pUC19, pKC30, pRep4, pHS1, pHS2, pPLc236, pMBL24, pLG200, pUR290, pIN-III113-B1, ⁇ gt11, pBdC1, and pET 11d (Studier et al, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 60-89 ; and Pouwels et al., eds.
  • Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-lac fusion promoter.
  • Target gene expression from the pET 11d vector relies on transcription from a T7 gn10-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident ⁇ prophage harboring a T7 gn1 gene under the transcriptional control of the lacUV 5 promoter. For transformation of other varieties of bacteria, appropriate vectors may be selected.
  • the plasmids pIJ101, pIJ364, pIJ702 and pIJ361 are known to be useful in transforming Streptomyces, while plasmids pUB110, pC194, or pBD214 are suited for transformation of Bacillus species.
  • plasmids pUB110, pC194, or pBD214 are suited for transformation of Bacillus species.
  • plasmids of use in the transfer of genetic information into Corynebacterium include pHM1519, pBL1, pSA77, or pAJ667 (Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: N.Y. IBSN 0 444 904018).
  • One strategy to maximize recombinant protein expression is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 119-128).
  • Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in the bacterium chosen for expression, such as C. glutamicum (Wada et al. (1992) Nucleic Acids Res. 20:2111-2118).
  • Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.
  • the MCT protein expression vector is a yeast expression vector.
  • yeast expression vectors for expression in yeast S. cerevisiae include pYepSec1 (Baldari, et al., (1987) Embo J. 6:229-234), 2 ⁇ , pAG-1, Yep6, Yep13, pEMBLYe23, pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al., (1987) Gene 54:113-123), and pYES2 (Invitrogen Corporation, San Diego, Calif.).
  • Vectors and methods for the construction of vectors appropriate for use in other fungi, such as the filamentous fungi include those detailed in: van den Hondel, C.A.M.J.J. & Punt, P. J. (1991) “Gene transfer systems and vector development for filamentous fungi, in: Applied Molecular Genetics of Fungi, J. F. Peberdy, et al., eds., p. 1-28, Cambridge University Press: Cambridge, and Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: N.Y. (IBSN 0 444 904018).
  • the MCT proteins of the invention can be expressed in insect cells using baculovirus expression vectors.
  • Baculovirus vectors available for expression of proteins in cultured insect cells include the pAc series (Smith et al. (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers (1989) Virology 170:31-39).
  • the MCT proteins of the invention may be expressed in unicellular plant cells (such as algae) or in plant cells from higher plants (e.g., the spermatophytes, such as crop plants).
  • plant expression vectors include those detailed in: Becker, D., Kemper, E., Schell, J. and Masterson, R. (1992) “New plant binary vectors with selectable markers located proximal to the left border”, Plant Mol. Biol. 20: 1195-1197; and Bevan, M. W. (1984) “Binary Agrobacterium vectors for plant transformation”, Nuc. Acid Res.
  • a nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector.
  • mammalian expression vectors include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC (Kaufman et al. (1987) EMBO J. 6:187-195).
  • the expression vector's control functions are often provided by viral regulatory elements.
  • commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40.
  • suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2 nd, ed., Cold Spring Harbor Laboratory , Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.
  • the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid).
  • tissue-specific regulatory elements are known in the art.
  • suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43:235-275), in particular promoters of T cell receptors (Winoto and Baltimore (1989) EMBO J.
  • promoters are also encompassed, for example the murine hox promoters (Kessel and Gruss (1990) Science 249:374-379) and the ⁇ -fetoprotein promoter (Campes and Tilghman (1989) Genes Dev. 3:537-546).
  • the invention further provides a recombinant expression vector comprising a DNA molecule of the invention cloned into the expression vector in an antisense orientation. That is, the DNA molecule is operatively linked to a regulatory sequence in a manner which allows for expression (by transcription of the DNA molecule) of an RNA molecule which is antisense to MCT mRNA. Regulatory sequences operatively linked to a nucleic acid cloned in the antisense orientation can be chosen which direct the continuous expression of the antisense RNA molecule in a variety of cell types, for instance viral promoters and/or enhancers, or regulatory sequences can be chosen which direct constitutive, tissue specific or cell type specific expression of antisense RNA.
  • the antisense expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which antisense nucleic acids are produced under the control of a high efficiency regulatory region, the activity of which can be determined by the cell type into which the vector is introduced.
  • a high efficiency regulatory region the activity of which can be determined by the cell type into which the vector is introduced.
  • host cell and “recombinant host cell” are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
  • a host cell can be any prokaryotic or eukaryotic cell.
  • an MCT protein can be expressed in bacterial cells such as C. glutamicum , insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells).
  • suitable host cells are known to one of ordinary skill in the art.
  • Microorganisms related to Corynebacterium glutamicum which may be conveniently used as host cells for the nucleic acid and protein molecules of the invention are set forth in Table 3.
  • Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques.
  • transformation and “transfection”, “conjugation” and “transduction” are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., linear DNA or RNA (e.g., a linearized vector or a gene construct alone without a vector) or nucleic acid in the form of a vector (e.g., a plasmid, phage, phasmid, phagemid, transposon or other DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, natural competence, chemical-mediated transfer, or electroporation.
  • foreign nucleic acid e.g., linear DNA or RNA (e.g., a linearized vector or a gene construct alone without a vector) or nucleic acid in the form of a vector (e.
  • Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. ( Molecular Cloning: A Laboratory Manual. 2 nd, ed., Cold Spring Harbor Laboratory , Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989), and other laboratory manuals.
  • a gene that encodes a selectable marker (e.g., resistance to antibiotics) is generally introduced into the host cells along with the gene of interest.
  • selectable markers include those which confer resistance to drugs, such as G418, hygromycin and methotrexate.
  • Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding an MCT protein or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by, for example, drug selection (e.g., cells that have incorporated the selectable marker gene will survive, while the other cells die).
  • a vector which contains at least a portion of an MCT gene into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the MCT gene.
  • this MCT gene is a Corynebacterium glutamicum MCT gene, but it can be a homologue from a related bacterium or even from a mammalian, yeast, or insect source.
  • the vector is designed such that, upon homologous recombination, the endogenous MCT gene is functionally disrupted (i.e., no longer encodes a functional protein; also referred to as a “knock out” vector).
  • the vector can be designed such that, upon homologous recombination, the endogenous MCT gene is mutated or otherwise altered but still encodes functional protein (e.g., the upstream regulatory region can be altered to thereby alter the expression of the endogenous MCT protein).
  • the altered portion of the MCT gene is flanked at its 5′ and 3′ ends by additional nucleic acid of the MCT gene to allow for homologous recombination to occur between the exogenous MCT gene carried by the vector and an endogenous MCT gene in a microorganism.
  • the additional flanking MCT nucleic acid is of sufficient length for successful homologous recombination with the endogenous gene.
  • flanking DNA both at the 5′ and 3′ ends
  • flanking DNA both at the 5′ and 3′ ends
  • the vector is introduced into a microorganism (e.g., by electroporation) and cells in which the introduced MCT gene has homologously recombined with the endogenous MCT gene are selected, using art-known techniques.
  • recombinant microorganisms can be produced which contain selected systems which allow for regulated expression of the introduced gene.
  • inclusion of an MCT gene on a vector placing it under control of the lac operon permits expression of the MCT gene only in the presence of IPTG.
  • Such regulatory systems are well known in the art.
  • an endogenous MCT gene in a host cell is disrupted (e.g., by homologous recombination or other genetic means known in the art) such that expression of its protein product does not occur.
  • an endogenous or introduced MCT gene in a host cell has been altered by one or more point mutations, deletions, or inversions, but still encodes a functional MCT protein.
  • one or more of the regulatory regions (e.g., a promoter, repressor, or inducer) of an MCT gene in a microorganism has been altered (e.g., by deletion, truncation, inversion, or point mutation) such that the expression of the MCT gene is modulated.
  • a host cell of the invention such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i.e., express) an MCT protein.
  • the invention further provides methods for producing MCT proteins using the host cells of the invention.
  • the method comprises culturing the host cell of invention (into which a recombinant expression vector encoding an MCT protein has been introduced, or into which genome has been introduced a gene encoding a wild-type or altered MCT protein) in a suitable medium until MCT protein is produced.
  • the method further comprises isolating MCT proteins from the medium or the host cell.
  • Another aspect of the invention pertains to isolated MCT proteins, and biologically active portions thereof.
  • An “isolated” or “purified” protein or biologically active portion thereof is substantially free of cellular material when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized.
  • the language “substantially free of cellular material” includes preparations of MCT protein in which the protein is separated from cellular components of the cells in which it is naturally or recombinantly produced.
  • the language “substantially free of cellular material” includes preparations of MCT protein having less than about 30% (by dry weight) of non-MCT protein (also referred to herein as a “contaminating protein”), more preferably less than about 20% of non-MCT protein, still more preferably less than about 10% of non-MCT protein, and most preferably less than about 5% non-MCT protein.
  • non-MCT protein also referred to herein as a “contaminating protein”
  • contaminating protein also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the protein preparation.
  • the language “substantially free of chemical precursors or other chemicals” includes preparations of MCT protein in which the protein is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein.
  • the language “substantially free of chemical precursors or other chemicals” includes preparations of MCT protein having less than about 30% (by dry weight) of chemical precursors or non-MCT chemicals, more preferably less than about 20% chemical precursors or non-MCT chemicals, still more preferably less than about 10% chemical precursors or non-MCT chemicals, and most preferably less than about 5% chemical precursors or non-MCT chemicals.
  • isolated proteins or biologically active portions thereof lack contaminating proteins from the same organism from which the MCT protein is derived. Typically, such proteins are produced by recombinant expression of, for example, a C. glutamicum MCT protein in a microorganism such as C. glutamicum.
  • an isolated MCT protein or a portion thereof of the invention can participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes, or has one or more of the activities set forth in Table 1.
  • the protein or portion thereof comprises an amino acid sequence which is sufficiently homologous to an amino acid sequence of Appendix B such that the protein or portion thereof maintains the ability participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes.
  • the portion of the protein is preferably a biologically active portion as described herein.
  • an MCT protein of the invention has an amino acid sequence shown in Appendix B.
  • the MCT protein has an amino acid sequence which is encoded by a nucleotide sequence which hybridizes, e.g., hybridizes under stringent conditions, to a nucleotide sequence of Appendix A.
  • the MCT protein has an amino acid sequence which is encoded by a nucleotide sequence that is at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%
  • Ranges and identity values intermediate to the above-recited values, are also intended to be encompassed by the present invention.
  • ranges of identity values using a combination of any of the above values recited as upper and/or lower limits are intended to be included.
  • the preferred MCT proteins of the present invention also preferably possess at least one of the MCT activities described herein.
  • a preferred MCT protein of the present invention includes an amino acid sequence encoded by a nucleotide sequence which hybridizes, e.g., hybridizes under stringent conditions, to a nucleotide sequence of Appendix A, and which can participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum , or in the transport of molecules across these membranes, or which has one or more of the activities set forth in Table 1.
  • the MCT protein is substantially homologous to an amino acid sequence of Appendix B and retains the functional activity of the protein of one of the sequences of Appendix B yet differs in amino acid sequence due to natural variation or mutagenesis, as described in detail in subsection I above.
  • the MCT protein is a protein which comprises an amino acid sequence which is at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more homologous to an entire amino acid sequence of Appendix B and which has at least one of the MCT activities described herein.
  • Ranges and identity values intermediate to the above-recited values are also intended to be encompassed by the present invention.
  • ranges of identity values using a combination of any of the above values recited as upper and/or lower limits are intended to be included.
  • the invention pertains to a full length C. glutamicum protein which is substantially homologous to an entire amino acid sequence of Appendix B.
  • Biologically active portions of an MCT protein include peptides comprising amino acid sequences derived from the amino acid sequence of an MCT protein, e.g., the an amino acid sequence shown in Appendix B or the amino acid sequence of a protein homologous to an MCT protein, which include fewer amino acids than a full length MCT protein or the full length protein which is homologous to an MCT protein, and exhibit at least one activity of an MCT protein.
  • biologically active portions peptides, e.g., peptides which are, for example, 5, 10, 15, 20, 30, 35, 36, 37, 38, 39, 40, 50, 100 or more amino acids in length
  • biologically active portions in which other regions of the protein are deleted, can be prepared by recombinant techniques and evaluated for one or more of the activities described herein.
  • the biologically active portions of an MCT protein include one or more selected domains/motifs or portions thereof having biological activity.
  • MCT proteins are preferably produced by recombinant DNA techniques.
  • a nucleic acid molecule encoding the protein is cloned into an expression vector (as described above), the expression vector is introduced into a host cell (as described above) and the MCT protein is expressed in the host cell.
  • the MCT protein can then be isolated from the cells by an appropriate purification scheme using standard protein purification techniques.
  • an MCT protein, polypeptide, or peptide can be synthesized chemically using standard peptide synthesis techniques.
  • native MCT protein can be isolated from cells (e.g., endothelial cells), for example using an anti-MCT antibody, which can be produced by standard techniques utilizing an MCT protein or fragment thereof of this invention.
  • an MCT “chimeric protein” or “fusion protein” comprises an MCT polypeptide operatively linked to a non-MCT polypeptide.
  • An “MCT polypeptide” refers to a polypeptide having an amino acid sequence corresponding to an MCT protein
  • a “non-MCT polypeptide” refers to a polypeptide having an amino acid sequence corresponding to a protein which is not substantially homologous to the MCT protein, e.g., a protein which is different from the MCT protein and which is derived from the same or a different organism.
  • the term “operatively linked” is intended to indicate that the MCT polypeptide and the non-MCT polypeptide are fused in-frame to each other.
  • the non-MCT polypeptide can be fused to the N-terminus or C-terminus of the MCT polypeptide.
  • the fusion protein is a GST-MCT fusion protein in which the MCT sequences are fused to the C-terminus of the GST sequences.
  • Such fusion proteins can facilitate the purification of recombinant MCT proteins.
  • the fusion protein is an MCT protein containing a heterologous signal sequence at its N-terminus. In certain host cells (e.g., mammalian host cells), expression and/or secretion of an MCT protein can be increased through use of a heterologous signal sequence.
  • an MCT chimeric or fusion protein of the invention is produced by standard recombinant DNA techniques.
  • DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, for example by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation.
  • the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers.
  • PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, for example, Current Protocols in Molecular Biology , eds. Ausubel et al. John Wiley & Sons: 1992).
  • anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence
  • many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide).
  • An MCT-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the MCT protein.
  • Homologues of the MCT protein can be generated by mutagenesis, e.g., discrete point mutation or truncation of the MCT protein.
  • the term “homologue” refers to a variant form of the MCT protein which acts as an agonist or antagonist of the activity of the MCT protein.
  • An agonist of the MCT protein can retain substantially the same, or a subset, of the biological activities of the MCT protein.
  • An antagonist of the MCT protein can inhibit one or more of the activities of the naturally occurring form of the MCT protein, by, for example, competitively binding to a downstream or upstream member of the cell membrane component metabolic cascade which includes the MCT protein, or by binding to an MCT protein which mediates transport of compounds across such membranes, thereby preventing translocation from taking place.
  • homologues of the MCT protein can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants, of the MCT protein for MCT protein agonist or antagonist activity.
  • a variegated library of MCT variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library.
  • a variegated library of MCT variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential MCT sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display) containing the set of MCT sequences therein.
  • a degenerate set of potential MCT sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display) containing the set of MCT sequences therein.
  • fusion proteins e.g., for phage display
  • degenerate set of genes allows for the provision, in one mixture, of all of the sequences encoding the desired set of potential MCT sequences.
  • Methods for synthesizing degenerate oligonucleotides are known in the art (see, e.g., Narang, S. A. (1983) Tetrahedron 39:3; Itakura et al. (1984) Annu. Rev. Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. 11:477.
  • libraries of fragments of the MCT protein coding can be used to generate a variegated population of MCT fragments for screening and subsequent selection of homologues of an MCT protein.
  • a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of an MCT coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double stranded DNA which can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with S1 nuclease, and ligating the resulting fragment library into an expression vector.
  • an expression library can be derived which encodes N-terminal, C-terminal and internal fragments of various sizes of the MCT protein.
  • REM Recursive ensemble mutagenesis
  • cell based assays can be exploited to analyze a variegated MCT library, using methods well known in the art.
  • nucleic acid molecules, proteins, protein homologues, fusion proteins, primers, vectors, and host cells described herein can be used in one or more of the following methods: identification of C. glutamicum and related organisms; mapping of genomes of organisms related to C. glutamicum ; identification and localization of C. glutamicum sequences of interest; evolutionary studies; determination of MCT protein regions required for function; modulation of an MCT protein activity; modulation of the metabolism of one or more cell membrane components; modulation of the transmembrane transport of one or more compounds; and modulation of cellular production of a desired compound, such as a fine chemical.
  • the MCT nucleic acid molecules of the invention have a variety of uses. First, they may be used to identify an organism as being Corynebacterium glutamicum or a close relative thereof. Also, they may be used to identify the presence of C. glutamicum or a relative thereof in a mixed population of microorganisms.
  • the invention provides the nucleic acid sequences of a number of C. glutamicum genes; by probing the extracted genomic DNA of a culture of a unique or mixed population of microorganisms under stringent conditions with a probe spanning a region of a C. glutamicum gene which is unique to this organism, one can ascertain whether this organism is present.
  • Corynebacterium glutamicum itself is nonpathogenic, it is related to pathogenic species, such as Corynebacterium diphtheriae.
  • Corynebacterium diphtheriae is the causative agent of diphtheria, a rapidly developing, acute, febrile infection which involves both local and systemic pathology.
  • a local lesion develops in the upper respiratory tract and involves necrotic injury to epithelial cells; the bacilli secrete toxin which is disseminated through this lesion to distal susceptible tissues of the body.
  • Degenerative changes brought about by the inhibition of protein synthesis in these tissues which include heart, muscle, peripheral nerves, adrenals, kidneys, liver and spleen, result in the systemic pathology of the disease.
  • the invention provides a method of identifying the presence or activity of Cornyebacterium diphtheriae in a subject. This method includes detection of one or more of the nucleic acid or amino acid sequences of the invention (e.g., the sequences set forth in Appendix A or Appendix B) in a subject, thereby detecting the presence or activity of Corynebacterium diphtheriae in the subject.
  • diphtheriae are related bacteria, and many of the nucleic acid and protein molecules in C. glutamicum are homologous to C. diphtheriae nucleic acid and protein molecules, and can therefore be used to detect C. diphtheriae in a subject.
  • the nucleic acid and protein molecules of the invention may also serve as markers for specific regions of the genome. This has utility not only in the mapping of the genome, but also for functional studies of C. glutamicum proteins. For example, to identify the region of the genome to which a particular C. glutamicum DNA-binding protein binds, the C. glutamicum genome could be digested, and the fragments incubated with the DNA-binding protein. Those which bind the protein may be additionally probed with the nucleic acid molecules of the invention, preferably with readily detectable labels; binding of such a nucleic acid molecule to the genome fragment enables the localization of the fragment to the genome map of C.
  • nucleic acid molecules of the invention may be sufficiently homologous to the sequences of related species such that these nucleic acid molecules may serve as markers for the construction of a genomic map in related bacteria, such as Brevibacterium lactofermentum.
  • the MCT nucleic acid molecules of the invention are also useful for evolutionary and protein structural studies.
  • the metabolic and transport processes in which the molecules of the invention participate are utilized by a wide variety of prokaryotic and eukaryotic cells; by comparing the sequences of the nucleic acid molecules of the present invention to those encoding similar enzymes from other organisms, the evolutionary relatedness of the organisms can be assessed. Similarly, such a comparison permits an assessment of which regions of the sequence are conserved and which are not, which may aid in determining those regions of the protein which are essential for the functioning of the enzyme. This type of determination is of value for protein engineering studies and may give an indication of what the protein can tolerate in terms of mutagenesis without losing function.
  • Manipulation of the MCT nucleic acid molecules of the invention may result in the production of MCT proteins having functional differences from the wild-type MCT proteins. These proteins may be improved in efficiency or activity, may be present in greater numbers in the cell than is usual, or may be decreased in efficiency or activity.
  • the invention provides methods for screening molecules which modulate the activity of an MCT protein, either by interacting with the protein itself or a substrate or binding partner of the MCT protein, or by modulating the transcription or translation of an MCT nucleic acid molecule of the invention.
  • a microorganism expressing one or more MCT proteins of the invention is contacted with one or more test compounds, and the effect of each test compound on the activity or level of expression of the MCT protein is assessed.
  • fatty acids and lipids are themselves desirable fine chemicals, so by optimizing the activity or increasing the number of one or more MCT proteins of the invention which participate in the biosynthesis of these compounds, or by impairing the activity of one or more MCT proteins which are involved in the degradation of these compounds, it may be possible to increase the yield, production, and/or efficiency of production of fatty acid and lipid molecules from C. glutamicum.
  • the engineering of one or more MCT genes of the invention may also result in MCT proteins having altered activities which indirectly impact the production of one or more desired fine chemicals from C. glutamicum .
  • the normal biochemical processes of metabolism result in the production of a variety of waste products (e.g., hydrogen peroxide and other reactive oxygen species) which may actively interfere with these same metabolic processes (for example, peroxynitrite is known to nitrate tyrosine side chains, thereby inactivating some enzymes having tyrosine in the active site (Groves, J. T. (1999) Curr. Opin. Chem. Biol. 3(2): 226-235). While these waste products are typically excreted, the C.
  • glutamicum strains utilized for large-scale fermentative production are optimized for the overproduction of one or more fine chemicals, and thus may produce more waste products than is typical for a wild-type C. glutamicum.
  • By optimizing the activity of one or more MCT proteins of the invention which are involved in the export of waste molecules it may be possible to improve the viability of the cell and to maintain efficient metabolic activity.
  • the presence of high intracellular levels of the desired fine chemical may actually be toxic to the cell, so by increasing the ability of the cell to secrete these compounds, one may improve the viability of the cell.
  • the MCT proteins of the invention may be manipulated such that the relative amounts of various lipid and fatty acid molecules produced are altered. This may have a profound effect on the lipid composition of the membrane of the cell. Since each type of lipid has different physical properties, an alteration in the lipid composition of a membrane may significantly alter membrane fluidity. Changes in membrane fluidity can impact the transport of molecules across the membrane, which, as previously explicated, may modify the export of waste products or the produced fine chemical or the import of necessary nutrients. Such membrane fluidity changes may also profoundly affect the integrity of the cell; cells with relatively weaker membranes are more vulnerable in the large-scale fermentor environment to mechanical stresses which may damage or kill the cell.
  • the nucleic acid and protein molecules of the invention may be utilized to generate C. glutamicum or related strains of bacteria expressing mutated MCT nucleic acid and protein molecules such that the yield, production, and/or efficiency of production of a desired compound is improved.
  • This desired compound may be any natural product of C. glutamicum , which includes the final products of biosynthesis pathways and intermediates of naturally-occurring metabolic pathways, as well as molecules which do not naturally occur in the metabolism of C. glutamicum , but which are produced by a C. glutamicum strain of the invention.
  • a culture of Corynebacterium glutamicum (ATCC 13032) was grown overnight at 30° C. with vigorous shaking in BHI medium (Difco). The cells were harvested by centrifugation, the supernatant was discarded and the cells were resuspended in 5 ml buffer-I (5% of the original volume of the culture—all indicated volumes have been calculated for 100 ml of culture volume).
  • composition of buffer-I 140.34 g/l sucrose, 2.46 g/l MgSO 4 ⁇ 7H 2 O, 10 ml/l KH 2 PO 4 solution (100 g/l, adjusted to pH 6.7 with KOH), 50 ml/l M12 concentrate (10 g/l (NH 4 ) 2 SO 4 , 1 g/l NaCl, 2 g/l MgSO 4 ⁇ 7 H 2 O, 0.2 g/l CaCl 2 , 0.5 g/l yeast extract (Difco), 10 ml/l trace-elements-mix (200 mg/l FeSO 4 ⁇ H 2 O, 10 mg/l ZnSO 4 ⁇ 7 H 2 O, 3 mg/l MnCl 2 ⁇ 4 H 2 O, 30 mg/l H 3 BO 3 20 mg/l CoCl 2 ⁇ 6 H 2 O, 1 mg/l NiCl 2 ⁇ 6 H 2 O, 3 mg/l Na 2 MoO 4 ⁇ 2 H 2 O, 500 mg/l complexing agent
  • Lysozyme was added to the suspension to a final concentration of 2.5 mg/ml. After an approximately 4 h incubation at 37° C., the cell wall was degraded and the resulting protoplasts are harvested by centrifugation. The pellet was washed once with 5 ml buffer-1 and once with 5 ml TE-buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8). The pellet was resuspended in 4 ml TE-buffer and 0.5 ml SDS solution (10%) and 0.5 ml NaCl solution (5 M) are added. After adding of proteinase K to a final concentration of 200 ⁇ g/ml, the suspension is incubated for ca. 18 h at 37° C.
  • the DNA was purified by extraction with phenol, phenol-chloroform-isoamylalcohol and chloroform-isoamylalcohol using standard procedures. Then, the DNA was precipitated by adding 1/50 volume of 3 M sodium acetate and 2 volumes of ethanol, followed by a 30 min incubation at ⁇ 20° C. and a 30 min centrifugation at 12,000 rpm in a high speed centrifuge using a SS34 rotor (Sorvall). The DNA was dissolved in 1 ml TE-buffer containing 20 ⁇ g/ml RNaseA and dialysed at 4° C. against 1000 ml TE-buffer for at least 3 hours. During this time, the buffer was exchanged 3 times.
  • plasmids pBR322 Suddens, J. G. (1979) Proc. Natl. Acad. Sci. USA, 75:3737-3741); pACYC177 (Change & Cohen (1978) J. Bacteriol 134:1141-1156), plasmids of the pBS series (pBSSK+, pBSSK ⁇ and others; Stratagene, LaJolla, USA), or cosmids as SuperCos1 (Stratagene, LaJolla, USA) or Lorist6 (Gibson, T. J., Rosenthal A. and Waterson, R. H. (1987) Gene 53:283-286.
  • Gene libraries specifically for use in C. glutamicum may be constructed using plasmid pSL109 (Lee, H.-S. and A. J. Sinskey (1994) J. Microbiol. Biotechnol. 4: 256-263).
  • Genomic libraries as described in Example 2 were used for DNA sequencing according to standard methods, in particular by the chain termination method using ABI377 sequencing machines (see e.g., Fleischman, R. D. et al. (1995) “Whole-genome Random Sequencing and Assembly of Haemophilus Influenzae Rd., Science, 269:496-512). Sequencing primers with the following nucleotide sequences were used: 5′-GGAAACAGTATGACCATG-3′ or 5′-GTAAAACGACGGCCAGT-3′.
  • In vivo mutagenesis of Corynebacterium glutamicum can be performed by passage of plasmid (or other vector) DNA through E. coli or other microorganisms (e.g. Bacillus spp. or yeasts such as Saccharomyces cerevisiae ) which are impaired in their capabilities to maintain the integrity of their genetic information.
  • E. coli or other microorganisms e.g. Bacillus spp. or yeasts such as Saccharomyces cerevisiae
  • Typical mutator strains have mutations in the genes for the DNA repair system (e.g., mutHLS, mutD, mutT, etc.; for reference, see Rupp, W. D. (1996) DNA repair mechanisms, in: Escherichia coli and Salmonella , p. 2277-2294, ASM: Washington.)
  • Such strains are well known to those of ordinary skill in the art. The use of such strains is illustrated, for example, in Greener, A. and Call
  • Corynebacterium and Brevibacterium species contain endogenous plasmids (as e.g., pHM1519 or pBL1) which replicate autonomously (for review see, e.g., Martin, J. F. et al. (1987) Biotechnology, 5:137-146).
  • Shuttle vectors for Escherichia coli and Corynebacterium glutamicum can be readily constructed by using standard vectors for E. coli (Sambrook, J. et al. (1989), “Molecular Cloning: A Laboratory Manual”, Cold Spring Harbor Laboratory Press or Ausubel, F. M. et al.
  • origins of replication are preferably taken from endogenous plasmids isolated from Corynebacterium and Brevibacterium species.
  • transformation markers are genes for kanamycin resistance (such as those derived from the Tn5 or Tn903 transposons) or chloramphenicol (Winnacker, E. L. (1987) “From Genes to Clones—Introduction to Gene Technology, VCH, Weinheim).
  • kanamycin resistance such as those derived from the Tn5 or Tn903 transposons
  • chloramphenicol Winnacker, E. L. (1987) “From Genes to Clones—Introduction to Gene Technology, VCH, Weinheim.
  • glutamicum which can be used for several purposes, including gene over-expression (for reference, see e.g., Yoshihama, M. et al. (1985) J. Bacteriol. 162:591-597, Martin J. F. et al. (1987) Biotechnology, 5:137-146 and Eikmanns, B. J. et al. (1991) Gene, 102:93-98).
  • E. coli glutamicum to E. coli by preparing plasmid DNA from C. glutamicum (using standard methods well-known in the art) and transforming it into E. coli .
  • This transformation step can be performed using standard methods, but it is advantageous to use an Mcr-deficient E. coli strain, such as NM522 (Gough & Murray (1983) J. Mol. Biol. 166:1-19).
  • Genes may be overexpressed in C. glutamicum strains using plasmids which comprise pCG1 (U.S. Pat. No. 4,617,267) or fragments thereof, and optionally the gene for kanamycin resistance from TN903 (Grindley, N. D. and Joyce, C. M. (1980) Proc. Natl. Acad. Sci. USA 77(12): 7176-7180).
  • genes may be overexpressed in C. glutamicum strains using plasmid pSL109 (Lee, H.-S. and A. J. Sinskey (1994) J. Microbiol. Biotechnol. 4: 256-263).
  • Genomic integration in C. glutamicum or other Corynebacterium or Brevibacterium species may be accomplished by well-known methods, such as homologous recombination with genomic region(s), restriction endonuclease mediated integration (REMI) (see, e.g., DE Patent 19823834), or through the use of transposons.
  • REMI restriction endonuclease mediated integration
  • a gene of interest by modifying the regulatory regions (e.g., a promoter, a repressor, and/or an enhancer) by sequence modification, insertion, or deletion using site-directed methods (such as homologous recombination) or methods based on random events (such as transposon mutagenesis or REMI).
  • Site-directed methods such as homologous recombination
  • random events such as transposon mutagenesis or REMI.
  • Nucleic acid sequences which function as transcriptional terminators may also be inserted 3′ to the coding region of one or more genes of the invention; such terminators are well-known in the art and are described, for example, in Winnacker, E. L. (1987) From Genes to Clones—Introduction to Gene Technology. VCH: Weinheim.
  • Observations of the activity of a mutated protein in a transformed host cell rely on the fact that the mutant protein is expressed in a similar fashion and in a similar quantity to that of the wild-type protein.
  • a useful method to ascertain the level of transcription of the mutant gene is to perform a Northern blot (for reference see, for example, Ausubel et al.
  • RNA of a culture of the organism is extracted, run on gel, transferred to a stable matrix and incubated with this probe, the binding and quantity of binding of the probe indicates the presence and also the quantity of mRNA for this gene. This information is evidence of the degree of transcription of the mutant gene.
  • a detectable tag usually radioactive or chemiluminescent
  • Corynebacteria are cultured in synthetic or natural growth media.
  • a number of different growth media for Corynebacteria are both well-known and readily available (Lieb et al. (1989) Appl. Microbiol. Biotechnol., 32:205-210; von der Osten et al. (1998) Biotechnology Letters, 11:11-16; Patent DE 4,120,867; Liebl (1992) “The Genus Corynebacterium, in: The Procaryotes, Volume II, Balows, A. et al., eds. Springer-Verlag).
  • These media consist of one or more carbon sources, nitrogen sources, inorganic salts, vitamins and trace elements.
  • Preferred carbon sources are sugars, such as mono-, di-, or polysaccharides.
  • sugars such as mono-, di-, or polysaccharides.
  • glucose, fructose, mannose, galactose, ribose, sorbose, ribulose, lactose, maltose, sucrose, raffinose, starch or cellulose serve as very good carbon sources.
  • sugar to the media via complex compounds such as molasses or other by-products from sugar refinement.
  • Other possible carbon sources are alcohols and organic acids, such as methanol, ethanol, acetic acid or lactic acid.
  • Nitrogen sources are usually organic or inorganic nitrogen compounds, or materials which contain these compounds.
  • Exemplary nitrogen sources include ammonia gas or ammonia salts, such as NH 4 Cl or (NH 4 ) 2 SO 4 , NH 4 OH, nitrates, urea, amino acids or complex nitrogen sources like corn steep liquor, soy bean flour, soy bean protein, yeast extract, meat extract and others.
  • Inorganic salt compounds which may be included in the media include the chloride-, phosphorous- or sulfate- salts of calcium, magnesium, sodium, cobalt, molybdenum, potassium, manganese, zinc, copper and iron.
  • Chelating compounds can be added to the medium to keep the metal ions in solution.
  • Particularly useful chelating compounds include dihydroxyphenols, like catechol or protocatechuate, or organic acids, such as citric acid. It is typical for the media to also contain other growth factors, such as vitamins or growth promoters, examples of which include biotin, riboflavin, thiamin, folic acid, nicotinic acid, pantothenate and pyridoxin.
  • the exact composition of the media compounds depends strongly on the immediate experiment and is individually decided for each specific case. Information about media optimization is available in the textbook “Applied Microbiol. Physiology, A Practical Approach (eds. P. M. Rhodes, P. F. Stanbury, IRL Press (1997) pp. 53-73, ISBN 0 19 963577 3). It is also possible to select growth media from commercial suppliers, like standard 1 (Merck) or BHI (grain heart infusion, DIFCO) or others.
  • All medium components are sterilized, either by heat (20 minutes at 1.5 bar and 121° C.) or by sterile filtration.
  • the components can either be sterilized together or, if necessary, separately. All media components can be present at the beginning of growth, or they can optionally be added continuously or batchwise.
  • the temperature should be in a range between 15° C. and 45° C.
  • the temperature can be kept constant or can be altered during the experiment.
  • the pH of the medium should be in the range of 5 to 8.5, preferably around 7.0, and can be maintained by the addition of buffers to the media.
  • An exemplary buffer for this purpose is a potassium phosphate buffer.
  • Synthetic buffers such as MOPS, HEPES, ACES and others can alternatively or simultaneously be used. It is also possible to maintain a constant culture pH through the addition of NaOH or NH 4 OH during growth. If complex medium components such as yeast extract are utilized, the necessity for additional buffers may be reduced, due to the fact that many complex compounds have high buffer capacities. If a fermentor is utilized for culturing the micro-organisms, the pH can also be controlled using gaseous ammonia.
  • the incubation time is usually in a range from several hours to several days. This time is selected in order to permit the maximal amount of product to accumulate in the broth.
  • the disclosed growth experiments can be carried out in a variety of vessels, such as microtiter plates, glass tubes, glass flasks or glass or metal fermentors of different sizes.
  • the microorganisms should be cultured in microtiter plates, glass tubes or shake flasks, either with or without baffles.
  • 100 ml shake flasks are used, filled with 10% (by volume) of the required growth medium.
  • the flasks should be shaken on a rotary shaker (amplitude 25 mm) using a speed-range of 100-300 rpm. Evaporation losses can be diminished by the maintenance of a humid atmosphere; alternatively, a mathematical correction for evaporation losses should be performed.
  • the medium is inoculated to an OD 600 of 0.5-1.5 using cells grown on agar plates, such as CM plates (10 g/l glucose, 2,5 g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeast extract, 5 g/l meat extract, 22 g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeast extract, 5 g/l meat extract, 22 g/l agar, pH 6.8 with 2M NaOH) that had been incubated at 30° C. Inoculation of the media is accomplished by either introduction of a saline suspension of C. glutamicum cells from CM plates or addition of a liquid preculture of this bacterium.
  • CM plates 10 g/l glucose, 2,5 g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeast extract, 5 g/l
  • DNA band-shift assays also called gel retardation assays
  • reporter gene assays such as that described in Kolmar, H. et al. (1995) EMBO J. 14: 3895-3904 and references cited therein. Reporter gene test systems are well known and established for applications in both pro- and eukaryotic cells, using enzymes such as beta-galactosidase, green fluorescent protein, and several others.
  • membrane-transport proteins The determination of activity of membrane-transport proteins can be performed according to techniques such as those described in Gennis, R. B. (1989) “Pores, Channels and Transporters”, in Biomembranes, Molecular Structure and Function, Springer: Heidelberg, p. 85-137; 199-234; and 270-322.
  • the effect of the genetic modification in C. glutamicum on production of a desired compound can be assessed by growing the modified microorganism under suitable conditions (such as those described above) and analyzing the medium and/or the cellular component for increased production of the desired product (i.e., an amino acid).
  • suitable conditions such as those described above
  • Such analysis techniques are well known to one of ordinary skill in the art, and include spectroscopy, thin layer chromatography, staining methods of various kinds, enzymatic and microbiological methods, and analytical chromatography such as high performance liquid chromatography (see, for example, Ullman, Encyclopedia of Industrial Chemistry, vol. A2, p. 89-90 and p. 443-613, VCH: Weinheim (1985); Fallon, A.
  • Recovery of the desired product from the C. glutamicum cells or supernatant of the above-described culture can be performed by various methods well known in the art. If the desired product is not secreted from the cells, the cells can be harvested from the culture by low-speed centrifugation, the cells can be lysed by standard techniques, such as mechanical force or sonication. The cellular debris is removed by centrifligation, and the supernatant fraction containing the soluble proteins is retained for further purification of the desired compound. If the product is secreted from the C. glutamicum cells, then the cells are removed from the culture by low-speed centrifugation, and the supernate fraction is retained for further purification.
  • the supernatant fraction from either purification method is subjected to chromatography with a suitable resin, in which the desired molecule is either retained on a chromatography resin while many of the impurities in the sample are not, or where the impurities are retained by the resin while the sample is not.
  • chromatography steps may be repeated as necessary, using the same or different chromatography resins.
  • One of ordinary skill in the art would be well-versed in the selection of appropriate chromatography resins and in their most efficacious application for a particular molecule to be purified.
  • the purified product may be concentrated by filtration or ultrafiltration, and stored at a temperature at which the stability of the product is maximized.
  • the identity and purity of the isolated compounds may be assessed by techniques standard in the art. These include high-performance liquid chromatography (HPLC), spectroscopic methods, staining methods, thin layer chromatography, NIRS, enzymatic assay, or microbiologically. Such analysis methods are reviewed in: Patek et al. (1994) Appl. Environ. Microbiol. 60: 133-140; Malakhova et al. (1996) Biotekhnologiya 11: 27-32; and Schmidt et al. (1998) Bioprocess Engineer. 19: 67-70. Ulmann's Encyclopedia of Industrial Chemistry, (1996) vol. A27, VCH: Weinheim, p. 89-90, p. 521-540, p. 540-547, p.
  • Gapped BLAST can be utilized as described in Altschul et al., (1997) Nucleic Acids Res. 25(17):3389-3402.
  • Another example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Meyers and Miller ((1988) Comput. Appl. Biosci. 4: 11-17). Such an algorithm is incorporated into the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM 120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. Additional algorithms for sequence analysis are known in the art, and include ADVANCE and ADAM. described in Torelli and Robotti (1994) Comput. Appl. Biosci. 10:3-5; and FASTA, described in Pearson and Lipman (1988) P.N.A.S. 85:2444-8.
  • the percent homology between two amino acid sequences can also be accomplished using the GAP program in the GCG software package (available at http://www.gcg.com), using either a Blosum 62 matrix or a PAM250 matrix, and a gap weight of 12, 10, 8, 6, or 4 and a length weight of 2, 3, or 4.
  • the percent homology between two nucleic acid sequences can be accomplished using the GAP program in the GCG software package, using standard parameters, such as a gap weight of 50 and a length weight of 3.
  • a comparative analysis of the gene sequences of the invention with those present in Genbank has been performed using techniques known in the art (see, e.g., Bexevanis and Ouellette, eds. (1998) Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. John Wiley and Sons: New York).
  • the gene sequences of the invention were compared to genes present in Genbank in a three-step process.
  • a BLASTN analysis e.g., a local alignment analysis
  • a subsequent FASTA search (e.g., a combined local and global alignment analysis, in which limited regions of the sequences are aligned) was performed on these 500 hits.
  • Each gene sequence of the invention was subsequently globally aligned to each of the top three FASTA hits, using the GAP program in the GCG software package (using standard parameters).
  • the length of the sequences extracted from Genbank were adjusted to the length of the query sequences by methods well-known in the art. The results of this analysis are set forth in Table 4.
  • sequences of the invention may additionally be used in the construction and application of DNA microarrays (the design, methodology, and uses of DNA arrays are well known in the art, and are described, for example, in Schena, M. et al. (1995) Science 270: 467-470; Wodicka, L. et al. (1997) Nature Biotechnology 15: 1359-1367; DeSaizieu, A. et al. (1998) Nature Biotechnology 16: 45-48; and DeRisi, J. L. et al. (1997) Science 278: 680-686).
  • DNA microarrays are solid or flexible supports consisting of nitrocellulose, nylon, glass, silicone, or other materials. Nucleic acid molecules may be attached to the surface in an ordered manner. After appropriate labeling, other nucleic acids or nucleic acid mixtures can be hybridized to the immobilized nucleic acid molecules, and the label may be used to monitor and measure the individual signal intensities of the hybridized molecules at defined regions. This methodology allows the simultaneous quantification of the relative or absolute amount of all or selected nucleic acids in the applied nucleic acid sample or mixture. DNA microarrays, therefore, permit an analysis of the expression of multiple (as many as 6800 or more) nucleic acids in parallel (see, e.g., Schena, M. (1996) BioEssays 18(5): 427-431).
  • sequences of the invention may be used to design oligonucleotide primers which are able to amplify defined regions of one or more C. glutamicum genes by a nucleic acid amplification reaction such as the polymerase chain reaction.
  • a nucleic acid amplification reaction such as the polymerase chain reaction.
  • the choice and design of the 5′ or 3′ oligonucleotide primers or of appropriate linkers allows the covalent attachment of the resulting PCR products to the surface of a support medium described above (and also described, for example, Schena, M. et al. (1995) Science 270: 467-470).
  • Nucleic acid microarrays may also be constructed by in situ oligonucleotide synthesis as described by Wodicka, L. et al. (1997) Nature Biotechnology 15: 1359-1367.
  • Photolithographic methods precisely defined regions of the matrix are exposed to light.
  • Protective groups which are photolabile are thereby activated and undergo nucleotide addition, whereas regions that are masked from light do not undergo any modification.
  • Subsequent cycles of protection and light activation permit the synthesis of different oligonucleotides at defined positions.
  • Small, defined regions of the genes of the invention may be synthesized on microarrays by solid phase oligonucleotide synthesis.
  • nucleic acid molecules of the invention present in a sample or mixture of nucleotides may be hybridized to the microarrays.
  • These nucleic acid molecules can be labeled according to standard methods.
  • nucleic acid molecules e.g., mRNA molecules or DNA molecules
  • Hybridization of labeled nucleic acids to microarrays is described (e.g., in Schena, M. et al. (1995) supra; Wodicka, L. et al. (1997), supra; and DeSaizieu A. et al. (1998), supra).
  • Radioactive labels can be detected, for example, as described in Schena, M. et al. (1995) supra) and fluorescent labels may be detected, for example, by the method of Shalon et al. (1996) Genome Research 6: 639-645).
  • sequences of the invention permits comparative analyses of different strains of C. glutamicum or other Corynebacteria .
  • studies of inter-strain variations based on individual transcript profiles and the identification of genes that are important for specific and/or desired strain properties such as pathogenicity, productivity and stress tolerance are facilitated by nucleic acid array methodologies.
  • comparisons of the profile of expression of genes of the invention during the course of a fermentation reaction are possible using nucleic acid array technology.
  • Protein populations of interest include, but are not limited to, the total protein population of C. glutamicum (e.g., in comparison with the protein populations of other organisms), those proteins which are active under specific environmental or metabolic conditions (e.g., during fermentation, at high or low temperature, or at high or low pH), or those proteins which are active during specific phases of growth and development.
  • Protein populations can be analyzed by various well-known techniques, such as gel electrophoresis.
  • Cellular proteins may be obtained, for example, by lysis or extraction, and may be separated from one another using a variety of electrophoretic techniques.
  • Sodium dodecyl sulfate polyacrylamide gel electrophoresis SDS-PAGE
  • Isoelectric focusing polyacrylamide gel electrophoresis Isoelectric focusing polyacrylamide gel electrophoresis (IEF-PAGE) separates proteins by their isoelectric point (which reflects not only the amino acid sequence but also posttranslational modifications of the protein).
  • Another, more preferred method of protein analysis is the consecutive combination of both IEF-PAGE and SDS-PAGE, known as 2-D-gel electrophoresis (described, for example, in Hermann et al. (1998) Electrophoresis 19: 3217-3221; Fountoulakis et al. (1998) Electrophoresis 19: 1193-1202; Langen et al. (1997) Electrophoresis 18: 1184-1192; Antelmann et al. (1997) Electrophoresis 18: 1451-1463).
  • Other separation techniques may also be utilized for protein separation, such as capillary gel electrophoresis; such techniques are well known in the art.
  • Proteins separated by these methodologies can be visualized by standard techniques, such as by staining or labeling. Suitable stains are known in the art, and include Coomassie Brilliant Blue, silver stain, or fluorescent dyes such as Sypro Ruby (Molecular Probes).
  • Suitable stains include Coomassie Brilliant Blue, silver stain, or fluorescent dyes such as Sypro Ruby (Molecular Probes).
  • the inclusion of radioactively labeled amino acids or other protein precursors e.g., 35 S-methionine, 35 S-cysteine, 14 C-labelled amino acids, 15 N-amino acids, 15 NO 3 or 15 NH 4 + or 13 C-labelled amino acids
  • fluorescent labels may be employed. These labeled proteins can be extracted, isolated and separated according to the previously described techniques.
  • Proteins visualized by these techniques can be further analyzed by measuring the amount of dye or label used.
  • the amount of a given protein can be determined quantitatively using, for example, optical methods and can be compared to the amount of other proteins in the same gel or in other gels. Comparisons of proteins on gels can be made, for example, by optical comparison, by spectroscopy, by image scanning and analysis of gels, or through the use of photographic films and screens. Such techniques are well-known in the art.
  • N- and/or C-terminal amino acid sequencing such as Edman degradation
  • mass spectrometry in particular MALDI or ESI techniques (see, e.g., Langen et al. (1997) Electrophoresis 18: 1184-1192)
  • MALDI or ESI techniques see, e.g., Langen et al. (1997) Electrophoresis 18: 1184-1192)
  • the information obtained by these methods can be used to compare patterns of protein presence, activity, or modification between different samples from various biological conditions (e.g., different organisms, time points of fermentation, media conditions, or different biotopes, among others). Data obtained from such experiments alone, or in combination with other techniques, can be used for various applications, such as to compare the behavior of various organisms in a given (e.g., metabolic) situation, to increase the productivity of strains which produce fine chemicals or to increase the efficiency of the production of fine chemicals.
  • various biological conditions e.g., different organisms, time points of fermentation, media conditions, or different biotopes, among others.
  • Data obtained from such experiments alone, or in combination with other techniques can be used for various applications, such as to compare the behavior of various organisms in a given (e.g., metabolic) situation, to increase the productivity of strains which produce fine chemicals or to increase the efficiency of the production of fine chemicals.
  • Corynebacterium glutamicum is equipped with four secondary carriers proline for compatible solutes: Identification, sequencing, and characterization of the proline/ectoine uptake system, ProP, and the ectoine/proline/glycine betaine carrier, EctP,” J. Bacteriol., 180(22): 6005-6012 (1998) AJ004934 dapD Tetrahydrodipicolinate succinylase Wehrmann, A. et al. “Different modes of diaminopimelate synthesis and their (incomplete i ) role in cell wall integrity: A study with Corynebacterium glutamicum ,” J.
  • DNA fragment having promoter function in coryneform bacterium Patent: JP 1995031476-A 1 Feb. 03, 1995 E08649 Aspartase Kohama, K. et al “DNA fragment having promoter function in coryneform bacterium ,” Patent: JP 1995031478-A 1 Feb. 03, 1995 E08900 Dihydrodipicolinate reductase Madori, M. et al. “DNA fragment containing gene coding Dihydrodipicolinate acid reductase and utilization thereof,” Patent: JP 1995075578-A 1 Mar. 20, 1995 E08901 Diaminopimelic acid decarboxylase Madori, M. et al.
  • Gram-positive bacteria with a high DNA G + C content are characterized by a common insertion within their 23S rRNA genes,” J. Gen. Microbiol., 138: 1167-1175 (1992) M85107, 23S rRNA gene insertion sequence Roller, C. et al.
  • Gram-positive bacteria with a high DNA G + C content are M85108 characterized by a common insertion within their 23S rRNA genes
  • Corynebacterium glutamicum aecD gene encodes a C-S uptake carrier; hypothetical protein yhbw lyase with alpha, beta-elimination activity that degrades aminoethylcysteine,” J. Bacteriol., 174(9): 2968-2977 (1992); Tauch, A. et al. “Isoleucine uptake in Corynebacterium glutamicum ATCC 13032 is directed by the brnQ gene product,” Arch. Microbiol., 169(4): 303-312 (1998) S59299 trp Leader gene (promoter) Herry, D. M. et al.
  • a gene encoding arginyl-tRNA synthetase is located in the decarboxylase (partial) upstream region of the lysA gene in Brevibacterium lactofermentum : Regulation of argS-lysA cluster expression by arginine,” J. Bacteriol., 175(22): 7356-7362 (1993) Z21502 dapA; dapB Dihydrodipicolinate synthase; Pisabarro, A. et al.
  • GB_HTG3 AC009685 210031 AC009685 Homo sapiens chromosome 15 clone 91_E_13 map 15, *** SEQUENCING IN Homo sapiens 34,247 29-Sep-99 PROGRESS ***, 27 unordered pieces.
  • GB_HTG7 AC009511 271896 AC009511 Homo sapiens clone RP11-860B13, *** SEQUENCING IN PROGRESS ***, 59 Homo sapiens 35,033 09-DEC-1999 unordered pieces.
  • GB_BA1 D50453 146191 D50453 Bacillus subtilis DNA for 25-36 degree region containing the amyE-srfA region, Bacillus subtilis 54,452 10-Feb-99 complete cds.
  • GB_BA1 SCI51 40745 AL109848 Streptomyces coelicolor cosmid I51. Streptomyces coelicolor 36,806 16-Aug-99 A3(2)
  • GB_BA1 ECOUW93 338534 U14003 Escherichia coli K-12 chromosomal region from 92.8 to 00.1 minutes.
  • GB_HTG3 AC011498_0 312343 AC011498 Homo sapiens chromosome 19 clone CIT978SKB_50L17, *** SEQUENCING IN Homo sapiens 37,117 13-Dec-99 PROGRESS ***, 190 unordered pieces.
  • rxa00104 879 GB_BA1: MTCY270 37586 Z95388 Mycobacterium tuberculosis H37Rv complete genome; segment 96/162.
  • GB_BA1 MTCY270 37586 Z95388 Mycobacterium tuberculosis H37Rv complete genome; segment 96/162.
  • Corynebacterium 57,259 14-OCT-1997 ammoniagenes GB_BA1: MTCY159 33818 Z83863 Mycobacterium tuberculosis H37Rv complete genome; segment 111/162.
  • GB_HTG2 HSJ1153D9 118360 AL109806 Homo sapiens chromosome 20 clone RP5-1153D9, *** SEQUENCING IN Homo sapiens 35,714 03-DEC-1999 PROGRESS ***, in unordered pieces.
  • GB_HTG2 HSJ1153D9 118360 AL109806 Homo sapiens chromosome 20 clone RP5-1153D9, *** SEQUENCING IN Homo sapiens 35,334 03-DEC-1999 PROGRESS ***, in unordered pieces.
  • rxa00181 1695 GB_BA1 CGPUTP 3791 Y09163 C. glutamicum putP gene.
  • GB_HTG2 Homo sapiens 37,315 5-Nov-98
  • GB_HTG2 HS745I14 133309 AL033532 Homo sapiens chromosome 1 clone RP4-745I14 map q23.1-24.3, *** SEQUENCING Homo sapiens 38,129 03-DEC-1999 IN PROGRESS ***, in unordered pieces.
  • GB_HTG2 HS745I14 133309 AL033532 Homo sapiens chromosome 1 clone RP4-745I14 map q23.1-24.3, *** SEQUENCING Homo sapiens 38,129 03-DEC-1999 IN PROGRESS ***, in unordered pieces.
  • GB_GSS10 AQ184082 506 AQ184082 HS_3216_A1_G08_T7 CIT Approved Human Genomic Sperm Library
  • GB_GSS10 AQ184082 506 AQ184082 HS_3216_A1_G08_T7 CIT Approved Human Genomic Sperm Library
  • GB_EST15 AA486042 515 AA486042 ab40c08.r1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone Homo sapiens 38,816 06-MAR-1998 IMAGE: 843278 5′, mRNA sequence. rxa00243 1140 GB_PR2: CNS01DS5 101584 AL121655 BAC sequence from the SPG4 candidate region at 2p21-2p22, complete sequence.
  • GB_HTG3 AC011408 79332 AC011408 Homo sapiens clone CIT978SKB_65D22, Homo sapiens 38,040 06-OCT-1999 *** SEQUENCING IN PROGRESS ***, 10 unordered pieces.
  • GB_HTG3 AC011408 79332 AC011408 Homo sapiens clone CIT978SKB_65D22, Homo sapiens 38,040 06-OCT-1999 *** SEQUENCING IN PROGRESS ***, 10 unordered pieces.
  • GB_HTG1 CEY62E10 254217 AL031580 Caenorhabditis elegans chromosome IV clone Y62E10, *** SEQUENCING IN Caenorhabditis elegans 36,776 6-Sep-99 PROGRESS ***, in unordered pieces.
  • GB_HTG1 CEY62E10 254217 AL031580 Caenorhabditis elegans chromosome IV clone Y62E10, *** SEQUENCING IN Caenorhabditis elegans 36,776 6-Sep-99 PROGRESS ***, in unordered pieces.
  • GB_PL2 YSCCHROMI 41988 L22015 Saccharomyces cerevisiae chromosome I centromere and right arm sequence. Saccharomyces 39,260 05-MAR-1998 cerevisiae rxa00269 912 GB_HTG4: AC009974 219565 AC009974 Homo sapiens chromosome unknown clone NH0459I19, WORKING DRAFT Homo sapiens 37,358 29-OCT-1999 SEQUENCE, in unordered pieces.
  • GB_HTG4 AC009974 219565 AC009974 Homo sapiens chromosome unknown clone NH0459I19, WORKING DRAFT Homo sapiens 37,358 29-OCT-1999 SEQUENCE, in unordered pieces.
  • GB_BA1 AB017508 32050 AB017508 Bacillus halodurans C-125 genomic DNA, 32 kb fragment, complete cds. Bacillus halodurans 44,622 14-Apr-99 rxa00281 766
  • GB_BA1 SCE8 24700 AL035654 Streptomyces coelicolor cosmid E8.
  • GB_BA1 SCU51332 3216 U51332 Streptomyces coelicolor histidine kinase homolog (absA1) and response regulator Streptomyces coelicolor 39,089 14-Sep-96 homolog (absA2) genes, complete cds.
  • GB_HTG4 AC011122 187123 AC011122 Homo sapiens chromosome 8 clone 23_D_19 map 8, *** SEQUENCING IN Homo sapiens 38,658 14-OCT-1999 PROGRESS ***, 27 ordered pieces.
  • GB_BA1 SC2E9 20850 AL021530 Streptomyces coelicolor cosmid 2E9. Streptomyces coelicolor 43,267 28-Jan-98 GB_BA1: SC9B1 24800 AL049727 Streptomyces coelicolor cosmid 9B1. Streptomyces coelicolor 44,613 27-Apr-99 GB_BA1: ECU70214 123171 U70214 Escherichia coli chromosome minutes 4-6.
  • GB_BA1 AEOCHIT1 6861 D63139 Aeromonas sp. gene for chitinase, complete and partial cds. Aeromonas sp. 10S-24 38,577 13-Feb-99 GB_EST4: D62996 314 D62996 HUM347G01B Clontech human aorta polyA+ mRNA (#6572) Homo sapiens cDNA Homo sapiens 41,613 29-Aug-95 clone GEN-347G01 5′, mRNA sequence.
  • GB_HTG2 AC005081 180096 AC005081 Homo sapiens clone RG270D13, *** SEQUENCING IN PROGRESS ***, 18 Homo sapiens 45,786 12-Jun-98 unordered pieces.
  • rxa00410 789 GB_BA1: ATPLOCC 8870 Z30328 A. tumefaciens Ti plasmid pTiAch5 genes for OccR, OccQ, OccM, OccP, OccT, Agrobacterium 46,490 10-OCT-1994 OoxB, OoxA and ornithine cyclodeaminase.
  • tumefaciens GB_BA2 U67591 9829 U67591 Methanococcus jannaschii section 133 of 150 of the complete genome. Methanococcus 45,677 28-Jan-98 jannaschii GB_BA1: TIPOCCQMPJ 4350 M80607 Plasmid pTiA6 (from Agribacterium tumefaciens ) periplasmic-type octopine Plasmid pTiA6 46,490 24-Apr-96 permease (occR, occQ, occM, occP, and occJ) and lysR-type regulatory protein (occR) genes, complete cds.
  • rxa00419 882 GB_BA2 MSU46844 16951 U46844 Mycobacterium smegmatis catalase-peroxidase (katG), putative arabinosyl Mycobacterium 57,029 12-MAY-1997 transferase (embC, embA, embB), genes complete cds and putative propionyl-coA smegmatis carboxylase beta chain (pccB) genes, partial cds.
  • GB_EST28 AI513245 471 AI513245 GH13311.3prime GH Drosophila melanogaster head pOT2 Drosophila melanogaster Drosophila melanogaster 37,696 16-MAR-1999 cDNA clone GH13311 3prime, mRNA sequence.
  • GB_HTG4 AC010066 187240 AC010066 Drosophila melanogaster chromosome 3L/72A4 clone RPCI98-25O1, *** Drosophila melanogaster 39,607 16-OCT-1999 SEQUENCING IN PROGRESS ***, 70 unordered pieces.
  • rxa00432 1608 GB_BA1 BSUB0015 218410 Z99118 Bacillus subtilis complete genome (section 15 of 21): from 2795131 to 3013540.
  • Bacillus subtilis 49,810 26-Nov-97 GB_PL1 CAC35A5 42565 AL033396 C. albicans cosmid Ca35A5.
  • GB_HTG2 AC008199 124050 AC008199 Drosophila melanogaster chromosome 3 clone BACR01K08 (D756) RPCI-98 01.K.8 Drosophila melanogaster 38,392 2-Aug-99 map 94D-94D strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 83 unordered pieces.
  • GB_RO RATLNKP2 177 M22337 Rat link protein gene, exon 2. Rattus sp.
  • GB_PR1 HSH33G4 1015 X05857 Human H3.3 gene exon 4.
  • NCI_CGAP_GC6 Homo sapiens cDNA clone IMAGE: 2240420 3′, Homo sapiens 35,417 27-Apr-99 mRNA sequence.
  • GB_HTG3 AC008708 83932 AC008708 Homo sapiens chromosome 5 clone CIT978SKB_78F1, *** SEQUENCING IN Homo sapiens 38,769 3-Aug-99 PROGRESS ***, 12 unordered pieces.
  • GB_HTG3 AC008708 83932 AC008708 Homo sapiens chromosome 5 clone CIT978SKB_78F1, *** SEQUENCING IN Homo sapiens 38,769 3-Aug-99 PROGRESS ***, 12 unordered pieces.
  • GB_HTG3 AC008708 83932 AC008708 Homo sapiens chromosome 5 clone CIT978SKB_78F1, *** SEQUENCING IN Homo sapiens 36,797 3-Aug-99 PROGRESS ***, 12 unordered pieces.
  • rxa00480 1239 GB_HTG1 HSJ575L21 94715 AL096841 Homo sapiens chromosome 1 clone RP4-575L21, *** SEQUENCING IN PROGRESS Homo sapiens 38,138 23-Nov-99 ***, In unordered pieces.
  • GB_HTG1 HSJ575L21 94715 AL096841 Homo sapiens chromosome 1 clone RP4-575L21, *** SEQUENCING IN PROGRESS Homo sapiens 38,138 23-Nov-99 ***, In unordered pieces.
  • GB_RO AC005960 158414 AC005960 Mus musculus chromosome 17 BAC cltb20h22 from the MHC region, complete Mus musculus 38,712 01-DEC-1998 sequence.
  • GB_BA1 SCI51 40745 AL109848 Streptomyces coelicolor cosmid I51.
  • GB_BA2 AF082879 3434 AF082879 Yersinia enterocolitica ABC transporter enterochelin/enterobactin gene cluster, Yersinia enterocolitica 55,634 20-OCT-1999 complete sequence.
  • GB_BA1 BSP132617 5192 AJ132617 Burkholderia sp. P-transporter operon and flanking genes. Burkholderia sp.
  • GB_BA2 CAU77910 3385 U77910 Corynebacterium ammoniagenes sequence upstream of the 5-phosphoribosyl-1- Corynebacterium 39,007 1-Jan-98 pyrophosphate amidotransferase (purF) gene.
  • cDNA clone RPCCK07 similar to Rattus sp.
  • GB_EST28 AI504741 568 AI504741 vl16c01.x1
  • GB_EST18 AA712043 68 AA712043 vu29f10.r1 Barstead mouse myotubes MPLRB5 Mus musculus cDNA clone Mus musculus 42,647 24-DEC-1997 IMAGE: 1182091 5′ similar to gb: L05093 60S RIBOSOMAL PROTEIN L18A (HUMAN);, mRNA sequence. rxa00571 1280 GB_BA1: MTCY78 33818 Z77165 Mycobacterium tuberculosis H37Rv complete genome; segment 145/162.
  • GB_HTG6 AC010932 203273 AC010932 Homo sapiens chromosome 15 clone RP11-296E22 map 15, *** SEQUENCING IN Homo sapiens 37,242 30-Nov-99 PROGRESS ***, 36 unordered pieces.
  • GB_HTG6 AC010932 203273 AC010932 Homo sapiens chromosome 15 clone RP11-296E22 map 15, *** SEQUENCING IN Homo sapiens 36,485 30-Nov-99 PROGRESS ***, 36 unordered pieces.
  • GB_BA1 MSGB26CS 37040 L78816 Mycobacterium leprae cosmid B26 DNA sequence.
  • GB_IN1 CEK09E9 30098 Z79602
  • Caenorhabditis elegans cosmid K09E9 complete sequence.
  • Caenorhabditis elegans 34,092 2-Sep-99 GB_PR4 AF135802 4965 AF135802 Homo sapiens thyroid hormone receptor-associated protein complex component Homo sapiens 36,310 9-Apr-99 TRAP170 mRNA, complete cds.
  • GB_PR4 AF104256 4365 AF104256 Homo sapiens transcriptional co-activator CRSP150 (CRSP150) mRNA, complete Homo sapiens 36,617 4-Feb-99 cds. rxa00596 576 GB_PR3: AC004659 129577 AC004659 Homo sapiens chromosome 19, CIT-HSP-87m17 BAC clone, complete sequence. Homo sapiens 34,321 02-MAY-1998 GB_PR3: AC004659 129577 AC004659 Homo sapiens chromosome 19, CIT-HSP-87m17 BAC clone, complete sequence.
  • Homo sapiens 40,404 6-Feb-99 rxa00607 504 GB_BA1: MTV010 3400 AL021186 Mycobacterium tuberculosis H37Rv complete genome; segment 119/162.
  • GB_BA1 MTCY428 26914 Z81451 Mycobacterium tuberculosis H37Rv complete genome; segment 107/162.
  • GB_HTG4 AC009766 170502 AC009766 Homo sapiens chromosome 11 clone 404_A_03 map 11, *** SEQUENCING IN Homo sapiens 37,984 19-OCT-1 999 PROGRESS ***, 27 unordered pieces.
  • GB_HTG4 AC009766 170502 AC009766 Homo sapiens chromosome 11 clone 404_A_03 map 11, *** SEQUENCING IN Homo sapiens 37,984 19-OCT-1999 PROGRESS ***, 27 unordered pieces.
  • GB_EST30 AU054038 245 AU054038 AU054038 Dictyostelium discoideum SL ( H. Urushihara ) Dictyostelium discoideum Dictyostelium discoideum 43,265 28-Apr-99 cDNA clone SLK472, mRNA sequence.
  • GB_EST30 AU054038 245 AU054038 AU054038 Dictyostelium discoideum SL ( H.
  • GB_PR4 AC007625 174701 AC007625 Genomic sequence of Homo sapiens clone 2314F2 from chromosome 18, complete Homo sapiens 38,014 30-Jun-99 sequence.
  • GB_EST14 AA427576 580 AA427576 zw54b04.s1 Soares_total_fetus_Nb2HF8_9w Homo sapiens cDNA clone Homo sapiens 42,731 16-OCT-1997 IMAGE: 773839 3′ similar to gb: M86852 PEROXISOME ASSEMBLY FACTOR-1 (HUMAN);, mRNA sequence.
  • GB_BA1 MTV022 13025 AL021925 Mycobacterium tuberculosis H37Rv complete genome; segment 100/162.
  • Mus musculus 39,398 9-Sep-97 GB_BA1 MTV022 13025 AL021925 Mycobacterium tuberculosis H37Rv complete genome; segment 100/162.
  • GB_BA1 DIHCLPBA 2441 M32229 B. nodosus clpB gene encoding a regulatory subunit of ATP-dependent protease.
  • GB_HTG3 AC008691_1 110000 AC008691 Homo sapiens chromosome 5 clone CIT978SKB_63A22, *** SEQUENCING IN Homo sapiens 38,270 3-Aug-99 PROGRESS ***, 253 unordered pieces.
  • GB_HTG3 AC009127 186591 AC009127 Homo sapiens chromosome 16 clone RPCI-11_498D10, *** SEQUENCING IN Homo sapiens 38,947 3-Aug-99 PROGRESS ***, 49 unordered pieces.
  • GB_HTG1 HS32B1 271488 AL023693 Homo sapiens chromosome 6 clone RP1-32B1, *** SEQUENCING IN PROGRESS Homo sapiens 36,565 23-Nov-99 ***, in unordered pieces.
  • GB_PR3 AC004919 75547 AC004919 Homo sapiens PAC clone DJ0895B23 from UL, complete sequence.
  • GB_EST6 W06539 300 W06539 T2367 MVAT4 bloodstream form of serodeme WRATat1.1 Trypanosoma brucei Trypanosoma brucei 40,000 12-Aug-96 rhodesiense cDNA 5′, mRNA sequence.
  • rhodesiense GB_PR4 AC008179 181745 AC008179 Homo sapiens clone NH0576F01, complete sequence.
  • GB_EST18 Homo sapiens 35,903 28-Sep-99 GB_EST18: AA710415 533 AA710415 vt53f08.r1 Barstead mouse irradiated colon MPLRB7 Mus musculus cDNA clone Mus musculus 41,562 24-DEC-1997 IMAGE: 1166823 5′, mRNA sequence. rxa00842 1323 GB_PR2: AC002379 118595 AC002379 Human BAC clone GS165I04 from 7q21, complete sequence.
  • GB_HTG4 AC007920 234529 AC007920 Homo sapiens chromosome 3q27 clone RPCI11-208N14, *** SEQUENCING IN Homo sapiens 33,742 21-OCT-1999 PROGRESS ***, 51 unordered pieces.
  • GB_HTG4 AC007920 234529 AC007920 Homo sapiens chromosome 3q27 clone RPCI11-208N14, *** SEQUENCING IN Homo sapiens 33,742 21-OCT-1999 PROGRESS ***, 51 unordered pieces.
  • GB_HTG2 AC004064 185000 AC004064 Homo sapiens chromosome 4, *** SEQUENCING IN PROGRESS ***, 10 unordered Homo sapiens 39,833 9-Jul-98 pieces.
  • GB_HTG2 AC004064 185000 AC004064 Homo sapiens chromosome 4, *** SEQUENCING IN PROGRESS ***, 10 unordered Homo sapiens 39,833 9-Jul-98 pieces.
  • GB_PR3 HSJ824F16 139330 AL050325 Human DNA sequence from clone 824F16 on chromosome 20, complete sequence.
  • GB_HTG3 AC010120 121582 AC010120 Drosophila melanogaster chromosome 3 clone BACR22N13 (D1061) RPCI-98 Drosophila melanogaster 36,855 24-Sep-99 22.N.13 map 96F-96F strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 83 unordered pieces.
  • GB_HTG2 AC006898 299308 AC006898 Caenorhabditis elegans clone Y73B6x, *** SEQUENCING IN PROGRESS ***, 9 Caenorhabditis elegans 36,768 24-Feb-99 unordered pieces.
  • GB_BA1 STMMSDA 3986 L48550 Streptomyces coelicolor methylmalonic acid semialdehyde dehydrogenase (msdA) Streptomyces coelicolor 63,743 09-MAY-1996 gene, complete cds.
  • GB_PAT I92043 713 I92043 Sequence 10 from patent U.S. Pat. No. 5726299. Unknown. 38,850 01-DEC-1998 GB_PAT: I78754 713 I78754 Sequence 10 from patent U.S. Pat. No. 5693781. Unknown. 38,850 3-Apr-98 rxa00875 690 GB_BA2: AF119715 549 AF119715 Escherichia coli isopentyl diphosphate isomerase (idi) gene, complete cds.
  • GB_HTG2 AC007472 114003 AC007472 Drosophila melanogaster chromosome 2 clone BACR30D19 (D587) RPCI-98 Drosophila melanogaster 36,592 2-Aug-99 30.D.19 map 49E-49F strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 79 unordered pieces.
  • GB_HTG2 AC006798 207370 AC006798 Caenorhabditis elegans clone Y51F8, *** SEQUENCING IN PROGRESS ***, 30 Caenorhabditis elegans 36,699 25-Feb-99 unordered pieces.
  • GB_EST4 H22888 468 H22888 ym54e12.r1 Soares infant brain 1NIB Home sapiens cDNA clone IMAGE: 52158 5′, Homo sapiens 37,179 6-Jul-95 mRNA sequence.
  • GB_GSS13 AQ426858 516 AQ426858 CITBI-E1-2578F1.
  • TF CITBI-E1 Home sapiens genomic clone 2578F1, genomic Homo sapiens 38,447 24-MAR-1999 survey sequence.
  • GB_PR1 AB002335 6289 AB002335 Human mRNA for KIAA0337 gene, complete cds.
  • GB_BA1 NGU58849 2401 U58849 Neisseria gonorrhoeae pilS6 silent pilus locus. Neisseria gonorrhoeae 40,623 20-Jun-96 GB_BA1: PLPDHOS 3119 L06822 Plasmid pSa (from Escherichia coli ) dihydropteroate synthase gene, 3′ end.
  • Plasmid pSa 38,966 20-MAR-1996 GB_BA1 PDGINTORF 6747 L06418 Integron In7 (from Plasmid pDGO100 from Escherichia coli ) integrase (int), Plasmid pDGO100 38,966 20-MAR-1996 aminoglycoside adenylyltransferase (aad), quaternary ammonium compound- resistance protein, dihydrofolate reductase (dhfrX), and dihydropteroate synthase (sull) genes.
  • GB_GSS9 AQ163442 658 AQ163442 nbxb0007A07f CUGI Rice BAC Library Oryza sativa genomic clone nbxb0007A07f, Oryza sativa 41,885 12-Sep-98 genomic survey sequence.
  • GB_PL1 PSST70 4974 X69213 P.
  • sativum Psst70 gene for heat-shock protein Pisum sativum 36,866 3-Jul-96 rxa00931 969 GB_GSS1: FR0025208 612 AL018047 F. rubripes GSS sequence, clone 145D10aA8, genomic survey sequence. Fugu rubripes 37,815 10-DEC-1997 GB_GSS1: FR0021844 252 AL014715 F. rubripes GSS sequence, clone 069K22aG5, genomic survey sequence.
  • Mycobacterium 37,902 17-Jun-98 tuberculosis GB_BA1 MTCY180 44201 Z97193 Mycobacterium tuberculosis H37Rv complete genome; segment 85/162.
  • Mycobacterium 39,140 17-Jun-98 tuberculosis GB_BA2 MSGKATG 1745 L14268 Mycobacterium tuberculosis ethyl methane sulphonate resistance protein (katG) Mycobacterium 42,517 26-Aug-99 gene, 3′end.
  • GB_HTG6 AC010998 144338 AC010998 Homo sapiens clone RP11-95I16, *** SEQUENCING IN PROGRESS ***, 17 Homo sapiens 39,497 08-DEC-1999 unordered pieces.
  • GB_GSS1 GGA340111 990 AJ232089 Gallus gallus anonymous sequence from Cosmid mapping to chromosome 2 Gallus gallus 37,970 25-Aug-98 (Cosmid 34 - Contig 15), genomic survey sequence.
  • GB_HTG6 AC010998 144338 AC010998 Homo sapiens clone RP11-95I16, *** SEQUENCING IN PROGRESS ***, 17 Homo sapiens 38,226 08-DEC-1999 unordered pieces.
  • rxa01060 1047 GB_BA1 ECTTN7 2280 AJ001816 Escherichia coli left end of transposon Tn7 including type 2 Integron.
  • GB_IN2 AF176377 8220 AF176377 Caenorhabditis briggsae CES-1 (ces-1) gene, complete cds; and CPN-1 (cpn-1) Caenorhabditis briggsae 39,921 09-DEC-1999 gene, partial cds.
  • GB_GSS10 AQ196728 429 AQ196728 CIT-HSP-2381F4.TR CIT-HSP Homo sapiens genomic clone 2381F4, genomic Homo sapiens 39,019 16-Sep-98 survey sequence.
  • GB_BA1 U00016 42931 U00016 Mycobacterium leprae cosmid B1937. Mycobacterium leprae 58,303 01-MAR-1994
  • GB_BA1 SYCGROESL 3256 D12677 Synechocystis sp. groES and groEL genes. Synechocystis sp. 34,593 3-Feb-99
  • GB_BA1 D90905 139467 D90905 Synechocystis sp. PCC6803 complete genome, 7/27, 781449-920915. Synechocystis sp.
  • GB_BA1 SC8D9 38681 AL035569 Streptomyces coelicolor cosmid 8D9. Streptomyces coelicolor 42,200 26-Feb-99 rxa01136 555 GB_EST11: AA244557 379 AA244557 mx07a01.r1 Soares mouse NML Mus musculus cDNA clone IMAGE: 679464 5′, Mus musculus 39,050 10-MAR-1997 mRNA sequence.
  • GB_EST14 AA407673 306 AA407673 EST01834 Mouse 7.5 dpc embryo ectoplacental cone cDNA library Mus musculus Mus musculus 38,562 26-Aug-98 cDNA clone C0014F02 3′, mRNA sequence.
  • GB_EST26 AI390328 604 AI390328 mx07a01.y1 Soares mouse NML Mus musculus cDNA clone IMAGE: 679464 5′, Mus musculus 33,136 2-Feb-99 mRNA sequence.
  • GB_PR4 AC006054 143738 AC006054 Homo sapiens Xq28 BAC RPCI11-382P7 (Roswell Park Cancer Institute Human Homo sapiens 36,053 1-Apr-99 BAC Library) complete sequence.
  • rxa01172 1578 GB_BA1 SCE39 23550 AL049573 Streptomyces coelicolor cosmid E39. Streptomyces coelicolor 62,357 31-MAR-1999
  • GB_BA1 MSU50335 5193 U50335 Mycobacterium smegmatis phage resistance (mpr) gene, complete cds.
  • GB_PR2 HS1191B2 60828 AL022237 Human DNA sequence from clone 1191B2 on chromosome 22q13.2-13.3.
  • GB_PL1 Mycobacterium 57,762 17-Jun-98 tuberculosis GB_PL1: ATY12776 38483 Y12776 Arabidopsis thaliana DNA, 40 kb surrounding ACS1 locus.
  • GB_BA1 SLGLYUB 2576 X65556 S. lividans tRNA-GlyU beta gene. Streptomyces lividans 54,493 20-DEC-1993 GB_BA1: SCH10 39524 AL049754 Streptomyces coelicolor cosmid H10. Streptomyces coelicolor 44,638 04-MAY-1999 rxa01219 1005 GB_PAT: A68024 520 A68024 Sequence 19 from Patent WO9743409.
  • GB_EST6 N99239 424 N99239 zb76h11.s1 Soares_senescent_fibroblasts_NbHSF Homo sapiens cDNA clone Homo sapiens 39,623 20-Aug-96 IMAGE: 309573 3′, mRNA sequence.
  • GB_EST16 AA554268 400 AA554268 nk36c09.s1 NCI_CGAP_GC2
  • Homo sapiens cDNA clone IMAGE 1015600 Homo sapiens 36,111 8-Sep-97 3′ similar to gb: X01677 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE, LIVER (HUMAN);, mRNA sequence.
  • rxa01221 849 GB_PR4 AF179633 96371 AF179633 Homo sapiens chromosome 16 map 16q23.3-q24.1 sequence.
  • GB_IN1 BBU44918 2791 U44918 Babesia bovis ATP-binding protein (babc) mRNA, complete cds.
  • GB_BA1 CGLPD 1800 Y16642 Corynebacterium glutamicum lpd gene, complete CDS.
  • GB_BA1 MTV038 16094 AL021933 Mycobacterium tuberculosis H37Rv complete genome; segment 24/162.
  • GB_PR3 AC005618 176714 AC005618 Homo sapiens chromosome 5, BAC clone 249h5 (LBNL H149), complete sequence.
  • GB_BA1 CGLPD 1800 Y16642 Corynebacterium glutamicum lpd gene, complete CDS.
  • GB_HTG4 AC010045 164829 AC010045 Drosophila melanogaster chromosome 3L/75A1 clone RPCI98-17C17, *** Drosophila melanogaster 50,512 16-OCT-1999 SEQUENCING IN PROGRESS ***, 50 unordered pieces.
  • GB_BA2 AF125164 26443 AF125164 Bacteroides fragilis 638R polysaccharide B (PS B2) biosynthesis locus, complete Bacteroides fragilis 56,071 01-DEC-1999 sequence; and unknown genes.
  • GB_BA1 AB002668 24907 AB002668 Actinobacillus actinomycetemcomitans DNA for glycosyltransferase, lytic Actinobacillus 46,679 21-Feb-98 transglycosylase, dTDP-4-rhamnose reductase, complete cds.
  • GB_STS AU027820 238 AU027820 Rattus norvegicus , OTSUKA clone, OT78.02/918b07, microsatellite sequence, Rattus norvegicus 34,874 02-MAR-1999 sequence tagged site.
  • GB_HTG3 AC006445 174547 AC006445 Homo sapiens chromosome 4, *** SEQUENCING IN PROGRESS ***, 7 unordered Homo sapiens 34,812 15-Sep-99 pieces. rxa01292 1308
  • GB_BA1 BSUB0017 217420 Z99120 Bacillus subtilis complete genome (section 17 of 21): from 3197001 to 3414420.
  • GB_HTG3 AC010580 121119 AC010580 Drosophila melanogaster chromosome 3 clone BACR48J06 (D1102) RPCI-98 48.J.6 Drosophila melanogaster 35,637 01-OCT-1999 map 96F-96F strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 71 unordered pieces.
  • rxa01293 450 GB_GSS8 AQ001809 705 AQ001809 CIT-HSP-2290D17.TF CIT-HSP Homo sapiens genomic clone 2290D17, genomic Homo sapiens 42,021 26-Jun-98 survey sequence.
  • GB_GSS8 AQ001809 705 AQ001809 CIT-HSP-2290D17.TF CIT-HSP Homo sapiens genomic clone 2290D17, genomic Homo sapiens 40,323 26-Jun-98 survey sequence. rxa01339 1111 GB_PL1: MGU60290 4614 U60290 Magnaporthe grisea nitrogen regulatory protein (NUT1) gene, complete cds.
  • NUT1 nitrogen regulatory protein
  • GB_HTG3 AC011371 189187 AC011371 Homo sapiens chromosome 5 clone CIT978SKB_107C20, *** SEQUENCING IN Homo sapiens 39,741 06-OCT-1999 PROGRESS ***, 31 unordered pieces.
  • GB_HTG3 AC011371 189187 AC011371 Homo sapiens chromosome 5 clone CIT978SKB_107C20, *** SEQUENCING IN Homo sapiens 39,741 06-OCT-1999 PROGRESS ***, 31 unordered pieces.
  • GB_HTG4 AC009892 138122 AC009892 Homo sapiens chromosome 19 clone CIT978SKB_83J4, *** SEQUENCING IN Homo sapiens 40,154 31-OCT-1999 PROGRESS ***, 6 ordered pieces.
  • GB_HTG4 AC009892 138122 AC009892 Homo sapiens chromosome 19 clone CIT978SKB_83J4, SEQUENCING IN Homo sapiens 40,154 31-OCT-1999 PROGRESS ***, 6 ordered pieces.
  • GB_PR3 AC002416 128915 AC002416 Human Chromosome X, complete sequence.
  • GB_EST37 AI982114 626 AI982114 pat.pk0074.e9.f chicken activated T cell cDNA Gallus gallus cDNA clone Gallus gallus 37,785 15-Sep-99 pat.pk0074.e9.f 5′ similar to H-ATPase B subunit, mRNA sequence.
  • GB_OV GGU20766 1645 U20766 Gallus gallus vacuolar H+-ATPase B subunit gene, complete cds.
  • GB_HTG2 AC006637 22092 AC006637 Caenorhabditis elegans clone F41B4, *** SEQUENCING IN PROGRESS ***, 1 Caenorhabditis elegans 37,488 23-Feb-99 unordered pieces.
  • GB_HTG1 CEY102G3_21 10000 AL020985 Caenorhabditis elegans chromosome V clone Y102G3, *** SEQUENCING IN Caenorhabditis elegans 35,437 3-Dec-98 GB_HTG1: CEY102G3_21 10000 AL020985 Caenorhabditis elegans chromosome V clone Y102G3, *** SEQUENCING IN Caenorhabditis elegans 35,437 3-Dec-98 GB_HTG1: CEY113G7_41 10000 AL031113 Caenorhabditis elegans chromosome V clone Y113G7, *** SEQUENCING IN Caenorhabditis elegans 35,437 12-Jan-99 rxa01576 882 GB_BA2: AF030975 2511 AF030975 Aeromon
  • GB_BA2 AF030975 2511 AF030975 Aeromonas salmonicida chaperonin GroES and chaperonin GroEL genes, complete Aeromonas salmonicida 38,171 2-Apr-98 cds.
  • GB_EST22 AI068560 965 AI068560 mgae0003aC11f Magnaporthe grisea Appressorium Stage cDNA Library Pyricularia Pyricularia grisea 40,073 09-DEC-1999 grisea cDNA clone mgae0003aC11f5′, mRNA sequence.
  • GB_GSS14 AQ554460 681 AQ554460 RPCI-11-419F2.TV RPCI-11 Homo sapiens genomic clone RPCI-11-419F2, genomic Homo sapiens 36,522 28-MAY-1999 survey sequence.
  • GB_IN2 AC005449 85518 AC005449 Drosophila melanogaster , chromosome 2R, region 44C4-44C5, P1 clone DS06765, Drosophila melanogaster 36,609 23-DEC-1998 complete sequence.
  • GB_IN2 AC005449 85518 AC005449 Drosophila melanogaster , chromosome 2R, region 44C4-44C5, P1 clone DS06765, Drosophila melanogaster 33,612 23-DEC-1998 complete sequence.
  • rxa01584 rxa01604 771 GB_HTG3 AC011352 160167 AC011352 Homo sapiens chromosome 5 clone CIT-HSPC_327F10, *** SEQUENCING IN Homo sapiens 33,688 06-OCT-1999 PROGRESS ***, 15 unordered pieces.
  • GB_HTG3 AC011352 160167 AC011352 Homo sapiens chromosome 5 clone CIT-HSPC_327F10, *** SEQUENCING IN Homo sapiens 33,688 06-OCT-1999 PROGRESS ***, 15 unordered pieces.
  • GB_HTG3 AC011402 168868 AC011402 Homo sapiens chromosome 5 clone CIT978SKB_38B5, *** SEQUENCING IN Homo sapiens 33,688 06-OCT-1999 PROGRESS ***, 7 unordered pieces.
  • GB_PR4 AC005377 102311 AC005377 Homo sapiens PAC clone DJ1136G02 from 7q32-q34, complete sequence. Homo sapiens 37,811 28-Apr-99 rxa01629 1635 GB_BA1: CGPROPGEN 2936 Y12537 C. glutamicum proP gene. Corynebacterium 100,000 17-Nov-98 glutamicum GB_BA1: CGPROPGEN 2936 Y12537 C. glutamicum proP gene.
  • GB_PR4 AF191071 88481 AF191071 Homo sapiens chromosome 8 clone BAC 388D06, complete sequence. Homo sapiens 35,612 11-OCT-1999 rxa01644 1401 GB_BA1: MSGB577COS 37770 L01263 M. leprae genomic dna sequence, cosmid b577. Mycobacterium leprae 55,604 14-Jun-96 GB_BA1: MLCB2407 35615 AL023596 Mycobacterium leprae cosmid B2407.
  • GB_BA1 Mycobacterium leprae 36,416 27-Aug-99 GB_BA1: MTV025 121125 AL022121 Mycobacterium tuberculosis H37Rv complete genome; segment 155/162. Mycobacterium 55,844 24-Jun-99 tuberculosis rxa01667 1329 GB_BA1: CGU43536 3464 U43536 Corynebacterium glutamicum heat shock, ATP-binding protein (clpB) gene, complete Corynebacterium 100,000 13-MAR-1997 cds.
  • clpB ATP-binding protein
  • GB_HTG4 AC009841 164434 AC009841 Drosophila melanogaster chromosome 3L/77E1 clone RPCI98-13F11, *** Drosophila melanogaster 33,205 16-OCT-1999 SEQUENCING IN PROGRESS ***, 70 unordered pieces.
  • GB_HTG4 AC009841 164434 AC009841 Drosophila melanogaster chromosome 3L/77E1 clone RPCI98-13F11, *** Drosophila melanogaster 33,205 16-OCT-1999 SEQUENCING IN PROGRESS ***, 70 unordered pieces.
  • GB_GSS1 FR0022586 522 AL015452
  • GB_BA2 CORCSLYS 2821 M89931 Corynebacterium glutamicum beta C-S lyase (aecD) and branched-chain amino acid Corynebacterium 99,929 4-Jun-98 uptake carrier (brnQ) genes, complete cds, and hypothetical protein Yhbw (yhbw) glutamicum gene, partial cds.
  • GB_HTG6 AC011037 167849 AC011037 Homo sapiens clone RP11-7F18, WORKING DRAFT SEQUENCE, 19 unordered Homo sapiens 36,903 30-Nov-99 pieces.
  • GB_HTG6 AC011037 167849 AC011037 Homo sapiens clone RP11-7F18, WORKING DRAFT SEQUENCE, 19 unordered Homo sapiens 35,642 30-Nov-99 pieces.
  • rxa01737 1182 GB_BA1 SCGD3 33779 AL096822 Streptomyces coelicolor cosmid GD3.
  • GB_HTG1 CNS01DSB 222193 AL121768 Homo sapiens chromosome 14 clone R-976B16, *** SEQUENCING IN PROGRESS Homo sapiens 35,147 05-OCT-1999 ***, in ordered pieces.
  • GB_HTG1 CNS01DSB 222193 AL121768 Homo sapiens chromosome 14 clone R-976B16, *** SEQUENCING IN PROGRESS Homo sapiens 35,147 05-OCT-1999 ***, in ordered pieces.
  • GB_BA1 MTCI28 36300 Z97050 Mycobacterium tuberculosis H37Rv complete genome; segment 10/162. Mycobacterium 49,574 23-Jun-98 tuberculosis GB_BA1: SC6G10 36734 AL049497 Streptomyces coelicolor cosmid 6G10. Streptomyces coelicolor 44,049 24-MAR-1999 GB_BA1: SCE29 26477 AL035707 Streptomyces coelicolor cosmid E29.
  • GB_EST38 AW066306 334 AW066306 687009D03.y1 687 Early embryo from Delaware Zea mays cDNA, mRNA Zea mays 46,108 12-OCT-1999 sequence.
  • GB_GSS13 AQ484750 375 AQ484750 RPCI-11-248N4.TV RPCI-11 Homo sapiens genomic clone RPCI-11-248N4, Homo sapiens 32,000 24-Apr-99 genomic survey sequence.
  • GB_GSS13 AQ489971 252 AQ489971 RPCI-11-247N23.TV RPCI-11 Homo sapiens genomic clone RPCI-11-247N23, Homo sapiens 36,111 24-Apr-99 genomic survey sequence. rxa01823 900 GB_BA1: SCI51 40745 AL109848 Streptomyces coelicolor cosmid I51. Streptomyces coelicolor 35,779 16-Aug-99 A3(2) GB_BA1: ECU82598 136742 U82598 Escherichia coli genomic sequence of minutes 9 to 12.
  • GB_HTG3 AC010189 265962 AC010189 Homo sapiens clone RPCI11-296K13, *** SEQUENCING IN PROGRESS ***, 80 Homo sapiens 39,006 16-Sep-99 unordered pieces.
  • GB_HTG3 AC010189 265962 AC010189 Homo sapiens clone RPCI11-296K13, *** SEQUENCING IN PROGRESS ***, 80 Homo sapiens 39,006 16-Sep-99 unordered pieces.
  • GB_HTG4 AC011117 148447 AC011117 Homo sapiens chromosome 4 clone 173_C_09 map 4, *** SEQUENCING IN Homo sapiens 39,130 14-OCT-1999 PROGRESS ***, 10 ordered pieces.
  • GB_HTG4 AC011117 148447 AC011117 Homo sapiens chromosome 4 clone 173_C_09 map 4, *** SEQUENCING IN Homo sapiens 39,130 14-OCT-1999 PROGRESS ***, 10 ordered pieces.
  • GB_BA1 MTCY2B12 20431 Z81011 Mycobacterium tuberculosis H37Rv complete genome; segment 61/162.
  • GB_HTG1 CEY48B6 293827 AL021151 Caenorhabditis elegans chromosome II clone Y48B6, *** SEQUENCING IN Caenorhabditis elegans 34,703 1-Apr-99 PROGRESS ***, in unordered pieces.
  • GB_HTG1 CEY48B6 293827 AL021151 Caenorhabditis elegans chromosome II clone Y48B6, *** SEQUENCING IN Caenorhabditis elegans 34,703 1-Apr-99 PROGRESS ***, in unordered pieces.
  • GB_HTG1 CEY53F4_2 110000 Z92860 Caenorhabditis elegans chromosome II clone Y53F4, *** SEQUENCING IN Caenorhabditis elegans 33,333 15-Oct-99 PROGRESS ***, in unordered pieces.
  • rxa01946 1298 GB_BA1 MTV007 32806 AL021184 Mycobacterium tuberculosis H37Rv complete genome; segment 64/162.
  • GB_HTG4 AC006467 175695 AC006467 Drosophila melanogaster chromosome 2 clone BACR03L08 (D532) RPCI-98 03.L.8 Drosophila melanogaster 36,672 27-OCT-1999 map 40A-40C strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 9 unordered pieces.
  • GB_HTG4 AC006467 175695 AC006467 Drosophila melanogaster chromosome 2 clone BACR03L08 (D532) RPCI-98 03.L.8 Drosophila melanogaster 32,367 27-OCT-1999 map 40A-40C strain y; cn bw sp, *** SEQUENCING IN PROGRESSo ***, 9 unordered pieces.
  • rxa02020 1111 GB_BA1 CGDNAAROP 2612 X85965 C. glutamicum ORF3 and aroP gene.
  • GB_PAT A58887 1612 A58887 Sequence 1 from Patent WO9701637. unidentified 100,000 06-MAR-1998
  • GB_BA1 STYCARABA 4378 M95047 Salmonella typhimurium transport protein, complete cds, and transfer RNA-Arg. Salmonella typhimurium 50,547 13-MAR-1996 rxa02029 1437
  • GB_HTG2 AC003023 104768 AC003023 Homo sapiens chromosome 11 clone pDJ363p2, *** SEQUENCING IN PROGRESS Homo sapiens 35,820 21-OCT-1997 ****, 22 unordered pieces.
  • GB_HTG2 AC003023 104768 AC003023 Homo sapiens chromosome 11 clone pDJ363p2, *** SEQUENCING IN PROGRESS Homo sapiens 35,820 21-OCT-1997 ***, 22 unordered pieces.
  • GB_HTG2 HS118B18 104729 AL034344 Homo sapiens chromosome 6 clone RP1-118B18 map p24.1-25.3, *** Homo sapiens 34,355 03-DEC-1999 SEQUENCING IN PROGRESS ***, in unordered pieces.
  • GB_PR4 AC007695 63247 AC007695 Homo sapiens 12q24 BAC RPCI11-124N23 (Roswell Park Cancer Institute Human Homo sapiens 38,681 1-Sep-99 BAC Library) complete sequence.
  • GB_PR4 AC006464 99908 AC006464 Homo sapiens BAC clone NH0436C12 from 2, complete sequence.
  • GB_PR4 AC006464 99908 AC006464 Homo sapiens BAC clone NH0436C12 from 2, complete sequence.
  • GB_BA1 Homo sapiens 35,968 22-OCT-1999 rxa02073 1653 GB_BA1: CGGDHA 2037 X72855 C. glutamicum GDHA gene. Corynebacterium 39,655 24-MAY-1993 glutamicum GB_BA1: CGGDH 2037 X59404 Corynebacterium glutamicum , gdh gen for glutamate dehydrogenase. Corynebacterium 44,444 30-Jul-99 glutamicum GB_BA2: SC2H4 25970 AL031514 Streptomyces coelicolor cosmid 2H4.
  • GB_HTG6 AC009769 122911 AC009769 Homo sapiens chromosome 8 clone RP11-202I12 map 8, LOW-PASS SEQUENCE Homo sapiens 35,473 07-DEC-1999 SAMPLING.
  • GB_EST7 W70175 436 W70175 zd52c02.r1 Soares_fetal_heart_NbHH19W Homo sapiens cDNA clone Homo sapiens 34,174 16-OCT-1996 IMAGE: 344258 5′ similar to contains LTR5.b2 LTR5 repetitive element;, mRNA sequence.
  • GB_BA1 CAJ10319 5368 AJ010319
  • GB_HTG3 AC011509 111353 AC011509
  • GB_HTG3 AC011509 111353 AC011509 Homo sapiens chromosome 19 clone CITB-H1_2189E23, *** SEQUENCING IN Homo sapiens 33,423 07-OCT-1999 PROGRESS ***, 35 unordered pieces.
  • rxa02115 1197 GB_HTG5 AC010126 175986 AC010126 Homo sapiens clone GS502B02, *** SEQUENCING IN PROGRESS ***, Homo sapiens 36,717 13-Nov-99 3 unordered pieces.
  • GB_HTG5 AC010126 175986 AC010126 Homo sapiens clone GS502B02, *** SEQUENCING IN PROGRESS ***, Homo sapiens 36,092 13-Nov-99 3 unordered pieces.
  • GB_PR1 HUMHM145 2214 D10925 Human mRNA for HM145.
  • GB_BA1 MTCY190 34150 Z70283 Mycobacterium tuberculosis H37Rv complete genome; segment 98/162.
  • rxa02133 329 GB_BA2 MPAE000058 28530 AE000058
  • Mycoplasma pneumoniae 32,317 18-Nov-96 GB_HTG4 AC008308 151373 AC008308 Drosophila melanogaster chromosome 3 clone BACR10M16 (D743) RPCI-98 Drosophila melanogaster 34,579 20-OCT-1999 10.M.16 map 93C-93D strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 186 unordered pieces.
  • GB_HTG4 AC008308 151373 AC008308 Drosophila melanogaster chromosome 3 clone BACR10M16 (D743) RPCI-98 Drosophila melanogaster 34,579 20-OCT-1999 10.M.16 map 93C-93D strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 186 unordered pieces.
  • GB_EST37 AW012260 358 AW012260 um06e09.y1 Sugano mouse kidney mkia Mus musculus cDNA clone Mus musculus 39,385 10-Sep-99 IMAGE: 2182312 5′ similar to SW: AMPL_BOVIN P00727 CYTOSOL AMINOPEPTIDASE;, mRNA sequence.
  • GB_GSS3 B87734 389 B87734 RPCI11-30D24.TP RPCI-11 Homo sapiens genomic clone RPCI-11-30D24, genomic Homo sapiens 37,629 9-Apr-99 survey sequence.
  • GB_PR4 AC005042 192218 AC005042
  • Homo sapiens clone NH0552E01 complete sequence.
  • GB_BA2 AF010496 189370
  • Rhodobacter capsulatus strain SB1003 partial genome.
  • GB_EST24 AI170522 367 AI170522 EST216450 Normalized rat lung, Bento Soares Rattus sp.
  • cDNA clone RLUCO75 3′ Rattus sp. 44,186 20-Jan-99 end, mRNA sequence.
  • GB_PL1 PHVDLECA 1441 K03288 P. vulgaris phytohemagglutinin gene encoding erythroagglutinating Phaseolus vulgaris 39,103 27-Apr-93 phytohemagglutinin (PHA-E), complete cds. rxa02173 1575
  • GB_BA1 CGGLTG 3013 X66112 C. glutamicum glt gene for citrate synthase and ORF.
  • GB_BA1 CGGLTG 3013 X66112 C. glutamicum glt gene for citrate synthase and ORF.
  • rxa02224 1920 GB_BA2 CXU21300 8990 U21300 Corynebacterium striatum hypothetical protein YbhB gene, partial cds; ABC Corynebacterium 37,264 9-Apr-99 transporter TetB (tetB), ABC transporter TetA (tetA), transposase, 23S rRNA striatum methyltransferase, and transposase genes, complete cds; and unknown genes.
  • GB_HTG3 AC009185 87184 AC009185 Homo sapiens chromosome 5 clone CIT-HSPC_248O19, *** SEQUENCING IN Homo sapiens 36,459 07-OCT-1999 PROGRESS ***, 2 ordered pieces.
  • GB_HTG3 AC009185 87184 AC009185 Homo sapiens chromosome 5 clone CIT-HSPC_248O19, *** SEQUENCING IN Homo sapiens 36,459 07-OCT-1999 PROGRESS ***, 2 ordered pieces.
  • rxa02225 905 GB_BA2 MPAE000058 28530 AE000058 Mycoplasma pneumoniae section 58 of 63 of the complete genome.
  • GB_EST26 AI337275 618 AI337275 tb96h11.x1 NCI_CGAP_Co16 Homo sapiens cDNA clone IMAGE: Homo sapiens 42,786 18-MAR-1999 2062245 3′ similar to TR: Q15392 Q15392 ORF, COMPLETE CDS.;, mRNA sequence.
  • rxa02233 1410 GB_BA1: ERWPNLB 1291 M65057 Erwinia carotovora pectin lyase (pnl) gene, complete cds.
  • GB_EST30 AV021947 313 AV021947 AV021947 Mus musculus 18-day embryo C57BL/6J Mus musculus cDNA clone Mus musculus 39,423 28-Aug-99 1190024M23, mRNA sequence.
  • GB_EST33 AV087117 251 AV087117 AV087117 Mus musculus tongue C57BL/6J adult Mus musculus cDNA clone Mus musculus 47,410 25-Jun-99 2310028C15, mRNA sequence.
  • GB_EST11 AA250210 532 AA250210 mx79g10.r1 Soares mouse NML Mus musculus cDNA clone IMAGE: 692610 5′ Mus musculus 36,136 12-MAR-1997 similar to TR: E236517 E236517 F44G4.1;, mRNA sequence.
  • GB_EST11 AA250210 532 AA250210 mx79g10.r1 Soares mouse NML Mus musculus cDNA clone IMAGE: 692610 5′ Mus musculus 36,202 12-MAR-1997 similar to TR: E236517 E236517 F44G4.1;, mRNA sequence.
  • GB_BA1 CGL007732 4460 AJ007732 Corynebacterium glutamicum 3′ ppc gene, secG gene, amt gene, ocd gene and 5′ Corynebacterium 100,000 7-Jan-99 soxA gene.
  • glutamicum GB_BA1 CGAMTGENE 2028 X93513 C. glutamicum amt gene.
  • GB_HTG3 AC009293 162944 AC009293 Homo sapiens chromosome 18 clone 53_I_06 map 18, *** SEQUENCING IN Homo sapiens 37,006 13-Aug-99 PROGRESS ***, 15 unordered pieces.
  • GB_HTG3 AC009293 162944 AC009293 Homo sapiens chromosome 18 clone 53_I_06 map 18, *** SEQUENCING IN Homo sapiens 37,006 13-Aug-99 PROGRESS ***, 15 unordered pieces.
  • GB_BA1 MTY25D10 40838 Z95558 Mycobacterium tuberculosis H37Rv complete genome; segment 28/162.
  • Mycobacterium 52,344 17-Jun-98 tuberculosis GB_BA1 MSGY224 40051 AD000004 Mycobacterium tuberculosis sequence from clone y224.
  • GB_BA1 MTY25D10 40838 Z95558 Mycobacterium tuberculosis H37Rv complete genome; segment 28/162.
  • Mycobacterium 36,861 17-Jun-98 tuberculosis GB_BA1 MSGY224 40051 AD000004 Mycobacterium tuberculosis sequence from clone y224.
  • GB_BA1 Homo sapiens 34,516 23-Nov-99 rxa02321 1752 GB_BA1: AB018531 4961 AB018531 Corynebacterium glutamicum dtsR1 and dtsR2 genes, complete cds. Corynebacterium 99,030 19-OCT-1998 glutamicum GB_PAT: E17019 4961 E17019 Brevibacterium lactofermentum dtsR and dtsR2 genes. Corynebacterium 98,973 28-Jul-99 glutamicum GB_BA1: AB018530 2855 AB018530 Corynebacterium glutamicum dtsR gene, complete cds.
  • glutamicum GB_BA1 U00012 33312 U00012 Mycobacterium leprae cosmid B1308.
  • GB_BA1 Mycobacterium leprae 40,247 30-Jan-96 GB_BA1: MTCY71 42729 Z92771 Mycobacterium tuberculosis H37Rv complete genome; segment 141/162. Mycobacterium 67,568 10-Feb-99 tuberculosis rxa02364 750 GB_BA1: AP000006 319000 AP000006 Pyrococcus horikoshii OT3 genomic DNA, 1166001-1485000 nt. position (6/7). Pyrococcus horikoshii 36,130 8-Feb-99 GB_BA1: AP000006 319000 AP000006 Pyrococcus horikoshii OT3 genomic DNA, 1166001-1485000 nt.
  • GB_HTG3 AC011461 100974 AC011461 Homo sapiens chromosome 19 clone CIT-HSPC_429L19, *** SEQUENCING IN Homo sapiens 36,138 07-OCT-1999 PROGRESS ***, 4 ordered pieces.
  • GB_HTG3 AC011461 100974 AC011461 Homo sapiens chromosome 19 clone CIT-HSPC_429L19, *** SEQUENCING IN Homo sapiens 36,138 07-OCT-1999 PROGRESS ***, 4 ordered pieces.
  • GB_EST21 AA992021 279 AA992021 ot36c01.s1 Soares_testis_NHT
  • Homo sapiens cDNA clone IMAGE 1618848 3′, Homo sapiens 41,219 3-Jun-98 mRNA sequence.
  • rxa02397 1119 GB_HTG4 AC009273 76175 AC009273 Arabidopsis thaliana chromosome 1 clone T1N6, *** SEQUENCING IN PROGRESS Arabidopsis thaliana 38,566 12-OCT-1999 ***, 2 ordered pieces.
  • GB_HTG4 AC009273 76175 AC009273 Arabidopsis thaliana chromosome 1 clone T1N6, *** SEQUENCING IN PROGRESS Arabidopsis thaliana 38,566 12-OCT-1999 ***, 2 ordered pieces.
  • GB_BA1 D90826 19493 D90826 E. coli genomic DNA, Kohara clone #335(40.9-41.3 min.).
  • GB_EST13 AA334108 275 AA334108 EST38262 Embryo, 9 week Homo sapiens cDNA 5′ end, mRNA sequence.
  • GB_BA2 Bacillus 40,338 26-Apr-93 stearothermophilus rxa02487 1827
  • GB_BA2 AF007101 32870 AF007101 Streptomyces hygroscopicus putative pteridine-dependent dioxygenase, PKS Streptomyces 43,298 13-Jan-98 modules 1, 2, 3 and 4, and putative regulatory protein genes, complete cds and hygroscopicus putative hydroxylase gene, partial cds.
  • GB_BA1 MTCI364 29540 Z93777 Mycobacterium tuberculosis H37Rv complete genome; segment 52/162.
  • GB_PR4 AC002470 235395 AC002470 Homo sapiens Chromosome 22q11.2 BAC Clone b135h6 in BCRL2-GGT Region, Homo sapiens 37,971 30-Nov-99 complete sequence.
  • GB_PR4 AC002472 147100 AC002472 Homo sapiens Chromosome 22q11.2 PAC Clone p_n5 in BCRL2-GGT Region, Homo sapiens 38,239 13-Sep-99 complete sequence.
  • GB_EST34 AI806938 118 AI806938 wf24b07.x1
  • Soares_NFL_T_GBC_S1 Homo sapiens cDNA clone IMAGE: Homo sapiens 38,983 7-Jul-99 2356501 3′ similar to SW: PLZF_HUMAN Q05516 ZINC FINGER PROTEIN PLZF;, mRNA sequence.
  • rxa02512 1086 GB_BA1 MTCY1A10 25949 Z95387 Mycobacterium tuberculosis H37Rv complete genome; segment 117/162.
  • GB_BA1 Mycobacterium 37,407 17-Jun-98 tuberculosis
  • GB_BA1 MLCL581 36225 Z96801
  • GB_OV GGU43396 2738
  • U43396 Gallus gallus tropomyosin receptor kinase A (ctrkA) mRNA, complete cds.
  • GB_BA2 AF008220 220060
  • Bacillus subtilis 37,395 4-Feb-98 GB_BA2 AF008220 220060 AF008220 Bacillus subtilis rrnB-dnaB genomic region.
  • Bacillus subtilis 36,218 4-Feb-98 GB_HTG2 AC005861 112369 AC005861 Arabidopsis thaliana clone F23B24, *** SEQUENCING IN PROGRESS ***, 6 Arabidopsis thaliana 38,407 29-Apr-99 unordered pieces.
  • GB_PL1 AB006530 7344 AB006530 Citrullus lanatus Sat gene for serine acetyltransferase, complete cds and 5′-flanking Citrullus lanatus 35,449 20-Aug-97 region.
  • GB_PL1 CNASA 5729 D85624 Citrullus vulgaris serine acetyltransferase (Sat) DNA, complete cds.
  • GB_EST32 AI727189 619 AI727189 BNLGHI7498 Six-day Cotton fiber Gossypium hirsutum cDNA 5′ similar to Gossypium hirsutum 35,099 11-Jun-99 (AB020715) KIAA0908 protein [ Homo sapiens ], mRNA sequence.
  • GB_BA1 CGPUTP 3791 Y09163 C. glutamicum putP gene.
  • GB_PL2 SPAC13G6 33481 Z54308 S. pombe chromosome I cosmid c13G6.
  • GB_BA1 CGU43535 2531 U43535
  • Corynebacterium glutamicum multidrug resistance protein (cmr) gene complete cds.
  • GB_EST35 AI857385 488 AI857385 wl55e03.x1
  • NCI_CGAP_Brn25 Homo sapiens cDNA clone IMAGE: 2428828 3′, Homo sapiens 39,139 26-Aug-99 mRNA sequence.
  • GB_BA1 CGU43535 2531 U43535
  • Corynebacterium glutamicum multidrug resistance protein (cmr) gene complete cds.
  • GB_PL1 AB016871 79109 AB016871 Arabldopsis thaliana genomic DNA, chromosome 5, TAC clone: K16L22, complete Arabidopsis thaliana 34,213 20-Nov-99 sequence.
  • GB_PL1 AB025602 55790 AB025602 Arabidopsis thaliana genomic DNA, chromosome 5, BAC clone: F14A1, complete Arabidopsis thaliana 36,461 20-Nov-99 sequence.
  • GB_IN1 CELF36H9 35985 AF016668 Caenorhabditis elegans cosmid F36H9. Caenorhabditis elegans 35,977 8-Aug-97 rxa02581 1983
  • GB_BA1 MTV005 37840 AL010186 Mycobacterium tuberculosis H37Rv complete genome; segment 51/162.
  • Mycobacterium 38,517 17-Jun-98 tuberculosis GB_BA1 MTV005 37840 AL010186 Mycobacterium tuberculosis H37Rv complete genome; segment 51/162.
  • GB_BA1 SEERYABS 20444 X62569
  • GB_BA2 AF113605 1593 AF113605 Streptomyces coelicolor proplonyl-CoA carboxylase complex B subunit (pccB) gene, Streptomyces coelicolor 58,397 08-DEC-1999 complete cds.
  • GB_BA1 SC1C2 42210 AL031124 Streptomyces coelicolor cosmid 1C2. Streptomyces coelicolor 52.916 15-Jan-99 GB_BA1: AB018531 4961 AB018531 Corynebacterium glutamicum dtsR1 and dtsR2 genes, complete cds. Corynebacterium 58,809 19-OCT-1998 glutamicum rxa02599 600 GB_BA1: AEMML 2585 X99639 Ralstonia eutropha mmlH, mmlI & mmlJ genes.
  • GB_EST15 AA508926 422 AA508926 MBAFCW1C08T3 Brugia malayi adult female cDNA (SAW96MLW-BmAF) Brugia Brugia malayi 43,377 8-Jul-97 malayi cDNA clone AFCW1C08 5′, mRNA sequence.
  • GB_BA1 AEMML 2585 X99639 Ralstonia eutropha mmlH, mmlI & mmlJ genes.
  • GB_IN1 MNE133341 399 AJ133341 Melarhaphe neritoides partial caM gene, exons 1-2. Melarhaphe neritoides 39,098 2-Jun-99 rxa02638 999 GB_BA2 AE001756 10938 AE001756 Thermotoga maritima section 68 of 136 of the complete genome. Thermotoga maritima 40,104 2-Jun-99 GB_GSS12: AQ423878 689 AQ423878 CITBI-E1-2575E20.TF CITBI-E1 Homo sapiens genomic clone 2575E20, genomic Homo sapiens 36,451 23-MAR-1999 survey sequence.
  • GB_HTG2 AC006765 274498 AC006765 Caenorhabditis elegans clone Y43H11, *** SEQUENCING IN PROGRESS***, 7 Caenorhabditis elegans 39,072 23-Feb-99 unordered pieces.
  • GB_GSS12 AQ342831 683 AQ342831 RPCI11-122K17.TJ RPCI-11 Homo sapiens genomic clone RPCI-11-122K17, Homo sapiens 34,762 07-MAY-1999 genomic survey sequence.
  • GB_EST36 AI900856 779 AI900856 sb95c11.y1 Gm-c1012 Glycine max cDNA clone GENOME SYSTEMS CLONE ID: Glycine max 39,063 06-DEC-1999 Gm-c1012-429 5′ similar to SW: PRS6_SOLTU P54778 26S PROTEASE REGULATORY SUBUNIT 6B HOMOLOG.;, mRNA sequence.
  • GB_IN2 CELB0213 39134 AF039050 Caenorhabditis elegans cosmid B0213. Caenorhabditis elegans 35,814 2-Jun-99 GB_GSS1: CNS00PZB 364 AL085157 Arabidopsis thaliana genome survey sequence SP6 end of BAC F10D11 of IGF Arabidopsis thaliana 38,462 28-Jun-99 library from strain Columbia of Arabidopsis thaliana , genomic survey sequence.
  • GB_RO RNITPR2R 10708 X61677 Rat ITPR2 gene for type 2 inositol triphosphate receptor.
  • rxa02691 930 GB_IN1 DME9736 7411 AJ009736 Drosophila melanogaster idefix retroelement: gag, pol and env genes, partial.
  • GB_PR4 AC004801 193561 AC004801 Homo sapiens 12q13.1 PAC RPCI1-228P16 (Roswell Park Cancer Institute Human Homo sapiens 39,341 2-Feb-99 PAC Library) complete sequence.
  • GB_PR4 AC004801 193561 AC004801 Homo sapiens 12q13.1 PAC RPCI1-228P16 (Roswell Park Cancer Institute Human Homo sapiens 37,037 2-Feb-99 PAC Library) complete sequence.
  • GB_EST34 AV132028 258 AV132028 AV132028 Mus musculus C57BL/6J 11-day embryo Mus musculus cDNA clone Mus musculus 43,529 1-Jul-99 2700087F01, mRNA sequence.
  • GB_GSS10 AQ240654 452 AQ240654 CIT-HSP-2385D24.TFB.1 CIT-HSP Homo sapiens genomic clone 2385D24, genomic Homo sapiens 40,044 30-Sep-98 survey sequence.
  • GB_GSS11 AQ309500 576 AQ309500 CIT-HSP-2384D24.TFD CIT-HSP Homo sapiens genomic clone 2384D24, genomic Homo sapiens 38,869 22-DEC-1998 survey sequence.
  • GB_BA2 AF086791 37867 AF086791 Zymomonas mobilis strain ZM4 clone 67E10 carbamoylphosphate synthetase small Zymomonas mobilis 39,024 4-Nov-98 subunit (carA), carbamoylphosphate synthetase large subunit (carB), transcription elongation factor (greA), enolase (eno), pyruvate dehydrogenase alpha subunit (pdhA), pyruvate dehydrogenase beta subunit (pdhB), ribonuclease H (mh), homoserine kinase homolog, alcohol dehydrogenase II (adhB), and excinuclease ABC subunit A (uvrA) genes, complete cds; and unknown genes.
  • carA carbamoylphosphate synthetase large subunit
  • greyA transcription elongation factor
  • GB_BA1 SYCSLRB 146271 D64000 Synechocystis sp. PCC6803 complete genome, 19/27, 2392729-2538999. Synechocystis sp. 34,573 13-Feb-99 GB_BA2: AE001306 13316 AE001306 Chlamydia trachomatis section 33 of 87 of the complete genome.
  • GB_BA2 Chlamydia trachomatis 38,940 2-Sep-98 rxa02767 906
  • GB_BA2 AF126953 1638 AF126953 Corynebacterium glutamicum cystathionine gamma-synthase (metB) gene, complete Corynebacterium 100,000 10-Sep-99 cds.
  • glutamicum GB_BA1 SCI5 6661 AL079332 Streptomyces coelicolor cosmid I5.
  • RPL15 60S Ribosomal Protein L15 pseudogene
  • GB_BA2 AF099015 5000 AF099015 Streptomyces coelicolor strain A3(2) integrase (int), Fe-containing superoxide Streptomyces coelicolor 36,721 1-Jun-99 dismutase II (sodF2), Fe uptake system permease (ftrE), and Fe uptake system integral membrane protein (ftrD) genes, complete cds.
  • GB_BA1 ECOUW93 338534 U14003 Escherichia coli K-12 chromosomal region from 92.8 to 00.1 minutes.
  • Escherichia coli 38,787 17-Apr-96 GB_HTG3 AC011361 186148 AC011361
  • Homo sapiens chromosome 5 clone CIT-HSPC_482N19 *** SEQUENCING IN Homo sapiens 43,577 06-OCT-1999 PROGRESS ***, 69 unordered pieces.
  • rxa02794 1197 GB_PR4 AC005998 96556 AC005998 Homo sapiens clone DJ0622E21, complete sequence.
  • Homo sapiens 37,298 29-Jul-99 GB_PR4 AC006008 57554 AC006008 Homo sapiens clone DJ0820A21, complete sequence.
  • GB_GSS5 AQ784593 515 AQ784593 HS_3248_A2_F02_T7C CIT Approved Human Genomic Sperm Library
  • GB_GSS13 AQ473140 397 AQ473140 CITBI-E1-2589G6.TF CITBI-E1 Homo sapiens genomic clone 2589G6, genomic Homo sapiens 34,761 23-Apr-99 survey sequence.
  • GB_EST18 AA696785 316 AA696785 GM08392.5prime GM Drosophila melanogaster ovary BlueScript Drosophila Drosophila melanogaster 40,604 28-Nov-98 melanogaster cDNA clone GM08392 5prime, mRNA sequence.
  • GB_EST18 AA696785 316 AA696785 GM08392.5prime GM Drosophila melanogaster ovary BlueScript Drosophila Drosophila melanogaster 38,281 28-Nov-98 melanogaster cDNA clone GM08392 5prime, mRNA sequence.
  • GB_BA1 CGBETPGEN 2339 X93514 C. glutamicum betP gene.
  • GB_PL1 Bacillus subtilis 40,000 4-Feb-98 rxs03220 725 GB_PL1: CKHUP2 2353 X66855 C. kessleri HUP2 mRNA. Chlorella kessleri 45,328 17-Feb-97 GB_EST38: AW048153 383 AW048153 UI-M-BH1-alq-h-05-0-UI.s1 NIH_BMAP_M_S2 Mus musculus cDNA Mus musculus 41,758 18-Sep-99 clone UI-M-BH1-alq-h-05-0-UI 3′, mRNA sequence. GB_PL1: CKHUP2 2353 X66855 C. kessleri HUP2 mRNA. Chlorella kessleri 38,106 17-Feb-97

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Abstract

Isolated nucleic acid molecules, designated MCT nucleic acid molecules, which encode novel MCT proteins from Corynebacterium glutamicum are described. The invention also provides antisense nucleic acid molecules, recombinant expression vectors containing MCT nucleic acid molecules, and host cells into which the expression vectors have been introduced. The invention still further provides isolated MCT proteins, mutated MCT proteins, fusion proteins, antigenic peptides and methods for the improvement of production of a desired compound from C. glutamicum based on genetic engineering of MCT genes in this organism.

Description

    RELATED APPLICATIONS
  • This application is a divisional of U.S. application Ser. No. 10/627,476, filed Jul. 25, 2003, which is a continuation of U.S. application Ser. No. 09/602,787, filed Jun. 23, 2000, which, in turn, claims priority to prior filed U.S. Provisional Patent Application Ser. No. 60/141031, filed Jun. 25, 1999. This application also claims priority to German Patent Application No. 19931454.3, filed Jul. 8, 1999, German Patent Application No. 19931478.0, filed Jul. 8, 1999, German Patent Application No. 19931563.9, filed Jul. 8, 1999, German Patent Application No. 19932122.1, filed Jul. 9, 1999, German Patent Application No. 19932124.8, filed Jul. 9, 1999, German Patent Application No. 19932125.6, filed Jul. 9, 1999, German Patent Application No. 19932128.0, filed Jul. 9, 1999, German Patent Application No. 19932180.9, filed Jul. 9, 1999, German Patent Application No. 19932182.5, filed Jul. 9, 1999, German Patent Application No. 19932190.6, filed Jul. 9, 1999, German Patent Application No. 19932191.4, filed Jul. 9, 1999, German Patent Application No. 19932209.0, filed Jul. 9, 1999, German Patent Application No. 19932212.0, filed Jul. 9, 1999, German Patent Application No. 19932227.9, filed Jul. 9, 1999, German Patent Application No. 19932228.7, filed Jul. 9, 1999, German Patent Application No. 19932229.5, filed Jul. 9, 1999, German Patent Application No. 19932230.9, filed Jul. 9, 1999, German Patent Application No. 19932927.3, filed Jul. 14, 1999, German Patent Application No. 19933005.0, filed Jul. 14, 1999, German Patent Application No. 19933006.9, filed Jul. 14, 1999, German Patent Application No. 19940764.9, filed Aug. 27, 1999, German Patent Application No. 19940765.7, filed Aug. 27, 1999, German Patent Application No. 19940766.5, filed Aug. 27, 1999, German Patent Application No. 19940830.0, filed Aug. 27, 1999, German Patent Application No. 19940831.9, filed Aug. 27, 1999, German Patent Application No. 19940832.7, filed Aug. 27, 1999, German Patent Application No. 19940833.5, filed Aug. 27, 1999, German Patent Application No. 19941378.9 filed Aug. 31, 1999, German Patent Application No. 19941379.7, filed Aug. 31, 1999, German Patent Application No. 19941395.9, filed Aug. 31, 1999, German Patent Application No. 19942077.7, filed Sep. 3, 1999, German Patent Application No. 19942078.5, filed September 3, 1999, German Patent Application No. 19942079.3, filed Sep. 3, 1999, and German Patent Application No. 19942088.2, filed Sep. 3, 1999. The entire contents of all of the above referenced applications are hereby expressly incorporated herein by this reference.
    • INCORPORATION OF MATERIAL SUBMITTED ON COMPACT DISCS
  • This application incorporates herein by reference the material contained on the compact discs submitted herewith as part of this application. Specifically, the file “seqlistcorr2” (2.43 MB) contained on each of Copy 1, Copy 2 and the CRF copy of the Sequence Listing is hereby incorporated herein by reference. This file was created on Jul. 31, 2006. In addition, the files “Appendix A” (399 KB) and “Appendix B” (140 KB) contained on each of the compact disks entitled “Appendices Copy 1” and “Appendices Copy 2” are hereby incorporated herein by reference. Each of these files were created on Jul. 31, 2006.
    • BACKGROUND OF THE INVENTION
  • Certain products and by-products of naturally-occurring metabolic processes in cells have utility in a wide array of industries, including the food, feed, cosmetics, and pharmaceutical industries. These molecules, collectively termed ‘fine chemicals’, include organic acids, both proteinogenic and non-proteinogenic amino acids, nucleotides and nucleosides, lipids and fatty acids, diols, carbohydrates, aromatic compounds, vitamins and cofactors, and enzymes. Their production is most conveniently performed through the large-scale culture of bacteria developed to produce and secrete large quantities of one or more desired molecules. One particularly useful organism for this purpose is Corynebacterium glutamicum, a gram positive, nonpathogenic bacterium. Through strain selection, a number of mutant strains have been developed which produce an array of desirable compounds. However, selection of strains improved for the production of a particular molecule is a time-consuming and difficult process.
    • SUMMARY OF THE INVENTION
  • The invention provides novel bacterial nucleic acid molecules which have a variety of uses. These uses include the identification of microorganisms which can be used to produce fine chemicals, the modulation of fine chemical production in C. glutamicum or related bacteria, the typing or identification of C. glutamicum or related bacteria, as reference points for mapping the C. glutamicum genome, and as markers for transformation. These novel nucleic acid molecules encode proteins, referred to herein as membrane construction and membrane transport (MCT) proteins.
  • C. glutamicum is a gram positive, aerobic bacterium which is commonly used in industry for the large-scale production of a variety of fine chemicals, and also for the degradation of hydrocarbons (such as in petroleum spills) and for the oxidation of terpenoids. The MCT nucleic acid molecules of the invention, therefore, can be used to identify microorganisms which can be used to produce fine chemicals, e.g., by fermentation processes. Modulation of the expression of the MCT nucleic acids of the invention, or modification of the sequence of the MCT nucleic acid molecules of the invention, can be used to modulate the production of one or more fine chemicals from a microorganism (e.g., to improve the yield or production of one or more fine chemicals from a Corynebacterium or Brevibacterium species).
  • The MCT nucleic acids of the invention may also be used to identify an organism as being Corynebacterium glutamicum or a close relative thereof, or to identify the presence of C. glutamicum or a relative thereof in a mixed population of microorganisms. The invention provides the nucleic acid sequences of a number of C. glutamicum genes; by probing the extracted genomic DNA of a culture of a unique or mixed population of microorganisms under stringent conditions with a probe spanning a region of a C. glutamicum gene which is unique to this organism, one can ascertain whether this organism is present. Although Corynebacterium glutamicum itself is nonpathogenic, it is related to species pathogenic in humans, such as Corynebacterium diphtheriae (the causative agent of diphtheria); the detection of such organisms is of significant clinical relevance.
  • The MCT nucleic acid molecules of the invention may also serve as reference points for mapping of the C. glutamicum genome, or of genomes of related organisms. Similarly, these molecules, or variants or portions thereof, may serve as markers for genetically engineered Corynebacterium or Brevibacterium species. e.g.e.g. The MCT proteins encoded by the novel nucleic acid molecules of the invention are capable of, for example, performing a function involved in the metabolism (e.g., the biosynthesis or degradation) of compounds necessary for membrane biosynthesis, or of assisting in the transmembrane transport of one or more compounds either into or out of the cell. Given the availability of cloning vectors for use in Corynebacterium glutamicum, such as those disclosed in Sinskey et al., U.S. Pat. No. 4,649,119, and techniques for genetic manipulation of C. glutamicum and the related Brevibacterium species (e.g., lactofermentum) (Yoshihama et al, J. Bacteriol. 162: 591-597 (1985); Katsumata et al., J. Bacteriol. 159: 306-311 (1984); and Santamaria et al., J. Gen. Microbiol. 130: 2237-2246 (1984)), the nucleic acid molecules of the invention may be utilized in the genetic engineering of this organism to make it a better or more efficient producer of one or more fine chemicals. This improved production or efficiency of production of a fine chemical may be due to a direct effect of manipulation of a gene of the invention, or it may be due to an indirect effect of such manipulation.
  • There are a number of mechanisms by which the alteration of an MCT protein of the invention may directly affect the yield, production, and/or efficiency of production of a fine chemical from a C. glutamicum strain incorporating such an altered protein. Those MCT proteins involved in the export of fine chemical molecules from the cell may be increased in number or activity such that greater quantities of these compounds are secreted to the extracellular medium, from which they are more readily recovered. Similarly, those MCT proteins involved in the import of nutrients necessary for the biosynthesis of one or more fine chemicals (e.g., phosphate, sulfate, nitrogen compounds, etc.) may be increased in number or activity such that these precursors, cofactors, or intermediate compounds are increased in concentration within the cell. Further, fatty acids and lipids themselves are desirable fine chemicals; by optimizing the activity or increasing the number of one or more MCT proteins of the invention which participate in the biosynthesis of these compounds, or by impairing the activity of one or more MCT proteins which are involved in the degradation of these compounds, it may be possible to increase the yield, production, and/or efficiency of production of fatty acid and lipid molecules from C. glutamicum.
  • The mutagenesis of one or more MCT genes of the invention may also result in MCT proteins having altered activities which indirectly impact the production of one or more desired fine chemicals from C. glutamicum. For example, MCT proteins of the invention involved in the export of waste products may be increased in number or activity such that the normal metabolic wastes of the cell (possibly increased in quantity due to the overproduction of the desired fine chemical) are efficiently exported before they are able to damage nucleotides and proteins within the cell (which would decrease the viability of the cell) or to interfere with fine chemical biosynthetic pathways (which would decrease the yield, production, or efficiency of production of the desired fine chemical). Further, the relatively large intracellular quantities of the desired fine chemical may in itself be toxic to the cell, so by increasing the activity or number of transporters able to export this compound from the cell, one may increase the viability of the cell in culture, in turn leading to a greater number of cells in the culture producing the desired fine chemical. The MCT proteins of the invention may also be manipulated such that the relative amounts of different lipid and fatty acid molecules are produced. This may have a profound effect on the lipid composition of the membrane of the cell. Since each type of lipid has different physical properties, an alteration in the lipid composition of a membrane may significantly alter membrane fluidity. Changes in membrane fluidity can impact the transport of molecules across the membrane, as well as the integrity of the cell, both of which have a profound effect on the production of fine chemicals from C. glutamicum in large-scale fermentative culture.
  • The invention provides novel nucleic acid molecules which encode proteins, referred to herein as MCT proteins, which are capable of, for example, participating in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes. Nucleic acid molecules encoding an MCT protein are referred to herein as MCT nucleic acid molecules. In a preferred embodiment, the MCT protein participates in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes. Examples of such proteins include those encoded by the genes set forth in Table 1.
  • Accordingly, one aspect of the invention pertains to isolated nucleic acid molecules (e.g., cDNAs, DNAs, or RNAs) comprising a nucleotide sequence encoding an MCT protein or biologically active portions thereof, as well as nucleic acid fragments suitable as primers or hybridization probes for the detection or amplification of MCT-encoding nucleic acid (e.g., DNA or mRNA). In particularly preferred embodiments, the isolated nucleic acid molecule comprises one of the nucleotide sequences set forth in Appendix A or the coding region or a complement thereof of one of these nucleotide sequences. In other particularly preferred embodiments, the isolated nucleic acid molecule of the invention comprises a nucleotide sequence which hybridizes to or is at least about 50%, preferably at least about 60%, more preferably at least about 70%, 80% or 90%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more homologous to a nucleotide sequence set forth in Appendix A, or a portion thereof. In other preferred embodiments, the isolated nucleic acid molecule encodes one of the amino acid sequences set forth in Appendix B. The preferred MCT proteins of the present invention also preferably possess at least one of the MCT activities described herein.
  • In another embodiment, the isolated nucleic acid molecule encodes a protein or portion thereof wherein the protein or portion thereof includes an amino acid sequence which is sufficiently homologous to an amino acid sequence of Appendix B, e.g., sufficiently homologous to an amino acid sequence of Appendix B such that the protein or portion thereof maintains an MCT activity. Preferably, the protein or portion thereof encoded by the nucleic acid molecule maintains the ability to participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes. In one embodiment, the protein encoded by the nucleic acid molecule is at least about 50%, preferably at least about 60%, and more preferably at least about 70%, 80%, or 90% and most preferably at least about 95%, 96%, 97%, 98%, or 99% or more homologous to an amino acid sequence of Appendix B (e.g., an entire amino acid sequence selected from those sequences set forth in Appendix B). In another preferred embodiment, the protein is a full length C. glutamicum protein which is substantially homologous to an entire amino acid sequence of Appendix B (encoded by an open reading frame shown in Appendix A).
  • In another preferred embodiment, the isolated nucleic acid molecule is derived from C. glutamicum and encodes a protein (e.g., an MCT fusion protein) which includes a biologically active domain which is at least about 50% or more homologous to one of the amino acid sequences of Appendix B and is able to participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes, or has one or more of the activities set forth in Table 1, and which also includes heterologous nucleic acid sequences encoding a heterologous polypeptide or regulatory regions.
  • In another embodiment, the isolated nucleic acid molecule is at least 15 nucleotides in length and hybridizes under stringent conditions to a nucleic acid molecule comprising a nucleotide sequence of Appendix A. Preferably, the isolated nucleic acid molecule corresponds to a naturally-occurring nucleic acid molecule. More preferably, the isolated nucleic acid encodes a naturally-occurring C. glutamicum MCT protein, or a biologically active portion thereof.
  • Another aspect of the invention pertains to vectors, e.g., recombinant expression vectors, containing the nucleic acid molecules of the invention, and host cells into which such vectors have been introduced. In one embodiment, such a host cell is used to produce an MCT protein by culturing the host cell in a suitable medium. The MCT protein can be then isolated from the medium or the host cell.
  • Yet another aspect of the invention pertains to a genetically altered microorganism in which an MCT gene has been introduced or altered. In one embodiment, the genome of the microorganism has been altered by introduction of a nucleic acid molecule of the invention encoding wild-type or mutated MCT sequence as a transgene. In another embodiment, an endogenous MCT gene within the genome of the microorganism has been altered, e.g., functionally disrupted, by homologous recombination with an altered MCT gene. In another embodiment, an endogenous or introduced MCT gene in a microorganism has been altered by one or more point mutations, deletions, or inversions, but still encodes a functional MCT protein. In still another embodiment, one or more of the regulatory regions (e.g., a promoter, repressor, or inducer) of an MCT gene in a microorganism has been altered (e.g., by deletion, truncation, inversion, or point mutation) such that the expression of the MCT gene is modulated. In a preferred embodiment, the microorganism belongs to the genus Corynebacterium or Brevibacterium, with Corynebacterium glutamicum being particularly preferred. In a preferred embodiment, the microorganism is also utilized for the production of a desired compound, such as an amino acid, with lysine being particularly preferred.
  • In another aspect, the invention provides a method of identifying the presence or activity of Cornyebacterium diphtheriae in a subject. This method includes detection of one or more of the nucleic acid or amino acid sequences of the invention (e.g., the sequences set forth in Appendix A or Appendix B) in a subject, thereby detecting the presence or activity of Corynebacterium diphtheriae in the subject.
  • Still another aspect of the invention pertains to an isolated MCT protein or a portion, e.g., a biologically active portion, thereof. In a preferred embodiment, the isolated MCT protein or portion thereof can participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes. In another preferred embodiment, the isolated MCT protein or portion thereof is sufficiently homologous to an amino acid sequence of Appendix B such that the protein or portion thereof maintains the ability to participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes.
  • The invention also provides an isolated preparation of an MCT protein. In preferred embodiments, the MCT protein comprises an amino acid sequence of Appendix B. In another preferred embodiment, the invention pertains to an isolated full length protein which is substantially homologous to an entire amino acid sequence of Appendix B (encoded by an open reading frame set forth in Appendix A). In yet another embodiment, the protein is at least about 50%, preferably at least about 60%, and more preferably at least about 70%, 80%, or 90%, and most preferably at least about 95%, 96%, 97%, 98%, or 99% or more homologous to an entire amino acid sequence of Appendix B. In other embodiments, the isolated MCT protein comprises an amino acid sequence which is at least about 50% or more homologous to one of the amino acid sequences of Appendix B and is able to participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes, or has one or more of the activities set forth in Table 1.
  • Alternatively, the isolated MCT protein can comprise an amino acid sequence which is encoded by a nucleotide sequence which hybridizes, e.g., hybridizes under stringent conditions, or is at least about 50%, preferably at least about 60%, more preferably at least about 70%, 80%, or 90%, and even more preferably at least about 95%, 96%, 97%, 98,%, or 99% or more homologous, to a nucleotide sequence of Appendix B. It is also preferred that the preferred forms of MCT proteins also have one or more of the MCT bioactivities described herein.
  • The MCT polypeptide, or a biologically active portion thereof, can be operatively linked to a non-MCT polypeptide to form a fusion protein. In preferred embodiments, this fusion protein has an activity which differs from that of the MCT protein alone. In other preferred embodiments, this fusion protein participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes. In particularly preferred embodiments, integration of this fusion protein into a host cell modulates production of a desired compound from the cell.
  • In another aspect, the invention provides methods for screening molecules which modulate the activity of an MCT protein, either by interacting with the protein itself or a substrate or binding partner of the MCT protein, or by modulating the transcription or translation of an MCT nucleic acid molecule of the invention.
  • Another aspect of the invention pertains to a method for producing a fine chemical. This method involves the culturing of a cell containing a vector directing the expression of an MCT nucleic acid molecule of the invention, such that a fine chemical is produced. In a preferred embodiment, this method further includes the step of obtaining a cell containing such a vector, in which a cell is transfected with a vector directing the expression of an MCT nucleic acid. In another preferred embodiment, this method further includes the step of recovering the fine chemical from the culture. In a particularly preferred embodiment, the cell is from the genus Corynebacterium or Brevibacterium, or is selected from those strains set forth in Table 3.
  • Another aspect of the invention pertains to methods for modulating production of a molecule from a microorganism. Such methods include contacting the cell with an agent which modulates MCT protein activity or MCT nucleic acid expression such that a cell associated activity is altered relative to this same activity in the absence of the agent. In a preferred embodiment, the cell is modulated for one or more C. glutamicum metabolic pathways for cell membrane components or is modulated for the transport of compounds across such membranes, such that the yields or rate of production of a desired fine chemical by this microorganism is improved. The agent which modulates MCT protein activity can be an agent which stimulates MCT protein activity or MCT nucleic acid expression. Examples of agents which stimulate MCT protein activity or MCT nucleic acid expression include small molecules, active MCT proteins, and nucleic acids encoding MCT proteins that have been introduced into the cell. Examples of agents which inhibit MCT activity or expression include small molecules and antisense MCT nucleic acid molecules.
  • Another aspect of the invention pertains to methods for modulating yields of a desired compound from a cell, involving the introduction of a wild-type or mutant MCT gene into a cell, either maintained on a separate plasmid or integrated into the genome of the host cell. If integrated into the genome, such integration can be random, or it can take place by homologous recombination such that the native gene is replaced by the introduced copy, causing the production of the desired compound from the cell to be modulated. In a preferred embodiment, said yields are increased. In another preferred embodiment, said chemical is a fine chemical. In a particularly preferred embodiment, said fine chemical is an amino acid. In especially preferred embodiments, said amino acid is L-lysine.
    • DETAILED DESCRIPTION OF THE INVENTION
  • The present invention provides MCT nucleic acid and protein molecules which are involved in the metabolism of cellular membrane components in C. glutamicum or in the transport of compounds across such membranes. The molecules of the invention may be utilized in the modulation of production of fine chemicals from microorganisms, such as C. glutamicum, either directly (e.g., where overexpression or optimization of a fatty acid biosynthesis protein has a direct impact on the yield, production, and/or efficiency of production of the fatty acid from modified C. glutamicum), or may have an indirect impact which nonetheless results in an increase of yield, production, and/or efficiency of production of the desired compound (e.g., where modulation of the metabolism of cell membrane components results in alterations in the yield, production, and/or efficiency of production or the composition of the cell membrane, which in turn may impact the production of one or more fine chemicals). Aspects of the invention are further explicated below.
  • I. Fine Chemicals
  • The term ‘fine chemical’ is art-recognized and includes molecules produced by an organism which have applications in various industries, such as, but not limited to, the pharmaceutical, agriculture, and cosmetics industries. Such compounds include organic acids, such as tartaric acid, itaconic acid, and diaminopimelic acid, both proteinogenic and non-proteinogenic amino acids, purine and pyrimidine bases, nucleosides, and nucleotides (as described e.g. in Kuninaka, A. (1996) Nucleotides and related compounds, p. 561-612, in Biotechnology vol. 6, Rehm et al., eds. VCH: Weinheim, and references contained therein), lipids, both saturated and unsaturated fatty acids (e.g., arachidonic acid), diols (e.g., propane diol, and butane diol), carbohydrates (e.g, hyaluronic acid and trehalose), aromatic compounds (e.g, aromatic amines, vanillin, and indigo), vitamins and cofactors (as described in Ullmann's Encyclopedia of Industrial Chemistry, vol. A27, “Vitamins”, p. 443-613 (1996) VCH: Weinheim and references therein; and Ong, A.S., Niki, E. & Packer, L. (1995) “Nutrition, Lipids, Health, and Disease” Proceedings of the UNESCO/Confederation of Scientific and Technological Associations in Malaysia, and the Society for Free Radical Research—Asia, held Sept. 1-3, 1994 at Penang, Malaysia, AOCS Press, (1995)), enzymes, polyketides (Cane et al. (1998) Science 282: 63-68), and all other chemicals described in Gutcho (1983) Chemicals by Fermentation, Noyes Data Corporation, ISBN: 0818805086 and references therein. The metabolism and uses of certain of these fine chemicals are further explicated below.
  • A. Amino Acid Metabolism and Uses
  • Amino acids comprise the basic structural units of all proteins, and as such are essential for normal cellular functioning in all organisms. The term “amino acid” is art-recognized. The proteinogenic amino acids, of which there are 20 species, serve as structural units for proteins, in which they are linked by peptide bonds, while the nonproteinogenic amino acids (hundreds of which are known) are not normally found in proteins (see Ulmann's Encyclopedia of Industrial Chemistry, vol. A2, p. 57-97 VCH: Weinheim (1985)). Amino acids may be in the D- or L-optical configuration, though L-amino acids are generally the only type found in naturally-occurring proteins. Biosynthetic and degradative pathways of each of the 20 proteinogenic amino acids have been well characterized in both prokaryotic and eukaryotic cells (see, for example, Stryer, L. Biochemistry, 3rd edition, pages 578-590 (1988)). The ‘essential’ amino acids (histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine), so named because they are generally a nutritional requirement due to the complexity of their biosyntheses, are readily converted by simple biosynthetic pathways to the remaining 11 ‘nonessential’ amino acids (alanine, arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine). Higher animals do retain the ability to synthesize some of these amino acids, but the essential amino acids must be supplied from the diet in order for normal protein synthesis to occur.
  • Aside from their function in protein biosynthesis, these amino acids are interesting chemicals in their own right, and many have been found to have various applications in the food, feed, chemical, cosmetics, agriculture, and pharmaceutical industries. Lysine is an important amino acid in the nutrition not only of humans, but also of monogastric animals such as poultry and swine. Glutamate is most commonly used as a flavor additive (mono-sodium glutamate, MSG) and is widely used throughout the food industry, as are aspartate, phenylalanine, glycine, and cysteine. Glycine, L-methionine and tryptophan are all utilized in the pharmaceutical industry. Glutamine, valine, leucine, isoleucine, histidine, arginine, proline, serine and alanine are of use in both the pharmaceutical and cosmetics industries. Threonine, tryptophan, and D/ L-methionine are common feed additives. (Leuchtenberger, W. (1996) Amino aids—technical production and use, p. 466-502 in Rehm et al. (eds.) Biotechnology vol. 6, chapter 14a, VCH: Weinheim). Additionally, these amino acids have been found to be useful as precursors for the synthesis of synthetic amino acids and proteins, such as N-acetylcysteine, S-carboxymethyl-L-cysteine, (S)-5-hydroxytryptophan, and others described in Ulmann's Encyclopedia of Industrial Chemistry, vol. A2, p. 57-97, VCH: Weinheim, 1985.
  • The biosynthesis of these natural amino acids in organisms capable of producing them, such as bacteria, has been well characterized (for review of bacterial amino acid biosynthesis and regulation thereof, see Umbarger, H. E.(1978) Ann. Rev. Biochem. 47: 533-606). Glutamate is synthesized by the reductive amination of α-ketoglutarate, an intermediate in the citric acid cycle. Glutamine, proline, and arginine are each subsequently produced from glutamate. The biosynthesis of serine is a three-step process beginning with 3-phosphoglycerate (an intermediate in glycolysis), and resulting in this amino acid after oxidation, transamination, and hydrolysis steps. Both cysteine and glycine are produced from serine; the former by the condensation of homocysteine with serine, and the latter by the transferal of the side-chain β-carbon atom to tetrahydrofolate, in a reaction catalyzed by serine transhydroxymethylase. Phenylalanine, and tyrosine are synthesized from the glycolytic and pentose phosphate pathway precursors erythrose 4-phosphate and phosphoenolpyruvate in a 9-step biosynthetic pathway that differ only at the final two steps after synthesis of prephenate. Tryptophan is also produced from these two initial molecules, but its synthesis is an 11-step pathway. Tyrosine may also be synthesized from phenylalanine, in a reaction catalyzed by phenylalanine hydroxylase. Alanine, valine, and leucine are all biosynthetic products of pyruvate, the final product of glycolysis. Aspartate is formed from oxaloacetate, an intermediate of the citric acid cycle. Asparagine, methionine, threonine, and lysine are each produced by the conversion of aspartate. Isoleucine is formed from threonine. A complex 9-step pathway results in the production of histidine from 5-phosphoribosyl-1-pyrophosphate, an activated sugar.
  • Amino acids in excess of the protein synthesis needs of the cell cannot be stored, and are instead degraded to provide intermediates for the major metabolic pathways of the cell (for review see Stryer, L. Biochemistry 3 rd ed. Ch. 21 “Amino Acid Degradation and the Urea Cycle” p. 495-516 (1988)). Although the cell is able to convert unwanted amino acids into useful metabolic intermediates, amino acid production is costly in terms of energy, precursor molecules, and the enzymes necessary to synthesize them. Thus it is not surprising that amino acid biosynthesis is regulated by feedback inhibition, in which the presence of a particular amino acid serves to slow or entirely stop its own production (for overview of feedback mechanisms in amino acid biosynthetic pathways, see Stryer, L. Biochemistry, 3rd ed. Ch. 24: “Biosynthesis of Amino Acids and Heme” p. 575-600 (1988)). Thus, the output of any particular amino acid is limited by the amount of that amino acid present in the cell.
  • B. Vitamin, Cofactor, and Nutraceutical Metabolism and Uses
  • Vitamins, cofactors, and nutraceuticals comprise another group of molecules which the higher animals have lost the ability to synthesize and so must ingest, although they are readily synthesized by other organisms such as bacteria. These molecules are either bioactive substances themselves, or are precursors of biologically active substances which may serve as electron carriers or intermediates in a variety of metabolic pathways. Aside from their nutritive value, these compounds also have significant industrial value as coloring agents, antioxidants, and catalysts or other processing aids. (For an overview of the structure, activity, and industrial applications of these compounds, see, for example, Ullman's Encyclopedia of Industrial Chemistry, “Vitamins” vol. A27, p. 443-613, VCH: Weinheim, 1996.) The term “vitamin” is art-recognized, and includes nutrients which are required by an organism for normal functioning, but which that organism cannot synthesize by itself. The group of vitamins may encompass cofactors and nutraceutical compounds. The language “cofactor” includes nonproteinaceous compounds required for a normal enzymatic activity to occur. Such compounds may be organic or inorganic; the cofactor molecules of the invention are preferably organic. The term “nutraceutical” includes dietary supplements having health benefits in plants and animals, particularly humans. Examples of such molecules are vitamins, antioxidants, and also certain lipids (e.g., polyunsaturated fatty acids).
  • The biosynthesis of these molecules in organisms capable of producing them, such as bacteria, has been largely characterized (Ullman's Encyclopedia of Industrial Chemistry, “Vitamins” vol. A27, p. 443-613, VCH: Weinheim, 1996; Michal, G. (1999) Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, John Wiley & Sons; Ong, A.S., Niki, E. & Packer, L. (1995) “Nutrition, Lipids, Health, and Disease” Proceedings of the UNESCO/Confederation of Scientific and Technological Associations in Malaysia, and the Society for Free Radical Research—Asia, held Sept. 1-3, 1994 at Penang, Malaysia, AOCS Press: Champaign, IL X, 374 S).
  • Thiamin (vitamin B1) is produced by the chemical coupling of pyrimidine and thiazole moieties. Riboflavin (vitamin B2) is synthesized from guanosine-5′-triphosphate (GTP) and ribose-5′-phosphate. Riboflavin, in turn, is utilized for the synthesis of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). The family of compounds collectively termed ‘vitamin B6’ (e.g., pyridoxine, pyridoxamine, pyridoxa-5′-phosphate, and the commercially used pyridoxin hydrochloride) are all derivatives of the common structural unit, 5-hydroxy-6-methylpyridine. Pantothenate (pantothenic acid, (R)-(+)-N-(2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)-β-alanine) can be produced either by chemical synthesis or by fermentation. The final steps in pantothenate biosynthesis consist of the ATP-driven condensation of β-alanine and pantoic acid. The enzymes responsible for the biosynthesis steps for the conversion to pantoic acid, to β-alanine and for the condensation to panthotenic acid are known. The metabolically active form of pantothenate is Coenzyme A, for which the biosynthesis proceeds in 5 enzymatic steps. Pantothenate, pyridoxal-5′-phosphate, cysteine and ATP are the precursors of Coenzyme A. These enzymes not only catalyze the formation of panthothante, but also the production of (R)-pantoic acid, (R)-pantolacton, (R)-panthenol (provitamin B5), pantetheine (and its derivatives) and coenzyme A.
  • Biotin biosynthesis from the precursor molecule pimeloyl-CoA in microorganisms has been studied in detail and several of the genes involved have been identified. Many of the corresponding proteins have been found to also be involved in Fe-cluster synthesis and are members of the nifS class of proteins. Lipoic acid is derived from octanoic acid, and serves as a coenzyme in energy metabolism, where it becomes part of the pyruvate dehydrogenase complex and the α-ketoglutarate dehydrogenase complex. The folates are a group of substances which are all derivatives of folic acid, which is turn is derived from L-glutamic acid, p-amino-benzoic acid and 6-methylpterin. The biosynthesis of folic acid and its derivatives, starting from the metabolism intermediates guanosine-5′-triphosphate (GTP), L-glutamic acid and p-amino-benzoic acid has been studied in detail in certain microorganisms.
  • Corrinoids (such as the cobalamines and particularly vitamin B12) and porphyrines belong to a group of chemicals characterized by a tetrapyrole ring system. The biosynthesis of vitamin B12 is sufficiently complex that it has not yet been completely characterized, but many of the enzymes and substrates involved are now known. Nicotinic acid (nicotinate), and nicotinamide are pyridine derivatives which are also termed ‘niacin’. Niacin is the precursor of the important coenzymes NAD (nicotinamide adenine dinucleotide) and NADP (nicotinamide adenine dinucleotide phosphate) and their reduced forms.
  • The large-scale production of these compounds has largely relied on cell-free chemical syntheses, though some of these chemicals have also been produced by large-scale culture of microorganisms, such as riboflavin, Vitamin B6, pantothenate, and biotin. Only Vitamin B12 is produced solely by fermentation, due to the complexity of its synthesis. In vitro methodologies require significant inputs of materials and time, often at great cost.
  • C. Purine, Pyrimidine, Nucleoside and Nucleotide Metabolism and Uses
  • Purine and pyrimidine metabolism genes and their corresponding proteins are important targets for the therapy of tumor diseases and viral infections. The language “purine” or “pyrimidine” includes the nitrogenous bases which are constituents of nucleic acids, co-enzymes, and nucleotides. The term “nucleotide” includes the basic structural units of nucleic acid molecules, which are comprised of a nitrogenous base, a pentose sugar (in the case of RNA, the sugar is ribose; in the case of DNA, the sugar is D-deoxyribose), and phosphoric acid. The language “nucleoside” includes molecules which serve as precursors to nucleotides, but which are lacking the phosphoric acid moiety that nucleotides possess. By inhibiting the biosynthesis of these molecules, or their mobilization to form nucleic acid molecules, it is possible to inhibit RNA and DNA synthesis; by inhibiting this activity in a fashion targeted to cancerous cells, the ability of tumor cells to divide and replicate may be inhibited. Additionally, there are nucleotides which do not form nucleic acid molecules, but rather serve as energy stores (i.e., AMP) or as coenzymes (i.e., FAD and NAD).
  • Several publications have described the use of these chemicals for these medical indications, by influencing purine and/or pyrimidine metabolism (e.g Christopherson, R. I. and Lyons, S. D. (1990) “Potent inhibitors of de novo pyrimidine and purine biosynthesis as chemotherapeutic agents.” Med. Res. Reviews 10: 505-548). Studies of enzymes involved in purine and pyrimidine metabolism have been focused on the development of new drugs which can be used, for example, as immunosuppressants or anti-proliferants (Smith, J. L., (1995) “Enzymes in nucleotide synthesis.” Curr. Opin. Struct. Biol. 5: 752-757; (1995) Biochem Soc. Transact. 23: 877-902). However, purine and pyrimidine bases, nucleosides and nucleotides have other utilities: as intermediates in the biosynthesis of several fine chemicals (e.g., thiamine, S-adenosyl-methionine, folates, or riboflavin), as energy carriers for the cell (e.g., ATP or GTP), and for chemicals themselves, commonly used as flavor enhancers (e.g., IMP or GMP) or for several medicinal applications (see, for example, Kuninaka, A. (1996) Nucleotides and Related Compounds in Biotechnology vol. 6, Rehm et al., eds. VCH: Weinheim, p. 561-612). Also, enzymes involved in purine, pyrimidine, nucleoside, or nucleotide metabolism are increasingly serving as targets against which chemicals for crop protection, including fungicides, herbicides and insecticides, are developed.
  • The metabolism of these compounds in bacteria has been characterized (for reviews see, for example, Zalkin, H. and Dixon, J. E. (1992) “de novo purine nucleotide biosynthesis”, in: Progress in Nucleic Acid Research and Molecular Biology, vol. 42, Academic Press:, p. 259-287; and Michal, G. (I 999) “Nucleotides and Nucleosides”, Chapter 8 in: Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, Wiley: New York). Purine metabolism has been the subject of intensive research, and is essential to the normal functioning of the cell. Impaired purine metabolism in higher animals can cause severe disease, such as gout. Purine nucleotides are synthesized from ribose-5-phosphate, in a series of steps through the intermediate compound inosine-5′-phosphate (IMP), resulting in the production of guanosine-5′-monophosphate (GMP) or adenosine-5′-monophosphate (AMP), from which the triphosphate forms utilized as nucleotides are readily formed. These compounds are also utilized as energy stores, so their degradation provides energy for many different biochemical processes in the cell. Pyrimidine biosynthesis proceeds by the formation of uridine-5′-monophosphate (UMP) from ribose-5-phosphate. UMP, in turn, is converted to cytidine-5′-triphosphate (CTP). The deoxy- forms of all of these nucleotides are produced in a one step reduction reaction from the diphosphate ribose form of the nucleotide to the diphosphate deoxyribose form of the nucleotide. Upon phosphorylation, these molecules are able to participate in DNA synthesis.
  • D. Trehalose Metabolism and Uses
  • Trehalose consists of two glucose molecules, bound in α, α-1,1 linkage. It is commonly used in the food industry as a sweetener, an additive for dried or frozen foods, and in beverages. However, it also has applications in the pharmaceutical, cosmetics and biotechnology industries (see, for example, Nishimoto et al., (1998) U.S. Pat. No. 5,759,610; Singer, M. A. and Lindquist, S. (1998) Trends Biotech. 16: 460-467; Paiva, C. L. A. and Panek, A. D. (1996) Biotech. Ann. Rev. 2: 293-314; and Shiosaka, M. (1997) J. Japan 172: 97-102). Trehalose is produced by enzymes from many microorganisms and is naturally released into the surrounding medium, from which it can be collected using methods known in the art.
  • II. Membrane Biosynthesis and Transmembrane Transport
  • Cellular membranes serve a variety of functions in a cell. First and foremost, a membrane differentiates the contents of a cell from the surrounding environment, thus giving integrity to the cell. Membranes may also serve as barriers to the influx of hazardous or unwanted compounds, and also to the efflux of desired compounds. Cellular membranes are by nature impervious to the unfacilitated diffusion of hydrophilic compounds such as proteins, water molecules and ions due to their structure: a bilayer of lipid molecules in which the polar head groups face outwards (towards the exterior and interior of the cell, respectively) and the nonpolar tails face inwards at the center of the bilayer, forming a hydrophobic core (for a general review of membrane structure and function, see Gennis, R. B. (1989) Biomembranes, Molecular Structure and Function, Springer: Heidelberg). This barrier enables cells to maintain a relatively higher concentration of desired compounds and a relatively lower concentration of undesired compounds than are contained within the surrounding medium, since the diffusion of these compounds is effectively blocked by the membrane. However, the membrane also presents an effective barrier to the import of desired compounds and the export of waste molecules. To overcome this difficulty, cellular membranes incorporate many kinds of transporter proteins which are able to facilitate the transmembrane transport of different kinds of compounds. There are two general classes of these transport proteins: pores or channels and transporters. The former are integral membrane proteins, sometimes complexes of proteins, which form a regulated hole through the membrane. This regulation, or ‘gating’ is generally specific to the molecules to be transported by the pore or channel, rendering these transmembrane constructs selectively permeable to a specific class of substrates; for example, a potassium channel is constructed such that only ions having a like charge and size to that of potassium may pass through. Channel and pore proteins tend to have discrete hydrophobic and hydrophilic domains, such that the hydrophobic face of the protein may associate with the interior of the membrane while the hydrophilic face lines the interior of the channel, thus providing a sheltered hydrophilic environment through which the selected hydrophilic molecule may pass. Many such pores/channels are known in the art, including those for potassium, calcium, sodium, and chloride ions.
  • This pore and channel-mediated system of facilitated diffusion is limited to very small molecules, such as ions, because pores or channels large enough to permit the passage of whole proteins by facilitated diffusion would be unable to prevent the passage of smaller hydrophilic molecules as well. Transport of molecules by this process is sometimes termed ‘facilitated diffusion’ since the driving force of a concentration gradient is required for the transport to occur. Permeases also permit facilitated diffusion of larger molecules, such as glucose or other sugars, into the cell when the concentration of these molecules on one side of the membrane is greater than that on the other (also called ‘uniport’). In contrast to pores or channels, these integral membrane proteins (often having between 6-14 membrane-spanning β-helices) do not form open channels through the membrane, but rather bind to the target molecule at the surface of the membrane and then undergo a conformational shift such that the target molecule is released on the opposite side of the membrane.
  • However, cells frequently require the import or export of molecules against the existing concentration gradient (‘active transport’), a situation in which facilitated diffusion cannot occur. There are two general mechanisms used by cells for such membrane transport: symport or antiport, and energy-coupled transport such as that mediated by the ABC transporters. Symport and antiport systems couple the movement of two different molecules across the membrane (via permeases having two separate binding sites for the two different molecules); in symport, both molecules are transported in the same direction, while in antiport, one molecule is imported while the other is exported. This is possible energetically because one of the two molecules moves in accordance with a concentration gradient, and this energetically favorable event is permitted only upon concomitant movement of a desired compound against the prevailing concentration gradient. Single molecules may be transported across the membrane against the concentration gradient in an energy-driven process, such as that utilized by the ABC transporters. In this system, the transport protein located in the membrane has an ATP-binding cassette; upon binding of the target molecule, the ATP is converted to ADP+Pi, and the resulting release of energy is used to drive the movement of the target molecule to the opposite face of the membrane, facilitated by the transporter. For more detailed descriptions of all of these transport systems, see: Bamberg, E. et al., (1993) “Charge transport of ion pumps on lipid bilayer membranes”, Q. Rev. Biophys. 26: 1-25; Findlay, J. B. C. (1991) “Structure and function in membrane transport systems”, Curr. Opin. Struct. Biol. 1:804-810; Higgins, C. F. (1992) “ABC transporters from microorganisms to man”, Ann. Rev. Cell Biol. 8: 67-113; Gennis, R. B. (1989) “Pores, Channels and Transporters”, in: Biomembranes, Molecular Structure and Function, Springer: Heidelberg, p. 270-322; and Nikaido, H. and Saier, H. (1992) “Transport proteins in bacteria: common themes in their design”, Science 258: 936-942, and references contained within each of these references.
  • The synthesis of membranes is a well-characterized process involving a number of components, the most important of which are lipid molecules. Lipid synthesis may be divided into two parts: the synthesis of fatty acids and their attachment to sn-glycerol-3-phosphate, and the addition or modification of a polar head group. Typical lipids utilized in bacterial membranes include phospholipids, glycolipids, sphingolipids, and phosphoglycerides. Fatty acid synthesis begins with the conversion of acetyl CoA either to malonyl CoA by acetyl CoA carboxylase, or to acetyl-ACP by acetyltransacylase. Following a condensation reaction, these two product molecules together form acetoacetyl-ACP, which is converted by a series of condensation, reduction and dehydration reactions to yield a saturated fatty acid molecule having a desired chain length. The production of unsaturated fatty acids from such molecules is catalyzed by specific desaturases either aerobically, with the help of molecular oxygen, or anaerobically (for reference on fatty acid synthesis, see F. C. Neidhardt et al. (1996) E. coli and Salmonella. ASM Press: Washington, D.C., p. 612-636 and references contained therein; Lengeler et al. (eds) (1999) Biology of Procaryotes. Thieme: Stuttgart, New York, and references contained therein; and Magnuson, K. et al., (1993) Microbiological Reviews 57: 522-542, and references contained therein). The cyclopropane fatty acids (CFA) are synthesized by a specific CFA-synthase using SAM as a cosubstrate. Branched chain fatty acids are synthesized from branched chain amino acids that are deaminated to yield branched chain 2-oxo-acids (see Lengeler et al., eds. (1999) Biology of Procaryotes. Thieme: Stuttgart, New York, and references contained therein). Another essential step in lipid synthesis is the transfer of fatty acids onto the polar head groups by, for example, glycerol-phosphate-acyltransferases. The combination of various precursor molecules and biosynthetic enzymes results in the production of different fatty acid molecules, which has a profound effect on the composition of the membrane.
  • III. Elements and Methods of the Invention
  • The present invention is based, at least in part, on the discovery of novel molecules, referred to herein as MCT nucleic acid and protein molecules, which control the production of cellular membranes in C. glutamicum and govern the movement of molecules across such membranes. In one embodiment, the MCT molecules participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes. In a preferred embodiment, the activity of the MCT molecules of the present invention to regulate membrane component production and membrane transport has an impact on the production of a desired fine chemical by this organism. In a particularly preferred embodiment, the MCT molecules of the invention are modulated in activity, such that the C. glutamicum metabolic pathways which the MCT proteins of the invention regulate are modulated in yield, production, and/or efficiency of production and the transport of compounds through the membranes is altered in efficiency, which either directly or indirectly modulates the yield, production, and/or efficiency of production of a desired fine chemical by C. glutamicum.
  • The language, “MCT protein” or “MCT polypeptide” includes proteins which participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes. Examples of MCT proteins include those encoded by the MCT genes set forth in Table 1 and Appendix A. The terms “MCT gene” or “MCT nucleic acid sequence” include nucleic acid sequences encoding an MCT protein, which consist of a coding region and also corresponding untranslated 5′ and 3′ sequence regions. Examples of MCT genes include those set forth in Table 1. The terms “production” or “productivity” are art-recognized and include the concentration of the fermentation product (for example, the desired fine chemical) formed within a given time and a given fermentation volume (e.g., kg product per hour per liter). The term “efficiency of production” includes the time required for a particular level of production to be achieved (for example, how long it takes for the cell to attain a particular rate of output of a fine chemical). The term “yield” or “product/carbon yield” is art-recognized and includes the efficiency of the conversion of the carbon source into the product (i.e., fine chemical). This is generally written as, for example, kg product per kg carbon source. By increasing the yield or production of the compound, the quantity of recovered molecules, or of useful recovered molecules of that compound in a given amount of culture over a given amount of time is increased. The terms “biosynthesis” or a “biosynthetic pathway” are art-recognized and include the synthesis of a compound, preferably an organic compound, by a cell from intermediate compounds in what may be a multistep and highly regulated process. The terms “degradation” or a “degradation pathway” are art-recognized and include the breakdown of a compound, preferably an organic compound, by a cell to degradation products (generally speaking, smaller or less complex molecules) in what may be a multistep and highly regulated process. The language “metabolism” is art-recognized and includes the totality of the biochemical reactions that take place in an organism. The metabolism of a particular compound, then, (e.g., the metabolism of an amino acid such as glycine) comprises the overall biosynthetic, modification, and degradation pathways in the cell related to this compound.
  • In another embodiment, the MCT molecules of the invention are capable of modulating the production of a desired molecule, such as a fine chemical, in a microorganism such as C. glutamicum. There are a number of mechanisms by which the alteration of an MCT protein of the invention may directly affect the yield, production, and/or efficiency of production of a fine chemical from a C. glutamicum strain incorporating such an altered protein. Those MCT proteins involved in the export of fine chemical molecules from the cell may be increased in number or activity such that greater quantities of these compounds are secreted to the extracellular medium, from which they are more readily recovered. Similarly, those MCT proteins involved in the import of nutrients necessary for the biosynthesis of one or more fine chemicals (e.g., phosphate, sulfate, nitrogen compounds, etc.) may be increased in number or activity such that these precursor, cofactor, or intermediate compounds are increased in concentration within the cell. Further, fatty acids and lipids themselves are desirable fine chemicals; by optimizing the activity or increasing the number of one or more MCT proteins of the invention which participate in the biosynthesis of these compounds, or by impairing the activity of one or more MCT proteins which are involved in the degradation of these compounds, it may be possible to increase the yield, production, and/or efficiency of production of fatty acid and lipid molecules from C. glutamicum.
  • The mutagenesis of one or more MCT genes of the invention may also result in MCT proteins having altered activities which indirectly impact the production of one or more desired fine chemicals from C. glutamicum. For example, MCT proteins of the invention involved in the export of waste products may be increased in number or activity such that the normal metabolic wastes of the cell (possibly increased in quantity due to the overproduction of the desired fine chemical) are efficiently exported before they are able to damage nucleotides and proteins within the cell (which would decrease the viability of the cell) or to interfere with fine chemical biosynthetic pathways (which would decrease the yield, production, or efficiency of production of the desired fine chemical). Further, the relatively large intracellular quantities of the desired fine chemical may in itself be toxic to the cell, so by increasing the activity or number of transporters able to export this compound from the cell, one may increase the viability of the cell in culture, in turn leading to a greater number of cells in the culture producing the desired fine chemical. The MCT proteins of the invention may also be manipulated such that the relative amounts of different lipid and fatty acid molecules are produced. This may have a profound effect on the lipid composition of the membrane of the cell. Since each type of lipid has different physical properties, an alteration in the lipid composition of a membrane may significantly alter membrane fluidity. Changes in membrane fluidity can impact the transport of molecules across the membrane, as well as the integrity of the cell, both of which have a profound effect on the production of fine chemicals from C. glutamicum in large-scale fermentative culture.
  • The isolated nucleic acid sequences of the invention are contained within the genome of a Corynebacterium glutamicum strain available through the American Type Culture Collection, given designation ATCC 13032. The nucleotide sequence of the isolated C. glutamicum MCT DNAs and the predicted amino acid sequences of the C. glutamicum MCT proteins are shown in Appendices A and B, respectively. Computational analyses were performed which classified and/or identified these nucleotide sequences as sequences which encode proteins involved in the metabolism of cellular membrane components or proteins involved in the transport of compounds across such membranes.
  • The present invention also pertains to proteins which have an amino acid sequence which is substantially homologous to an amino acid sequence of Appendix B. As used herein, a protein which has an amino acid sequence which is substantially homologous to a selected amino acid sequence is least about 50% homologous to the selected amino acid sequence, e.g., the entire selected amino acid sequence. A protein which has an amino acid sequence which is substantially homologous to a selected amino acid sequence can also be least about 50-60%, preferably at least about 60-70%, and more preferably at least about 70-80%, 80-90%, or 90-95%, and most preferably at least about 96%, 97%, 98%, 99% or more homologous to the selected amino acid sequence.
  • The MCT protein or a biologically active portion or fragment thereof of the invention can participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes, or have one or more of the activities set forth in Table 1.
  • Various aspects of the invention are described in further detail in the following subsections:
  • A. Isolated Nucleic Acid Molecules
  • One aspect of the invention pertains to isolated nucleic acid molecules that encode MCT polypeptides or biologically active portions thereof, as well as nucleic acid fragments sufficient for use as hybridization probes or primers for the identification or amplification of MCT-encoding nucleic acid (e.g., MCT DNA). As used herein, the term “nucleic acid molecule” is intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs. This term also encompasses untranslated sequence located at both the 3′ and 5′ ends of the coding region of the gene: at least about 100 nucleotides of sequence upstream from the 5′ end of the coding region and at least about 20 nucleotides of sequence downstream from the 3′ end of the coding region of the gene. The nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA. An “isolated” nucleic acid molecule is one which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid. Preferably, an “isolated” nucleic acid is free of sequences which naturally flank the nucleic acid (i.e., sequences located at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. For example, in various embodiments, the isolated MCT nucleic acid molecule can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived (e.g, a C. glutamicum cell). Moreover, an “isolated” nucleic acid molecule, such as a DNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or chemical precursors or other chemicals when chemically synthesized.
  • A nucleic acid molecule of the present invention, e.g., a nucleic acid molecule having a nucleotide sequence of Appendix A, or a portion thereof, can be isolated using standard molecular biology techniques and the sequence information provided herein. For example, a C. glutamicum MCT DNA can be isolated from a C. glutamicum library using all or portion of one of the sequences of Appendix A as a hybridization probe and standard hybridization techniques (e.g., as described in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989). Moreover, a nucleic acid molecule encompassing all or a portion of one of the sequences of Appendix A can be isolated by the polymerase chain reaction using oligonucleotide primers designed based upon this sequence (e.g., a nucleic acid molecule encompassing all or a portion of one of the sequences of Appendix A can be isolated by the polymerase chain reaction using oligonucleotide primers designed based upon this same sequence of Appendix A). For example, mRNA can be isolated from normal endothelial cells (e.g., by the guanidinium-thiocyanate extraction procedure of Chirgwin et al. (1979) Biochemistry 18: 5294-5299) and DNA can be prepared using reverse transcriptase (e.g., Moloney MLV reverse transcriptase, available from Gibco/BRL, Bethesda, Md.; or AMV reverse transcriptase, available from Seikagaku America, Inc., St. Petersburg, Fla.). Synthetic oligonucleotide primers for polymerase chain reaction amplification can be designed based upon one of the nucleotide sequences shown in Appendix A. A nucleic acid of the invention can be amplified using cDNA or, alternatively, genomic DNA, as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis. Furthermore, oligonucleotides corresponding to an MCT nucleotide sequence can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.
  • In a preferred embodiment, an isolated nucleic acid molecule of the invention comprises one of the nucleotide sequences shown in Appendix A. The sequences of Appendix A correspond to the Corynebacterium glutamicum MCT DNAs of the invention. This DNA comprises sequences encoding MCT proteins (i.e., the “coding region”, indicated in each sequence in Appendix A), as well as 5′ untranslated sequences and 3′ untranslated sequences, also indicated in Appendix A. Alternatively, the nucleic acid molecule can comprise only the coding region of any of the sequences in Appendix A.
  • For the purposes of this application, it will be understood that each of the sequences set forth in Appendix A has an identifying RXA, RXN, RXS, or RXC number having the designation “RXA”, “RXN”, “RXS” or “RXC” followed by 5 digits (i.e., RXA02099, RXN03097, RXS00148, or RXC01748). Each of these sequences comprises up to three parts: a 5′ upstream region, a coding region, and a downstream region. Each of these three regions is identified by the same RXA, RXN, RXS, or RXC designation to eliminate confusion. The recitation “one of the sequences in Appendix A”, then, refers to any of the sequences in Appendix A, which may be distinguished by their differing RXA, RXN, RXS, or RXC designations. The coding region of each of these sequences is translated into a corresponding amino acid sequence, which is set forth in Appendix B. The sequences of Appendix B are identified by the same RXA, RXN, RXS, or RXC designations as Appendix A, such that they can be readily correlated. For example, the amino acid sequences in Appendix B designated RXA02099, RXN03097, RXS00148, and RXC01748 are translations of the coding region of the nucleotide sequences of nucleic acid molecules RXA02099, RXN03097, RXS00148, and RXC01748, respectively, in Appendix A. Each of the RXA, RXN, RXS, and RXC nucleotide and amino acid sequences of the invention has also been assigned a SEQ ID NO, as indicated in Table 1. For example, as set forth in Table 1, the nucleotide sequence of RXA00104 is SEQ ID NO:5, and the amino acid sequence of RXA00104 is SEQ ID NO:6.
  • Several of the genes of the invention are “F-designated genes”. An F-designated gene includes those genes set forth in Table 1 which have an ‘F’ in front of the RXA, RXN, RXS, or RXC designation. For example, SEQ ID NO:11, designated, as indicated on Table 1, as “F RXA02581”, is an F-designated gene, as are SEQ ID NOs: 31, 33, and 43 (designated on Table 1 as “F RXA02487”, “F RXA02490”, and “F RXA02809”, respectively).
  • In one embodiment, the nucleic acid molecules of the present invention are not intended to include those compiled in Table 2. In the case of the dapD gene, a sequence for this gene was published in Wehrmann, A., et al. (1998) J. Bacteriol. 180(12): 3159-3165. However, the sequence obtained by the inventors of the present application is significantly longer than the published version. It is believed that the published version relied on an incorrect start codon, and thus represents only a fragment of the actual coding region.
  • In another preferred embodiment, an isolated nucleic acid molecule of the invention comprises a nucleic acid molecule which is a complement of one of the nucleotide sequences shown in Appendix A, or a portion thereof. A nucleic acid molecule which is complementary to one of the nucleotide sequences shown in Appendix A is one which is sufficiently complementary to one of the nucleotide sequences shown in Appendix A such that it can hybridize to one of the nucleotide sequences shown in Appendix A, thereby forming a stable duplex.
  • In still another preferred embodiment, an isolated nucleic acid molecule of the invention comprises a nucleotide sequence which is at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more homologous to a nucleotide sequence shown in Appendix A, or a portion thereof. Ranges and identity values intermediate to the above-recited ranges, (e.g., 70-90% identical or 80-95% identical) are also intended to be encompassed by the present invention. For example, ranges of identity values using a combination of any of the above values recited as upper and/or lower limits are intended to be included. In an additional preferred embodiment, an isolated nucleic acid molecule of the invention comprises a nucleotide sequence which hybridizes, e.g., hybridizes under stringent conditions, to one of the nucleotide sequences shown in Appendix A, or a portion thereof.
  • Moreover, the nucleic acid molecule of the invention can comprise only a portion of the coding region of one of the sequences in Appendix A, for example a fragment which can be used as a probe or primer or a fragment encoding a biologically active portion of an MCT protein. The nucleotide sequences determined from the cloning of the MCT genes from C. glutamicum allows for the generation of probes and primers designed for use in identifying and/or cloning MCT homologues in other cell types and organisms, as well as MCT homologues from other Corynebacteria or related species. The probe/primer typically comprises substantially purified oligonucleotide. The oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12, preferably about 25, more preferably about 40, 50 or 75 consecutive nucleotides of a sense strand of one of the sequences set forth in Appendix A, an anti-sense sequence of one of the sequences set forth in Appendix A, or naturally occurring mutants thereof. Primers based on a nucleotide sequence of Appendix A can be used in PCR reactions to clone MCT homologues. Probes based on the MCT nucleotide sequences can be used to detect transcripts or genomic sequences encoding the same or homologous proteins. In preferred embodiments, the probe further comprises a label group attached thereto, e.g. the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor. Such probes can be used as a part of a diagnostic test kit for identifying cells which misexpress an MCT protein, such as by measuring a level of an MCT-encoding nucleic acid in a sample of cells, e.g., detecting MCT mRNA levels or determining whether a genomic MCT gene has been mutated or deleted.
  • In one embodiment, the nucleic acid molecule of the invention encodes a protein or portion thereof which includes an amino acid sequence which is sufficiently homologous to an amino acid sequence of Appendix B such that the protein or portion thereof maintains the ability to participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes. As used herein, the language “sufficiently homologous” refers to proteins or portions thereof which have amino acid sequences which include a minimum number of identical or equivalent (e.g., an amino acid residue which has a similar side chain as an amino acid residue in one of the sequences of Appendix B) amino acid residues to an amino acid sequence of Appendix B such that the protein or portion thereof is able to participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes. Protein members of such membrane component metabolic pathways or membrane transport systems, as described herein, may play a role in the production and secretion of one or more fine chemicals. Examples of such activities are also described herein. Thus, “the function of an MCT protein” contributes either directly or indirectly to the yield, production, and/or efficiency of production of one or more fine chemicals. Examples of MCT protein activities are set forth in Table 1.
  • In another embodiment, the protein is at least about 50-60%, preferably at least about 60-70%, and more preferably at least about 70-80%, 80-90%, 90-95%, and most preferably at least about 96%, 97%, 98%, 99% or more homologous to an entire amino acid sequence of Appendix B.
  • Portions of proteins encoded by the MCT nucleic acid molecules of the invention are preferably biologically active portions of one of the MCT proteins. As used herein, the term “biologically active portion of an MCT protein” is intended to include a portion, e.g., a domain/motif, of an MCT protein that participates in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes, or has an activity as set forth in Table 1. To determine whether an MCT protein or a biologically active portion thereof can participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes, an assay of enzymatic activity may be performed. Such assay methods are well known to those of ordinary skill in the art, as detailed in Example 8 of the Exemplification.
  • Additional nucleic acid fragments encoding biologically active portions of an MCT protein can be prepared by isolating a portion of one of the sequences in Appendix B, expressing the encoded portion of the MCT protein or peptide (e.g., by recombinant expression in vitro) and assessing the activity of the encoded portion of the MCT protein or peptide.
  • The invention further encompasses nucleic acid molecules that differ from one of the nucleotide sequences shown in Appendix A (and portions thereof) due to degeneracy of the genetic code and thus encode the same MCT protein as that encoded by the nucleotide sequences shown in Appendix A. In another embodiment, an isolated nucleic acid molecule of the invention has a nucleotide sequence encoding a protein having an amino acid sequence shown in Appendix B. In a still further embodiment, the nucleic acid molecule of the invention encodes a full length C. glutamicum protein which is substantially homologous to an amino acid sequence of Appendix B (encoded by an open reading frame shown in Appendix A).
  • It will be understood by one of ordinary skill in the art that in one embodiment the sequences of the invention are not meant to include the sequences of the prior art, such as those Genbank sequences set forth in Tables 2 or 4 which were available prior to the present invention. In one embodiment, the invention includes nucleotide and amino acid sequences having a percent identity to a nucleotide or amino acid sequence of the invention which is greater than that of a sequence of the prior art (e.g., a Genbank sequence (or the protein encoded by such a sequence) set forth in Tables 2 or 4). For example, the invention includes a nucleotide sequence which is greater than and/or at least 38% identical to the nucleotide sequence designated RXA01420 (SEQ ID NO:7), a nucleotide sequence which is greater than and/or at least 43% identical to the nucleotide sequence designated RXA00104 (SEQ ID NO:5), and a nucleotide sequence which is greater than and/or at least 45% identical to the nucleotide sequence designated RXA02173 (SEQ ID NO:25). One of ordinary skill in the art would be able to calculate the lower threshold of percent identity for any given sequence of the invention by examining the GAP-calculated percent identity scores set forth in Table 4 for each of the three top hits for the given sequence, and by subtracting the highest GAP-calculated percent identity from 100 percent. One of ordinary skill in the art will also appreciate that nucleic acid and amino acid sequences having percent identities greater than the lower threshold so calculated (e.g., at least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more identical) are also encompassed by the invention.
  • In addition to the C. glutamicum MCT nucleotide sequences shown in Appendix A, it will be appreciated by one of ordinary skill in the art that DNA sequence polymorphisms that lead to changes in the amino acid sequences of MCT proteins may exist within a population (e.g., the C. glutamicum population). Such genetic polymorphism in the MCT gene may exist among individuals within a population due to natural variation. As used herein, the terms “gene” and “recombinant gene” refer to nucleic acid molecules comprising an open reading frame encoding an MCT protein, preferably a C. glutamicum MCT protein. Such natural variations can typically result in 1-5% variance in the nucleotide sequence of the MCT gene. Any and all such nucleotide variations and resulting amino acid polymorphisms in MCT that are the result of natural variation and that do not alter the functional activity of MCT proteins are intended to be within the scope of the invention.
  • Nucleic acid molecules corresponding to natural variants and non-C. glutamicum homologues of the C. glutamicum MCT DNA of the invention can be isolated based on their homology to the C. glutamicum MCT nucleic acid disclosed herein using the C. glutamicum DNA, or a portion thereof, as a hybridization probe according to standard hybridization techniques under stringent hybridization conditions. Accordingly, in another embodiment, an isolated nucleic acid molecule of the invention is at least 15 nucleotides in length and hybridizes under stringent conditions to the nucleic acid molecule comprising a nucleotide sequence of Appendix A. In other embodiments, the nucleic acid is at least 30, 50, 100, 250 or more nucleotides in length. As used herein, the term “hybridizes under stringent conditions” is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 60% homologous to each other typically remain hybridized to each other. Preferably, the conditions are such that sequences at least about 65%, more preferably at least about 70%, and even more preferably at least about 75% or more homologous to each other typically remain hybridized to each other. Such stringent conditions are known to those of ordinary skill in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. A preferred, non-limiting example of stringent hybridization conditions are hybridization in 6× sodium chloride/sodium citrate (SSC) at about 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 50-65° C. Preferably, an isolated nucleic acid molecule of the invention that hybridizes under stringent conditions to a sequence of Appendix A corresponds to a naturally-occurring nucleic acid molecule. As used herein, a “naturally-occurring” nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural protein). In one embodiment, the nucleic acid encodes a natural C. glutamicum MCT protein.
  • In addition to naturally-occurring variants of the MCT sequence that may exist in the population, one of ordinary skill in the art will further appreciate that changes can be introduced by mutation into a nucleotide sequence of Appendix A, thereby leading to changes in the amino acid sequence of the encoded MCT protein, without altering the functional ability of the MCT protein. For example, nucleotide substitutions leading to amino acid substitutions at “non-essential” amino acid residues can be made in a sequence of Appendix A. A “non-essential” amino acid residue is a residue that can be altered from the wild-type sequence of one of the MCT proteins (Appendix B) without altering the activity of said MCT protein, whereas an “essential” amino acid residue is required for MCT protein activity. Other amino acid residues, however, (e.g., those that are not conserved or only semi-conserved in the domain having MCT activity) may not be essential for activity and thus are likely to be amenable to alteration without altering MCT activity.
  • Accordingly, another aspect of the invention pertains to nucleic acid molecules encoding MCT proteins that contain changes in amino acid residues that are not essential for MCT activity. Such MCT proteins differ in amino acid sequence from a sequence contained in Appendix B yet retain at least one of the MCT activities described herein. In one embodiment, the isolated nucleic acid molecule comprises a nucleotide sequence encoding a protein, wherein the protein comprises an amino acid sequence at least about 50% homologous to an amino acid sequence of Appendix B and is capable of participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes, or has one or more activities set forth in Table 1. Preferably, the protein encoded by the nucleic acid molecule is at least about 50-60% homologous to one of the sequences in Appendix B, more preferably at least about 60-70% homologous to one of the sequences in Appendix B, even more preferably at least about 70-80%, 80-90%, 90-95% homologous to one of the sequences in Appendix B, and most preferably at least about 96%, 97%, 98%, or 99% homologous to one of the sequences in Appendix B.
  • To determine the percent homology of two amino acid sequences (e.g., one of the sequences of Appendix B and a mutant form thereof) or of two nucleic acids, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of one protein or nucleic acid for optimal alignment with the other protein or nucleic acid). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in one sequence (e.g., one of the sequences of Appendix B) is occupied by the same amino acid residue or nucleotide as the corresponding position in the other sequence (e.g., a mutant form of the sequence selected from Appendix B), then the molecules are homologous at that position (i.e., as used herein amino acid or nucleic acid “homology” is equivalent to amino acid or nucleic acid “identity”). The percent homology between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % homology=# of identical positions/total# of positions×100).
  • An isolated nucleic acid molecule encoding an MCT protein homologous to a protein sequence of Appendix B can be created by introducing one or more nucleotide substitutions, additions or deletions into a nucleotide sequence of Appendix A such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced into one of the sequences of Appendix A by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more predicted non-essential amino acid residues. A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Thus, a predicted nonessential amino acid residue in an MCT protein is preferably replaced with another amino acid residue from the same side chain family. Alternatively, in another embodiment, mutations can be introduced randomly along all or part of an MCT coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for an MCT activity described herein to identify mutants that retain MCT activity. Following mutagenesis of one of the sequences of Appendix A, the encoded protein can be expressed recombinantly and the activity of the protein can be determined using, for example, assays described herein (see Example 8 of the Exemplification).
  • In addition to the nucleic acid molecules encoding MCT proteins described above, another aspect of the invention pertains to isolated nucleic acid molecules which are antisense thereto. An “antisense” nucleic acid comprises a nucleotide sequence which is complementary to a “sense” nucleic acid encoding a protein, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. Accordingly, an antisense nucleic acid can hydrogen bond to a sense nucleic acid. The antisense nucleic acid can be complementary to an entire MCT coding strand, or to only a portion thereof. In one embodiment, an antisense nucleic acid molecule is antisense to a “coding region” of the coding strand of a nucleotide sequence encoding an MCT protein. The term “coding region” refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues (e.g., the entire coding region of SEQ ID NO:5 (RXA00104 in Appendix A) comprises nucleotides 1 to 756). In another embodiment, the antisense nucleic acid molecule is antisense to a “noncoding region” of the coding strand of a nucleotide sequence encoding MCT. The term “noncoding region” refers to 5′ and 3′ sequences which flank the coding region that are not translated into amino acids (i.e., also referred to as 5′ and 3′ untranslated regions).
  • Given the coding strand sequences encoding MCT disclosed herein (e.g., the sequences set forth in Appendix A), antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of MCT mRNA, but more preferably is an oligonucleotide which is antisense to only a portion of the coding or noncoding region of MCT mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of MCT mRNA. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length. An antisense nucleic acid of the invention can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used. Examples of modified nucleotides which can be used to generate the antisense nucleic acid include 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5′-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).
  • The antisense nucleic acid molecules of the invention are typically administered to a cell or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding an MCT protein to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove of the double helix. The antisense molecule can be modified such that it specifically binds to a receptor or an antigen expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecule to a peptide or an antibody which binds to a cell surface receptor or antigen. The antisense nucleic acid molecule can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of the antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong prokaryotic, viral, or eukaryotic promoter are preferred.
  • In yet another embodiment, the antisense nucleic acid molecule of the invention is an α-anomeric nucleic acid molecule. An α-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual β-units, the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids. Res. 15:6625-6641). The antisense nucleic acid molecule can also comprise a 2′-o-methylribonucleotide (Inoue et al. (1987) Nucleic Acids Res. 15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215:327-330).
  • In still another embodiment, an antisense nucleic acid of the invention is a ribozyme. Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to catalytically cleave MCT mRNA transcripts to thereby inhibit translation of MCT mRNA. A ribozyme having specificity for an MCT-encoding nucleic acid can be designed based upon the nucleotide sequence of an MCT DNA disclosed herein (i.e., SEQ ID NO. 5 (RXA00104) in Appendix A)). For example, a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in an MCT-encoding mRNA. See, e.g., Cech et al. U.S. Pat. No. 4,987,071 and Cech et al. U.S. Pat. No. 5,116,742. Alternatively, MCT mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel, D. and Szostak, J. W. (1993) Science 261:1411-1418.
  • Alternatively, MCT gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of an MCT nucleotide sequence (e.g., an MCT promoter and/or enhancers) to form triple helical structures that prevent transcription of an MCT gene in target cells. See generally, Helene, C. (1991) Anticancer Drug Des. 6(6):569-84; Helene, C. et al. (1992) Ann. N.Y. Acad. Sci. 660:27-36; and Maher, L. J. (1992) Bioassays 14(12):807-15.
  • B. Recombinant Expression Vectors and Host Cells
  • Another aspect of the invention pertains to vectors, preferably expression vectors, containing a nucleic acid encoding an MCT protein (or a portion thereof). As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a “plasmid”, which refers to a circular double stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as “expression vectors”. In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, “plasmid” and “vector” can be used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.
  • The recombinant expression vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, “operably linked” is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell). The term “regulatory sequence” is intended to include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cell and those which direct expression of the nucleotide sequence only in certain host cells. Preferred regulatory sequences are, for example, promoters such as cos-, tac-, trp-, tet-, trp-tet-, lpp-, lac-, lpp-lac-, lacIq-, T7-, T5-, T3-, gal-, trc-, ara-, SP6-, amy, SPO2, λ-PR-or λ PL, which are used preferably in bacteria. Additional regulatory sequences are, for example, promoters from yeasts and fungi, such as ADC1, MFα, AC, P-60, CYC1, GAPDH, TEF, rp28, ADH, promoters from plants such as CaMV/35S, SSU, OCS, lib4, usp, STLS1, B33, nos or ubiquitin- or phaseolin-promoters. It is also possible to use artificial promoters. It will be appreciated by one of ordinary skill in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc. The expression vectors of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein (e.g., MCT proteins, mutant forms of MCT proteins, fusion proteins, etc.).
  • The recombinant expression vectors of the invention can be designed for expression of MCT proteins in prokaryotic or eukaryotic cells. For example, MCT genes can be expressed in bacterial cells such as C. glutamicum, insect cells (using baculovirus expression vectors), yeast and other fungal cells (see Romanos, M. A. et al. (1992) “Foreign gene expression in yeast: a review”, Yeast 8: 423-488; van den Hondel, C.A.M.J.J. et al. (1991) “Heterologous gene expression in filamentous fungi” in: More Gene Manipulations in Fungi, J. W. Bennet & L. L. Lasure, eds., p. 396-428: Academic Press: San Diego; and van den Hondel, C.A.M.J.J. & Punt, P. J. (1991) “Gene transfer systems and vector development for filamentous fungi, in: Applied Molecular Genetics of Fungi, Peberdy, J. F. et al., eds., p. 1-28, Cambridge University Press: Cambridge), algae and multicellular plant cells (see Schmidt, R. and Willmitzer, L. (1988) High efficiency Agrobacterium tumefaciens—mediated transformation of Arabidopsis thaliana leaf and cotyledon explants” Plant Cell Rep.: 583-586), or mammalian cells. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.
  • Expression of proteins in prokaryotes is most often carried out with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein but also to the C-terminus or fused within suitable regions in the proteins. Such fusion vectors typically serve three purposes: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase.
  • Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D. B. and Johnson, K. S. (1988) Gene 67:31-40), pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein. In one embodiment, the coding sequence of the MCT protein is cloned into a pGEX expression vector to create a vector encoding a fusion protein comprising, from the N-terminus to the C-terminus, GST-thrombin cleavage site-X protein. The fusion protein can be purified by affinity chromatography using glutathione-agarose resin. Recombinant MCT protein unfused to GST can be recovered by cleavage of the fusion protein with thrombin.
  • Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al., (1988) Gene 69:301-315) pLG338, pACYC184, pBR322, pUC18, pUC19, pKC30, pRep4, pHS1, pHS2, pPLc236, pMBL24, pLG200, pUR290, pIN-III113-B1, λgt11, pBdC1, and pET 11d (Studier et al, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 60-89 ; and Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: New York IBSN 0 444 904018). Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-lac fusion promoter. Target gene expression from the pET 11d vector relies on transcription from a T7 gn10-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident λ prophage harboring a T7 gn1 gene under the transcriptional control of the lacUV 5 promoter. For transformation of other varieties of bacteria, appropriate vectors may be selected. For example, the plasmids pIJ101, pIJ364, pIJ702 and pIJ361 are known to be useful in transforming Streptomyces, while plasmids pUB110, pC194, or pBD214 are suited for transformation of Bacillus species. Several plasmids of use in the transfer of genetic information into Corynebacterium include pHM1519, pBL1, pSA77, or pAJ667 (Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: N.Y. IBSN 0 444 904018).
  • One strategy to maximize recombinant protein expression is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 119-128). Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in the bacterium chosen for expression, such as C. glutamicum (Wada et al. (1992) Nucleic Acids Res. 20:2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.
  • In another embodiment, the MCT protein expression vector is a yeast expression vector. Examples of vectors for expression in yeast S. cerevisiae include pYepSec1 (Baldari, et al., (1987) Embo J. 6:229-234), 2μ, pAG-1, Yep6, Yep13, pEMBLYe23, pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al., (1987) Gene 54:113-123), and pYES2 (Invitrogen Corporation, San Diego, Calif.). Vectors and methods for the construction of vectors appropriate for use in other fungi, such as the filamentous fungi, include those detailed in: van den Hondel, C.A.M.J.J. & Punt, P. J. (1991) “Gene transfer systems and vector development for filamentous fungi, in: Applied Molecular Genetics of Fungi, J. F. Peberdy, et al., eds., p. 1-28, Cambridge University Press: Cambridge, and Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: N.Y. (IBSN 0 444 904018).
  • Alternatively, the MCT proteins of the invention can be expressed in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells (e.g., Sf9 cells) include the pAc series (Smith et al. (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers (1989) Virology 170:31-39).
  • In another embodiment, the MCT proteins of the invention may be expressed in unicellular plant cells (such as algae) or in plant cells from higher plants (e.g., the spermatophytes, such as crop plants). Examples of plant expression vectors include those detailed in: Becker, D., Kemper, E., Schell, J. and Masterson, R. (1992) “New plant binary vectors with selectable markers located proximal to the left border”, Plant Mol. Biol. 20: 1195-1197; and Bevan, M. W. (1984) “Binary Agrobacterium vectors for plant transformation”, Nuc. Acid Res. 12: 8711-8721, and include pLGV23, pGHlac+, pBIN19, pAK2004, and pDH51 (Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: N.Y. IBSN 0 444 904018).
  • In yet another embodiment, a nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC (Kaufman et al. (1987) EMBO J. 6:187-195). When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40. For other suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.
  • In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43:235-275), in particular promoters of T cell receptors (Winoto and Baltimore (1989) EMBO J. 8:729-733) and immunoglobulins (Banerji et al. (1983) Cell 33:729-740; Queen and Baltimore (1983) Cell 33:741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle (1989) PNAS 86:5473-5477), pancreas-specific promoters (Edlund et al. (1985) Science 230:912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166). Developmentally-regulated promoters are also encompassed, for example the murine hox promoters (Kessel and Gruss (1990) Science 249:374-379) and the α-fetoprotein promoter (Campes and Tilghman (1989) Genes Dev. 3:537-546).
  • The invention further provides a recombinant expression vector comprising a DNA molecule of the invention cloned into the expression vector in an antisense orientation. That is, the DNA molecule is operatively linked to a regulatory sequence in a manner which allows for expression (by transcription of the DNA molecule) of an RNA molecule which is antisense to MCT mRNA. Regulatory sequences operatively linked to a nucleic acid cloned in the antisense orientation can be chosen which direct the continuous expression of the antisense RNA molecule in a variety of cell types, for instance viral promoters and/or enhancers, or regulatory sequences can be chosen which direct constitutive, tissue specific or cell type specific expression of antisense RNA. The antisense expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which antisense nucleic acids are produced under the control of a high efficiency regulatory region, the activity of which can be determined by the cell type into which the vector is introduced. For a discussion of the regulation of gene expression using antisense genes see Weintraub, H. et al., Antisense RNA as a molecular tool for genetic analysis, Reviews—Trends in Genetics, Vol. 1(1) 1986.
  • Another aspect of the invention pertains to host cells into which a recombinant expression vector of the invention has been introduced. The terms “host cell” and “recombinant host cell” are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
  • A host cell can be any prokaryotic or eukaryotic cell. For example, an MCT protein can be expressed in bacterial cells such as C. glutamicum, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells). Other suitable host cells are known to one of ordinary skill in the art. Microorganisms related to Corynebacterium glutamicum which may be conveniently used as host cells for the nucleic acid and protein molecules of the invention are set forth in Table 3.
  • Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. As used herein, the terms “transformation” and “transfection”, “conjugation” and “transduction” are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., linear DNA or RNA (e.g., a linearized vector or a gene construct alone without a vector) or nucleic acid in the form of a vector (e.g., a plasmid, phage, phasmid, phagemid, transposon or other DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, natural competence, chemical-mediated transfer, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989), and other laboratory manuals.
  • For stable transfection of mammalian cells, it is known that, depending upon the expression vector and transfection technique used, only a small fraction of cells may integrate the foreign DNA into their genome. In order to identify and select these integrants, a gene that encodes a selectable marker (e.g., resistance to antibiotics) is generally introduced into the host cells along with the gene of interest. Preferred selectable markers include those which confer resistance to drugs, such as G418, hygromycin and methotrexate. Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding an MCT protein or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by, for example, drug selection (e.g., cells that have incorporated the selectable marker gene will survive, while the other cells die).
  • To create a homologous recombinant microorganism, a vector is prepared which contains at least a portion of an MCT gene into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the MCT gene. Preferably, this MCT gene is a Corynebacterium glutamicum MCT gene, but it can be a homologue from a related bacterium or even from a mammalian, yeast, or insect source. In a preferred embodiment, the vector is designed such that, upon homologous recombination, the endogenous MCT gene is functionally disrupted (i.e., no longer encodes a functional protein; also referred to as a “knock out” vector). Alternatively, the vector can be designed such that, upon homologous recombination, the endogenous MCT gene is mutated or otherwise altered but still encodes functional protein (e.g., the upstream regulatory region can be altered to thereby alter the expression of the endogenous MCT protein). In the homologous recombination vector, the altered portion of the MCT gene is flanked at its 5′ and 3′ ends by additional nucleic acid of the MCT gene to allow for homologous recombination to occur between the exogenous MCT gene carried by the vector and an endogenous MCT gene in a microorganism. The additional flanking MCT nucleic acid is of sufficient length for successful homologous recombination with the endogenous gene. Typically, several kilobases of flanking DNA (both at the 5′ and 3′ ends) are included in the vector (see e.g., Thomas, K. R., and Capecchi, M. R. (1987) Cell 51: 503 for a description of homologous recombination vectors). The vector is introduced into a microorganism (e.g., by electroporation) and cells in which the introduced MCT gene has homologously recombined with the endogenous MCT gene are selected, using art-known techniques.
  • In another embodiment, recombinant microorganisms can be produced which contain selected systems which allow for regulated expression of the introduced gene. For example, inclusion of an MCT gene on a vector placing it under control of the lac operon permits expression of the MCT gene only in the presence of IPTG. Such regulatory systems are well known in the art.
  • In another embodiment, an endogenous MCT gene in a host cell is disrupted (e.g., by homologous recombination or other genetic means known in the art) such that expression of its protein product does not occur. In another embodiment, an endogenous or introduced MCT gene in a host cell has been altered by one or more point mutations, deletions, or inversions, but still encodes a functional MCT protein. In still another embodiment, one or more of the regulatory regions (e.g., a promoter, repressor, or inducer) of an MCT gene in a microorganism has been altered (e.g., by deletion, truncation, inversion, or point mutation) such that the expression of the MCT gene is modulated. One of ordinary skill in the art will appreciate that host cells containing more than one of the described MCT gene and protein modifications may be readily produced using the methods of the invention, and are meant to be included in the present invention.
  • A host cell of the invention, such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i.e., express) an MCT protein. Accordingly, the invention further provides methods for producing MCT proteins using the host cells of the invention. In one embodiment, the method comprises culturing the host cell of invention (into which a recombinant expression vector encoding an MCT protein has been introduced, or into which genome has been introduced a gene encoding a wild-type or altered MCT protein) in a suitable medium until MCT protein is produced. In another embodiment, the method further comprises isolating MCT proteins from the medium or the host cell.
  • C. Isolated MCT Proteins
  • Another aspect of the invention pertains to isolated MCT proteins, and biologically active portions thereof. An “isolated” or “purified” protein or biologically active portion thereof is substantially free of cellular material when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. The language “substantially free of cellular material” includes preparations of MCT protein in which the protein is separated from cellular components of the cells in which it is naturally or recombinantly produced. In one embodiment, the language “substantially free of cellular material” includes preparations of MCT protein having less than about 30% (by dry weight) of non-MCT protein (also referred to herein as a “contaminating protein”), more preferably less than about 20% of non-MCT protein, still more preferably less than about 10% of non-MCT protein, and most preferably less than about 5% non-MCT protein. When the MCT protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the protein preparation. The language “substantially free of chemical precursors or other chemicals” includes preparations of MCT protein in which the protein is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein. In one embodiment, the language “substantially free of chemical precursors or other chemicals” includes preparations of MCT protein having less than about 30% (by dry weight) of chemical precursors or non-MCT chemicals, more preferably less than about 20% chemical precursors or non-MCT chemicals, still more preferably less than about 10% chemical precursors or non-MCT chemicals, and most preferably less than about 5% chemical precursors or non-MCT chemicals. In preferred embodiments, isolated proteins or biologically active portions thereof lack contaminating proteins from the same organism from which the MCT protein is derived. Typically, such proteins are produced by recombinant expression of, for example, a C. glutamicum MCT protein in a microorganism such as C. glutamicum.
  • An isolated MCT protein or a portion thereof of the invention can participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes, or has one or more of the activities set forth in Table 1. In preferred embodiments, the protein or portion thereof comprises an amino acid sequence which is sufficiently homologous to an amino acid sequence of Appendix B such that the protein or portion thereof maintains the ability participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes. The portion of the protein is preferably a biologically active portion as described herein. In another preferred embodiment, an MCT protein of the invention has an amino acid sequence shown in Appendix B. In yet another preferred embodiment, the MCT protein has an amino acid sequence which is encoded by a nucleotide sequence which hybridizes, e.g., hybridizes under stringent conditions, to a nucleotide sequence of Appendix A. In still another preferred embodiment, the MCT protein has an amino acid sequence which is encoded by a nucleotide sequence that is at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more homologous to one of the nucleic acid sequences of Appendix A, or a portion thereof. Ranges and identity values intermediate to the above-recited values, (e.g., 70-90% identical or 80-95% identical) are also intended to be encompassed by the present invention. For example, ranges of identity values using a combination of any of the above values recited as upper and/or lower limits are intended to be included. The preferred MCT proteins of the present invention also preferably possess at least one of the MCT activities described herein. For example, a preferred MCT protein of the present invention includes an amino acid sequence encoded by a nucleotide sequence which hybridizes, e.g., hybridizes under stringent conditions, to a nucleotide sequence of Appendix A, and which can participate in the metabolism of compounds necessary for the construction of cellular membranes in C. glutamicum, or in the transport of molecules across these membranes, or which has one or more of the activities set forth in Table 1.
  • In other embodiments, the MCT protein is substantially homologous to an amino acid sequence of Appendix B and retains the functional activity of the protein of one of the sequences of Appendix B yet differs in amino acid sequence due to natural variation or mutagenesis, as described in detail in subsection I above. Accordingly, in another embodiment, the MCT protein is a protein which comprises an amino acid sequence which is at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more homologous to an entire amino acid sequence of Appendix B and which has at least one of the MCT activities described herein. Ranges and identity values intermediate to the above-recited values, (e.g., 70-90% identical or 80-95% identical) are also intended to be encompassed by the present invention. For example, ranges of identity values using a combination of any of the above values recited as upper and/or lower limits are intended to be included. In another embodiment, the invention pertains to a full length C. glutamicum protein which is substantially homologous to an entire amino acid sequence of Appendix B.
  • Biologically active portions of an MCT protein include peptides comprising amino acid sequences derived from the amino acid sequence of an MCT protein, e.g., the an amino acid sequence shown in Appendix B or the amino acid sequence of a protein homologous to an MCT protein, which include fewer amino acids than a full length MCT protein or the full length protein which is homologous to an MCT protein, and exhibit at least one activity of an MCT protein. Typically, biologically active portions (peptides, e.g., peptides which are, for example, 5, 10, 15, 20, 30, 35, 36, 37, 38, 39, 40, 50, 100 or more amino acids in length) comprise a domain or motif with at least one activity of an MCT protein. Moreover, other biologically active portions, in which other regions of the protein are deleted, can be prepared by recombinant techniques and evaluated for one or more of the activities described herein. Preferably, the biologically active portions of an MCT protein include one or more selected domains/motifs or portions thereof having biological activity.
  • MCT proteins are preferably produced by recombinant DNA techniques. For example, a nucleic acid molecule encoding the protein is cloned into an expression vector (as described above), the expression vector is introduced into a host cell (as described above) and the MCT protein is expressed in the host cell. The MCT protein can then be isolated from the cells by an appropriate purification scheme using standard protein purification techniques. Alternative to recombinant expression, an MCT protein, polypeptide, or peptide can be synthesized chemically using standard peptide synthesis techniques. Moreover, native MCT protein can be isolated from cells (e.g., endothelial cells), for example using an anti-MCT antibody, which can be produced by standard techniques utilizing an MCT protein or fragment thereof of this invention.
  • The invention also provides MCT chimeric or fusion proteins. As used herein, an MCT “chimeric protein” or “fusion protein” comprises an MCT polypeptide operatively linked to a non-MCT polypeptide. An “MCT polypeptide” refers to a polypeptide having an amino acid sequence corresponding to an MCT protein, whereas a “non-MCT polypeptide” refers to a polypeptide having an amino acid sequence corresponding to a protein which is not substantially homologous to the MCT protein, e.g., a protein which is different from the MCT protein and which is derived from the same or a different organism. Within the fusion protein, the term “operatively linked” is intended to indicate that the MCT polypeptide and the non-MCT polypeptide are fused in-frame to each other. The non-MCT polypeptide can be fused to the N-terminus or C-terminus of the MCT polypeptide. For example, in one embodiment the fusion protein is a GST-MCT fusion protein in which the MCT sequences are fused to the C-terminus of the GST sequences. Such fusion proteins can facilitate the purification of recombinant MCT proteins. In another embodiment, the fusion protein is an MCT protein containing a heterologous signal sequence at its N-terminus. In certain host cells (e.g., mammalian host cells), expression and/or secretion of an MCT protein can be increased through use of a heterologous signal sequence.
  • Preferably, an MCT chimeric or fusion protein of the invention is produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, for example by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al. John Wiley & Sons: 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide). An MCT-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the MCT protein.
  • Homologues of the MCT protein can be generated by mutagenesis, e.g., discrete point mutation or truncation of the MCT protein. As used herein, the term “homologue” refers to a variant form of the MCT protein which acts as an agonist or antagonist of the activity of the MCT protein. An agonist of the MCT protein can retain substantially the same, or a subset, of the biological activities of the MCT protein. An antagonist of the MCT protein can inhibit one or more of the activities of the naturally occurring form of the MCT protein, by, for example, competitively binding to a downstream or upstream member of the cell membrane component metabolic cascade which includes the MCT protein, or by binding to an MCT protein which mediates transport of compounds across such membranes, thereby preventing translocation from taking place.
  • In an alternative embodiment, homologues of the MCT protein can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants, of the MCT protein for MCT protein agonist or antagonist activity. In one embodiment, a variegated library of MCT variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library. A variegated library of MCT variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential MCT sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display) containing the set of MCT sequences therein. There are a variety of methods which can be used to produce libraries of potential MCT homologues from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be performed in an automatic DNA synthesizer, and the synthetic gene then ligated into an appropriate expression vector. Use of a degenerate set of genes allows for the provision, in one mixture, of all of the sequences encoding the desired set of potential MCT sequences. Methods for synthesizing degenerate oligonucleotides are known in the art (see, e.g., Narang, S. A. (1983) Tetrahedron 39:3; Itakura et al. (1984) Annu. Rev. Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. 11:477.
  • In addition, libraries of fragments of the MCT protein coding can be used to generate a variegated population of MCT fragments for screening and subsequent selection of homologues of an MCT protein. In one embodiment, a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of an MCT coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double stranded DNA which can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with S1 nuclease, and ligating the resulting fragment library into an expression vector. By this method, an expression library can be derived which encodes N-terminal, C-terminal and internal fragments of various sizes of the MCT protein.
  • Several techniques are known in the art for screening gene products of combinatorial libraries made by point mutations or truncation, and for screening cDNA libraries for gene products having a selected property. Such techniques are adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of MCT homologues. The most widely used techniques, which are amenable to high through-put analysis, for screening large gene libraries typically include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates isolation of the vector encoding the gene whose product was detected. Recursive ensemble mutagenesis (REM), a new technique which enhances the frequency of functional mutants in the libraries, can be used in combination with the screening assays to identify MCT homologues (Arkin and Yourvan (1992) PNAS 89:7811-7815; Delgrave et al. (1993) Protein Engineering 6(3):327-331).
  • In another embodiment, cell based assays can be exploited to analyze a variegated MCT library, using methods well known in the art.
  • D. Uses and Methods of the Invention
  • The nucleic acid molecules, proteins, protein homologues, fusion proteins, primers, vectors, and host cells described herein can be used in one or more of the following methods: identification of C. glutamicum and related organisms; mapping of genomes of organisms related to C. glutamicum ; identification and localization of C. glutamicum sequences of interest; evolutionary studies; determination of MCT protein regions required for function; modulation of an MCT protein activity; modulation of the metabolism of one or more cell membrane components; modulation of the transmembrane transport of one or more compounds; and modulation of cellular production of a desired compound, such as a fine chemical.
  • The MCT nucleic acid molecules of the invention have a variety of uses. First, they may be used to identify an organism as being Corynebacterium glutamicum or a close relative thereof. Also, they may be used to identify the presence of C. glutamicum or a relative thereof in a mixed population of microorganisms. The invention provides the nucleic acid sequences of a number of C. glutamicum genes; by probing the extracted genomic DNA of a culture of a unique or mixed population of microorganisms under stringent conditions with a probe spanning a region of a C. glutamicum gene which is unique to this organism, one can ascertain whether this organism is present.
  • Although Corynebacterium glutamicum itself is nonpathogenic, it is related to pathogenic species, such as Corynebacterium diphtheriae. Corynebacterium diphtheriae is the causative agent of diphtheria, a rapidly developing, acute, febrile infection which involves both local and systemic pathology. In this disease, a local lesion develops in the upper respiratory tract and involves necrotic injury to epithelial cells; the bacilli secrete toxin which is disseminated through this lesion to distal susceptible tissues of the body. Degenerative changes brought about by the inhibition of protein synthesis in these tissues, which include heart, muscle, peripheral nerves, adrenals, kidneys, liver and spleen, result in the systemic pathology of the disease. Diphtheria continues to have high incidence in many parts of the world, including Africa, Asia, Eastern Europe and the independent states of the former Soviet Union. An ongoing epidemic of diphtheria in the latter two regions has resulted in at least 5,000 deaths since 1990. In one embodiment, the invention provides a method of identifying the presence or activity of Cornyebacterium diphtheriae in a subject. This method includes detection of one or more of the nucleic acid or amino acid sequences of the invention (e.g., the sequences set forth in Appendix A or Appendix B) in a subject, thereby detecting the presence or activity of Corynebacterium diphtheriae in the subject. C. glutamicum and C. diphtheriae are related bacteria, and many of the nucleic acid and protein molecules in C. glutamicum are homologous to C. diphtheriae nucleic acid and protein molecules, and can therefore be used to detect C. diphtheriae in a subject.
  • The nucleic acid and protein molecules of the invention may also serve as markers for specific regions of the genome. This has utility not only in the mapping of the genome, but also for functional studies of C. glutamicum proteins. For example, to identify the region of the genome to which a particular C. glutamicum DNA-binding protein binds, the C. glutamicum genome could be digested, and the fragments incubated with the DNA-binding protein. Those which bind the protein may be additionally probed with the nucleic acid molecules of the invention, preferably with readily detectable labels; binding of such a nucleic acid molecule to the genome fragment enables the localization of the fragment to the genome map of C. glutamicum, and, when performed multiple times with different enzymes, facilitates a rapid determination of the nucleic acid sequence to which the protein binds. Further, the nucleic acid molecules of the invention may be sufficiently homologous to the sequences of related species such that these nucleic acid molecules may serve as markers for the construction of a genomic map in related bacteria, such as Brevibacterium lactofermentum.
  • The MCT nucleic acid molecules of the invention are also useful for evolutionary and protein structural studies. The metabolic and transport processes in which the molecules of the invention participate are utilized by a wide variety of prokaryotic and eukaryotic cells; by comparing the sequences of the nucleic acid molecules of the present invention to those encoding similar enzymes from other organisms, the evolutionary relatedness of the organisms can be assessed. Similarly, such a comparison permits an assessment of which regions of the sequence are conserved and which are not, which may aid in determining those regions of the protein which are essential for the functioning of the enzyme. This type of determination is of value for protein engineering studies and may give an indication of what the protein can tolerate in terms of mutagenesis without losing function.
  • Manipulation of the MCT nucleic acid molecules of the invention may result in the production of MCT proteins having functional differences from the wild-type MCT proteins. These proteins may be improved in efficiency or activity, may be present in greater numbers in the cell than is usual, or may be decreased in efficiency or activity.
  • The invention provides methods for screening molecules which modulate the activity of an MCT protein, either by interacting with the protein itself or a substrate or binding partner of the MCT protein, or by modulating the transcription or translation of an MCT nucleic acid molecule of the invention. In such methods, a microorganism expressing one or more MCT proteins of the invention is contacted with one or more test compounds, and the effect of each test compound on the activity or level of expression of the MCT protein is assessed.
  • There are a number of mechanisms by which the alteration of an MCT protein of the invention may directly affect the yield, production, and/or efficiency of production of a fine chemical from a C. glutamicum strain incorporating such an altered protein. Recovery of fine chemical compounds from large-scale cultures of C. glutamicum is significantly improved if C. glutamicum secretes the desired compounds, since such compounds may be readily purified from the culture medium (as opposed to extracted from the mass of C. glutamicum cells). By either increasing the number or the activity of transporter molecules which export fine chemicals from the cell, it may be possible to increase the amount of the produced fine chemical which is present in the extracellular medium, thus permitting greater ease of harvesting and purification. Conversely, in order to efficiently overproduce one or more fine chemicals, increased amounts of the cofactors, precursor molecules, and intermediate compounds for the appropriate biosynthetic pathways are required. Therefore, by increasing the number and/or activity of transporter proteins involved in the import of nutrients, such as carbon sources (i.e., sugars), nitrogen sources (i.e., amino acids, ammonium salts), phosphate, and sulfur, it may be possible to improve the production of a fine chemical, due to the removal of any nutrient supply limitations on the biosynthetic process. Further, fatty acids and lipids are themselves desirable fine chemicals, so by optimizing the activity or increasing the number of one or more MCT proteins of the invention which participate in the biosynthesis of these compounds, or by impairing the activity of one or more MCT proteins which are involved in the degradation of these compounds, it may be possible to increase the yield, production, and/or efficiency of production of fatty acid and lipid molecules from C. glutamicum.
  • The engineering of one or more MCT genes of the invention may also result in MCT proteins having altered activities which indirectly impact the production of one or more desired fine chemicals from C. glutamicum. For example, the normal biochemical processes of metabolism result in the production of a variety of waste products (e.g., hydrogen peroxide and other reactive oxygen species) which may actively interfere with these same metabolic processes (for example, peroxynitrite is known to nitrate tyrosine side chains, thereby inactivating some enzymes having tyrosine in the active site (Groves, J. T. (1999) Curr. Opin. Chem. Biol. 3(2): 226-235). While these waste products are typically excreted, the C. glutamicum strains utilized for large-scale fermentative production are optimized for the overproduction of one or more fine chemicals, and thus may produce more waste products than is typical for a wild-type C. glutamicum. By optimizing the activity of one or more MCT proteins of the invention which are involved in the export of waste molecules, it may be possible to improve the viability of the cell and to maintain efficient metabolic activity. Also, the presence of high intracellular levels of the desired fine chemical may actually be toxic to the cell, so by increasing the ability of the cell to secrete these compounds, one may improve the viability of the cell.
  • Further, the MCT proteins of the invention may be manipulated such that the relative amounts of various lipid and fatty acid molecules produced are altered. This may have a profound effect on the lipid composition of the membrane of the cell. Since each type of lipid has different physical properties, an alteration in the lipid composition of a membrane may significantly alter membrane fluidity. Changes in membrane fluidity can impact the transport of molecules across the membrane, which, as previously explicated, may modify the export of waste products or the produced fine chemical or the import of necessary nutrients. Such membrane fluidity changes may also profoundly affect the integrity of the cell; cells with relatively weaker membranes are more vulnerable in the large-scale fermentor environment to mechanical stresses which may damage or kill the cell. By manipulating MCT proteins involved in the production of fatty acids and lipids for membrane construction such that the resulting membrane has a membrane composition more amenable to the environmental conditions extant in the cultures utilized to produce fine chemicals, a greater proportion of the C. glutamicum cells should survive and multiply. Greater numbers of C. glutamicum cells in a culture should translate into greater yields, production, or efficiency of production of the fine chemical from the culture.
  • The aforementioned mutagenesis strategies for MCT proteins to result in increased yields of a fine chemical from C. glutamicum are not meant to be limiting; variations on these strategies will be readily apparent to one of ordinary skill in the art. Using such strategies, and incorporating the mechanisms disclosed herein, the nucleic acid and protein molecules of the invention may be utilized to generate C. glutamicum or related strains of bacteria expressing mutated MCT nucleic acid and protein molecules such that the yield, production, and/or efficiency of production of a desired compound is improved. This desired compound may be any natural product of C. glutamicum, which includes the final products of biosynthesis pathways and intermediates of naturally-occurring metabolic pathways, as well as molecules which do not naturally occur in the metabolism of C. glutamicum, but which are produced by a C. glutamicum strain of the invention.
  • This invention is further illustrated by the following examples which should not be construed as limiting. The contents of all references, patent applications, patents, published patent applications, Tables, Appendices, and the sequence listing cited throughout this application are hereby incorporated by reference.
  • Exemplification
    • EXAMPLE 1 Preparation of Total Genomic DNA of Corynebacterium glutamicum ATCC 13032
  • A culture of Corynebacterium glutamicum (ATCC 13032) was grown overnight at 30° C. with vigorous shaking in BHI medium (Difco). The cells were harvested by centrifugation, the supernatant was discarded and the cells were resuspended in 5 ml buffer-I (5% of the original volume of the culture—all indicated volumes have been calculated for 100 ml of culture volume). Composition of buffer-I: 140.34 g/l sucrose, 2.46 g/l MgSO4×7H2O, 10 ml/l KH2PO4 solution (100 g/l, adjusted to pH 6.7 with KOH), 50 ml/l M12 concentrate (10 g/l (NH4)2SO4, 1 g/l NaCl, 2 g/l MgSO4×7 H2O, 0.2 g/l CaCl2, 0.5 g/l yeast extract (Difco), 10 ml/l trace-elements-mix (200 mg/l FeSO4×H2O, 10 mg/l ZnSO4×7 H2O, 3 mg/l MnCl2×4 H2O, 30 mg/l H3BO3 20 mg/l CoCl2×6 H2O, 1 mg/l NiCl2×6 H2O, 3 mg/l Na2MoO4×2 H2O, 500 mg/l complexing agent (EDTA or critic acid), 100 ml/l vitamins-mix (0.2 mg/l biotin, 0.2 mg/l folic acid, 20 mg/l p-amino benzoic acid, 20 mg/l riboflavin, 40 mg/l ca-panthothenate, 140 mg/l nicotinic acid, 40 mg/l pyridoxole hydrochloride, 200 mg/l myo-inositol). Lysozyme was added to the suspension to a final concentration of 2.5 mg/ml. After an approximately 4 h incubation at 37° C., the cell wall was degraded and the resulting protoplasts are harvested by centrifugation. The pellet was washed once with 5 ml buffer-1 and once with 5 ml TE-buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8). The pellet was resuspended in 4 ml TE-buffer and 0.5 ml SDS solution (10%) and 0.5 ml NaCl solution (5 M) are added. After adding of proteinase K to a final concentration of 200 μg/ml, the suspension is incubated for ca. 18 h at 37° C. The DNA was purified by extraction with phenol, phenol-chloroform-isoamylalcohol and chloroform-isoamylalcohol using standard procedures. Then, the DNA was precipitated by adding 1/50 volume of 3 M sodium acetate and 2 volumes of ethanol, followed by a 30 min incubation at −20° C. and a 30 min centrifugation at 12,000 rpm in a high speed centrifuge using a SS34 rotor (Sorvall). The DNA was dissolved in 1 ml TE-buffer containing 20 μg/ml RNaseA and dialysed at 4° C. against 1000 ml TE-buffer for at least 3 hours. During this time, the buffer was exchanged 3 times. To aliquots of 0.4 ml of the dialysed DNA solution, 0.4 ml of 2 M LiCl and 0.8 ml of ethanol are added. After a 30 min incubation at −20° C., the DNA was collected by centrifugation (13,000 rpm, Biofuge Fresco, Heraeus, Hanau, Germany). The DNA pellet was dissolved in TE-buffer. DNA prepared by this procedure could be used for all purposes, including southern blotting or construction of genomic libraries.
    • EXAMPLE 2 Construction of Genomic Libraries in Escherichia coli of Corynebacterium glutamicum ATCC13032.
  • Using DNA prepared as described in Example 1, cosmid and plasmid libraries were constructed according to known and well established methods (see e.g., Sambrook, J. et al. (1989) “Molecular Cloning: A Laboratory Manual”, Cold Spring Harbor Laboratory Press, or Ausubel, F. M. et al. (1994) “Current Protocols in Molecular Biology”, John Wiley & Sons.)
  • Any plasmid or cosmid could be used. Of particular use were the plasmids pBR322 (Sutcliffe, J. G. (1979) Proc. Natl. Acad. Sci. USA, 75:3737-3741); pACYC177 (Change & Cohen (1978) J. Bacteriol 134:1141-1156), plasmids of the pBS series (pBSSK+, pBSSK− and others; Stratagene, LaJolla, USA), or cosmids as SuperCos1 (Stratagene, LaJolla, USA) or Lorist6 (Gibson, T. J., Rosenthal A. and Waterson, R. H. (1987) Gene 53:283-286. Gene libraries specifically for use in C. glutamicum may be constructed using plasmid pSL109 (Lee, H.-S. and A. J. Sinskey (1994) J. Microbiol. Biotechnol. 4: 256-263).
    • EXAMPLE 3 DNA Sequencing and Computational Functional Analysis
  • Genomic libraries as described in Example 2 were used for DNA sequencing according to standard methods, in particular by the chain termination method using ABI377 sequencing machines (see e.g., Fleischman, R. D. et al. (1995) “Whole-genome Random Sequencing and Assembly of Haemophilus Influenzae Rd., Science, 269:496-512). Sequencing primers with the following nucleotide sequences were used: 5′-GGAAACAGTATGACCATG-3′ or 5′-GTAAAACGACGGCCAGT-3′.
    • EXAMPLE 4 In vivo Mutagenesis
  • In vivo mutagenesis of Corynebacterium glutamicum can be performed by passage of plasmid (or other vector) DNA through E. coli or other microorganisms (e.g. Bacillus spp. or yeasts such as Saccharomyces cerevisiae) which are impaired in their capabilities to maintain the integrity of their genetic information. Typical mutator strains have mutations in the genes for the DNA repair system (e.g., mutHLS, mutD, mutT, etc.; for reference, see Rupp, W. D. (1996) DNA repair mechanisms, in: Escherichia coli and Salmonella, p. 2277-2294, ASM: Washington.) Such strains are well known to those of ordinary skill in the art. The use of such strains is illustrated, for example, in Greener, A. and Callahan, M. (1994) Strategies 7: 32-34.
    • EXAMPLE 5 DNA Transfer Between Escherichia coli and Corynebacterium glutamicum
  • Several Corynebacterium and Brevibacterium species contain endogenous plasmids (as e.g., pHM1519 or pBL1) which replicate autonomously (for review see, e.g., Martin, J. F. et al. (1987) Biotechnology, 5:137-146). Shuttle vectors for Escherichia coli and Corynebacterium glutamicum can be readily constructed by using standard vectors for E. coli (Sambrook, J. et al. (1989), “Molecular Cloning: A Laboratory Manual”, Cold Spring Harbor Laboratory Press or Ausubel, F. M. et al. (1994) “Current Protocols in Molecular Biology”, John Wiley & Sons) to which a origin or replication for and a suitable marker from Corynebacterium glutamicum is added. Such origins of replication are preferably taken from endogenous plasmids isolated from Corynebacterium and Brevibacterium species. Of particular use as transformation markers for these species are genes for kanamycin resistance (such as those derived from the Tn5 or Tn903 transposons) or chloramphenicol (Winnacker, E. L. (1987) “From Genes to Clones—Introduction to Gene Technology, VCH, Weinheim). There are numerous examples in the literature of the construction of a wide variety of shuttle vectors which replicate in both E. coli and C. glutamicum, and which can be used for several purposes, including gene over-expression (for reference, see e.g., Yoshihama, M. et al. (1985) J. Bacteriol. 162:591-597, Martin J. F. et al. (1987) Biotechnology, 5:137-146 and Eikmanns, B. J. et al. (1991) Gene, 102:93-98).
  • Using standard methods, it is possible to clone a gene of interest into one of the shuttle vectors described above and to introduce such a hybrid vectors into strains of Corynebacterium glutamicum. Transformation of C. glutamicum can be achieved by protoplast transformation (Kastsumata, R. et al. (1984) J. Bacteriol. 159306-311), electroporation (Liebl, E. et al. (1989) FEMS Microbiol. Letters, 53:399-303) and in cases where special vectors are used, also by conjugation (as described e.g. in Schäfer, A et al. (1990) J. Bacteriol. 172:1663-1666). It is also possible to transfer the shuttle vectors for C. glutamicum to E. coli by preparing plasmid DNA from C. glutamicum (using standard methods well-known in the art) and transforming it into E. coli. This transformation step can be performed using standard methods, but it is advantageous to use an Mcr-deficient E. coli strain, such as NM522 (Gough & Murray (1983) J. Mol. Biol. 166:1-19).
  • Genes may be overexpressed in C. glutamicum strains using plasmids which comprise pCG1 (U.S. Pat. No. 4,617,267) or fragments thereof, and optionally the gene for kanamycin resistance from TN903 (Grindley, N. D. and Joyce, C. M. (1980) Proc. Natl. Acad. Sci. USA 77(12): 7176-7180). In addition, genes may be overexpressed in C. glutamicum strains using plasmid pSL109 (Lee, H.-S. and A. J. Sinskey (1994) J. Microbiol. Biotechnol. 4: 256-263).
  • Aside from the use of replicative plasmids, gene overexpression can also be achieved by integration into the genome. Genomic integration in C. glutamicum or other Corynebacterium or Brevibacterium species may be accomplished by well-known methods, such as homologous recombination with genomic region(s), restriction endonuclease mediated integration (REMI) (see, e.g., DE Patent 19823834), or through the use of transposons. It is also possible to modulate the activity of a gene of interest by modifying the regulatory regions (e.g., a promoter, a repressor, and/or an enhancer) by sequence modification, insertion, or deletion using site-directed methods (such as homologous recombination) or methods based on random events (such as transposon mutagenesis or REMI). Nucleic acid sequences which function as transcriptional terminators may also be inserted 3′ to the coding region of one or more genes of the invention; such terminators are well-known in the art and are described, for example, in Winnacker, E. L. (1987) From Genes to Clones—Introduction to Gene Technology. VCH: Weinheim.
    • EXAMPLE 6 Assessment of the Expression of the Mutant Protein
  • Observations of the activity of a mutated protein in a transformed host cell rely on the fact that the mutant protein is expressed in a similar fashion and in a similar quantity to that of the wild-type protein. A useful method to ascertain the level of transcription of the mutant gene (an indicator of the amount of mRNA available for translation to the gene product) is to perform a Northern blot (for reference see, for example, Ausubel et al. (1988) Current Protocols in Molecular Biology, Wiley: N.Y.), in which a primer designed to bind to the gene of interest is labeled with a detectable tag (usually radioactive or chemiluminescent), such that when the total RNA of a culture of the organism is extracted, run on gel, transferred to a stable matrix and incubated with this probe, the binding and quantity of binding of the probe indicates the presence and also the quantity of mRNA for this gene. This information is evidence of the degree of transcription of the mutant gene. Total cellular RNA can be prepared from Corynebacterium glutamicum by several methods, all well-known in the art, such as that described in Bormann, E. R. et al. (1992) Mol. Microbiol. 6: 317-326.
  • To assess the presence or relative quantity of protein translated from this mRNA, standard techniques, such as a Western blot, may be employed (see, for example, Ausubel et al. (1988) Current Protocols in Molecular Biology, Wiley: N.Y.). In this process, total cellular proteins are extracted, separated by gel electrophoresis, transferred to a matrix such as nitrocellulose, and incubated with a probe, such as an antibody, which specifically binds to the desired protein. This probe is generally tagged with a chemiluminescent or colorimetric label which may be readily detected. The presence and quantity of label observed indicates the presence and quantity of the desired mutant protein present in the cell.
    • EXAMPLE 7 Growth of Genetically Modified Corynebacterium glutamicum—Media and Culture Conditions
  • Genetically modified Corynebacteria are cultured in synthetic or natural growth media. A number of different growth media for Corynebacteria are both well-known and readily available (Lieb et al. (1989) Appl. Microbiol. Biotechnol., 32:205-210; von der Osten et al. (1998) Biotechnology Letters, 11:11-16; Patent DE 4,120,867; Liebl (1992) “The Genus Corynebacterium, in: The Procaryotes, Volume II, Balows, A. et al., eds. Springer-Verlag). These media consist of one or more carbon sources, nitrogen sources, inorganic salts, vitamins and trace elements. Preferred carbon sources are sugars, such as mono-, di-, or polysaccharides. For example, glucose, fructose, mannose, galactose, ribose, sorbose, ribulose, lactose, maltose, sucrose, raffinose, starch or cellulose serve as very good carbon sources. It is also possible to supply sugar to the media via complex compounds such as molasses or other by-products from sugar refinement. It can also be advantageous to supply mixtures of different carbon sources. Other possible carbon sources are alcohols and organic acids, such as methanol, ethanol, acetic acid or lactic acid. Nitrogen sources are usually organic or inorganic nitrogen compounds, or materials which contain these compounds. Exemplary nitrogen sources include ammonia gas or ammonia salts, such as NH 4Cl or (NH4)2SO4, NH4OH, nitrates, urea, amino acids or complex nitrogen sources like corn steep liquor, soy bean flour, soy bean protein, yeast extract, meat extract and others.
  • Inorganic salt compounds which may be included in the media include the chloride-, phosphorous- or sulfate- salts of calcium, magnesium, sodium, cobalt, molybdenum, potassium, manganese, zinc, copper and iron. Chelating compounds can be added to the medium to keep the metal ions in solution. Particularly useful chelating compounds include dihydroxyphenols, like catechol or protocatechuate, or organic acids, such as citric acid. It is typical for the media to also contain other growth factors, such as vitamins or growth promoters, examples of which include biotin, riboflavin, thiamin, folic acid, nicotinic acid, pantothenate and pyridoxin. Growth factors and salts frequently originate from complex media components such as yeast extract, molasses, corn steep liquor and others. The exact composition of the media compounds depends strongly on the immediate experiment and is individually decided for each specific case. Information about media optimization is available in the textbook “Applied Microbiol. Physiology, A Practical Approach (eds. P. M. Rhodes, P. F. Stanbury, IRL Press (1997) pp. 53-73, ISBN 0 19 963577 3). It is also possible to select growth media from commercial suppliers, like standard 1 (Merck) or BHI (grain heart infusion, DIFCO) or others.
  • All medium components are sterilized, either by heat (20 minutes at 1.5 bar and 121° C.) or by sterile filtration. The components can either be sterilized together or, if necessary, separately. All media components can be present at the beginning of growth, or they can optionally be added continuously or batchwise.
  • Culture conditions are defined separately for each experiment. The temperature should be in a range between 15° C. and 45° C. The temperature can be kept constant or can be altered during the experiment. The pH of the medium should be in the range of 5 to 8.5, preferably around 7.0, and can be maintained by the addition of buffers to the media. An exemplary buffer for this purpose is a potassium phosphate buffer. Synthetic buffers such as MOPS, HEPES, ACES and others can alternatively or simultaneously be used. It is also possible to maintain a constant culture pH through the addition of NaOH or NH4OH during growth. If complex medium components such as yeast extract are utilized, the necessity for additional buffers may be reduced, due to the fact that many complex compounds have high buffer capacities. If a fermentor is utilized for culturing the micro-organisms, the pH can also be controlled using gaseous ammonia.
  • The incubation time is usually in a range from several hours to several days. This time is selected in order to permit the maximal amount of product to accumulate in the broth. The disclosed growth experiments can be carried out in a variety of vessels, such as microtiter plates, glass tubes, glass flasks or glass or metal fermentors of different sizes. For screening a large number of clones, the microorganisms should be cultured in microtiter plates, glass tubes or shake flasks, either with or without baffles. Preferably 100 ml shake flasks are used, filled with 10% (by volume) of the required growth medium. The flasks should be shaken on a rotary shaker (amplitude 25 mm) using a speed-range of 100-300 rpm. Evaporation losses can be diminished by the maintenance of a humid atmosphere; alternatively, a mathematical correction for evaporation losses should be performed.
  • If genetically modified clones are tested, an unmodified control clone or a control clone containing the basic plasmid without any insert should also be tested. The medium is inoculated to an OD600 of 0.5-1.5 using cells grown on agar plates, such as CM plates (10 g/l glucose, 2,5 g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeast extract, 5 g/l meat extract, 22 g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeast extract, 5 g/l meat extract, 22 g/l agar, pH 6.8 with 2M NaOH) that had been incubated at 30° C. Inoculation of the media is accomplished by either introduction of a saline suspension of C. glutamicum cells from CM plates or addition of a liquid preculture of this bacterium.
    • EXAMPLE 8 In vitro Analysis of the Function of Mutant Proteins
  • The determination of activities and kinetic parameters of enzymes is well established in the art. Experiments to determine the activity of any given altered enzyme must be tailored to the specific activity of the wild-type enzyme, which is well within the ability of one of ordinary skill in the art. Overviews about enzymes in general, as well as specific details concerning structure, kinetics, principles, methods, applications and examples for the determination of many enzyme activities may be found, for example, in the following references: Dixon, M., and Webb, E. C., (1979) Enzymes. Longmans: London; Fersht, (1985) Enzyme Structure and Mechanism. Freeman: New York; Walsh, (1979) Enzymatic Reaction Mechanisms. Freeman: San Francisco; Price, N. C., Stevens, L. (1982) Fundamentals of Enzymology. Oxford Univ. Press: Oxford; Boyer, P. D., ed. (1983) The Enzymes, 3rd ed. Academic Press: New York; Bisswanger, H., (1994) Enzymkinetik, 2nd ed. VCH: Weinheim (ISBN 3527300325); Bergmeyer, H. U., Bergmeyer, J., Gralβl, M., eds. (1983-1986) Methods of Enzymatic Analysis, 3rd ed., vol. I-XII, Verlag Chemie: Weinheim; and Ullmann's Encyclopedia of Industrial Chemistry (1987) vol. A9, “Enzymes”. VCH: Weinheim, p. 352-363.
  • The activity of proteins which bind to DNA can be measured by several well-established methods, such as DNA band-shift assays (also called gel retardation assays). The effect of such proteins on the expression of other molecules can be measured using reporter gene assays (such as that described in Kolmar, H. et al. (1995) EMBO J. 14: 3895-3904 and references cited therein). Reporter gene test systems are well known and established for applications in both pro- and eukaryotic cells, using enzymes such as beta-galactosidase, green fluorescent protein, and several others.
  • The determination of activity of membrane-transport proteins can be performed according to techniques such as those described in Gennis, R. B. (1989) “Pores, Channels and Transporters”, in Biomembranes, Molecular Structure and Function, Springer: Heidelberg, p. 85-137; 199-234; and 270-322.
    • EXAMPLE 9 Analysis of Impact of Mutant Protein on the Production of the Desired Product
  • The effect of the genetic modification in C. glutamicum on production of a desired compound (such as an amino acid) can be assessed by growing the modified microorganism under suitable conditions (such as those described above) and analyzing the medium and/or the cellular component for increased production of the desired product (i.e., an amino acid). Such analysis techniques are well known to one of ordinary skill in the art, and include spectroscopy, thin layer chromatography, staining methods of various kinds, enzymatic and microbiological methods, and analytical chromatography such as high performance liquid chromatography (see, for example, Ullman, Encyclopedia of Industrial Chemistry, vol. A2, p. 89-90 and p. 443-613, VCH: Weinheim (1985); Fallon, A. et al., (1987) “Applications of HPLC in Biochemistry” in: Laboratory Techniques in Biochemistry and Molecular Biology, vol. 17; Rehm et al. (1993) Biotechnology, vol. 3, Chapter III: “Product recovery and purification”, page 469-714, VCH: Weinheim; Belter, P. A. et al. (1988) Bioseparations: downstream processing for biotechnology, John Wiley and Sons; Kennedy, J. F. and Cabral, J. M. S. (1992) Recovery processes for biological materials, John Wiley and Sons; Shaeiwitz, J. A. and Henry, J. D. (1988) Biochemical separations, in: Ulmann's Encyclopedia of Industrial Chemistry, vol. B3, Chapter 11, page 1-27, VCH: Weinheim; and Dechow, F. J. (1989) Separation and purification techniques in biotechnology, Noyes Publications.)
  • In addition to the measurement of the final product of fermentation, it is also possible to analyze other components of the metabolic pathways utilized for the production of the desired compound, such as intermediates and side-products, to determine the overall efficiency of production of the compound. Analysis methods include measurements of nutrient levels in the medium (e.g., sugars, hydrocarbons, nitrogen sources, phosphate, and other ions), measurements of biomass composition and growth, analysis of the production of common metabolites of biosynthetic pathways, and measurement of gasses produced during fermentation. Standard methods for these measurements are outlined in Applied Microbial Physiology, A Practical Approach, P. M. Rhodes and P. F. Stanbury, eds., IRL Press, p. 103-129; 131-163; and 165-192 (ISBN: 0199635773) and references cited therein.
    • EXAMPLE 10 Purification of the Desired Product from C. glutamicum Culture
  • Recovery of the desired product from the C. glutamicum cells or supernatant of the above-described culture can be performed by various methods well known in the art. If the desired product is not secreted from the cells, the cells can be harvested from the culture by low-speed centrifugation, the cells can be lysed by standard techniques, such as mechanical force or sonication. The cellular debris is removed by centrifligation, and the supernatant fraction containing the soluble proteins is retained for further purification of the desired compound. If the product is secreted from the C. glutamicum cells, then the cells are removed from the culture by low-speed centrifugation, and the supernate fraction is retained for further purification.
  • The supernatant fraction from either purification method is subjected to chromatography with a suitable resin, in which the desired molecule is either retained on a chromatography resin while many of the impurities in the sample are not, or where the impurities are retained by the resin while the sample is not. Such chromatography steps may be repeated as necessary, using the same or different chromatography resins. One of ordinary skill in the art would be well-versed in the selection of appropriate chromatography resins and in their most efficacious application for a particular molecule to be purified. The purified product may be concentrated by filtration or ultrafiltration, and stored at a temperature at which the stability of the product is maximized.
  • There are a wide array of purification methods known to the art and the preceding method of purification is not meant to be limiting. Such purification techniques are described, for example, in Bailey, J. E. & Ollis, D. F. Biochemical Engineering Fundamentals, McGraw-Hill: N.Y. (1986).
  • The identity and purity of the isolated compounds may be assessed by techniques standard in the art. These include high-performance liquid chromatography (HPLC), spectroscopic methods, staining methods, thin layer chromatography, NIRS, enzymatic assay, or microbiologically. Such analysis methods are reviewed in: Patek et al. (1994) Appl. Environ. Microbiol. 60: 133-140; Malakhova et al. (1996) Biotekhnologiya 11: 27-32; and Schmidt et al. (1998) Bioprocess Engineer. 19: 67-70. Ulmann's Encyclopedia of Industrial Chemistry, (1996) vol. A27, VCH: Weinheim, p. 89-90, p. 521-540, p. 540-547, p. 559-566, 575-581 and p. 581-587; Michal, G. (1999) Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, John Wiley and Sons; Fallon, A. et al. (1987) Applications of HPLC in Biochemistry in: Laboratory Techniques in Biochemistry and Molecular Biology, vol. 17.
    • EXAMPLE 11 Analysis of the Gene Sequences of the Invention
  • The comparison of sequences and determination of percent homology between two sequences are art-known techniques, and can be accomplished using a mathematical algorithm, such as the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad Sci. USA 87:2264-68, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-77. Such an algorithm is incorporated into the NBLAST and XBLAST programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10. BLAST nucleotide searches can be performed with the NBLAST program, score=100, wordlength=12 to obtain nucleotide sequences homologous to MCT nucleic acid molecules of the invention. BLAST protein searches can be performed with the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences homologous to MCT protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., (1997) Nucleic Acids Res. 25(17):3389-3402. When utilizing BLAST and Gapped BLAST programs, one of ordinary skill in the art will know how to optimize the parameters of the program (e.g., XBLAST and NBLAST) for the specific sequence being analyzed.
  • Another example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Meyers and Miller ((1988) Comput. Appl. Biosci. 4: 11-17). Such an algorithm is incorporated into the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM 120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. Additional algorithms for sequence analysis are known in the art, and include ADVANCE and ADAM. described in Torelli and Robotti (1994) Comput. Appl. Biosci. 10:3-5; and FASTA, described in Pearson and Lipman (1988) P.N.A.S. 85:2444-8.
  • The percent homology between two amino acid sequences can also be accomplished using the GAP program in the GCG software package (available at http://www.gcg.com), using either a Blosum 62 matrix or a PAM250 matrix, and a gap weight of 12, 10, 8, 6, or 4 and a length weight of 2, 3, or 4. The percent homology between two nucleic acid sequences can be accomplished using the GAP program in the GCG software package, using standard parameters, such as a gap weight of 50 and a length weight of 3.
  • A comparative analysis of the gene sequences of the invention with those present in Genbank has been performed using techniques known in the art (see, e.g., Bexevanis and Ouellette, eds. (1998) Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. John Wiley and Sons: New York). The gene sequences of the invention were compared to genes present in Genbank in a three-step process. In a first step, a BLASTN analysis (e.g., a local alignment analysis) was performed for each of the sequences of the invention against the nucleotide sequences present in Genbank, and the top 500 hits were retained for further analysis. A subsequent FASTA search (e.g., a combined local and global alignment analysis, in which limited regions of the sequences are aligned) was performed on these 500 hits. Each gene sequence of the invention was subsequently globally aligned to each of the top three FASTA hits, using the GAP program in the GCG software package (using standard parameters). In order to obtain correct results, the length of the sequences extracted from Genbank were adjusted to the length of the query sequences by methods well-known in the art. The results of this analysis are set forth in Table 4. The resulting data is identical to that which would have been obtained had a GAP (global) analysis alone been performed on each of the genes of the invention in comparison with each of the references in Genbank, but required significantly reduced computational time as compared to such a database-wide GAP (global) analysis. Sequences of the invention for which no alignments above the cutoff values were obtained are indicated on Table 4 by the absence of alignment information. It will further be understood by one of ordinary skill in the art that the GAP alignment homology percentages set forth in Table 4 under the heading “% homology (GAP)” are listed in the European numerical format, wherein a ‘,’ represents a decimal point. For example, a value of “40,345” in this column represents “40.345%”.
    • EXAMPLE 12 Construction and Operation of DNA Microarrays
  • The sequences of the invention may additionally be used in the construction and application of DNA microarrays (the design, methodology, and uses of DNA arrays are well known in the art, and are described, for example, in Schena, M. et al. (1995) Science 270: 467-470; Wodicka, L. et al. (1997) Nature Biotechnology 15: 1359-1367; DeSaizieu, A. et al. (1998) Nature Biotechnology 16: 45-48; and DeRisi, J. L. et al. (1997) Science 278: 680-686).
  • DNA microarrays are solid or flexible supports consisting of nitrocellulose, nylon, glass, silicone, or other materials. Nucleic acid molecules may be attached to the surface in an ordered manner. After appropriate labeling, other nucleic acids or nucleic acid mixtures can be hybridized to the immobilized nucleic acid molecules, and the label may be used to monitor and measure the individual signal intensities of the hybridized molecules at defined regions. This methodology allows the simultaneous quantification of the relative or absolute amount of all or selected nucleic acids in the applied nucleic acid sample or mixture. DNA microarrays, therefore, permit an analysis of the expression of multiple (as many as 6800 or more) nucleic acids in parallel (see, e.g., Schena, M. (1996) BioEssays 18(5): 427-431).
  • The sequences of the invention may be used to design oligonucleotide primers which are able to amplify defined regions of one or more C. glutamicum genes by a nucleic acid amplification reaction such as the polymerase chain reaction. The choice and design of the 5′ or 3′ oligonucleotide primers or of appropriate linkers allows the covalent attachment of the resulting PCR products to the surface of a support medium described above (and also described, for example, Schena, M. et al. (1995) Science 270: 467-470).
  • Nucleic acid microarrays may also be constructed by in situ oligonucleotide synthesis as described by Wodicka, L. et al. (1997) Nature Biotechnology 15: 1359-1367. By photolithographic methods, precisely defined regions of the matrix are exposed to light. Protective groups which are photolabile are thereby activated and undergo nucleotide addition, whereas regions that are masked from light do not undergo any modification. Subsequent cycles of protection and light activation permit the synthesis of different oligonucleotides at defined positions. Small, defined regions of the genes of the invention may be synthesized on microarrays by solid phase oligonucleotide synthesis.
  • The nucleic acid molecules of the invention present in a sample or mixture of nucleotides may be hybridized to the microarrays. These nucleic acid molecules can be labeled according to standard methods. In brief, nucleic acid molecules (e.g., mRNA molecules or DNA molecules) are labeled by the incorporation of isotopically or fluorescently labeled nucleotides, e.g., during reverse transcription or DNA synthesis. Hybridization of labeled nucleic acids to microarrays is described (e.g., in Schena, M. et al. (1995) supra; Wodicka, L. et al. (1997), supra; and DeSaizieu A. et al. (1998), supra). The detection and quantification of the hybridized molecule are tailored to the specific incorporated label. Radioactive labels can be detected, for example, as described in Schena, M. et al. (1995) supra) and fluorescent labels may be detected, for example, by the method of Shalon et al. (1996) Genome Research 6: 639-645).
  • The application of the sequences of the invention to DNA microarray technology, as described above, permits comparative analyses of different strains of C. glutamicum or other Corynebacteria. For example, studies of inter-strain variations based on individual transcript profiles and the identification of genes that are important for specific and/or desired strain properties such as pathogenicity, productivity and stress tolerance are facilitated by nucleic acid array methodologies. Also, comparisons of the profile of expression of genes of the invention during the course of a fermentation reaction are possible using nucleic acid array technology.
    • EXAMPLE 13 Analysis of the Dynamics of Cellular Protein Populations (Proteomics)
  • The genes, compositions, and methods of the invention may be applied to study the interactions and dynamics of populations of proteins, termed ‘proteomics’. Protein populations of interest include, but are not limited to, the total protein population of C. glutamicum (e.g., in comparison with the protein populations of other organisms), those proteins which are active under specific environmental or metabolic conditions (e.g., during fermentation, at high or low temperature, or at high or low pH), or those proteins which are active during specific phases of growth and development.
  • Protein populations can be analyzed by various well-known techniques, such as gel electrophoresis. Cellular proteins may be obtained, for example, by lysis or extraction, and may be separated from one another using a variety of electrophoretic techniques. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) separates proteins largely on the basis of their molecular weight. Isoelectric focusing polyacrylamide gel electrophoresis (IEF-PAGE) separates proteins by their isoelectric point (which reflects not only the amino acid sequence but also posttranslational modifications of the protein). Another, more preferred method of protein analysis is the consecutive combination of both IEF-PAGE and SDS-PAGE, known as 2-D-gel electrophoresis (described, for example, in Hermann et al. (1998) Electrophoresis 19: 3217-3221; Fountoulakis et al. (1998) Electrophoresis 19: 1193-1202; Langen et al. (1997) Electrophoresis 18: 1184-1192; Antelmann et al. (1997) Electrophoresis 18: 1451-1463). Other separation techniques may also be utilized for protein separation, such as capillary gel electrophoresis; such techniques are well known in the art.
  • Proteins separated by these methodologies can be visualized by standard techniques, such as by staining or labeling. Suitable stains are known in the art, and include Coomassie Brilliant Blue, silver stain, or fluorescent dyes such as Sypro Ruby (Molecular Probes). The inclusion of radioactively labeled amino acids or other protein precursors (e.g., 35S-methionine, 35S-cysteine, 14C-labelled amino acids, 15N-amino acids, 15NO3 or 15NH4 + or 13C-labelled amino acids) in the medium of C. glutamicum permits the labeling of proteins from these cells prior to their separation. Similarly, fluorescent labels may be employed. These labeled proteins can be extracted, isolated and separated according to the previously described techniques.
  • Proteins visualized by these techniques can be further analyzed by measuring the amount of dye or label used. The amount of a given protein can be determined quantitatively using, for example, optical methods and can be compared to the amount of other proteins in the same gel or in other gels. Comparisons of proteins on gels can be made, for example, by optical comparison, by spectroscopy, by image scanning and analysis of gels, or through the use of photographic films and screens. Such techniques are well-known in the art.
  • To determine the identity of any given protein, direct sequencing or other standard techniques may be employed. For example, N- and/or C-terminal amino acid sequencing (such as Edman degradation) may be used, as may mass spectrometry (in particular MALDI or ESI techniques (see, e.g., Langen et al. (1997) Electrophoresis 18: 1184-1192)). The protein sequences provided herein can be used for the identification of C. glutamicum proteins by these techniques.
  • The information obtained by these methods can be used to compare patterns of protein presence, activity, or modification between different samples from various biological conditions (e.g., different organisms, time points of fermentation, media conditions, or different biotopes, among others). Data obtained from such experiments alone, or in combination with other techniques, can be used for various applications, such as to compare the behavior of various organisms in a given (e.g., metabolic) situation, to increase the productivity of strains which produce fine chemicals or to increase the efficiency of the production of fine chemicals.
  • Equivalents
  • Those of ordinary skill in the art will recognize, or will be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.
    TABLE 1
    GENES IN THE APPLICATION
    Nucleic Amino
    Acid Acid
    SEQ SEQ
    ID ID Identification NT NT
    NO NO Code Contig. Start Stop Function
    1 2 RXN03097 VV0062 3 557 AMMONIUM TRANSPORT SYSTEM
    3 4 RXA02099 GR00630 6198 6470 AMMONIUM TRANSPORT SYSTEM
    5 6 RXA00104 GR00014 15895 16650 CYSQ PROTEIN, ammonium transport protein
    Polyketide Synthesis
    7 8 RXA01420 GR00416 775 17 4″-MYCAROSYL ISOVALERYL-COA TRANSFERASE (EC 2.—.—.—)
    9 10 RXN02581 VV0098 30482 28623 POLYKETIDE SYNTHASE
    11 12 F RXA02581 GR00741 1 1527 POLYKETIDE SYNTHASE
    13 14 RXA02582 GR00741 1890 6719 PROBABLE POLYKETIDE SYNTHASE CY338.20
    15 16 RXA01138 GR00318 1656 2072 ACTINORHODIN POLYKETIDE DIMERASE (EC —.—.—.—)
    17 18 RXA01980 GR00573 1470 838 POLYKETIDE CYCLASE
    19 20 RXN01007 VV0021 2572 866 FRNA
    21 22 RXN00784 VV0103 27531 28265 FRNE
    Fatty acid and lipid synthesis
    23 24 RXA02335 GR00672 550 2322 BIOTIN CARBOXYLASE (EC 6.3.4.14)
    25 26 RXA02173 GR00641 7473 8924 ACETYL-COENZYME A CARBOXYLASE CARBOXYL
    TRANSFERASE SUBUNIT BETA (EC 6.4.1.2)
    27 28 RXA01764 GR00500 2178 3110 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE (EC 1.1.1.100)
    29 30 RXN02487 VV0007 6367 4664 LONG-CHAIN-FATTY-ACID—COA LIGASE (EC 6.2.1.3)
    31 32 F RXA02487 GR00718 4937 4650 LONG-CHAIN-FATTY-ACID—COA LIGASE (EC 6.2.1.3)
    33 34 F RXA02490 GR00720 817 5 LONG-CHAIN-FATTY-ACID—COA LIGASE (EC 6.2.1.3)
    35 36 RXA01467 GR00422 920 1210 ACYL CARRIER PROTEIN
    37 38 RXA00796 GR00212 202 5 Acyl carrier protein phosphodiesterase
    39 40 RXA01897 GR00544 617 1159 Acyl carrier protein phosphodiesterase
    41 42 RXN02809 VV0342 380 6 Acyl carrier protein phosphodiesterase
    43 44 F RXA02809 GR00790 277 5 Acyl carrier protein phosphodiesterase
    45 46 RXN00113 VV0129 103 5724 FATTY ACID SYNTHASE (EC 2.3.1.85) [INCLUDES: EC 2.3.1.38;
    EC 2.3.1.39; EC 2.3.1.41;
    47 48 F RXA00113 GR00017 2 3295 FATTY-ACID SYNTHASE (EC 2.3.1.85)
    49 50 RXN03111 VV0084 6040 5 FATTY ACID SYNTHASE (EC 2.3.1.85) [INCLUDES: EC 2.3.1.38;
    EC 2.3.1.39; EC 2.3.1.41; EC 1.1.1.100; EC 4.2.1.61;
    EC 1.3.1.10; EC 3.1.2.14]
    51 52 F RXA00158 GR00024 2088 4 FATTY ACID SYNTHASE (EC 2.3.1.85)
    53 54 F RXA00572 GR00155 2 3832 FATTY ACID SYNTHASE (EC 2.3.1.85)
    55 56 RXA02582 GR00741 1890 6719 PROBABLE POLYKETIDE SYNTHASE CY338.20
    57 58 RXA02691 GR00754 15347 14541 FATTY ACYL RESPONSIVE REGULATOR
    59 60 RXA00880 GR00242 6213 8057 LONG-CHAIN-FATTY-ACID—COA LIGASE (EC 6.2.1.3)
    61 62 RXA01060 GR00296 9566 10489 OMEGA-3 FATTY ACID DESATURASE (EC 1.14.99.—)
    63 64 RXN01722 VV0036 2938 1214 MEDIUM-CHAIN-FATTY-ACID—COA LIGASE (EC 6.2.1.—)
    65 66 F RXA01722 GR00488 5746 4022 MEDIUM-CHAIN-FATTY-ACID—COA LIGASE (EC 6.2.1.—)
    67 68 RXA01644 GR00456 9854 8577 CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE (EC 2.1.1.79)
    69 70 RXA02029 GR00618 356 1669 CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE (EC 2.1.1.79)
    71 72 RXA01801 GR00509 3396 2380 ENOYL-COA HYDRATASE (EC 4.2.1.17)
    73 74 RXN02512 VV0171 16147 15185 LIPID A BIOSYNTHESIS LAUROYL ACYLTRANSFERASE (EC 2.3.1.—)
    75 76 F RXA02512 GR00721 3303 4259 LIPID A BIOSYNTHESIS LAUROYL ACYLTRANSFERASE (EC 2.3.1.—)
    77 78 RXA00899 GR00245 1599 2864 CARDIOLIPIN SYNTHETASE (EC 2.7.8.—)
    79 80 RXN00819 VV0054 18127 19455 ACYL-COA DEHYDROGENASE (EC 1.3.99.—)
    81 82 F RXA00819 GR00221 18 1007 ACYL-COA DEHYDROGENASE (EC 1.3.99.—)
    83 84 F RXA01766 GR00500 4081 4371 ACYL-COA DEHYDROGENASE (EC 1.3.99.—)
    85 86 RXN01762 VV0054 15318 13783 LONG-CHAIN-FATTY-ACID—COA LIGASE (EC 6.2.1.3)
    87 88 F RXA01762 GR00500 1272 10 LONG-CHAIN-FATTY-ACID—COA LIGASE (EC 6.2.1.3)
    89 90 RXA00681 GR00179 3405 2662 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE (EC 1.1.1.100)
    91 92 RXA00802 GR00214 3803 4516 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE (EC 1.1.1.100)
    93 94 RXA02133 GR00639 3 308 3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE (EC 1.1.1.100)
    95 96 RXN01114 VV0182 9118 10341 3-KETOACYL-COA THIOLASE (EC 2.3.1.16)
    97 98 F RXA01114 GR00308 2 793 3-KETOACYL-COA THIOLASE (EC 2.3.1.16)
    99 100 RXA01894 GR00542 1622 2476 PHOSPHATIDATE CYTIDYLYLTRANSFERASE (EC 2.7.7.41)
    101 102 RXA02599 GR00742 3179 3655 PHOSPHATIDYLGLYCEROPHOSPHATASE B (EC 3.1.3.27)
    103 104 RXN02638 VV0098 54531 53656 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE (EC 2.3.1.51)
    105 106 F RXA02638 GR00749 8 511 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE (EC 2.3.1.51)
    107 108 RXA00856 GR00232 720 1256 CDP-DIACYLGLYCEROL—GLYCEROL-3-PHOSPHATE 3-
    PHOSPHATIDYLTRANSFERASE (EC 2.7.8.5)
    109 110 RXA02511 GR00721 2621 3277 CDP-DIACYLGLYCEROL—GLYCEROL-3-PHOSPHATE 3-
    PHOSPHATIDYLTRANSFERASE (EC 2.7.8.5)
    111 112 RXN02836 VV0102 32818 33372 KETOACYL REDUCTASE HETN (EC 1.3.1.—)
    113 114 F RXA02836 GR00827 106 411 KETOACYL REDUCTASE HETN (EC 1.3.1.—)
    115 116 RXA02578 GR00740 2438 3541 PUTATIVE ACYLTRANSFERASE
    117 118 RXA02150 GR00639 18858 19658 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE (EC 2.3.1.51)
    119 120 RXA00607 GR00160 1869 2249 POLY(3-HYDROXYALKANOATE) POLYMERASE (EC 2.3.1.—)
    121 122 RXA02397 GR00698 1688 2683 POLY-BETA-HYDROXYBUTYRATE POLYMERASE (EC 2.3.1.—)
    123 124 RXN03110 VV0083 16568 17929 HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6)
    125 126 F RXA00660 GR00171 1027 5 HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6)
    127 128 RXA00801 GR00214 3138 3770 HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6)
    129 130 RXA00821 GR00221 1469 2311 HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6)
    131 132 RXN02966 VV0143 12056 13462 HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6)
    133 134 F RXA01833 GR00517 1666 260 HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6)
    135 136 RXA01853 GR00525 5561 5010 HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6)
    137 138 RXN02424 VV0116 10570 11169 HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6)
    139 140 F RXA02424 GR00706 808 428 HYDROXYACYLGLUTATHIONE HYDROLASE (EC 3.1.2.6)
    141 142 RXN00419 VV0112 1024 266 ACETOACETYL-COA REDUCTASE (EC 1.1.1.36)
    143 144 F RXA00419 GR00095 3 464 ACETOACETYL-COA REDUCTASE (EC 1.1.1.36)
    145 146 F RXA00421 GR00096 565 723 ACETOACETYL-COA REDUCTASE (EC 1.1.1.36)
    147 148 RXN02923 VV0088 3301 2564 ACETOACETYL-COA REDUCTASE (EC 1.1.1.36)
    149 150 RXN02922 VV0321 11407 10328 ACYL-COA DEHYDROGENASE, SHORT-CHAIN SPECIFIC (EC 1.3.99.2)
    151 152 RXN03065 VV0038 6237 6629 HOLO-[ACYL-CARRIER PROTEIN] SYNTHASE (EC 2.7.8.7)
    153 154 RXN03132 VV0127 39053 39472 POLY-BETA-HYDROXYBUTYRATE POLYMERASE (EC 2.3.1.—)
    155 156 RXN03157 VV0188 1607 1170 LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN KDTB
    157 158 RXN00934 VV0171 15181 14099 (AE000805) LPS biosynthesis RfbU related protein [Methanobacterium
    thermoautotrophicum]
    159 160 RXN00792 VV0321 10328 9132 ACYL-COA DEHYDROGENASE, SHORT-CHAIN SPECIFIC (EC 1.3.99.2)
    161 162 RXN00931 VV0171 13011 12166 ACYL-COA THIOESTERASE II (EC 3.1.2.—)
    163 164 F RXA00931 GR00253 4959 4114 thioesterase II
    165 166 RXN01421 VV0122 16024 15638 ACYLTRANSFERASE (EC 2.3.1.—)
    167 168 RXN02342 VV0078 3460 4266 BIOTIN—[ACETYL-COA-CARBOXYLASE] SYNTHETASE (EC 6.3.4.15)
    169 170 RXN00563 VV0038 1 2739 FATTY ACID SYNTHASE (EC 2.3.1.85) [INCLUDES: EC 2.3.1.38;
    EC 2.3.1.39; EC 2.3.1.41; EC 1.1.1.100; EC 4.2.1.61; EC 1.3.1.10; EC 3.1.2.14]
    171 172 RXN02168 VV0100 2894 81 FATTY ACID SYNTHASE (EC 2.3.1.85) [INCLUDES: EC 2.3.1.38;
    EC 2.3.1.39; EC 2.3.1.41; EC 1.1.1.100; EC 4.2.1.61; EC 1.3.1.10;
    EC 3.1.2.14]
    173 174 RXN01090 VV0155 6483 5686 KETOACYL REDUCTASE HETN (EC 1.3.1.—)
    175 176 RXN02062 VV0222 3159 1990 Lipopolysaccharide N-acetylglucosaminyltransferase
    177 178 RXN02148 VV0300 16561 17703 Lipopolysaccharide N-acetylglucosaminyltransferase
    179 180 RXN02595 VV0098 11098 9935 Lipopolysaccharide N-acetylglucosaminyltransferase
    181 182 RXS00148 VV0167 9849 12059 METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT (EC 5.4.99.2)
    183 184 RXS00149 VV0167 7995 9842 METHYLMALONYL-COA MUTASE BETA-SUBUNIT (EC 5.4.99.2)
    185 186 RXS02106 VV0123 22649 21594 LIPOATE-PROTEIN LIGASE A (EC 6.—.—.—)
    187 188 RXS01746 VV0185 934 1686 LIPOATE-PROTEIN LIGASE B (EC 6.—.—.—)
    189 190 RXS01747 VV0185 1826 2869 LIPOIC ACID SYNTHETASE
    191 192 RXC01748 VV0185 3001 3780 protein involved in lipid metabolism
    193 194 RXC00354 VV0135 33604 32792 Cytosolic Protein involved in lipid metabolism
    195 196 RXC01749 VV0185 3953 5569 Membrane Spanning Protein involved in lipid metabolism
    Fatty acid degradation
    197 198 RXA02268 GR00655 2182 3081 LIPASE (EC 3.1.1.3)
    199 200 RXA02269 GR00655 3094 4065 LIPASE (EC 3.1.1.3)
    201 202 RXA01614 GR00449 8219 7197 LYSOPHOSPHOLIPASE L2 (EC 3.1.1.5)
    203 204 RXA01983 GR00573 3559 3053 LIPASE (EC 3.1.1.3)
    205 206 RXN02947 VV0078 1319 6 PROPIONYL-COA CARBOXYLASE BETA CHAIN (EC 6.4.1.3)
    207 208 F RXA02320 GR00667 593 6 PROPIONYL-COA CARBOXYLASE BETA CHAIN (EC 6.4.1.3)
    209 210 F RXA02851 GR00851 524 6 PROPIONYL-COA CARBOXYLASE BETA CHAIN (EC 6.4.1.3)
    211 212 RXN02321 VV0078 3291 1663 PROPIONYL-COA CARBOXYLASE BETA CHAIN (EC 6.4.1.3)
    213 214 F RXA02321 GR00667 1380 937 PROPIONYL-COA CARBOXYLASE BETA CHAIN (EC 6.4.1.3)
    215 216 F RXA02343 GR00675 1403 1816 PROPIONYL-COA CARBOXYLASE BETA CHAIN (EC 6.4.1.3)
    217 218 F RXA02850 GR00850 2 493 PROPIONYL-COA CARBOXYLASE BETA CHAIN (EC 6.4.1.3)
    219 220 RXA02583 GR00741 6743 8290 PROPIONYL-COA CARBOXYLASE BETA CHAIN (EC 6.4.1.3)
    221 222 RXA00870 GR00239 809 2320 METHYLMALONATE-SEMIALDEHYDE DEHYDROGENASE
    (ACYLATING) (EC 1.2.1.27) 2-Methyl-3-oxopropanoate:
    NAD+ oxidoreductase (CoA-propanoylating)
    223 224 RXA01260 GR00367 2381 1200 LIPOAMIDE DEHYDROGENASE COMPONENT (E3) OF BRANCHED-CHAIN
    ALPHA-KETO ACID DEHYDROGENASE COMPLEX (EC 1.8.1.4)
    225 226 RXA01261 GR00367 2607 2437 LIPOAMIDE DEHYDROGENASE COMPONENT (E3) OF BRANCHED-CHAIN
    ALPHA-KETO ACID DEHYDROGENASE COMPLEX (EC 1.8.1.4)
    227 228 RXA01136 GR00318 685 1116 ISOVALERYL-COA DEHYDROGENASE (EC 1.3.99.10)
    229 230 RXN00559 VV0103 7568 6552 PROTEIN VDLD
    231 232 F RXA00559 GR00149 218 6 PROTEIN VDLD
    233 234 RXA01580 GR00440 707 6 Glycerophosphoryl diester phosphodiesterase
    235 236 RXA02677 GR00754 3119 3877 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE (EC 3.1.4.46)
    237 238 RXS01166 VV0117 18142 16838 EXTRACELLULAR LIPASE PRECURSOR (EC 3.1.1.3)
    Terpenoid biosynthesis
    239 240 RXA00875 GR00241 2423 1857 ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE (EC 5.3.3.2)
    241 242 RXA01292 GR00373 1204 2388 PHYTOENE DEHYDROGENASE (EC 1.3.—.—)
    243 244 RXA01293 GR00373 2370 2696 PHYTOENE DEHYDROGENASE (EC 1.3.—.—)
    245 246 RXA02310 GR00665 1132 2394 GERANYLGERANYL HYDROGENASE
    247 248 RXA02718 GR00758 18539 19585 GERANYLGERANYL PYROPHOSPHATE SYNTHASE (EC 2.5.1.1)
    249 250 RXA01067 GR00298 1453 2181 undecaprenyl-diphosphate synthase (EC 2.5.1.31)
    251 252 RXA01269 GR00367 20334 19894 UNDECAPRENYL-PHOSPHATE GALACTOSEPHOSPHOTRANSFERASE (EC
    2.7.8.6)
    253 254 RXA01205 GR00346 3 533 PUTATIVE UNDECAPRENYL-PHOSPHATE ALPHA-N-
    ACETYLGLUCOSAMINYLTRANSFERASE (EC 2.4.1.—)
    255 256 RXA01576 GR00438 8053 8811 DOLICHYL-PHOSPHATE BETA-GLUCOSYLTRANSFERASE (EC 2.4.1.117)
    257 258 RXN02309 VV0025 28493 29542 OCTAPRENYL-DIPHOSPHATE SYNTHASE (EC 2.5.1.—)
    259 260 F RXA02309 GR00665 978 4 OCTAPRENYL-DIPHOSPHATE SYNTHASE (EC 2.5.1.—)
    261 262 RXN00477 VV0086 38905 37262 PHYTOENE DEHYDROGENASE (EC 1.3.—.—)
    263 264 F RXA00477 GR00119 13187 11544 PHYTOENE DEHYDROGENASE (EC 1.3.—.—)
    265 266 RXA00478 GR00119 14020 13190 PHYTOENE SYNTHASE (EC 2.5.1.—)
    267 268 RXA01291 GR00373 345 1277 PHYTOENE SYNTHASE (EC 2.5.1.—)
    269 270 RXA00480 GR00119 17444 16329 FARNESYL DIPHOSPHATE SYNTHASE (EC 2.5.1.1) (EC 2.5.1.10)
    271 272 RXS01879 VV0105 1505 573 isopentenyl-phosphate kinase (EC 2.7.4.—)
    273 274 RXS02023 VV0160 3234 4001 P450 cytochrome, isopentenyltransf, ferridox
    275 276 RXS00948 VV0107 4266 5384 12-oxophytodienoate reductase (EC 1.3.1.42)
    277 278 RXS02228 VV0068 1876 2778 TRNA DELTA(2)-ISOPENTENYLPYROPHOSPHATE
    TRANSFERASE (EC 2.5.1.8)
    279 280 RXC01971 VV0105 4545 3715 Metal-Dependent Hydrolase involved in metabolism of terpenoids
    281 282 RXC02697 VV0017 31257 32783 membrane protein involved in metabolism of terpenoids
    ABC-Transporter
    283 284 RXN01946 VV0228 2 1276 Hypothetical ABC Transporter ATP-Binding Protein
    285 286 F RXA01946 GR00559 1849 575 (AL021184) ABC transporter ATP binding protein [Mycobacterium tuberculosis]
    287 288 RXN00164 VV0232 1782 94 Hypothetical ABC Transporter ATP-Binding Protein
    289 290 F RXA00164 GR00025 1782 94 , P, G, R ATPase subunits of ABC transporters
    291 292 RXN00243 VV0057 28915 27899 , P, G, R ATPase subunits of ABC transporters
    293 294 F RXA00243 GR00037 930 4 , P, G, R ATPase subunits of ABC transporters
    295 296 RXA00259 GR00039 8469 6268 , P, G, R ATPase subunits of ABC transporters
    297 298 RXN00410 VV0086 51988 51323 GLUTAMINE TRANSPORT ATP-BINDING PROTEIN GLNQ
    299 300 F RXA00410 GR00092 829 164 , P, G, R ATPase subunits of ABC transporters
    301 302 RXN00456 VV0076 6780 8156 , P, G, R ATPase subunits of ABC transporters
    303 304 F RXA00456 GR00114 316 5 , P, G, R ATPase subunits of ABC transporters
    305 306 F RXA00459 GR00115 1231 245 , P, G, R ATPase subunits of ABC transporters
    307 308 RXN01604 VV0137 8117 7470 , P, G, R ATPase subunits of ABC transporters
    309 310 F RXA01604 GR00448 2 607 , P, G, R ATPase subunits of ABC transporters
    311 312 RXN02547 VV0057 27726 25588 , P, G, R ATPase subunits of ABC transporters
    313 314 F RXA02547 GR00726 22055 19932 , P, G, R ATPase subunits of ABC transporters
    315 316 RXN02571 VV0101 12331 13359 MALTOSE/MALTODEXTRIN TRANSPORT ATP-BINDING PROTEIN MALK
    317 318 F RXA02571 GR00736 1469 2497 , P, G, R ATPase subunits of ABC transporters
    319 320 RXN02074 VV0318 12775 11153 TRANSPORT ATP-BINDING PROTEIN CYDD
    321 322 F RXA02074 GR00628 5798 4176 , P, G, R ATPase subunits of ABC transporters
    323 324 RXA02095 GR00629 14071 15474 , P, G, R ATPase subunits of ABC transporters
    325 326 RXA02225 GR00652 3156 2275 , P, G, R ATPase subunits of ABC transporters
    327 328 RXA02253 GR00654 20480 21406 , P, G, R ATPase subunits of ABC transporters
    329 330 RXN01881 VV0105 529 95 Hypothetical ABC Transporter ATP-Binding Protein
    331 332 F RXA01881 GR00537 3092 3532 ATPase components of ABC transporters with duplicated ATPase domains
    333 334 RXA00526 GR00136 1353 664 Hypothetical ABC Transporter ATP-Binding Protein
    335 336 RXN00733 VV0132 1647 2531 Hypothetical ABC Transporter ATP-Binding Protein
    337 338 F RXA00733 GR00197 411 4 Hypothetical ABC Transporter ATP-Binding Protein
    339 340 RXA00735 GR00198 849 181 Hypothetical ABC Transporter ATP-Binding Protein
    341 342 RXA00878 GR00242 3733 1871 Hypothetical ABC Transporter ATP-Binding Protein
    343 344 RXN01191 VV0169 10478 12067 Hypothetical ABC Transporter ATP-Binding Protein
    345 346 F RXA01191 GR00341 1571 165 Hypothetical ABC Transporter ATP-Binding Protein
    347 348 RXN01212 VV0169 3284 4207 Hypothetical ABC Transporter ATP-Binding Protein
    349 350 F RXA01212 GR00350 1 813 Hypothetical ABC Transporter ATP-Binding Protein
    351 352 RXA02749 GR00764 4153 5028 Hypothetical ABC Transporter ATP-Binding Protein
    353 354 RXA02224 GR00652 2271 475 Hypothetical ABC Transporter ATP-Binding Protein
    355 356 RXN01602 VV0229 1109 2638 Hypothetical ABC Transporter ATP-Binding Protein
    357 358 RXN02515 VV0087 962 1717 Hypothetical ABC Transporter ATP-Binding Protein
    359 360 RXN00525 VV0079 26304 27566 Hypothetical ABC Transporter Permease Protein
    361 362 RXN02096 VV0126 20444 22135 Hypothetical ABC Transporter Permease Protein
    363 364 RXN00412 VV0086 53923 52844 Hypothetical Amino Acid ABC Transporter ATP-Binding Protein
    365 366 RXN00411 VV0086 52844 52170 Hypothetical Amino Acid ABC Transporter Permease Protein
    367 368 RXN02614 VV0313 5964 5236 TAURINE TRANSPORT ATP-BINDING PROTEIN TAUB
    369 370 RXN02613 VV0313 5223 4267 TAURINE-BINDING PERIPLASMIC PROTEIN PRECURSOR
    371 372 RXN00368 VV0226 2300 726 SPERMIDINE/PUTRESCINE TRANSPORT ATP-BINDING PROTEIN POTA
    373 374 F RXA00368 GR00076 1 579 SPERMIDINE/PUTRESCINE TRANSPORT ATP-BINDING PROTEIN POTA
    375 376 F RXA00370 GR00077 6 803 SPERMIDINE/PUTRESCINE TRANSPORT ATP-BINDING PROTEIN POTA
    377 378 RXN01285 VV0215 1780 1055 FERRIC ENTEROBACTIN TRANSPORT ATP-BINDING PROTEIN FEPC
    379 380 RXN00523 VV0194 1363 338 FERRIC ENTEROBACTIN TRANSPORT PROTEIN FEPG
    381 382 RXN01142 VV0077 5805 6302 NITRATE TRANSPORT ATP-BINDING PROTEIN NRTD
    383 384 RXN01141 VV0077 4644 5468 NITRATE TRANSPORT PROTEIN NRTA
    385 386 RXN01002 VV0106 8858 8055 PHOSPHONATES TRANSPORT ATP-BINDING PROTEIN PHNC
    387 388 RXN01000 VV0106 7252 6407 PHOSPHONATES TRANSPORT SYSTEM PERMEASE PROTEIN PHNE
    389 390 RXN01732 VV0106 9944 8895 PHOSPHONATES-BINDING PERIPLASMIC PROTEIN PRECURSOR
    391 392 RXN03080 VV0045 1670 2449 FERRIC ENTEROBACTIN TRANSPORT ATP-BINDING PROTEIN FEPC
    393 394 RXN03081 VV0045 2476 2934 FERRIENTEROBACTIN-BINDING PERIPLASMIC PROTEIN PRECURSOR
    395 396 RXN03082 VV0045 3131 3451 FERRIENTEROBACTIN-BINDING PERIPLASMIC PROTEIN PRECURSOR
    Other transporters
    397 398 RXA02261 GR00654 30936 32291 AMMONIUM TRANSPORT SYSTEM
    399 400 RXA02020 GR00613 1015 5 AROMATIC AMINO ACID TRANSPORT PROTEIN AROP
    401 402 RXA00281 GR00043 4721 5404 BACITRACIN TRANSPORT ATP-BINDING PROTEIN BCRA
    403 404 RXN00570 VV0147 855 4 BENZOATE MEMBRANE TRANSPORT PROTEIN
    405 406 F RXA00570 GR00153 1 498 BENZOATE MEMBRANE TRANSPORT PROTEIN
    407 408 RXN00571 VV173 1298 42 BENZOATE MEMBRANE TRANSPORT PROTEIN
    409 410 F RXA00571 GR00154 2 1186 BENZOATE MEMBRANE TRANSPORT PROTEIN
    411 412 RXA00962 GR00268 2 667 BENZOATE MEMBRANE TRANSPORT PROTEIN
    413 414 RXA02811 GR00792 177 560 BENZOATE MEMBRANE TRANSPORT PROTEIN
    415 416 RXA02115 GR00635 2 1198 BENZOATE MEMBRANE TRANSPORT PROTEIN
    417 418 RXN00590 VV0178 5043 6230 BRANCHED CHAIN AMINO ACID TRANSPORT SYSTEM II
    CARRIER PROTEIN
    419 420 F RXA00590 GR00157 178 564 BRANCHED CHAIN AMINO ACID TRANSPORT SYSTEM II
    CARRIER PROTEIN
    421 422 F RXA01538 GR00427 5040 5429 BRANCHED CHAIN AMINO ACID TRANSPORT SYSTEM II
    CARRIER PROTEIN
    423 424 RXA01727 GR00489 1471 194 BRANCHED-CHAIN AMINO ACID TRANSPORT SYSTEM
    CARRIER PROTEIN
    425 426 RXA00623 GR00163 6525 7862 C4-DICARBOXYLATE TRANSPORT PROTEIN
    427 428 RXA01584 GR00441 55 597 CHROMATE TRANSPORT PROTEIN
    429 430 RXA00852 GR00231 3137 2448 COBALT TRANSPORT ATP-BINDING PROTEIN CBIO
    431 432 RXA00690 GR00181 1213 68 COBALT TRANSPORT PROTEIN CBIQ
    433 434 RXA00827 GR00223 1319 567 COBALT TRANSPORT PROTEIN CBIQ
    435 436 RXA00851 GR00231 2448 1840 COBALT TRANSPORT PROTEIN CBIQ
    437 438 RXS03220 D-XYLOSE-PROTON SYMPORT
    439 440 F RXA02762 GR00768 346 630 D-XYLOSE PROTON-SYMPORTER
    441 442 RXN00092 VV0129 27509 26844 GLUTAMINE TRANSPORT ATP-BINDING PROTEIN GLNQ
    443 444 F RXA00092 GR00014 1 204 GLUTAMINE TRANSPORT ATP-BINDING PROTEIN GLNQ
    445 446 RXN03060 VV0030 6227 5376 GLUTAMINE TRANSPORT ATP-BINDING PROTEIN GLNQ
    447 448 F RXA02618 GR00745 1914 2351 GLUTAMINE TRANSPORT ATP-BINDING PROTEIN GLNQ
    449 450 F RXA02900 GR10040 2979 2128 GLUTAMINE TRANSPORT ATP-BINDING PROTEIN GLNQ
    451 452 RXS03212 GLYCINE BETAINE TRANSPORTER BETP
    453 454 F RXA01591 GR00446 3 947 GLYCINE BETAINE TRANSPORTER BETP
    455 456 RXN00201 VV0096 197 6 HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
    457 458 F RXA00201 GR00032 191 6 HIGH AFFINITY RIBOSE TRANSPORT PROTEIN RBSD
    459 460 RXA01221 GR00354 2108 2833 HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID
    TRANSPORT ATP-BINDING PROTEIN BRAG
    461 462 RXA01222 GR00354 2844 3542 HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID
    TRANSPORT ATP-BINDING PROTEIN LIVF
    463 464 RXA01219 GR00354 151 1032 HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID
    TRANSPORT PERMEASE PROTEIN LIVH
    465 466 RXA01220 GR00354 1032 2108 HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID
    TRANSPORT PERMEASE PROTEIN LIVM
    467 468 RXA00091 GR00013 7762 8514 IRON(III) DICITRATE TRANSPORT ATP-BINDING PROTEIN FECE
    469 470 RXA00228 GR00032 29232 28642 IRON(III) DICITRATE TRANSPORT ATP-BINDING PROTEIN FECE
    471 472 RXA00346 GR00064 1054 1743 IRON(III) DICITRATE TRANSPORT ATP-BINDING PROTEIN FECE
    473 474 RXA00524 GR00135 779 1111 IRON(III) DICITRATE TRANSPORT ATP-BINDING PROTEIN FECE
    475 476 RXA01823 GR00516 591 1367 IRON(III) DICITRATE TRANSPORT ATP-BINDING PROTEIN FECE
    477 478 RXA02767 GR00770 1032 1814 IRON(III) DICITRATE TRANSPORT ATP-BINDING PROTEIN FECE
    479 480 RXA02792 GR00777 8581 7829 IRON(III) DICITRATE TRANSPORT ATP-BINDING PROTEIN FECE
    481 482 RXN02929 VV0090 36837 37874 IRON(III) DICITRATE TRANSPORT SYSTEM PERMEASE PROTEIN FECD
    483 484 F RXA01235 GR00358 1165 194 IRON(III) DICITRATE TRANSPORT SYSTEM PERMEASE PROTEIN FECD
    485 486 RXN02794 VV0134 10625 9552 IRON(III) DICITRATE TRANSPORT SYSTEM PERMEASE PROTEIN FECD
    487 488 F RXA01419 GR00415 888 1151 IRON(III) DICITRATE TRANSPORT SYSTEM PERMEASE PROTEIN FECD
    489 490 F RXA02794 GR00777 10172 9552 IRON(III) DICITRATE TRANSPORT SYSTEM PERMEASE PROTEIN FECD
    491 492 RXN03079 VV0045 644 1660 IRON(III) DICITRATE TRANSPORT SYSTEM PERMEASE PROTEIN FECD
    493 494 F RXA02865 GR10007 3832 2816 IRON(III) DICITRATE TRANSPORT SYSTEM PERMEASE PROTEIN FECD
    495 496 RXA00181 GR00028 3954 2383 PROLINE TRANSPORT SYSTEM
    497 498 RXA00591 GR00158 229 1581 PROLINE/BETAINE TRANSPORTER
    499 500 RXA01629 GR00453 3476 1965 PROLINE/BETAINE TRANSPORTER
    501 502 RXA02030 GR00618 3072 1687 PROLINE/BETAINE TRANSPORTER
    503 504 RXA00186 GR00028 12242 12988 SHORT-CHAIN FATTY ACIDS TRANSPORTER
    505 506 RXA00187 GR00028 13097 13447 SHORT-CHAIN FATTY ACIDS TRANSPORTER
    507 508 RXA01667 GR00464 703 1908 SODIUM/GLUTAMATE SYMPORT CARRIER PROTEIN
    509 510 RXA02171 GR00641 6571 4919 SODIUM/PROLINE SYMPORTER
    511 512 RXA00902 GR00245 4643 5875 SODIUM-DEPENDENT PHOSPHATE TRANSPORT PROTEIN
    513 514 RXA00941 GR00257 1999 683 sodium-dependent phosphate transport protein
    515 516 RXN00449 VV0112 30992 32572 Sodium-Dicarboxylate Symport Protein
    517 518 F RXA00449 GR00109 2040 1036 Sodium-Dicarboxylate Symport Protein
    519 520 F RXA01755 GR00498 352 5 Sodium-Dicarboxylate Symport Protein
    521 522 RXA00269 GR00041 1826 1038 SPERMIDINE/PUTRESCINE TRANSPORT ATP-BINDING PROTEIN POTA
    523 524 RXA00369 GR00076 583 1299 SPERMIDINE/PUTRESCINE TRANSPORT ATP-BINDING PROTEIN POTA
    525 526 RXA02073 GR00628 4176 2647 TRANSPORT ATP-BINDING PROTEIN CYDC
    527 528 RXA01399 GR00409 1 1119 TRANSPORT ATP-BINDING PROTEIN CYDD
    529 530 RXA01339 GR00389 8408 7164 TYROSINE-SPECIFIC TRANSPORT PROTEIN
    531 532 RXA02527 GR00725 5519 6847 2-OXOGLUTARATE/MALATE TRANSLOCATOR PRECURSOR
    533 534 RXN00298 VV0176 40228 42072 HIGH-AFFINITY CHOLINE TRANSPORT PROTEIN
    535 536 F RXA00298 GR00048 4459 6303 Ectoine/Proline/Glycine betaine carrier ectP
    537 538 RXA00596 GR00159 335 787 potassium efflux system protein phaE
    539 540 RXA02364 GR00686 841 215 C4-DICARBOXYLATE-BINDING PERIPLASMIC PROTEIN
    PRECURSOR, transport protein
    541 542 RXN01411 VV0050 26015 26779 SHIKIMATE TRANSPORTER
    543 544 RXN00960 VV0075 1139 105 PROTON/SODIUM-GLUTAMATE SYMPORT PROTEIN
    545 546 RXN02447 VV0107 14297 13203 GALACTOSE-PROTON SYMPORT
    547 548 RXN02395 VV0176 16747 14858 GLYCINE BETAINE TRANSPORTER BETP
    549 550 RXN02348 VV0078 6027 7910 KUP SYSTEM POTASSIUM UPTAKE PROTEIN
    551 552 RXN00297 VV0176 38630 39541 Hypothetical Malonate Transporter
    553 554 RXN03103 VV0070 845 1087 GLUTAMATE-BINDING PROTEIN PRECURSOR
    555 556 RXN02993 VV0071 736 65 GLUTAMINE-BINDING PROTEIN
    557 558 RXN00349 VV0135 35187 36653 Hypothetical Trehalose Transport Protein
    559 560 RXN03095 VV0057 4056 4424 CADMIUM EFFLUX SYSTEM ACCESSORY PROTEIN HOMOLOG
    561 562 RXN03160 VV0189 5150 5617 CHROMATE TRANSPORT PROTEIN
    563 564 RXN02955 VV0176 8666 9187 DICARBOXYLATE TRANSPORTER
    565 566 RXN03109 VV0082 659 6 HEMIN TRANSPORT SYSTEM PERMEASE PROTEIN HMUU
    567 568 RXN02979 VV0149 2150 2383 MERCURIC TRANSPORT PROTEIN PERIPLASMIC
    COMPONENT PRECURSOR
    569 570 RXN02987 VV0234 527 294 MERCURIC TRANSPORT PROTEIN PERIPLASMIC
    COMPONENT PRECURSOR
    571 572 RXN03084 VV0048 900 1817 IRON(III) DICITRATE-BINDING PERIPLASMIC PROTEIN PRECURSOR
    573 574 RXN03183 VV0372 1 417 TREHALOSE/MALTOSE BINDING PROTEIN
    575 576 RXN01139 VV0077 2776 1823 CATION EFFLUX SYSTEM PROTEIN CZCD
    577 578 RXN00378 VV0223 8027 5418 Cation transport ATPases
    579 580 RXN01338 VV0032 2 1903 CATION-TRANSPORTING ATPASE PACS (EC 3.6.1.—)
    581 582 RXN00980 VV0149 2635 4428 CATION-TRANSPORTING P-TYPE ATPASE B (EC 3.6.1.—)
    583 584 RXN00099 VV0129 18876 17704 CYANATE TRANSPORT PROTEIN CYNX
    585 586 RXN02662 VV0315 1461 1724 DIPEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN DPPC
    587 588 RXN02442 VV0217 5970 6818 zinc transport system membrane protein
    589 590 RXN02443 VV0217 6818 7771 zinc-binding periplasmic protein precursor
    591 592 RXN00842 VV0138 8686 7487 BRANCHED CHAIN AMINO ACID TRANSPORT SYSTEM II
    CARRIER PROTEIN
    593 594 F RXA00842 GR00228 3208 2009 Permeases
    595 596 RXN00832 VV0180 3133 4182 CALCIUM/PROTON ANTIPORTER
    597 598 RXN00466 VV0086 63271 64266 Ferrichrome transport proteins
    599 600 RXN01936 VV0127 40116 41387 MACROLIDE-EFFLUX PROTEIN
    601 602 RXN01995 VV0182 2139 3476 PUTATIVE 3-(3-HYDROXYPHENYL) PROPIONATE TRANSPORT PROTEIN
    603 604 RXN00661 VV0142 9718 9029 PNUC PROTEIN
    Permeases
    605 606 RXN02566 VV0154 11823 13031 NUCLEOSIDE PERMEASE NUPG
    607 608 F RXA02561 GR00732 664 5 NUCLEOSIDE PERMEASE NUPG
    609 610 F RXA02566 GR00733 782 345 NUCLEOSIDE PERMEASE NUPG
    611 612 RXA00051 GR00008 5770 7173 PROLINE-SPECIFIC PERMEASE PROY
    613 614 RXA01172 GR00334 2687 4141 SULFATE PERMEASE
    615 616 RXA02128 GR00637 2906 4600 SULFATE PERMEASE
    617 618 RXA02634 GR00748 6045 7655 SULFATE PERMEASE
    619 620 RXN02233 VV0068 6856 8142 URACIL PERMEASE
    621 622 F RXA02233 GR00653 6856 8067 URACIL PERMEASE
    623 624 RXN02372 VV0213 9311 11197 XANTHINE PERMEASE
    625 626 F RXA02372 GR00688 6 560 XANTHINE PERMEASE
    627 628 F RXA02377 GR00689 3336 4526 XANTHINE PERMEASE
    629 630 RXA02676 GR00754 2697 1309 GLUCONATE PERMEASE
    631 632 RXN00432 VV0112 14751 13267 NA(+)-LINKED D-ALANINE GLYCINE PERMEASE
    633 634 F RXA00432 GR00100 1 891 NA(+)-LINKED D-ALANINE GLYCINE PERMEASE
    635 636 F RXA00436 GR00101 45 569 NA(+)-LINKED D-ALANINE GLYCINE PERMEASE
    637 638 RXA00847 GR00230 1829 381 OLIGOPEPTIDE-BINDING PROTEIN APPA PRECURSOR (permease)
    639 640 RXN01382 VV0119 8670 9761 OLIGOPEPTIDE-BINDING PROTEIN OPPA PRECURSOR
    641 642 F RXA01382 GR00405 1067 6 OLIGOPEPTIDE-BINDING PROTEIN OPPA PRECURSOR (permease)
    643 644 RXA02659 GR00753 2 313 OLIGOPEPTIDE-BINDING PROTEIN OPPA PRECURSOR (permease)
    645 646 RXN02933 VV0176 30042 29233 DIPEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN DPPC
    647 648 RXN02991 VV0072 618 4 GLUTAMINE TRANSPORT SYSTEM PERMEASE PROTEIN GLNP
    649 650 RXN02992 VV0072 842 621 GLUTAMINE TRANSPORT SYSTEM PERMEASE PROTEIN GLNP
    651 652 RXN02996 VV0069 1980 2648 HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID
    TRANSPORT PERMEASE PROTEIN LIVH
    653 654 RXN03126 VV0112 9894 9001 TEICHOIC ACID TRANSLOCATION PERMEASE PROTEIN TAGG
    655 656 RXN00443 VV0112 21572 20769 MOLYBDATE-BINDING PERIPLASMIC PROTEIN PRECURSOR
    657 658 RXN00444 VV0112 20785 19949 MOLYBDENUM TRANSPORT SYSTEM PERMEASE PROTEIN MODB
    659 660 RXN00193 VV0371 1 594 POTENTIAL STARCH DEGRADATION PRODUCTS TRANSPORT SYSTEM
    PERMEASE PROTEIN AMYD
    661 662 RXN01298 VV0116 2071 1142 POTENTIAL STARCH DEGRADATION PRODUCTS TRANSPORT SYSTEM
    PERMEASE PROTEIN AMYD
    Channel Proteins
    663 664 RXA01737 GR00493 2913 3971 POTASSIUM CHANNEL PROTEIN
    665 666 RXN02348 VV0078 6027 7910 KUP SYSTEM POTASSIUM UPTAKE PROTEIN
    667 668 RXA02426 GR00707 2165 633 PROBABLE NA(+)/H(+) ANTIPORTER
    669 670 RXN03164 VV0277 1586 2455 POTASSIUM CHANNEL BETA SUBUNIT
    671 672 RXN00024 VV0127 64219 63275 POTASSIUM CHANNEL BETA SUBUNIT
    Lipoprotein and Lipopolysaccharide synthesis
    673 674 RXN01164 VV0117 15894 14260 DOLICHOL-PHOSPHATE MANNOSYLTRANSFERASE (EC 2.4.1.83)/
    APOLIPOPROTEIN N-ACYLTRANSFERASE (EC 2.3.1.—)
    675 676 RXN01168 VV0117 14224 13415 DOLICHOL-PHOSPHATE MANNOSYLTRANSFERASE (EC 2.4.1.83)/
    APOLIPOPROTEIN N-ACYLTRANSFERASE (EC 2.3.1.—)
  • TABLE 2
    GENES IDENTIFIED FROM GENBANK
    GenBank ™ Accession No. Gene Name Gene Function Reference
    A09073 ppg Phosphoenol pyruvate carboxylase Bachmann, B. et al. “DNA fragment coding for phosphoenolpyruvat
    corboxylase, recombinant DNA carrying said fragment, strains carrying the
    recombinant DNA and method for producing L-aminino acids using said strains,” Patent:
    EP 0358940-A 3 Mar. 21, 1990
    A45579, Threonine dehydratase Moeckel, B. et al. “Production of L-isoleucine by means of recombinant
    A45581, micro-organisms with deregulated threonine dehydratase,” Patent: WO
    A45583, 9519442-A 5 Jul. 20, 1995
    A45585
    A45587
    AB003132 murC; ftsQ; ftsZ Kobayashi, M. et al. “Cloning, sequencing, and characterization of the ftsZ
    gene from coryneform bacteria,” Biochem. Biophys. Res. Commun.,
    236(2): 383-388 (1997)
    AB015023 murC; ftsQ Wachi, M. et al. “A murC gene from Coryneform bacteria, ” Appl. Microbiol.
    Biotechnol., 51(2): 223-228 (1999)
    AB018530 dtsR Kimura, E. et al. “Molecular cloning of a novel gene, dtsR, which rescues the
    detergent sensitivity of a mutant derived from Brevibacterium
    lactofermentum, ” Biosci. Biotechnol. Biochem., 60(10): 1565-1570 (1996)
    AB018531 dtsR1; dtsR2
    AB020624 murI D-glutamate racemase
    AB023377 tkt transketolase
    AB024708 gltB; gltD Glutamine 2-oxoglutarate aminotransferase
    large and small subunits
    AB025424 acn aconitase
    AB027714 rep Replication protein
    AB027715 rep; aad Replication protein; aminoglycoside
    adenyltransferase
    AF005242 argC N-acetylglutamate-5-semialdehyde
    dehydrogenase
    AF005635 glnA Glutamine synthetase
    AF030405 hisF cyclase
    AF030520 argG Argininosuccinate synthetase
    AF031518 argF Ornithine carbamolytransferase
    AF036932 aroD 3-dehydroquinate dehydratase
    AF038548 pyc Pyruvate carboxylase
    AF038651 dciAE; apt; rel Dipeptide-binding protein; adenine Wehmeier, L. et al. “The role of the Corynebacterium glutamicum rel gene in (p)ppGpp
    phosphoribosyltransferase; GTP metabolism,” Microbiology, 144: 1853-1862 (1998)
    pyrophosphokinase
    AF041436 argR Arginine repressor
    AF045998 impA Inositol monophosphate phosphatase
    AF048764 argH Argininosuccinate lyase
    AF049897 argC; argJ; argB; N-acetylglutamylphosphate reductase;
    argD; argF; argR; ornithine acetyltransferase; N-
    argG; argH acetylglutamate kinase; acetylornithine
    transminase; ornithine
    carbamoyltransferase; arginine repressor;
    argininosuccinate synthase;
    argininosuccinate lyase
    AF050109 inhA Enoyl-acyl carrier protein reductase
    AF050166 hisG ATP phosphoribosyltransferase
    AF051846 hisA Phosphoribosylformimino-5-amino-1-
    phosphoribosyl-4-imidazolecarboxamide
    isomerase
    AF052652 metA Homoserine O-acetyltransferase Park, S. et al. “Isolation and analysis of metA, a methionine biosynthetic gene
    encoding homoserine acetyltransferase in Corynebacterium glutamicum,” Mol.
    Cells., 8(3): 286-294 (1998)
    AF053071 aroB Dehydroquinate synthetase
    AF060558 hisH Glutamine amidotransferase
    AF086704 hisE Phosphoribosyl-ATP-
    pyrophosphohydrolase
    AF114233 aroA 5-enolpyruvylshikimate 3-phosphate
    synthase
    AF116184 panD L-aspartate-alpha-decarboxylase precursor Dusch, N. et al. “Expression of the Corynebacterium glutamicum panD gene
    encoding L-aspartate-alpha-decarboxylase leads to pantothenate
    overproduction in Escherichia coli,” Appl. Environ. Microbiol., 65(4)1530-1539
    (1999)
    AF124518 aroD; aroE 3-dehydroquinase; shikimate
    dehydrogenase
    AF124600 aroC; aroK; aroB; Chorismate synthase; shikimate kinase; 3-
    pepQ dehydroquinate synthase; putative
    cytoplasmic peptidase
    AF145897 inhA
    AF145898 inhA
    AJ001436 ectP Transport of ectoine, glycine betaine, Peter, H. et al. “Corynebacterium glutamicum is equipped with four secondary carriers
    proline for compatible solutes: Identification, sequencing, and characterization
    of the proline/ectoine uptake system, ProP, and the ectoine/proline/glycine
    betaine carrier, EctP,” J. Bacteriol., 180(22): 6005-6012 (1998)
    AJ004934 dapD Tetrahydrodipicolinate succinylase Wehrmann, A. et al. “Different modes of diaminopimelate synthesis and their
    (incompletei) role in cell wall integrity: A study with Corynebacterium glutamicum,” J.
    Bacteriol., 180(12): 3159-3165 (1998)
    AJ007732 ppc; secG; amt; ocd; Phosphoenolpyruvate-carboxylase; ?; high
    soxA affinity ammonium uptake protein; putative
    ornithine-cyclodecarboxylase; sarcosine
    oxidase
    AJ010319 ftsY, glnB, glnD; srp; amtP Involved in cell division; PII protein; Jakoby, M. et al. “Nitrogen regulation in Corynebacterium glutamicum ;
    uridylyltransferase (uridylyl-removing Isolation of genes involved in biochemical characterization of corresponding
    enzmye); signal recognition particle; low proteins,” FEMS Microbiol., 173(2): 303-310 (1999)
    affinity ammonium uptake protein
    AJ132968 cat Chloramphenicol aceteyl transferase
    AJ224946 mqo L-malate: quinone oxidoreductase Molenaar, D. et al. “Biochemical and genetic characterization of the
    membrane-associated malate dehydrogenase (acceptor) from Corynebacterium
    glutamicum,” Eur. J. Biochem., 254(2): 395-403 (1998)
    AJ238250 ndh NADH dehydrogenase
    AJ238703 porA Porin Lichtinger, T. et al. “Biochemical and biophysical characterization of the cell
    wall porin of Corynebacterium glutamicum: The channel is formed by a low
    molecular mass polypeptide,” Biochemistry, 37(43): 15024-15032 (1998)
    D17429 Transposable element IS31831 Vertes, A. A. et al. “Isolation and characterization of IS31831, a transposable
    element from Corynebacterium glutamicum,” Mol. Microbiol., 11(4): 739-746
    (1994)
    D84102 odhA 2-oxoglutarate dehydrogenase Usuda, Y. et al. “Molecular cloning of the Corynebacterium glutamicum
    (Brevibacterium lactofermentum AJ12036) odhA gene encoding a novel type
    of 2-oxoglutarate dehydrogenase,” Microbiology, 142: 3347-3354 (1996)
    E01358 hdh; hk Homoserine dehydrogenase; homoserine Katsumata, R. et al. “Production of L-thereonine and L-isoleucine,” Patent: JP
    kinase 1987232392-A 1 Oct. 12, 1987
    E01359 Upstream of the start codon of homoserine Katsumata, R. et al. “Production of L-thereonine and L-isoleucine,” Patent: JP
    kinase gene 1987232392-A 2 Oct. 12, 1987
    E01375 Tryptophan operon
    E01376 trpL; trpE Leader peptide; anthranilate synthase Matsui, K. et al. “Tryptophan operon, peptide and protein coded thereby,
    utilization of tryptophan operon gene expression and production of
    tryptophan,” Patent: JP 1987244382-A 1 Oct. 24, 1987
    E01377 Promoter and operator regions of Matsui, K. et al. “Tryptophan operon, peptide and protein coded thereby,
    tryptophan operon utilization of tryptophan operon gene expression and production of
    tryptophan,” Patent: JP 1987244382-A 1 Oct. 24, 1987
    E03937 Biotin-synthase Hatakeyama, K. et al. “DNA fragment containing gene capable of coding
    biotin synthetase and its utilization,” Patent: JP 1992278088-A 1 Oct. 02, 1992
    E04040 Diamino pelargonic acid aminotransferase Kohama, K. et al. “Gene coding diaminopelargonic acid aminotransferase and
    desthiobiotin synthetase and its utilization,” Patent: JP 1992330284-A 1
    Nov. 18, 1992
    E04041 Desthiobiotinsynthetase Kohama, K. et al. “Gene coding diaminopelargonic acid aminotransferase and
    desthiobiotin synthetase and its utilization,” Patent: JP 1992330284-A 1
    Nov. 18, 1992
    E04307 Flavum aspartase Kurusu, Y. et al. “Gene DNA coding aspartase and utilization thereof,” Patent:
    JP 1993030977-A 1 Feb. 09, 1993
    E04376 Isocitric acid lyase Katsumata, R. et al. “Gene manifestation controlling DNA,” Patent: JP
    1993056782-A 3 Mar. 09, 1993
    A09073 ppg Phosphoenol pyruvate carboxylase Bachmann, B. et al. “DNA fragment coding for phosphoenolpyruvat
    E04377 Isocitric acid lyase N-terminal fragment Katsumata, R. et al. “Gene manifestation controlling DNA,” Patent: JP
    1993056782-A 3 Mar. 09, 1993
    E04484 Prephenate dehydratase Sotouchi, N. et al. “Production of L-phenylalanine by fermentation,” Patent: JP
    1993076352-A 2 Mar. 30, 1993
    E05108 Aspartokinase Fugono, N. et al. “Gene DNA coding Aspartokinase and its use,” Patent: JP
    1993184366-A 1 Jul. 27, 1993
    E05112 Dihydro-dipichorinate synthetase Hatakeyama, K. et al. “Gene DNA coding dihydrodipicolinic acid synthetase
    and its use,” Patent: JP 1993184371-A 1 Jul. 27, 1993
    E05776 Diaminopimelic acid dehydrogenase Kobayashi, M. et al. “Gene DNA coding Diaminopimelic acid dehydrogenase
    and its use,” Patent: JP 1993284970-A 1 Nov. 02, 1993
    E05779 Threonine synthase Kohama, K. et al. “Gene DNA coding threonine synthase and its use,” Patent:
    JP 1993284972-A 1 Nov. 02, 1993
    E06110 Prephenate dehydratase Kikuchi, T. et al. “Production of L-phenylalanine by fermentation method,”
    Patent: JP 1993344881-A 1 Dec. 27, 1993
    E06111 Mutated Prephenate dehydratase Kikuchi, T. et al. “Production of L-phenylalanine by fermentation method,”
    Patent: JP 1993344881-A 1 Dec. 27, 1993
    E06146 Acetohydroxy acid synthetase Inui, M. et al. “Gene capable of coding Acetohydroxy acid synthetase and its
    use,” Patent: JP 1993344893-A 1 Dec. 27, 1993
    E06825 Aspartokinase Sugimoto, M. et al. “Mutant aspartokinase gene,” patent: JP 1994062866-A 1
    Mar. 08, 1994
    E06826 Mutated aspartokinase alpha subunit Sugimoto, M. et al. “Mutant aspartokinase gene,” patent: JP 1994062866-A 1
    Mar. 08, 1994
    E06827 Mutated aspartokinase alpha subunit Sugimoto, M. et al. “Mutant aspartokinase gene,” patent: JP 1994062866-A 1
    Mar. 08, 1994
    E07701 secY Honno, N. et al. “Gene DNA participating in integration of membraneous
    protein to membrane,” Patent: JP 1994169780-A 1 Jun. 21, 1994
    E08177 Aspartokinase Sato, Y. et al. “Genetic DNA capable of coding Aspartokinase released from
    feedback inhibition and its utilization,” Patent: JP 1994261766-A 1 Sep. 20, 1994
    E08178, Feedback inhibition-released Aspartokinase Sato, Y. et al. “Genetic DNA capable of coding Aspartokinase released from
    E08179, feedback inhibition and its utilization,” Patent: JP 1994261766-A 1 Sep. 20, 1994
    E08180,
    E08181,
    E08182
    E08232 Acetohydroxy-acid isomeroreductase Inui, M. et al. “Gene DNA coding acetohydroxy acid isomeroreductase,”
    Patent: JP 1994277067-A 1 Oct. 04, 1994
    E08234 secE Asai, Y. et al. “Gene DNA coding for translocation machinery of protein,”
    Patent: JP 1994277073-A 1 Oct. 04, 1994
    E08643 FT aminotransferase and desthiobiotin Hatakeyama, K. et al. “DNA fragment having promoter function in
    synthetase promoter region coryneform bacterium,” Patent: JP 1995031476-A 1 Feb. 03, 1995
    E08646 Biotin synthetase Hatakeyama, K. et al. “DNA fragment having promoter function in
    coryneform bacterium,” Patent: JP 1995031476-A 1 Feb. 03, 1995
    E08649 Aspartase Kohama, K. et al “DNA fragment having promoter function in coryneform
    bacterium,” Patent: JP 1995031478-A 1 Feb. 03, 1995
    E08900 Dihydrodipicolinate reductase Madori, M. et al. “DNA fragment containing gene coding Dihydrodipicolinate
    acid reductase and utilization thereof,” Patent: JP 1995075578-A 1 Mar. 20, 1995
    E08901 Diaminopimelic acid decarboxylase Madori, M. et al. “DNA fragment containing gene coding Diaminopimelic acid
    decarboxylase and utilization thereof,” Patent: JP 1995075579-A 1 Mar. 20, 1995
    E12594 Serine hydroxymethyltransferase Hatakeyama, K. et al. “Production of L-trypophan,” Patent: JP 1997028391-A
    1 Feb. 4, 1997
    E12760, transposase Moriya, M. et al. “Amplification of gene using artificial transposon,” Patent:
    E12759, JP 1997070291-A Mar. 18, 1997
    E12758
    E12764 Arginyl-tRNA synthetase; diaminopimelic Moriya, M. et al. “Amplification of gene using artificial transposon,” Patent:
    acid decarboxylase JP 1997070291-A Mar. 18, 1997
    E12767 Dihydrodipicolinic acid synthetase Moriya, M. et al. “Amplification of gene using artificial transposon,” Patent:
    JP 1997070291-A Mar. 18, 1997
    E12770 aspartokinase Moriya, M. et al. “Amplification of gene using artificial transposon,” Patent:
    JP 1997070291-A Mar. 18, 1997
    E12773 Dihydrodipicolinic acid reductase Moriya, M. et al. “Amplification of gene using artificial transposon,” Patent:
    JP 1997070291-A Mar. 18, 1997
    E13655 Glucose-6-phosphate dehydrogenase Hatakeyama, K. et al. “Glucose-6-phosphate dehydrogenase and DNA capable
    of coding the same,” Patent: JP 1997224661-A 1 Sep. 02, 1997
    L01508 IlvA Threonine dehydratase Moeckel, B. et al. “Functional and structural analysis of the threonine
    dehydratase of Corynebacterium glutamicum,” J. Bacteriol., 174: 8065-8072
    (1992)
    L07603 EC 4.2.1.15 3-deoxy-D-arabinoheptulosonate-7- Chen, C. et al. “The cloning and nucleotide sequence of Corynebacterium
    phosphate synthase glutamicum 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase gene,”
    FEMS Microbiol. Lett., 107: 223-230 (1993)
    L09232 IlvB; ilvN; ilvC Acetohydroxy acid synthase large subunit; Keilhauer, C. et al. “Isoleucine synthesis in Corynebacterium glutamicum:
    Acetohydroxy acid synthase small subunit; molecular analysis of the ilvB-ilvN-ilvC operon,” J. Bacteriol., 175(17): 5595-5603
    Acetohydroxy acid isomeroreductase (1993)
    L18874 PtsM Phosphoenolpyruvate sugar Fouet, A et al. “Bacillus subtilis sucrose-specific enzyme II of the
    phosphotransferase phosphotransferase system: expression in Escherichia coli and homology to
    enzymes II from enteric bacteria,” PNAS USA, 84(24): 8773-8777 (1987); Lee, J. K.
    et al. “Nucleotide sequence of the gene encoding the Corynebacterium
    glutamicum mannose enzyme II and analyses of the deduced protein
    sequence,” FEMS Microbiol. Lett., 119(1-2): 137-145 (1994)
    L27123 aceB Malate synthase Lee, H-S. et al. “Molecular characterization of aceB, a gene encoding malate
    synthase in Corynebacterium glutamicum,” J. Microbiol. Biotechnol.,
    4(4): 256-263 (1994)
    L27126 Pyruvate kinase Jetten, M. S. et al. “Structural and functional analysis of pyruvate kinase from
    Corynebacterium glutamicum,” Appl. Environ. Microbiol., 60(7): 2501-2507
    (1994)
    L28760 aceA Isocitrate lyase
    L35906 dtxr Diphtheria toxin repressor Oguiza, J. A. et al. “Molecular cloning, DNA sequence analysis, and
    characterization of the Corynebacterium diphtheriae dtxR from Brevibacterium
    lactofermentum,” J. Bacteriol., 177(2): 465-467 (1995)
    M13774 Prephenate dehydratase Follettie, M. T. et al. “Molecular cloning and nucleotide sequence of the
    Corynebacterium glutamicum pheA gene,” J. Bacteriol., 167: 695-702 (1986)
    M16175 5S rRNA Park, Y-H. et al. “Phylogenetic analysis of the coryneform bacteria by 56
    rRNA sequences,” J. Bacteriol., 169: 1801-1806 (1987)
    M16663 trpE Anthranilate synthase, 5′ end Sano, K. et al. “Structure and function of the trp operon control regions of
    Brevibacterium lactofermentum , a glutamic-acid-producing bacterium,” Gene,
    52: 191-200 (1987)
    M16664 trpA Tryptophan synthase, 3′end Sano, K. et al. “Structure and function of the trp operon control regions of
    Brevibacterium lactofermentum , a glutamic-acid-producing bacterium,” Gene,
    52: 191-200 (1987)
    M25819 Phosphoenolpyruvate carboxylase O'Regan, M. et al. “Cloning and nucleotide sequence of the
    Phosphoenolpyruvate carboxylase-coding gene of Corynebacterium
    glutamicum ATCC13032,” Gene, 77(2): 237-251 (1989)
    M85106 23S rRNA gene insertion sequence Roller, C. et al. “Gram-positive bacteria with a high DNA G + C content are
    characterized by a common insertion within their 23S rRNA genes,” J. Gen.
    Microbiol., 138: 1167-1175 (1992)
    M85107, 23S rRNA gene insertion sequence Roller, C. et al. “Gram-positive bacteria with a high DNA G + C content are
    M85108 characterized by a common insertion within their 23S rRNA genes,” J. Gen.
    Microbiol., 138: 1167-1175 (1992)
    M89931 aecD; brnQ; yhbw Beta C-S lyase; branched-chain amino acid Rossol, I. et al. “The Corynebacterium glutamicum aecD gene encodes a C-S
    uptake carrier; hypothetical protein yhbw lyase with alpha, beta-elimination activity that degrades aminoethylcysteine,”
    J. Bacteriol., 174(9): 2968-2977 (1992); Tauch, A. et al. “Isoleucine uptake in
    Corynebacterium glutamicum ATCC 13032 is directed by the brnQ gene
    product,” Arch. Microbiol., 169(4): 303-312 (1998)
    S59299 trp Leader gene (promoter) Herry, D. M. et al. “Cloning of the trp gene cluster from a tryptophan-
    hyperproducing strain of Corynebacterium glutamicum: identification of a
    mutation in the trp leader sequence,” Appl. Environ. Microbiol., 59(3): 791-799
    (1993)
    U11545 trpD Anthranilate phosphoribosyltransferase O'Gara, J. P. and Dunican, L. K. (1994) Complete nucleotide sequence of the
    Corynebacterium glutamicum ATCC 21850 tpD gene.” Thesis, Microbiology
    Department, University College Galway, Ireland.
    U13922 cglIM; cglIR; clgIIR Putative type II 5-cytosoine Schafer, A. et al. “Cloning and characterization of a DNA region encoding a
    methyltransferase; putative type II stress-sensitive restriction system from Corynebacterium glutamicum ATCC
    restriction endonuclease; putative type I or 13032 and analysis of its role in intergeneric conjugation with Escherichia
    type III restriction endonuclease coli,” J. Bacteriol., 176(23): 7309-7319 (1994); Schafer, A. et al. “The
    Corynebacterium glutamicum cglIM gene encoding a 5-cytosine in an McrBC-
    deficient Escherichia coli strain,” Gene, 203(2): 95-101 (1997)
    U14965 recA
    U31224 ppx Ankri, S. et al. “Mutations in the Corynebacterium glutamicum proline
    biosynthetic pathway: A natural bypass of the proA step,” J. Bacteriol.,
    178(15): 4412-4419 (1996)
    U31225 proC L-proline: NADP+ 5-oxidoreductase Ankri, S. et al. “Mutations in the Corynebacterium glutamicum proline
    biosynthetic pathway: A natural bypass of the proA step,” J. Bacteriol.,
    178(15): 4412-4419 (1996)
    U31230 obg; proB; unkdh ?; gamma glutamyl kinase; similar to D- Ankri, S. et al. “Mutations in the Corynebacterium glutamicum proline
    isomer specific 2-hydroxyacid biosynthetic pathway: A natural bypass of the proA step,” J. Bacteriol.,
    dehydrogenases 178(15): 4412-4419 (1996)
    U31281 bioB Biotin synthase Serebriiskii, I. G., “Two new members of the bio B superfamily: Cloning,
    sequencing and expression of bio B genes of Methylobacillus flagellatum and
    Corynebacterium glutamicum,” Gene, 175: 15-22 (1996)
    U35023 thtR; accBC Thiosulfate sulfurtransferase; acyl CoA Jager, W. et al. “A Corynebacterium glutamicum gene encoding a two-domain
    carboxylase protein similar to biotin carboxylases and biotin-carboxyl-carrier proteins,”
    Arch. Microbiol., 166(2); 76-82 (1996)
    U43535 cmr Multidrug resistance protein Jager, W. et al. “A Corynebacterium glutamicum gene conferring multidrug
    resistance in the heterologous host Escherichia coli,” J. Bacteriol.,
    179(7): 2449-2451 (1997)
    U43536 clpB Heat shock ATP-binding protein
    U53587 aphA-3 3′5″-aminoglycoside phosphotransferase
    U89648 Corynebacterium glutamicum unidentified
    sequence involved in histidine biosynthesis,
    partial sequence
    X04960 trpA; trpB; trpC; trpD; trpE; trpG; trpL Tryptophan operon Matsui, K. et al. “Complete nucleotide and deduced amino acid sequences of
    the Brevibacterium lactofermentum tryptophan operon,” Nucleic Acids Res., 14(24):
    10113-10114 (1986)
    X07563 lys A DAP decarboxylase (meso-diaminopimelate Yeh, P. et al. “Nucleic sequence of the lysA gene of Corynebacterium
    decarboxylase, EC 4.1.1.20) glutamicum and possible mechanisms for modulation of its expression,” Mol.
    Gen. Genet., 212(1): 112-119 (1988)
    X14234 EC 4.1.1.31 Phosphoenolpyruvate carboxylase Eikmanns, B. J. et al. “The Phosphoenolpyruvate carboxylase gene of
    Corynebacterium glutamicum: Molecular cloning, nucleotide sequence, and
    expression,” Mol. Gen. Genet., 218(2): 330-339 (1989); Lepiniec, L. et al.
    “Sorghum Phosphoenolpyruvate carboxylase gene family: structure, function
    and molecular evolution,” Plant. Mol. Biol., 21 (3): 487-502 (1993)
    X17313 fda Fructose-bisphosphate aldolase Von der Osten, C. H. et al. “Molecular cloning, nucleotide sequence and fine-
    structural analysis of the Corynebacterium glutamicum fda gene: structural
    comparison of C. glutamicum fructose-1,6-biphosphate aldolase to class I and
    class II aldolases,” Mol. Microbiol.,
    X53993 dapA L-2,3-dihydrodipicolinate synthetase (EC Bonnassie, S. et al. “Nucleic sequence of the dapA gene from
    4.2.1.52) Corynebacterium glutamicum,” Nucleic Acids Res., 18(21): 6421 (1990)
    X54223 AttB-related site Cianciotto, N. et al. “DNA sequence homology between att B-related sites of
    Corynebacterium diphtheriae, Corynebacterium ulcerans, Corynebacterium
    glutamicum, and the attP site of lambdacorynephage,” FEMS. Microbiol,
    Lett., 66: 299-302 (1990)
    X54740 argS; lysA Arginyl-tRNA synthetase; Diaminopimelate Marcel, T. et al. “Nucleotide sequence and organization of the upstream region
    decarboxylase of the Corynebacterium glutamicum lysA gene,” Mol. Microbiol., 4(11): 1819-1830
    (1990)
    X55994 trpL; trpE Putative leader peptide; anthranilate Heery, D. M. et al. “Nucleotide sequence of the Corynebacterium glutamicum
    synthase component 1 trpE gene,” Nucleic Acids Res., 18(23): 7138 (1990)
    X56037 thrC Threonine synthase Han, K. S. et al. “The molecular structure of the Corynebacterium glutamicum
    threonine synthase gene,” Mol. Microbiol., 4(10): 1693-1702 (1990)
    X56075 attB-related site Attachment site Cianciotto, N. et al. “DNA sequence homology between att B-related sites of
    Corynebacterium diphtheriae, Corynebacterium ulcerans , Corynebacterium
    glutamicum, and the attP site of lambdacorynephage,” FEMS. Microbiol,
    Lett., 66: 299-302 (1990)
    X57226 lysC-alpha; lysC-beta; Aspartokinase-alpha subunit; Kalinowski, J. et al. “Genetic and biochemical analysis of the Aspartokinase
    asd Aspartokinase-beta subunit; aspartate beta from Corynebacterium glutamicum,” Mol. Microbiol., 5(5): 1197-1204 (1991);
    semialdehyde dehydrogenase Kalinowski, J. et al. “Aspartokinase genes lysC alpha and lysC beta overlap
    and are adjacent to the aspertate beta-semialdehyde dehydrogenase gene asd in
    Corynebacterium glutamicum,” Mol. Gen. Genet., 224(3): 317-324 (1990)
    X59403 gap; pgk; tpi Glyceraldehyde-3-phosphate; Eikmanns, B. J. “Identification, sequence analysis, and expression of a
    phosphoglycerate kinase; triosephosphate Corynebacterium glutamicum gene cluster encoding the three glycolytic
    isomerase enzymes glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate
    kinase, and triosephosphate isomeras,” J. Bacteriol., 174(19): 6076-6086
    (1992)
    X59404 gdh Glutamate dehydrogenase Bormann, E. R. et al. “Molecular analysis of the Corynebacterium glutamicum
    gdh gene encoding glutamate dehydrogenase,” Mol. Microbiol., 6(3): 317-326
    (1992)
    X60312 lysI L-lysine permease Seep-Feldhaus, A. H. et al. “Molecular analysis of the Corynebacterium
    glutamicum lysI gene involved in lysine uptake,” Mol. Microbiol., 5(12): 2995-3005
    (1991)
    X66078 cop1 Ps1 protein Joliff, G. et al. “Cloning and nucleotide sequence of the csp1 gene encoding
    PS1, one of the two major secreted proteins of Corynebacterium glutamicum:
    The deduced N-terminal region of PS1 is similar to the Mycobacterium antigen
    85 complex,” Mol. Microbiol., 6(16): 2349-2362 (1992)
    X66112 glt Citrate synthase Eikmanns, B. J. et al. “Cloning sequence, expression and transcriptional
    analysis of the Corynebacterium glutamicum gltA gene encoding citrate
    synthase,” Microbiol., 140: 1817-1828 (1994)
    X67737 dapB Dihydrodipicolinate reductase
    X69103 csp2 Surface layer protein PS2 Peyret, J. L. et al. “Characterization of the cspB gene encoding PS2, an ordered
    surface-layer protein in Corynebacterium glutamicum,” Mol. Microbiol.,
    9(1): 97-109 (1993)
    X69104 IS3 related insertion element Bonamy, C. et al. “Identification of IS1206, a Corynebacterium glutamicum
    IS3-related insertion sequence and phylogenetic analysis,” Mol. Microbiol.,
    14(3): 571-581 (1994)
    X70959 leuA Isopropylmalate synthase Patek, M. et al. “Leucine synthesis in Corynebacterium glutamicum: enzyme
    activities, structure of leuA, and effect of leuA inactivation on lysine
    synthesis,” Appl. Environ. Microbiol., 60(1): 133-140 (1994)
    X71489 icd Isocitrate dehydrogenase (NADP+) Eikmanns, B. J. et al. “Cloning sequence analysis, expression, and inactivation
    of the Corynebacterium glutamicum icd gene encoding isocitrate
    dehydrogenase and biochemical characterization of the enzyme,” J. Bacteriol.,
    177(3): 774-782 (1995)
    X72855 GDHA Glutamate dehydrogenase (NADP+)
    X75083, mtrA 5-methyltryptophan resistance Heery, D. M. et al. “A sequence from a tryptophan-hyperproducing strain of
    X70584 Corynebacterium glutamicum encoding resistance to 5-methyltryptophan,”
    Biochem. Biophys. Res. Commun., 201(3): 1255-1262 (1994)
    X75085 recA Fitzpatrick, R. et al. “Construction and characterization of recA mutant strains
    of Corynebacterium glutamicum and Brevibacterium lactofermentum,” Appl.
    Microbiol. Biotechnol., 42(4): 575-580 (1994)
    X75504 aceA; thiX Partial Isocitrate lyase; ? Reinscheid, D. J. et al. “Characterization of the isocitrate lyase gene from
    Corynebacterium glutamicum and biochemical analysis of the enzyme,” J.
    Bacteriol., 176(12): 3474-3483 (1994)
    X76875 ATPase beta-subunit Ludwig, W. et al. “Phylogenetic relationships of bacteria based on comparative
    sequence analysis of elongation factor Tu and ATP-synthase beta-subunit
    genes,” Antonie Van Leeuwenhoek, 64: 285-305 (1993)
    X77034 tuf Elongation factor Tu Ludwig, W. et al. “Phylogenetic relationships of bacteria based on comparative
    sequence analysis of elongation factor Tu and ATP-synthase beta-subunit
    genes,” Antonie Van Leeuwenhoek, 64: 285-305 (1993)
    X77384 recA Billman-Jacobe, H. “Nucleotide sequence of a recA gene from
    Corynebacterium glutamicum,” DNA Seq., 4(6): 403-404 (1994)
    X78491 aceB Malate synthase Reinscheid, D. J. et al. “Malate synthase from Corynebacterium glutamicum
    pta-ack operon encoding phosphotransacetylase: sequence analysis,”
    Microbiology, 140: 3099-3108 (1994)
    X80629 16S rDNA 16S ribosomal RNA Rainey, F. A. et al. “Phylogenetic analysis of the genera Rhodococcus and
    Norcardia and evidence for the evolutionary origin of the genus Norcardia
    from within the radiation of Rhodococcus species,” Microbiol., 141: 523-528
    (1995)
    X81191 gluA; gluB; gluC; Glutamate uptake system Kronemeyer, W. et al. “Structure of the gluABCD cluster encoding the
    gluD glutamate uptake system of Corynebacterium glutamicum,” J. Bacteriol.,
    177(5): 1152-1158 (1995)
    X81379 dapE Succinyldiaminopimelate desuccinylase Wehrmann, A. et al. “Analysis of different DNA fragments of
    Corynebacterium glutamicum complementing dapE of Escherichia coli,”
    Microbiology, 40: 3349-56 (1994)
    X82061 16S rDNA 16S ribosomal RNA Ruimy, R. et al. “Phylogeny of the genus Corynebacterium deduced from
    analyses of small-subunit ribosomal DNA sequences,” Int. J. Syst. Bacteriol.,
    45(4): 740-746 (1995)
    X82928 asd; lysC Aspartate-semialdehyde dehydrogenase; ? Serebrijski, I. et al. “Multicopy suppression by asd gene and osmotic stress-
    dependent complementation by heterologous proA in proA mutants,” J.
    Bacteriol., 177(24): 7255-7260 (1995)
    X82929 proA Gamma-glutamyl phosphate reductase Serebrijski, I. et al. “Multicopy suppression by asd gene and osmotic stress-
    dependent complementation by heterologous proA in proA mutants,” J.
    Bacteriol., 177(24): 7255-7260 (1995)
    X84257 16S rDNA 16S ribosomal RNA Pascual, C. et al. “Phylogenetic analysis of the genus Corynebacterium based
    on 16S rRNA gene sequences,” Int. J. Syst. Bacteriol., 45(4): 724-728 (1995)
    X85965 aroP; dapE Aromatic amino acid permease; ? Wehrmann, A. et al. “Functional analysis of sequences adjacent to dapE of
    Corynebacterium glutamicum proline reveals the presence of aroP, which
    encodes the aromatic amino acid transporter,” J. Bacteriol., 177(20): 5991-5993
    (1995)
    X86157 argB; argC; argD; Acetylglutamate kinase; N-acetyl-gamma- Sakanyan, V. et al. “Genes and enzymes of the acetyl cycle of arginine
    argF; argJ glutamyl-phosphate reductase; biosynthesis in Corynebacterium glutamicum: enzyme evolution in the early
    acetylornithine aminotransferase; ornithine steps of the arginine pathway,” Microbiology, 142: 99-108 (1996)
    carbamoyltransferase; glutamate N-
    acetyltransferase
    X89084 pta; ackA Phosphate acetyltransferase; acetate kinase Reinscheid, D. J. et al. “Cloning, sequence analysis, expression and inactivation
    of the Corynebacterium glutamicum pta-ack operon encoding
    phosphotransacetylase and acetate kinase,” Microbiology, 145: 503-513 (1999)
    X89850 attB Attachment site Le Marrec, C. et al. “Genetic characterization of site-specific integration
    functions of phi AAU2 infecting “Arthrobacter aureus C70,” J. Bacteriol.,
    178(7): 1996-2004 (1996)
    X90356 Promoter fragment F1 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X90357 Promoter fragment F2 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X90358 Promoter fragment F10 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X90359 Promoter fragment F13 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X90360 Promoter fragment F22 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X90361 Promoter fragment F34 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X90362 Promoter fragment F37 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X90363 Promoter fragment F45 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X90364 Promoter fragment F64 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X90365 Promoter fragment F75 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X90366 Promoter fragment PF101 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X90367 Promoter fragment PF104 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X90368 Promoter fragment PF109 Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,
    molecular analysis and search for a consensus motif,” Microbiology,
    142: 1297-1309 (1996)
    X93513 amt Ammonium transport system Siewe, R. M. et al. “Functional and genetic characterization of the (methyl)
    ammonium uptake carrier of Corynebacterium glutamicum,” J. Biol. Chem.,
    271(10): 5398-5403 (1996)
    X93514 betP Glycine betaine transport system Peter, H. et al. “Isolation, characterization, and expression of the
    Corynebacterium glutamicum betP gene, encoding the transport system for the
    compatible solute glycine betaine,” J. Bacteriol., 178(17): 5229-5234 (1996)
    X95649 orf4 Patek, M. et al. “Identification and transcriptional analysis of the dapB-ORF2-
    dapA-ORF4 operon of Corynebacterium glutamicum, encoding two enzymes
    involved in L-lysine synthesis,” Biotechnol. Lett., 19: 1113-1117 (1997)
    X96471 lysE; lysG Lysine exporter protein; Lysine export Vrljic, M. et al. “A new type of transporter with a new type of cellular
    regulator protein function: L-lysine export from Corynebacterium glutamicum,” Mol.
    Microbiol., 22(5): 815-826 (1996)
    X96580 panB; panC; xylB 3-methyl-2-oxobutanoate Sahm, H. et al. “D-pantothenate synthesis in Corynebacterium glutamicum and
    hydroxymethyltransferase; pantoate-beta- use of panBC and genes encoding L-valine synthesis for D-pantothenate
    alanine ligase; xylulokinase overproduction,” Appl. Environ. Microbiol., 65(5): 1973-1979 (1999)
    X96962 Insertion sequence IS1207 and transposase
    X99289 Elongation factor P Ramos, A. et al. “Cloning, sequencing and expression of the gene encoding
    elongation factor P in the amino-acid producer Brevibacterium lactofermentum
    (Corynebacterium glutamicum ATCC 13869),” Gene, 198: 217-222 (1997)
    Y00140 thrB Homoserine kinase Mateos, L. M. et al. “Nucleotide sequence of the homoserine kinase (thrB) gene
    of the Brevibacterium lactofermentum,” Nucleic Acids Res., 15(9): 3922 (1987)
    Y00151 ddh Meso-diaminopimelate D-dehydrogenase Ishino, S. et al. “Nucleotide sequence of the meso-diaminopimelate D-
    (EC 1.4.1.16) dehydrogenase gene from Corynebacterium glutamicum,” Nucleic Acids Res.,
    15(9): 3917 (1987)
    Y00476 thrA Homoserine dehydrogenase Mateos, L. M. et al. “Nucleotide sequence of the homoserine dehydrogenase
    (thrA) gene of the Brevibacterium lactofermentum,” Nucleic Acids Res.,
    15(24): 10598 (1987)
    Y00546 hom; thrB Homoserine dehydrogenase; homoserine Peoples, O. P. et al. “Nucleotide sequence and fine structural analysis of the
    kinase Corynebacterium glutamicum hom-thrB operon,” Mol. Microbiol., 2(1): 63-72
    (1988)
    Y08964 murC; ftsQ/divD; ftsZ UPD-N-acetylmuramate-alanine ligase; Honrubia, M. P. et al. “Identification, characterization, and chromosomal
    division initiation protein or cell division organization of the ftsZ gene from Brevibacterium lactofermentum,” Mol. Gen.
    protein; cell division protein Genet., 259(1): 97-104 (1998)
    Y09163 putP High affinity proline transport system Peter, H. et al. “Isolation of the putP gene of Corynebacterium
    glutamicumproline and characterization of a low-affinity uptake system for
    compatible solutes,” Arch. Microbiol., 168(2): 143-151 (1997)
    Y09548 pyc Pyruvate carboxylase Peters-Wendisch, P. G. et al. “Pyruvate carboxylase from Corynebacterium
    glutamicum: characterization, expression and inactivation of the pyc gene,”
    Microbiology, 144: 915-927 (1998)
    Y09578 leuB 3-isopropylmalate dehydrogenase Patek, M. et al. “Analysis of the leuB gene from Corynebacterium
    glutamicum,” Appl. Microbiol. Biotechnol., 50(1): 42-47 (1998)
    Y12472 Attachment site bacteriophage Phi-16 Moreau, S. et al. “Site-specific integration of corynephage Phi-16: The
    construction of an integration vector,” Microbiol., 145: 539-548 (1999)
    Y12537 proP Proline/ectoine uptake system protein Peter, H. et al. “Corynebacterium glutamicum is equipped with four secondary
    carriers for compatible solutes: Identification, sequencing, and characterization
    of the proline/ectoine uptake system, ProP, and the ectoine/proline/glycine
    betaine carrier, EctP,” J. Bacteriol., 180(22): 6005-6012 (1998)
    Y13221 glnA Glutamine synthetase I Jakoby, M. et al. “Isolation of Corynebacterium glutamicum glnA gene
    encoding glutamine synthetase I,” FEMS Microbiol. Lett., 154(1): 81-88 (1997)
    Y16642 lpd Dihydrolipoamide dehydrogenase
    Y18059 Attachment site Corynephage 304L Moreau, S. et al. “Analysis of the integration functions of φ 304L: An
    integrase module among corynephages,” Virology, 255(1): 150-159 (1999)
    Z21501 argS; lysA Arginyl-tRNA synthetase; diaminopimelate Oguiza, J. A. et al. “A gene encoding arginyl-tRNA synthetase is located in the
    decarboxylase (partial) upstream region of the lysA gene in Brevibacterium lactofermentum:
    Regulation of argS-lysA cluster expression by arginine,” J. Bacteriol.,
    175(22): 7356-7362 (1993)
    Z21502 dapA; dapB Dihydrodipicolinate synthase; Pisabarro, A. et al. “A cluster of three genes (dapA, orf2, and dapB) of
    dihydrodipicolinate reductase Brevibacterium lactofermentum encodes dihydrodipicolinate reductase, and a
    third polypeptide of unknown function,” J. Bacteriol., 175(9): 2743-2749
    (1993)
    Z29563 thrC Threonine synthase Malumbres, M. et al. “Analysis and expression of the thrC gene of the encoded
    threonine synthase,” Appl. Environ. Microbiol., 60(7)2209-2219 (1994)
    Z46753 16S rDNA Gene for 16S ribosomal RNA
    A09073 ppg Phosphoenol pyruvate carboxylase Bachmann, B. et al. “DNA fragment coding for phosphoenolpyruvat
    Z49822 sigA SigA sigma factor Oguiza, J. A. et al “Multiple sigma factor genes in Brevibacterium
    lactofermentum: Characterization of sigA and sigB,” J. Bacteriol., 178(2): 550-553
    (1996)
    Z49823 galE; dtxR Catalytic activity UDP-galactose 4- Oguiza, J. A. et al “The galE gene encoding the UDP-galactose 4-epimerase of
    epimerase; diphtheria toxin regulatory Brevibacterium lactofermentum is coupled transcriptionally to the dmdR
    protein gene,” Gene, 177: 103-107 (1996)
    Z49824 orfl; sigB ?; SigB sigma factor Oguiza, J. A. et al “Multiple sigma factor genes in Brevibacterium
    lactofermentum: Characterization of sigA and sigB,” J. Bacteriol., 178(2): 550-553
    (1996)
    Z66534 Transposase Correia, A. et al. “Cloning and characterization of an IS-like element present in
    the genome of Brevibacterium lactofermentum ATCC 13869,” Gene,
    170(1): 91-94 (1996)

    1A sequence for this gene was published in the indicated reference. However, the sequence obtained by the inventors of the present application is significantly longer than the published version. It is believed that the published version relied on an incorrect start codon, and thus represents only a fragment of the actual coding region.
  • TABLE 3
    Corynebacterium and Brevibacterium Strains Which May be Used in the Practice of the Invention
    Genus species ATCC FERM NRRL CECT NCIMB CBS NCTC DSMZ
    Brevibacterium ammoniagenes 21054
    Brevibacterium ammoniagenes 19350
    Brevibacterium ammoniagenes 19351
    Brevibacterium ammoniagenes 19352
    Brevibacterium ammoniagenes 19353
    Brevibacterium ammoniagenes 19354
    Brevibacterium ammoniagenes 19355
    Brevibacterium ammoniagenes 19356
    Brevibacterium ammoniagenes 21055
    Brevibacterium ammoniagenes 21077
    Brevibacterium ammoniagenes 21553
    Brevibacterium ammoniagenes 21580
    Brevibacterium ammoniagenes 39101
    Brevibacterium butanicum 21196
    Brevibacterium divaricatum 21792 P928
    Brevibacterium flavum 21474
    Brevibacterium flavum 21129
    Brevibacterium flavum 21518
    Brevibacterium flavum B11474
    Brevibacterium flavum B11472
    Brevibacterium flavum 21127
    Brevibacterium flavum 21128
    Brevibacterium flavum 21427
    Brevibacterium flavum 21475
    Brevibacterium flavum 21517
    Brevibacterium flavum 21528
    Brevibacterium flavum 21529
    Brevibacterium flavum B11477
    Brevibacterium flavum B11478
    Brevibacterium flavum 21127
    Brevibacterium flavum B11474
    Brevibacterium healii 15527
    Brevibacterium ketoglutamicum 21004
    Brevibacterium ketoglutamicum 21089
    Brevibacterium ketosoreductum 21914
    Brevibacterium lactofermentum 70
    Brevibacterium lactofermentum 74
    Brevibacterium lactofermentum 77
    Brevibacterium lactofermentum 21798
    Brevibacterium lactofermentum 21799
    Brevibacterium lactofermentum 21800
    Brevibacterium lactofermentum 21801
    Brevibacterium lactofermentum B11470
    Brevibacterium lactofermentum B11471
    Brevibacterium lactofermentum 21086
    Brevibacterium lactofermentum 21420
    Brevibacterium lactofermentum 21086
    Brevibacterium lactofermentum 31269
    Brevibacterium linens 9174
    Brevibacterium linens 19391
    Brevibacterium linens 8377
    Brevibacterium paraffinolyticum 11160
    Brevibacterium spec. 717.73
    Brevibacterium spec. 717.73
    Brevibacterium spec. 14604
    Brevibacterium spec. 21860
    Brevibacterium spec. 21864
    Brevibacterium spec. 21865
    Brevibacterium spec. 21866
    Brevibacterium spec. 19240
    Corynebacterium acetoacidophilum 21476
    Corynebacterium acetoacidophilum 13870
    Corynebacterium acetoglutamicum B11473
    Corynebacterium acetoglutamicum B11475
    Corynebacterium acetoglutamicum 15806
    Corynebacterium acetoglutamicum 21491
    Corynebacterium acetoglutamicum 31270
    Corynebacterium acetophilum B3671
    Corynebacterium ammoniagenes 6872 2399
    Corynebacterium ammoniagenes 15511
    Corynebacterium fujiokense 21496
    Corynebacterium glutamicum 14067
    Corynebacterium glutamicum 39137
    Corynebacterium glutamicum 21254
    Corynebacterium glutamicum 21255
    Corynebacterium glutamicum 31830
    Corynebacterium glutamicum 13032
    Corynebacterium glutamicum 14305
    Corynebacterium glutamicum 15455
    Corynebacterium glutamicum 13058
    Corynebacterium glutamicum 13059
    Corynebacterium glutamicum 13060
    Corynebacterium glutamicum 21492
    Corynebacterium glutamicum 21513
    Corynebacterium glutamicum 21526
    Corynebacterium glutamicum 21543
    Corynebacterium glutamicum 13287
    Corynebacterium glutamicum 21851
    Corynebacterium glutamicum 21253
    Corynebacterium glutamicum 21514
    Corynebacterium glutamicum 21516
    Corynebacterium glutamicum 21299
    Corynebacterium glutamicum 21300
    Corynebacterium glutamicum 39684
    Corynebacterium glutamicum 21488
    Corynebacterium glutamicum 21649
    Corynebacterium glutamicum 21650
    Corynebacterium glutamicum 19223
    Corynebacterium glutamicum 13869
    Corynebacterium glutamicum 21157
    Corynebacterium glutamicum 21158
    Corynebacterium glutamicum 21159
    Corynebacterium glutamicum 21355
    Corynebacterium glutamicum 31808
    Corynebacterium glutamicum 21674
    Corynebacterium glutamicum 21562
    Corynebacterium glutamicum 21563
    Corynebacterium glutamicum 21564
    Corynebacterium glutamicum 21565
    Corynebacterium glutamicum 21566
    Corynebacterium glutamicum 21567
    Corynebacterium glutamicum 21568
    Corynebacterium glutamicum 21569
    Corynebacterium glutamicum 21570
    Corynebacterium glutamicum 21571
    Corynebacterium glutamicum 21572
    Corynebacterium glutamicum 21573
    Corynebacterium glutamicum 21579
    Corynebacterium glutamicum 19049
    Corynebacterium glutamicum 19050
    Corynebacterium glutamicum 19051
    Corynebacterium glutamicum 19052
    Corynebacterium glutamicum 19053
    Corynebacterium glutamicum 19054
    Corynebacterium glutamicum 19055
    Corynebacterium glutamicum 19056
    Corynebacterium glutamicum 19057
    Corynebacterium glutamicum 19058
    Corynebacterium glutamicum 19059
    Corynebacterium glutamicum 19060
    Corynebacterium glutamicum 19185
    Corynebacterium glutamicum 13286
    Corynebacterium glutamicum 21515
    Corynebacterium glutamicum 21527
    Corynebacterium glutamicum 21544
    Corynebacterium glutamicum 21492
    Corynebacterium glutamicum B8183
    Corynebacterium glutamicum B8182
    Corynebacterium glutamicum B12416
    Corynebacterium glutamicum B12417
    Corynebacterium glutamicum B12418
    Corynebacterium glutamicum B11476
    Corynebacterium glutamicum 21608
    Corynebacterium lilium P973
    Corynebacterium nitrilophilus 21419 11594
    Corynebacterium spec. P4445
    Corynebacterium spec. P4446
    Corynebacterium spec. 31088
    Corynebacterium spec. 31089
    Corynebacterium spec. 31090
    Corynebacterium spec. 31090
    Corynebacterium spec. 31090
    Corynebacterium spec. 15954 20145
    Corynebacterium spec. 21857
    Corynebacterium spec. 21862
    Corynebacterium spec. 21863

    ATCC: American Type Culture Collection, Rockville, MD, USA

    FERM: Fermentation Research Institute, Chiba, Japan

    NRRL: ARS Culture Collection, Northern Regional Research Laboratory, Peoria, IL, USA

    CECT: Coleccion Espanola de Cultivos Tipo, Valencia, Spain

    NCIMB: National Collection of Industrial and Marine Bacteria Ltd., Aberdeen, UK

    CBS: Centraalbureau voor Schimmelcultures, Baarn, NL

    NCTC: National Collection of Type Cultures, London, UK

    DSMZ: Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany

    For reference see Sugawara, H. et al. (1993) World directory of collections of cultures of microorganisms: Bacteria, fungi and yeasts (4th edn), World federation for culture collections world data center on microorganisms, Saimata, Japen.
  • TABLE 4
    ALIGNMENT RESULTS
    %
    length homology Date of
    ID # (NT) Genbank Hit Length Accession Name of Genbank Hit Source of Genbank Hit (GAP) Deposit
    rxa00051 1527 GB_HTG3: AC009685 210031 AC009685 Homo sapiens chromosome 15 clone 91_E_13 map 15, *** SEQUENCING IN Homo sapiens 34,247 29-Sep-99
    PROGRESS ***, 27 unordered pieces.
    GB_HTG3: AC009685 210031 AC009685 Homo sapiens chromosome 15 clone 91_E_13 map 15, *** SEQUENCING IN Homo sapiens 34,247 29-Sep-99
    PROGRESS ***, 27 unordered pieces.
    GB_HTG7: AC009511 271896 AC009511 Homo sapiens clone RP11-860B13, *** SEQUENCING IN PROGRESS ***, 59 Homo sapiens 35,033 09-DEC-1999
    unordered pieces.
    rxa00091 876 GB_BA1: D50453 146191 D50453 Bacillus subtilis DNA for 25-36 degree region containing the amyE-srfA region, Bacillus subtilis 54,452 10-Feb-99
    complete cds.
    GB_BA1: SCI51 40745 AL109848 Streptomyces coelicolor cosmid I51. Streptomyces coelicolor 36,806 16-Aug-99
    A3(2)
    GB_BA1: ECOUW93 338534 U14003 Escherichia coli K-12 chromosomal region from 92.8 to 00.1 minutes. Escherichia coli 38,642 17-Apr-96
    rxa00092 789 GB_BA1: SCH35 45396 AL078610 Streptomyces coelicolor cosmid H35. Streptomyces coelicolor 49,934 4-Jun-99
    GB_HTG3: AC011498_0 312343 AC011498 Homo sapiens chromosome 19 clone CIT978SKB_50L17, *** SEQUENCING IN Homo sapiens 37,117 13-Dec-99
    PROGRESS ***, 190 unordered pieces.
    GB_HTG3: AC011498_0 312343 AC011498 Homo sapiens chromosome 19 clone CIT978SKB_50L17, *** SEQUENCING IN Homo sapiens 37,117 13-Dec-99
    PROGRESS ***, 190 unordered pieces.
    rxa00104 879 GB_BA1: MTCY270 37586 Z95388 Mycobacterium tuberculosis H37Rv complete genome; segment 96/162. Mycobacterium 36,732 10-Feb-99
    tuberculosis
    GB_PL2: T24M8 68251 AF077409 Arabidopsis thaliana BAC T24M8. Arabidopsis thaliana 37,150 3-Aug-98
    GB_BA1: MTCY270 37586 Z95388 Mycobacterium tuberculosis H37Rv complete genome; segment 96/162. Mycobacterium 42,874 10-Feb-99
    tuberculosis
    rxa00113 5745 GB_BA1: MAFASGEN 10520 X87822 B. ammoniagenes FAS gene. Corynebacterium 68,381 03-OCT-1996
    ammoniagenes
    GB_BA1: BAFASAA 10549 X64795 B. ammoniagenes FAS gene. Corynebacterium 57,259 14-OCT-1997
    ammoniagenes
    GB_BA1: MTCY159 33818 Z83863 Mycobacterium tuberculosis H37Rv complete genome; segment 111/162. Mycobacterium 39,870 17-Jun-98
    tuberculosis
    rxa00164 1812 GB_HTG2: HSJ1153D9 118360 AL109806 Homo sapiens chromosome 20 clone RP5-1153D9, *** SEQUENCING IN Homo sapiens 35,714 03-DEC-1999
    PROGRESS ***, in unordered pieces.
    GB_HTG2: HSJ1153D9 118360 AL109806 Homo sapiens chromosome 20 clone RP5-1153D9, *** SEQUENCING IN Homo sapiens 35,714 03-DEC-1999
    PROGRESS ***, in unordered pieces.
    GB_HTG2: HSJ1153D9 118360 AL109806 Homo sapiens chromosome 20 clone RP5-1153D9, *** SEQUENCING IN Homo sapiens 35,334 03-DEC-1999
    PROGRESS ***, in unordered pieces.
    rxa00181 1695 GB_BA1: CGPUTP 3791 Y09163 C. glutamicum putP gene. Corynebacterium 100,000 8-Sep-97
    glutamicum
    GB_BA2: U32814 10393 U32814 Haemophilus influenzae Rd section 129 of 163 of the complete genome. Haemophilus influenzae 36,347 29-MAY-1998
    Rd
    GB_BA1: CGPUTP 3791 Y09163 C. glutamicum putP gene. Corynebacterium 37,454 8-Sep-97
    glutamicum
    rxa00186 870 GB_PR3: AC004843 136655 AC004843 Homo sapiens PAC clone DJ0612F12 from 7p12-p14, complete sequence. Homo sapiens 37,315 5-Nov-98
    GB_HTG2: HS745I14 133309 AL033532 Homo sapiens chromosome 1 clone RP4-745I14 map q23.1-24.3, *** SEQUENCING Homo sapiens 38,129 03-DEC-1999
    IN PROGRESS ***, in unordered pieces.
    GB_HTG2: HS745I14 133309 AL033532 Homo sapiens chromosome 1 clone RP4-745I14 map q23.1-24.3, *** SEQUENCING Homo sapiens 38,129 03-DEC-1999
    IN PROGRESS ***, in unordered pieces.
    rxa00187 474 GB_GSS10: AQ184082 506 AQ184082 HS_3216_A1_G08_T7 CIT Approved Human Genomic Sperm Library D Homo Homo sapiens 37,297 1-Nov-98
    sapiens genomic clone Plate = 3216 Col = 15 Row = M, genomic survey sequence.
    GB_GSS1: CNS008ZZ 1101 AL052951 Drosophila melanogaster genome survey sequence T7 end of BAC # BACR18L01 of Drosophila melanogaster 34,120 3-Jun-99
    RPCI-98 library from Drosophila melanogaster (fruit fly), genomic survey sequence.
    GB_GSS10: AQ184082 506 AQ184082 HS_3216_A1_G08_T7 CIT Approved Human Genomic Sperm Library D Homo Homo sapiens 39,655 1-Nov-98
    sapiens genomic clone Plate = 3216 Col = 15 Row = M, genomic survey sequence.
    rxa00201 292 GB_PR3: HSJ824F16 139330 AL050325 Human DNA sequence from clone 824F16 on chromosome 20, complete sequence. Homo sapiens 34,520 23-Nov-99
    GB_BA1: RCSECA 2724 X89411 R. capsulatus DNA for secA gene. Rhodobacter capsulatus 38,163 6-Jan-96
    GB_EST34: AV122904 242 AV122904 AV122904 Mus musculus C57BL/6J 10-day embryo Mus musculus cDNA clone Mus musculus 38,889 1-Jul-99
    2610529H07, mRNA sequence.
    rxa00228 714 GB_EST15: AA486042 515 AA486042 ab40c08.r1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone Homo sapiens 37,500 06-MAR-1998
    IMAGE: 843278 5′, mRNA sequence.
    GB_EST15: AA486042 515 AA486042 ab40c08.r1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone Homo sapiens 38,816 06-MAR-1998
    IMAGE: 843278 5′, mRNA sequence.
    rxa00243 1140 GB_PR2: CNS01DS5 101584 AL121655 BAC sequence from the SPG4 candidate region at 2p21-2p22, complete sequence. Homo sapiens 37,001 29-Sep-99
    GB_HTG3: AC011408 79332 AC011408 Homo sapiens clone CIT978SKB_65D22, Homo sapiens 38,040 06-OCT-1999
    *** SEQUENCING IN PROGRESS ***, 10 unordered pieces.
    GB_HTG3: AC011408 79332 AC011408 Homo sapiens clone CIT978SKB_65D22, Homo sapiens 38,040 06-OCT-1999
    *** SEQUENCING IN PROGRESS ***, 10 unordered pieces.
    rxa00259 2325 GB_HTG1: CEY62E10 254217 AL031580 Caenorhabditis elegans chromosome IV clone Y62E10, *** SEQUENCING IN Caenorhabditis elegans 36,776 6-Sep-99
    PROGRESS ***, in unordered pieces.
    GB_HTG1: CEY62E10 254217 AL031580 Caenorhabditis elegans chromosome IV clone Y62E10, *** SEQUENCING IN Caenorhabditis elegans 36,776 6-Sep-99
    PROGRESS ***, in unordered pieces.
    GB_PL2: YSCCHROMI 41988 L22015 Saccharomyces cerevisiae chromosome I centromere and right arm sequence. Saccharomyces 39,260 05-MAR-1998
    cerevisiae
    rxa00269 912 GB_HTG4: AC009974 219565 AC009974 Homo sapiens chromosome unknown clone NH0459I19, WORKING DRAFT Homo sapiens 37,358 29-OCT-1999
    SEQUENCE, in unordered pieces.
    GB_HTG4: AC009974 219565 AC009974 Homo sapiens chromosome unknown clone NH0459I19, WORKING DRAFT Homo sapiens 37,358 29-OCT-1999
    SEQUENCE, in unordered pieces.
    GB_BA1: AB017508 32050 AB017508 Bacillus halodurans C-125 genomic DNA, 32 kb fragment, complete cds. Bacillus halodurans 44,622 14-Apr-99
    rxa00281 766 GB_BA1: SCE8 24700 AL035654 Streptomyces coelicolor cosmid E8. Streptomyces coelicolor 36,328 11-MAR-1999
    GB_BA1: SCU51332 3216 U51332 Streptomyces coelicolor histidine kinase homolog (absA1) and response regulator Streptomyces coelicolor 39,089 14-Sep-96
    homolog (absA2) genes, complete cds.
    GB_HTG4: AC011122 187123 AC011122 Homo sapiens chromosome 8 clone 23_D_19 map 8, *** SEQUENCING IN Homo sapiens 38,658 14-OCT-1999
    PROGRESS ***, 27 ordered pieces.
    rxa00298 1968 GB_BA1: CGECTP 2719 AJ001436 Corynebacterium glutamicum ectP gene. Corynebacterium 100,000 20-Nov-98
    glutamicum
    GB_BA1: CGECTP 2719 AJ001436 Corynebacterium glutamicum ectP gene. Corynebacterium 100,000 20-Nov-98
    glutamicum
    GB_EST24: AI234006 432 AI234006 EST230694 Normalized rat lung, Bento Soares Rattus sp. cDNA clone RLUCU01 3′ Rattus sp. 46,552 31-Jan-99
    end, mRNA sequence.
    rxa00346 813 GB_BA1: SC2E9 20850 AL021530 Streptomyces coelicolor cosmid 2E9. Streptomyces coelicolor 43,267 28-Jan-98
    GB_BA1: SC9B1 24800 AL049727 Streptomyces coelicolor cosmid 9B1. Streptomyces coelicolor 44,613 27-Apr-99
    GB_BA1: ECU70214 123171 U70214 Escherichia coli chromosome minutes 4-6. Escherichia coli 39,490 21-Sep-96
    rxa00368 1698 GB_BA2: AF065159 35209 AF065159 Bradyrhizobium japonicum putative arylsulfatase (arsA), putative soluble lytic Bradyrhizobium 40,409 27-OCT-1999
    transglycosylase precursor (sltA), dihydrodipicolinate synthase (dapA), MscL (mscL), japonicum
    SmpB (smpB), BcpB (bcpB), RnpO (rnpO), RelA/SpoT homolog (relA), PdxJ (pdxJ),
    and acyl carrier protein synthase AcpS (acpS) genes, complete cds; prokaryotic type
    I signal peptidase SipF (sipF) gene, sipF-sipS allele, complete cds; RNase III (rnc)
    gene, complete cds; GTP-binding protein Era (era) gene, partial cds; and unknown
    genes.
    GB_BA1: AEOCHIT1 6861 D63139 Aeromonas sp. gene for chitinase, complete and partial cds. Aeromonas sp. 10S-24 38,577 13-Feb-99
    GB_EST4: D62996 314 D62996 HUM347G01B Clontech human aorta polyA+ mRNA (#6572) Homo sapiens cDNA Homo sapiens 41,613 29-Aug-95
    clone GEN-347G01 5′, mRNA sequence.
    rxa00369 817 GB_BA1: YP102KB 119443 AL031866 Yersinia pestis 102 kbases unstable region: from 1 to 119443. Yersinia pestis 35,396 4-Jan-99
    GB_GSS8: AQ012142 501 AQ012142 8750H1A037010398 Cosmid library of chromosome II Rhodobacter sphaeroides Rhodobacter sphaeroides 54,800 4-Jun-98
    genomic clone 8750H1A037010398, genomic survey sequence.
    GB_HTG2: AC005081 180096 AC005081 Homo sapiens clone RG270D13, *** SEQUENCING IN PROGRESS ***, 18 Homo sapiens 45,786 12-Jun-98
    unordered pieces.
    rxa00410 789 GB_BA1: ATPLOCC 8870 Z30328 A. tumefaciens Ti plasmid pTiAch5 genes for OccR, OccQ, OccM, OccP, OccT, Agrobacterium 46,490 10-OCT-1994
    OoxB, OoxA and ornithine cyclodeaminase. tumefaciens
    GB_BA2: U67591 9829 U67591 Methanococcus jannaschii section 133 of 150 of the complete genome. Methanococcus 45,677 28-Jan-98
    jannaschii
    GB_BA1: TIPOCCQMPJ 4350 M80607 Plasmid pTiA6 (from Agribacterium tumefaciens) periplasmic-type octopine Plasmid pTiA6 46,490 24-Apr-96
    permease (occR, occQ, occM, occP, and occJ) and lysR-type regulatory protein
    (occR) genes, complete cds.
    rxa00419 882 GB_BA2: MSU46844 16951 U46844 Mycobacterium smegmatis catalase-peroxidase (katG), putative arabinosyl Mycobacterium 57,029 12-MAY-1997
    transferase (embC, embA, embB), genes complete cds and putative propionyl-coA smegmatis
    carboxylase beta chain (pccB) genes, partial cds.
    GB_EST28: AI513245 471 AI513245 GH13311.3prime GH Drosophila melanogaster head pOT2 Drosophila melanogaster Drosophila melanogaster 37,696 16-MAR-1999
    cDNA clone GH13311 3prime, mRNA sequence.
    GB_HTG4: AC010066 187240 AC010066 Drosophila melanogaster chromosome 3L/72A4 clone RPCI98-25O1, *** Drosophila melanogaster 39,607 16-OCT-1999
    SEQUENCING IN PROGRESS ***, 70 unordered pieces.
    rxa00432 1608 GB_BA1: BSUB0015 218410 Z99118 Bacillus subtilis complete genome (section 15 of 21): from 2795131 to 3013540. Bacillus subtilis 49,810 26-Nov-97
    GB_PL1: CAC35A5 42565 AL033396 C. albicans cosmid Ca35A5. Candida albicans 35,041 5-Nov-98
    GB_EST13: AA336266 378 AA336266 EST40981 Endometrial tumor Homo sapiens cDNA 5′ end, mRNA sequence. Homo sapiens 39,733 21-Apr-97
    rxa00449 1704 GB_HTG2: AC008199 124050 AC008199 Drosophila melanogaster chromosome 3 clone BACR01K08 (D756) RPCI-98 01.K.8 Drosophila melanogaster 38,392 2-Aug-99
    map 94D-94D strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 83
    unordered pieces.
    GB_HTG2: AC008199 124050 AC008199 Drosophila melanogaster chromosome 3 clone BACR01K08 (D756) RPCI-98 01.K.8 Drosophila melanogaster 38,392 2-Aug-99
    map 94D-94D strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 83
    unordered pieces.
    GB_RO: RATLNKP2 177 M22337 Rat link protein gene, exon 2. Rattus sp. 40,678 27-Apr-93
    rxa00456 1500 GB_GSS1: FR0030597 476 AL026966 Fugu rubripes GSS sequence, clone 091C22aF9, genomic survey sequence. Fugu rubripes 47,407 25-Jun-98
    GB_GSS5: AQ786587 556 AQ786587 HS_3086_B1_H05_MR CIT Approved Human Genomic Sperm Library D Homo Homo sapiens 38,406 3-Aug-99
    sapiens genomic clone Plate = 3086 Col = 9 Row = P, genomic survey sequence.
    GB_GSS14: AQ526586 434 AQ526586 HS_5198_B1_B03_SP6E RPCI-11 Human Male BAC Library Homo sapiens Homo sapiens 36,951 11-MAY-1999
    genomic clone Plate = 774 Col = 5 Row = D, genomic survey sequence.
    rxa00477 1767 GB_EST17: AA610489 407 AA610489 np93e05.s1 NCI_CGAP_Thy1 Homo sapiens cDNA clone IMAGE: 1133888 similar Homo sapiens 41,791 09-DEC-1997
    to gb: M11353 HISTONE H3.3 (HUMAN);, mRNA sequence.
    GB_PR1: HSH33G4 1015 X05857 Human H3.3 gene exon 4. Homo sapiens 38,182 24-Jan-96
    GB_EST30: AI637667 579 AI637667 tt10g11.x1 NCI_CGAP_GC6 Homo sapiens cDNA clone IMAGE: 2240420 3′, Homo sapiens 35,417 27-Apr-99
    mRNA sequence.
    rxa00478 954 GB_HTG3: AC008708 83932 AC008708 Homo sapiens chromosome 5 clone CIT978SKB_78F1, *** SEQUENCING IN Homo sapiens 38,769 3-Aug-99
    PROGRESS ***, 12 unordered pieces.
    GB_HTG3: AC008708 83932 AC008708 Homo sapiens chromosome 5 clone CIT978SKB_78F1, *** SEQUENCING IN Homo sapiens 38,769 3-Aug-99
    PROGRESS ***, 12 unordered pieces.
    GB_HTG3: AC008708 83932 AC008708 Homo sapiens chromosome 5 clone CIT978SKB_78F1, *** SEQUENCING IN Homo sapiens 36,797 3-Aug-99
    PROGRESS ***, 12 unordered pieces.
    rxa00480 1239 GB_HTG1: HSJ575L21 94715 AL096841 Homo sapiens chromosome 1 clone RP4-575L21, *** SEQUENCING IN PROGRESS Homo sapiens 38,138 23-Nov-99
    ***, In unordered pieces.
    GB_HTG1: HSJ575L21 94715 AL096841 Homo sapiens chromosome 1 clone RP4-575L21, *** SEQUENCING IN PROGRESS Homo sapiens 38,138 23-Nov-99
    ***, In unordered pieces.
    GB_RO: AC005960 158414 AC005960 Mus musculus chromosome 17 BAC cltb20h22 from the MHC region, complete Mus musculus 38,712 01-DEC-1998
    sequence.
    rxa00524 433 GB_BA1: SCI51 40745 AL109848 Streptomyces coelicolor cosmid I51. Streptomyces coelicolor 40,284 16-Aug-99
    A3(2)
    GB_BA2: AF082879 3434 AF082879 Yersinia enterocolitica ABC transporter enterochelin/enterobactin gene cluster, Yersinia enterocolitica 55,634 20-OCT-1999
    complete sequence.
    GB_BA1: BSP132617 5192 AJ132617 Burkholderia sp. P-transporter operon and flanking genes. Burkholderia sp. 40,793 13-Jul-99
    rxa00526 813 GB_BA1: BSUB0008 208230 Z99111 Bacillus subtilis complete genome (section 8 of 21): from 1394791 to 1603020. Bacillus subtilis 54,534 26-Nov-97
    GB_BA2: AF012285 46864 AF012285 Bacillus subtilis mobA-nprE gene region. Bacillus subtilis 54,534 1-Jul-98
    GB_BA1: D90725 13796 D90725 Escherichia coli genomic DNA. (19.7-20.0 min). Escherichia coli 51,481 7-Feb-99
    rxa00559 1140 GB_BA2: CAU77910 3385 U77910 Corynebacterium ammoniagenes sequence upstream of the 5-phosphoribosyl-1- Corynebacterium 39,007 1-Jan-98
    pyrophosphate amidotransferase (purF) gene. ammoniagenes
    GB_EST4: H34952 382 H34952 EST108261 Rat PC-12 cells, untreated Rattus sp. cDNA clone RPCCK07 similar to Rattus sp. 39,267 2-Apr-98
    NADH-ubiquinone oxidoreductase complex I 23 kDa precursor (iron-sulfur protein),
    mRNA sequence.
    GB_BA2: AE000963 22014 AE000963 Archaeoglobus fulgidus section 144 of 172 of the complete genome. Archaeoglobus fulgidus 38,338 15-DEC-1997
    rxa00570 852 GB_GSS12: AQ422451 563 AQ422451 RPCI-11-185C3.TV RPCI-11 Homo sapiens genomic clone RPCI-11-185C3, Homo sapiens 38,767 23-MAR-1999
    genomic survey sequence.
    GB_EST28: AI504741 568 AI504741 vl16c01.x1 Stratagene mouse Tcell 937311 Mus musculus cDNA clone Mus musculus 37,900 11-MAR-1999
    IMAGE: 972384 3′ similar to gb: Z14044 M. musculus mRNA for valosin-containing
    protein (MOUSE);, mRNA sequence.
    GB_EST18: AA712043 68 AA712043 vu29f10.r1 Barstead mouse myotubes MPLRB5 Mus musculus cDNA clone Mus musculus 42,647 24-DEC-1997
    IMAGE: 1182091 5′ similar to gb: L05093 60S RIBOSOMAL PROTEIN L18A
    (HUMAN);, mRNA sequence.
    rxa00571 1280 GB_BA1: MTCY78 33818 Z77165 Mycobacterium tuberculosis H37Rv complete genome; segment 145/162. Mycobacterium 38,468 17-Jun-98
    tuberculosis
    GB_PR3: AC005788 36224 AC005788 Homo sapiens chromosome 19, cosmid R26652, complete sequence. Homo sapiens 36,911 06-OCT-1998
    GB_PR3: AC005338 34541 AC005338 Homo sapiens chromosome 19, cosmid R31646, complete sequence. Homo sapiens 36,911 30-Jul-98
    rxa00590 1288 GB_HTG6: AC010932 203273 AC010932 Homo sapiens chromosome 15 clone RP11-296E22 map 15, *** SEQUENCING IN Homo sapiens 37,242 30-Nov-99
    PROGRESS ***, 36 unordered pieces.
    GB_HTG6: AC010932 203273 AC010932 Homo sapiens chromosome 15 clone RP11-296E22 map 15, *** SEQUENCING IN Homo sapiens 36,485 30-Nov-99
    PROGRESS ***, 36 unordered pieces.
    GB_BA1: MSGB26CS 37040 L78816 Mycobacterium leprae cosmid B26 DNA sequence. Mycobacterium leprae 39,272 15-Jun-96
    rxa00591 1476 GB_IN1: CEK09E9 30098 Z79602 Caenorhabditis elegans cosmid K09E9, complete sequence. Caenorhabditis elegans 34,092 2-Sep-99
    GB_PR4: AF135802 4965 AF135802 Homo sapiens thyroid hormone receptor-associated protein complex component Homo sapiens 36,310 9-Apr-99
    TRAP170 mRNA, complete cds.
    GB_PR4: AF104256 4365 AF104256 Homo sapiens transcriptional co-activator CRSP150 (CRSP150) mRNA, complete Homo sapiens 36,617 4-Feb-99
    cds.
    rxa00596 576 GB_PR3: AC004659 129577 AC004659 Homo sapiens chromosome 19, CIT-HSP-87m17 BAC clone, complete sequence. Homo sapiens 34,321 02-MAY-1998
    GB_PR3: AC004659 129577 AC004659 Homo sapiens chromosome 19, CIT-HSP-87m17 BAC clone, complete sequence. Homo sapiens 35,739 02-MAY-1998
    GB_PR1: HUMCBP2 2047 D83174 Human mRNA for collagen binding protein 2, complete cds. Homo sapiens 40,404 6-Feb-99
    rxa00607 504 GB_BA1: MTV010 3400 AL021186 Mycobacterium tuberculosis H37Rv complete genome; segment 119/162. Mycobacterium 40,862 23-Jun-99
    tuberculosis
    GB_BA1: MTV010 3400 AL021186 Mycobacterium tuberculosis H37Rv complete genome; segment 119/162. Mycobacterium 38,833 23-Jun-99
    tuberculosis
    rxa00623 1461 GB_BA1: MTCY428 26914 Z81451 Mycobacterium tuberculosis H37Rv complete genome; segment 107/162. Mycobacterium 60,552 17-Jun-98
    tuberculosis
    GB_BA1: RSPNGR234 34010 Z68203 Rhizobium sp. plasmid NGR234a DNA. Rhizobium sp. 51,992 8-Aug-96
    GB_BA2: AE000101 10057 AE000101 Rhizobium sp, NGR234 plasmid pNGR234a, section 38 of 46 of the complete Rhizobium sp. NGR234 51,992 12-DEC-1997
    plasmid sequence.
    rxa00681
    rxa00690 1269 GB_HTG5: AC008338 136685 AC008338 Drosophila melanogaster chromosome X clone BACR30J04 (D908) RPCI-98 30.J.4 Drosophila melanogaster 35,341 15-Nov-99
    map 19C-19E strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 93
    unordered pieces.
    GB_HTG4: AC009766 170502 AC009766 Homo sapiens chromosome 11 clone 404_A_03 map 11, *** SEQUENCING IN Homo sapiens 37,984 19-OCT-1 999
    PROGRESS ***, 27 unordered pieces.
    GB_HTG4: AC009766 170502 AC009766 Homo sapiens chromosome 11 clone 404_A_03 map 11, *** SEQUENCING IN Homo sapiens 37,984 19-OCT-1999
    PROGRESS ***, 27 unordered pieces.
    rxa00733 1008 GB_EST30: AU054038 245 AU054038 AU054038 Dictyostelium discoideum SL (H. Urushihara) Dictyostelium discoideum Dictyostelium discoideum 43,265 28-Apr-99
    cDNA clone SLK472, mRNA sequence.
    GB_EST30: AU054038 245 AU054038 AU054038 Dictyostelium discoideum SL (H. Urushihara) Dictyostelium discoideum Dictyostelium discoideum 43,265 28-Apr-99
    cDNA clone SLK472, mRNA sequence.
    rxa00735 692 GB_BA1: MTCY50 36030 Z77137 Mycobacterium tuberculosis H37Rv complete genome; segment 55/162. Mycobacterium 36,819 17-Jun-98
    tuberculosis
    GB_BA1: D90904 150894 D90904 Synechocystis sp. PCC6803 complete genome, 6/27, 630555-781448. Synechocystis sp. 52,585 7-Feb-99
    GB_BA1: D90904 150894 D90904 Synechocystis sp. PCC6803 complete genome, 6/27, 630555-781448. Synechocystis sp. 39,699 7-Feb-99
    rxa00796 298 GB_GSS14: AQ579838 651 AQ579838 T135342b shotgun sub-library of BAC clone 31P06 Medicago truncatula genomic Medicago truncatula 37,153 27-Sep-99
    clone 31-P-06-C-054, genomic survey sequence.
    GB_PR4: AC007625 174701 AC007625 Genomic sequence of Homo sapiens clone 2314F2 from chromosome 18, complete Homo sapiens 38,014 30-Jun-99
    sequence.
    GB_EST14: AA427576 580 AA427576 zw54b04.s1 Soares_total_fetus_Nb2HF8_9w Homo sapiens cDNA clone Homo sapiens 42,731 16-OCT-1997
    IMAGE: 773839 3′ similar to gb: M86852 PEROXISOME ASSEMBLY FACTOR-1
    (HUMAN);, mRNA sequence.
    rxa00801 756 GB_BA1: MTV022 13025 AL021925 Mycobacterium tuberculosis H37Rv complete genome; segment 100/162. Mycobacterium 59,350 17-Jun-98
    tuberculosis
    GB_RO: AC002109 160048 AC002109 Genomic sequence from Mouse 9, complete sequence. Mus musculus 39,398 9-Sep-97
    GB_BA1: MTV022 13025 AL021925 Mycobacterium tuberculosis H37Rv complete genome; segment 100/162. Mycobacterium 36,842 17-Jun-98
    tuberculosis
    rxa00802 837 GB_GSS14: AQ563349 642 AQ563349 HS_5335_B2_A09_T7A RPCI-11 Human Male BAC Library Homo Homo sapiens 37,649 29-MAY-1999
    sapiens genomic clone Plate = 911 Col = 18 Row = B, genomic survey sequence.
    GB_BA1: DIHCLPBA 2441 M32229 B. nodosus clpB gene encoding a regulatory subunit of ATP-dependent protease. Dichelobacter nodosus 41,140 26-Apr-93
    GB_GSS3: B61538 698 B61538 T17M17TR TAMU Arabidopsis thaliana genomic clone T17M17, genomic survey Arabidopsis thaliana 36,946 21-Nov-97
    sequence.
    rxa00819 1452 GB_HTG3: AC008691_1 110000 AC008691 Homo sapiens chromosome 5 clone CIT978SKB_63A22, *** SEQUENCING IN Homo sapiens 38,270 3-Aug-99
    PROGRESS ***, 253 unordered pieces.
    GB_HTG3: AC008691_1 110000 AC008691 Homo sapiens chromosome 5 clone CIT978SKB_63A22, *** SEQUENCING IN Homo sapiens 38,270 3-Aug-99
    PROGRESS ***, 253 unordered pieces.
    GB_HTG3: AC009127 186591 AC009127 Homo sapiens chromosome 16 clone RPCI-11_498D10, *** SEQUENCING IN Homo sapiens 38,947 3-Aug-99
    PROGRESS ***, 49 unordered pieces.
    rxa00821 966 GB_HTG1: HS32B1 271488 AL023693 Homo sapiens chromosome 6 clone RP1-32B1, *** SEQUENCING IN PROGRESS Homo sapiens 36,565 23-Nov-99
    ***, in unordered pieces.
    GB_HTG1: HS32B1 271488 AL023693 Homo sapiens chromosome 6 clone RP1-32B1, *** SEQUENCING IN PROGRESS Homo sapiens 36,565 23-Nov-99
    ***, in unordered pieces.
    GB_PR3: AC004919 75547 AC004919 Homo sapiens PAC clone DJ0895B23 from UL, complete sequence. Homo sapiens 34,346 19-Sep-98
    rxa00827 876 GB_EST6: W06539 300 W06539 T2367 MVAT4 bloodstream form of serodeme WRATat1.1 Trypanosoma brucei Trypanosoma brucei 40,000 12-Aug-96
    rhodesiense cDNA 5′, mRNA sequence. rhodesiense
    GB_PR4: AC008179 181745 AC008179 Homo sapiens clone NH0576F01, complete sequence. Homo sapiens 35,903 28-Sep-99
    GB_EST18: AA710415 533 AA710415 vt53f08.r1 Barstead mouse irradiated colon MPLRB7 Mus musculus cDNA clone Mus musculus 41,562 24-DEC-1997
    IMAGE: 1166823 5′, mRNA sequence.
    rxa00842 1323 GB_PR2: AC002379 118595 AC002379 Human BAC clone GS165I04 from 7q21, complete sequence. Homo sapiens 36,321 23-Jul-97
    GB_PR2: AC002379 118595 AC002379 Human BAC clone GS165I04 from 7q21, complete sequence. Homo sapiens 37,284 23-Jul-97
    GB_IN1: CEF02D8 31624 Z78411 Caenorhabditis elegans cosmid F02D8, complete sequence. Caenorhabditis elegans 38,163 23-Nov-98
    rxa00847 1572 GB_OV: XELRDS38A 1209 L79915 Xenopus laevis rds/peripherin (rds38) mRNA, complete cds. Xenopus laevis 36,044 30-Jul-97
    GB_HTG4: AC007920 234529 AC007920 Homo sapiens chromosome 3q27 clone RPCI11-208N14, *** SEQUENCING IN Homo sapiens 33,742 21-OCT-1999
    PROGRESS ***, 51 unordered pieces.
    GB_HTG4: AC007920 234529 AC007920 Homo sapiens chromosome 3q27 clone RPCI11-208N14, *** SEQUENCING IN Homo sapiens 33,742 21-OCT-1999
    PROGRESS ***, 51 unordered pieces.
    rxa00851 732 GB_HTG2: AC004064 185000 AC004064 Homo sapiens chromosome 4, *** SEQUENCING IN PROGRESS ***, 10 unordered Homo sapiens 39,833 9-Jul-98
    pieces.
    GB_HTG2: AC004064 185000 AC004064 Homo sapiens chromosome 4, *** SEQUENCING IN PROGRESS ***, 10 unordered Homo sapiens 39,833 9-Jul-98
    pieces.
    GB_PR3: HSJ824F16 139330 AL050325 Human DNA sequence from clone 824F16 on chromosome 20, complete sequence. Homo sapiens 39,833 23-Nov-99
    rxa00852 813 GB_HTG3: AC010120 121582 AC010120 Drosophila melanogaster chromosome 3 clone BACR22N13 (D1061) RPCI-98 Drosophila melanogaster 36,855 24-Sep-99
    22.N.13 map 96F-96F strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 83
    unordered pieces.
    GB_HTG3: AC010120 121582 AC010120 Drosophila melanogaster chromosome 3 clone BACR22N13 (D1061) RPCI-98 Drosophila melanogaster 36,855 24-Sep-99
    22.N.13 map 96F-96F strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 83
    unordered pieces.
    GB_HTG2: AC006898 299308 AC006898 Caenorhabditis elegans clone Y73B6x, *** SEQUENCING IN PROGRESS ***, 9 Caenorhabditis elegans 36,768 24-Feb-99
    unordered pieces.
    rxa00856
    rxa00870 1635 GB_BA1: STMMSDA 3986 L48550 Streptomyces coelicolor methylmalonic acid semialdehyde dehydrogenase (msdA) Streptomyces coelicolor 63,743 09-MAY-1996
    gene, complete cds.
    GB_PAT: I92043 713 I92043 Sequence 10 from patent U.S. Pat. No. 5726299. Unknown. 38,850 01-DEC-1998
    GB_PAT: I78754 713 I78754 Sequence 10 from patent U.S. Pat. No. 5693781. Unknown. 38,850 3-Apr-98
    rxa00875 690 GB_BA2: AF119715 549 AF119715 Escherichia coli isopentyl diphosphate isomerase (idi) gene, complete cds. Escherichia coli 54,827 22-Apr-99
    GB_BA2: AE000372 12144 AE000372 Escherichia coli K-12 MG1655 section 262 of 400 of the complete genome. Escherichia coli 51,416 12-Nov-98
    GB_BA1: ECU28375 55175 U28375 Escherichia coli K-12 genome; approximately 64 to 65 minutes. Escherichia coli 51,416 08-DEC-1995
    rxa00878 1986 GB_HTG2: AC007472 114003 AC007472 Drosophila melanogaster chromosome 2 clone BACR30D19 (D587) RPCI-98 Drosophila melanogaster 36,592 2-Aug-99
    30.D.19 map 49E-49F strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 79
    unordered pieces.
    GB_HTG2: AC007472 114003 AC007472 Drosophila melanogaster chromosome 2 clone BACR30D19 (D587) RPCI-98 Drosophila melanogaster 36,592 2-Aug-99
    30.D.19 map 49E-49F strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 79
    unordered pieces.
    GB_HTG2: AC006798 207370 AC006798 Caenorhabditis elegans clone Y51F8, *** SEQUENCING IN PROGRESS ***, 30 Caenorhabditis elegans 36,699 25-Feb-99
    unordered pieces.
    rxa00880 1968 GB_EST4: H22888 468 H22888 ym54e12.r1 Soares infant brain 1NIB Home sapiens cDNA clone IMAGE: 52158 5′, Homo sapiens 37,179 6-Jul-95
    mRNA sequence.
    GB_GSS13: AQ426858 516 AQ426858 CITBI-E1-2578F1.TF CITBI-E1 Home sapiens genomic clone 2578F1, genomic Homo sapiens 38,447 24-MAR-1999
    survey sequence.
    GB_PR1: AB002335 6289 AB002335 Human mRNA for KIAA0337 gene, complete cds. Homo sapiens 35,799 13-Feb-99
    rxa00899 1389 GB_BA1: NGU58849 2401 U58849 Neisseria gonorrhoeae pilS6 silent pilus locus. Neisseria gonorrhoeae 40,623 20-Jun-96
    GB_BA1: PLPDHOS 3119 L06822 Plasmid pSa (from Escherichia coli) dihydropteroate synthase gene, 3′ end. Plasmid pSa 38,966 20-MAR-1996
    GB_BA1: PDGINTORF 6747 L06418 Integron In7 (from Plasmid pDGO100 from Escherichia coli) integrase (int), Plasmid pDGO100 38,966 20-MAR-1996
    aminoglycoside adenylyltransferase (aad), quaternary ammonium compound-
    resistance protein, dihydrofolate reductase (dhfrX), and dihydropteroate
    synthase (sull) genes.
    rxa00902 1333 GB_GSS15: AQ606873 581 AQ606873 HS_5404_B2_H05_T7A RPCI-11 Human Male BAC Library Homo sapiens Homo sapiens 37,900 10-Jun-99
    genomic clone Plate = 980 Col = 10 Row = P, genomic survey sequence.
    GB_GSS9: AQ163442 658 AQ163442 nbxb0007A07f CUGI Rice BAC Library Oryza sativa genomic clone nbxb0007A07f, Oryza sativa 41,885 12-Sep-98
    genomic survey sequence.
    GB_PL1: PSST70 4974 X69213 P. sativum Psst70 gene for heat-shock protein. Pisum sativum 36,866 3-Jul-96
    rxa00931 969 GB_GSS1: FR0025208 612 AL018047 F. rubripes GSS sequence, clone 145D10aA8, genomic survey sequence. Fugu rubripes 37,815 10-DEC-1997
    GB_GSS1: FR0021844 252 AL014715 F. rubripes GSS sequence, clone 069K22aG5, genomic survey sequence. Fugu rubripes 37,698 10-DEC-1997
    GB_GSS12: AQ403344 593 AQ403344 HS_2257_B1_B03_T7C CIT Approved Human Genomic Sperm Library D Homo Homo sapiens 31,552 13-MAR-1999
    sapiens genomic clone Plate = 2257 Col = 5 Row = D, genomic survey sequence.
    rxa00941 1440 GB_BA1: MTCY180 44201 Z97193 Mycobacterium tuberculosis H37Rv complete genome; segment 85/162. Mycobacterium 37,902 17-Jun-98
    tuberculosis
    GB_BA1: MTCY180 44201 Z97193 Mycobacterium tuberculosis H37Rv complete genome; segment 85/162. Mycobacterium 39,140 17-Jun-98
    tuberculosis
    GB_BA2: MSGKATG 1745 L14268 Mycobacterium tuberculosis ethyl methane sulphonate resistance protein (katG) Mycobacterium 42,517 26-Aug-99
    gene, 3′end. tuberculosis
    rxa00962 689 GB_HTG6: AC010998 144338 AC010998 Homo sapiens clone RP11-95I16, *** SEQUENCING IN PROGRESS ***, 17 Homo sapiens 39,497 08-DEC-1999
    unordered pieces.
    GB_GSS1: GGA340111 990 AJ232089 Gallus gallus anonymous sequence from Cosmid mapping to chromosome 2 Gallus gallus 37,970 25-Aug-98
    (Cosmid 34 - Contig 15), genomic survey sequence.
    GB_HTG6: AC010998 144338 AC010998 Homo sapiens clone RP11-95I16, *** SEQUENCING IN PROGRESS ***, 17 Homo sapiens 38,226 08-DEC-1999
    unordered pieces.
    rxa01060 1047 GB_BA1: ECTTN7 2280 AJ001816 Escherichia coli left end of transposon Tn7 including type 2 Integron. Escherichia coli 38,822 4-Nov-97
    GB_IN2: AF176377 8220 AF176377 Caenorhabditis briggsae CES-1 (ces-1) gene, complete cds; and CPN-1 (cpn-1) Caenorhabditis briggsae 39,921 09-DEC-1999
    gene, partial cds.
    GB_GSS10: AQ196728 429 AQ196728 CIT-HSP-2381F4.TR CIT-HSP Homo sapiens genomic clone 2381F4, genomic Homo sapiens 39,019 16-Sep-98
    survey sequence.
    rxa01067 852 GB_BA1: U00016 42931 U00016 Mycobacterium leprae cosmid B1937. Mycobacterium leprae 58,303 01-MAR-1994
    GB_BA1: SYCGROESL 3256 D12677 Synechocystis sp. groES and groEL genes. Synechocystis sp. 34,593 3-Feb-99
    GB_BA1: D90905 139467 D90905 Synechocystis sp. PCC6803 complete genome, 7/27, 781449-920915. Synechocystis sp. 34,593 7-Feb-99
    rxa01114 1347 GB_BA1: PSEFAOAB 3480 D10390 P. fragi faoA and faoB genes, complete cds. Pseudomonas fragi 51,919 2-Feb-99
    GB_BA1: AB014757 6057 AB014757 Pseudomonas sp. 61-3 genes for PhbR, acetoacetyl-CoA reductase, beta- Pseudomonas sp. 61-3 50,573 26-DEC-1998
    ketothiolase and PHB synthase, complete cds.
    GB_BA1: SC8D9 38681 AL035569 Streptomyces coelicolor cosmid 8D9. Streptomyces coelicolor 42,200 26-Feb-99
    rxa01136 555 GB_EST11: AA244557 379 AA244557 mx07a01.r1 Soares mouse NML Mus musculus cDNA clone IMAGE: 679464 5′, Mus musculus 39,050 10-MAR-1997
    mRNA sequence.
    GB_EST14: AA407673 306 AA407673 EST01834 Mouse 7.5 dpc embryo ectoplacental cone cDNA library Mus musculus Mus musculus 38,562 26-Aug-98
    cDNA clone C0014F02 3′, mRNA sequence.
    GB_EST26: AI390328 604 AI390328 mx07a01.y1 Soares mouse NML Mus musculus cDNA clone IMAGE: 679464 5′, Mus musculus 33,136 2-Feb-99
    mRNA sequence.
    rxa01138 540 GB_OV: XLXINT1 1278 X13138 Xenopus laevis int-1 mRNA for int-1 protein. Xenopus laevis 40,038 31-MAR-1995
    GB_PR4: AC006054 143738 AC006054 Homo sapiens Xq28 BAC RPCI11-382P7 (Roswell Park Cancer Institute Human Homo sapiens 37,996 1-Apr-99
    BAC Library) complete sequence.
    GB_PR4: AC006054 143738 AC006054 Homo sapiens Xq28 BAC RPCI11-382P7 (Roswell Park Cancer Institute Human Homo sapiens 36,053 1-Apr-99
    BAC Library) complete sequence.
    rxa01172 1578 GB_BA1: SCE39 23550 AL049573 Streptomyces coelicolor cosmid E39. Streptomyces coelicolor 62,357 31-MAR-1999
    GB_BA1: MSU50335 5193 U50335 Mycobacterium smegmatis phage resistance (mpr) gene, complete cds. Mycobacterium 37,853 1-Feb-97
    smegmatis
    GB_BA1: BACTHRTRNA 15467 D84213 Bacillus subtilis genome, trnl-feuABC region. Bacillus subtilis 53,807 6-Feb-99
    rxa01191 1713 GB_PR2: HS1191B2 60828 AL022237 Human DNA sequence from clone 1191B2 on chromosome 22q13.2-13.3. Contains Homo sapiens 38,366 23-Nov-99
    part of the BIK (NBK, BP4, BIP1) gene for BCL2-interacting killer (apoptosis-
    inducing), a 40S Ribososmal Protein S25 pseudogene and part of an
    alternatively spliced novel Acyl Transferase gene similar to C. elegans C50D2.7.
    Contains ESTs, STSs, GSSs, two putative CpG islands and genomic marker
    D22S1151, complete sequence.
    GB_PR2: HS1191B2 60828 AL022237 Human DNA sequence from clone 1191B2 on chromosome 22q13.2-13.3. Contains Homo sapiens 39,595 23-Nov-99
    part of the BIK (NBK, BP4, BIP1) gene for BCL2-interacting killer (apoptosis-
    inducing), a 40S Ribososmal Protein S25 pseudogene and part of an
    alternatively spliced novel Acyl Transferase gene similar to C. elegans C50D2.7.
    Contains ESTs, STSs, GSSs, two putative CpG islands and genomic marker
    D22S1151, complete sequence.
    rxa01205 554 GB_BA1: MTCY373 35516 Z73419 Mycobacterium tuberculosis H37Rv complete genome; segment 57/162. Mycobacterium 57,762 17-Jun-98
    tuberculosis
    GB_PL1: ATY12776 38483 Y12776 Arabidopsis thaliana DNA, 40 kb surrounding ACS1 locus. Arabidopsis thaliana 32,971 7-Sep-98
    GB_PL2: ATT6K21 99643 AL021889 Arabidopsis thaliana DNA chromosome 4, BAC clone T6K21 (ESSA project). Arabidopsis thaliana 35,273 16-Aug-99
    rxa01212 1047 GB_BA2: SCD25 41622 AL118514 Streptomyces coelicolor cosmid D25. Streptomyces coelicolor 39,654 21-Sep-99
    A3(2)
    GB_BA1: SLGLYUB 2576 X65556 S. lividans tRNA-GlyU beta gene. Streptomyces lividans 54,493 20-DEC-1993
    GB_BA1: SCH10 39524 AL049754 Streptomyces coelicolor cosmid H10. Streptomyces coelicolor 44,638 04-MAY-1999
    rxa01219 1005 GB_PAT: A68024 520 A68024 Sequence 19 from Patent WO9743409. unidentified 42,553 05-MAY-1999
    GB_PAT: A68025 193 A68025 Sequence 20 from Patent WO9743409. unidentified 43,229 05-MAY-1999
    GB_PAT: A68027 193 A68027 Sequence 22 from Patent WO9743409. unidentified 38,342 05-MAY-1999
    rxa01220 1200 GB_PR3: HS512B11 64356 AL031058 Human DNA sequence from clone 512B11 on chromosome 6p24-25. Contains the Homo sapiens 35,478 23-Nov-99
    Desmoplakin I (DPI) gene, ESTs, STSs and GSSs, complete sequence.
    GB_EST6: N99239 424 N99239 zb76h11.s1 Soares_senescent_fibroblasts_NbHSF Homo sapiens cDNA clone Homo sapiens 39,623 20-Aug-96
    IMAGE: 309573 3′, mRNA sequence.
    GB_EST16: AA554268 400 AA554268 nk36c09.s1 NCI_CGAP_GC2 Homo sapiens cDNA clone IMAGE: 1015600 Homo sapiens 36,111 8-Sep-97
    3′ similar to gb: X01677 GLYCERALDEHYDE 3-PHOSPHATE
    DEHYDROGENASE, LIVER (HUMAN);, mRNA sequence.
    rxa01221 849 GB_PR4: AF179633 96371 AF179633 Homo sapiens chromosome 16 map 16q23.3-q24.1 sequence. Homo sapiens 40,199 5-Sep-99
    GB_VI: EHVU20824 184427 U20824 Equine herpesvirus 2, complete genome. Equine herpesvirus 2 37,001 2-Feb-96
    GB_BA2: AE000407 10601 AE000407 Escherichia coli K-12 MG1655 section 297 of 400 of the complete genome. Escherichia coli 39,471 12-Nov-98
    rxa01222 822 GB_PAT: AR068625 28804 AR068625 Sequence 1 from patent U.S. Pat. No. 5854034. Unknown. 40,574 29-Sep-99
    GB_BA2: SSU51197 28804 U51197 Sphingomonas S88 sphingan polysaccharide synthesis (spsG), (spsS), (spsR), Sphingomonas sp. S88 40,574 16-MAY-1996
    glycosyl transferase (spsQ), (spsl), glycosyl transferase (spsK), glycosyl transferase
    (spsL), (spsJ), (spsF), (spsD), (spsC), (spsE), Urf 32, Urf 26, ATP-binding
    cassette transporter (atrD), ATP-binding cassette transporter (atrB), glucosyl-
    isoprenylphosphate transferase (spsB), glucose-1-phosphate thymidylyltransferase
    (rhsA), dTDP-6-deoxy-D-glucose-3,5-epimerase (rhsC) dTDP-D-glucose-4,6-
    dehydratase (rhsB), dTDP-6-deoxy-L-mannose-dehydrogenase (rhsD), Urf 31, and
    Urf 34 genes, complete cds.
    GB_IN1: BBU44918 2791 U44918 Babesia bovis ATP-binding protein (babc) mRNA, complete cds. Babesia bovis 39,228 9-Aug-97
    rxa01260 1305 GB_BA1: CGLPD 1800 Y16642 Corynebacterium glutamicum lpd gene, complete CDS. Corynebacterium 99,923 1-Feb-99
    glutamicum
    GB_BA1: MTV038 16094 AL021933 Mycobacterium tuberculosis H37Rv complete genome; segment 24/162. Mycobacterium 59,056 17-Jun-98
    tuberculosis
    GB_PR3: AC005618 176714 AC005618 Homo sapiens chromosome 5, BAC clone 249h5 (LBNL H149), complete sequence. Homo sapiens 36,270 5-Sep-98
    rxa01261 294 GB_BA1: CGLPD 1800 Y16642 Corynebacterium glutamicum lpd gene, complete CDS. Corynebacterium 100,000 1-Feb-99
    glutamicum
    GB_HTG4: AC010045 164829 AC010045 Drosophila melanogaster chromosome 3L/75A1 clone RPCI98-17C17, *** Drosophila melanogaster 50,512 16-OCT-1999
    SEQUENCING IN PROGRESS ***, 50 unordered pieces.
    GB_HTG4: AC010045 164829 AC010045 Drosophila melanogaster chromosome 3L/75A1 clone RPCI98-17C17, *** Drosophila melanogaster 50,512 16-OCT-1999
    SEQUENCING IN PROGRESS ***, 50 unordered pieces.
    rxa01269 564 GB_BA2: AF125164 26443 AF125164 Bacteroides fragilis 638R polysaccharide B (PS B2) biosynthesis locus, complete Bacteroides fragilis 56,071 01-DEC-1999
    sequence; and unknown genes.
    GB_BA1: AB002668 24907 AB002668 Actinobacillus actinomycetemcomitans DNA for glycosyltransferase, lytic Actinobacillus 46,679 21-Feb-98
    transglycosylase, dTDP-4-rhamnose reductase, complete cds. actinomycetemcomitans
    GB_BA1: AB010415 23112 AB010415 Actinobacillus actinomycetemcomitans gene cluster for 6-deoxy-L-talan synthesis, Actinobacillus 46,679 13-Feb-99
    complete cds. actinomycetemcomitans
    rxa01291 1056 GB_STS: AU027820 238 AU027820 Rattus norvegicus, OTSUKA clone, OT78.02/918b07, microsatellite sequence, Rattus norvegicus 34,874 02-MAR-1999
    sequence tagged site.
    GB_STS: AU027820 238 AU027820 Rattus norvegicus, OTSUKA clone, OT78.02/918b07, microsatellite sequence, Rattus norvegicus 34,874 02-MAR-1999
    sequence tagged site.
    GB_HTG3: AC006445 174547 AC006445 Homo sapiens chromosome 4, *** SEQUENCING IN PROGRESS ***, 7 unordered Homo sapiens 34,812 15-Sep-99
    pieces.
    rxa01292 1308 GB_BA1: BSUB0017 217420 Z99120 Bacillus subtilis complete genome (section 17 of 21): from 3197001 to 3414420. Bacillus subtilis 37,802 26-Nov-97
    GB_HTG3: AC010580 121119 AC010580 Drosophila melanogaster chromosome 3 clone BACR48J06 (D1102) RPCI-98 48.J.6 Drosophila melanogaster 35,637 01-OCT-1999
    map 96F-96F strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 71
    unordered pieces.
    GB_HTG3: AC010580 121119 AC010580 Drosophila melanogaster chromosome 3 clone BACR48J06 (D1102) RPCI-98 48.J.6 Drosophila melanogaster 35,637 01-OCT-1999
    map 96F-96F strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 71
    unordered pieces.
    rxa01293 450 GB_GSS8: AQ001809 705 AQ001809 CIT-HSP-2290D17.TF CIT-HSP Homo sapiens genomic clone 2290D17, genomic Homo sapiens 42,021 26-Jun-98
    survey sequence.
    GB_GSS8: AQ001809 705 AQ001809 CIT-HSP-2290D17.TF CIT-HSP Homo sapiens genomic clone 2290D17, genomic Homo sapiens 40,323 26-Jun-98
    survey sequence.
    rxa01339 1111 GB_PL1: MGU60290 4614 U60290 Magnaporthe grisea nitrogen regulatory protein (NUT1) gene, complete cds. Magnaporthe grisea 38,707 3-Jul-96
    GB_HTG3: AC011371 189187 AC011371 Homo sapiens chromosome 5 clone CIT978SKB_107C20, *** SEQUENCING IN Homo sapiens 39,741 06-OCT-1999
    PROGRESS ***, 31 unordered pieces.
    GB_HTG3: AC011371 189187 AC011371 Homo sapiens chromosome 5 clone CIT978SKB_107C20, *** SEQUENCING IN Homo sapiens 39,741 06-OCT-1999
    PROGRESS ***, 31 unordered pieces.
    rxa01382 1192 GB_HTG4: AC009892 138122 AC009892 Homo sapiens chromosome 19 clone CIT978SKB_83J4, *** SEQUENCING IN Homo sapiens 40,154 31-OCT-1999
    PROGRESS ***, 6 ordered pieces.
    GB_HTG4: AC009892 138122 AC009892 Homo sapiens chromosome 19 clone CIT978SKB_83J4, SEQUENCING IN Homo sapiens 40,154 31-OCT-1999
    PROGRESS ***, 6 ordered pieces.
    GB_PR3: AC002416 128915 AC002416 Human Chromosome X, complete sequence. Homo sapiens 37,521 29-Jan-98
    rxa01399 1142 GB_EST9: AA096601 524 AA096601 mo03b09.r1 Stratagene mouse lung 937302 Mus musculus cDNA clone Mus musculus 40,525 15-Feb-97
    IMAGE: 552473 5′ similar to gb: L06505 60S RIBOSOMAL PROTEIN L12
    (HUMAN); gb: L04280 Mus musculus ribosomal protein (MOUSE);,
    mRNA sequence.
    GB_EST37: AI982114 626 AI982114 pat.pk0074.e9.f chicken activated T cell cDNA Gallus gallus cDNA clone Gallus gallus 37,785 15-Sep-99
    pat.pk0074.e9.f 5′ similar to H-ATPase B subunit, mRNA sequence.
    GB_OV: GGU20766 1645 U20766 Gallus gallus vacuolar H+-ATPase B subunit gene, complete cds. Gallus gallus 38,244 07-DEC-1995
    rxa01420 1065 GB_HTG2: AC005690 193424 AC005690 Homo sapiens chromosome 4, *** SEQUENCING IN PROGRESS ***, 7 unordered Homo sapiens 37,464 11-Apr-99
    pieces.
    GB_HTG2: AC005690 193424 AC005690 Homo sapiens chromosome 4, *** SEQUENCING IN PROGRESS ***, 7 unordered Homo sapiens 37,464 11-Apr-99
    pieces.
    GB_HTG2: AC006637 22092 AC006637 Caenorhabditis elegans clone F41B4, *** SEQUENCING IN PROGRESS ***, 1 Caenorhabditis elegans 37,488 23-Feb-99
    unordered pieces.
    rxa01467 414 GB_HTG1: CEY102G3_21 10000 AL020985 Caenorhabditis elegans chromosome V clone Y102G3, *** SEQUENCING IN Caenorhabditis elegans 35,437 3-Dec-98
    GB_HTG1: CEY102G3_21 10000 AL020985 Caenorhabditis elegans chromosome V clone Y102G3, *** SEQUENCING IN Caenorhabditis elegans 35,437 3-Dec-98
    GB_HTG1: CEY113G7_41 10000 AL031113 Caenorhabditis elegans chromosome V clone Y113G7, *** SEQUENCING IN Caenorhabditis elegans 35,437 12-Jan-99
    rxa01576 882 GB_BA2: AF030975 2511 AF030975 Aeromonas salmonicida chaperonin GroES and chaperonin GroEL genes, complete Aeromonas salmonicida 41,516 2-Apr-98
    cds.
    GB_BA2: AF030975 2511 AF030975 Aeromonas salmonicida chaperonin GroES and chaperonin GroEL genes, complete Aeromonas salmonicida 38,171 2-Apr-98
    cds.
    GB_EST22: AI068560 965 AI068560 mgae0003aC11f Magnaporthe grisea Appressorium Stage cDNA Library Pyricularia Pyricularia grisea 40,073 09-DEC-1999
    grisea cDNA clone mgae0003aC11f5′, mRNA sequence.
    rxa01580 840 GB_GSS14: AQ554460 681 AQ554460 RPCI-11-419F2.TV RPCI-11 Homo sapiens genomic clone RPCI-11-419F2, genomic Homo sapiens 36,522 28-MAY-1999
    survey sequence.
    GB_IN2: AC005449 85518 AC005449 Drosophila melanogaster, chromosome 2R, region 44C4-44C5, P1 clone DS06765, Drosophila melanogaster 36,609 23-DEC-1998
    complete sequence.
    GB_IN2: AC005449 85518 AC005449 Drosophila melanogaster, chromosome 2R, region 44C4-44C5, P1 clone DS06765, Drosophila melanogaster 33,612 23-DEC-1998
    complete sequence.
    rxa01584
    rxa01604 771 GB_HTG3: AC011352 160167 AC011352 Homo sapiens chromosome 5 clone CIT-HSPC_327F10, *** SEQUENCING IN Homo sapiens 33,688 06-OCT-1999
    PROGRESS ***, 15 unordered pieces.
    GB_HTG3: AC011352 160167 AC011352 Homo sapiens chromosome 5 clone CIT-HSPC_327F10, *** SEQUENCING IN Homo sapiens 33,688 06-OCT-1999
    PROGRESS ***, 15 unordered pieces.
    GB_HTG3: AC011402 168868 AC011402 Homo sapiens chromosome 5 clone CIT978SKB_38B5, *** SEQUENCING IN Homo sapiens 33,688 06-OCT-1999
    PROGRESS ***, 7 unordered pieces.
    rxa01614 1146 GB_BA1: CGA224946 2408 AJ224946 Corynebacterium glutamicum DNA for L-Malate:quinone oxidoreductase. Corynebacterium 42,284 11-Aug-98
    glutamicum
    GB_EST17: AA608825 439 AA608825 af03g07.s1 Soares_testis_NHT Homo sapiens cDNA clone IMAGE: 1030620 3′ Homo sapiens 40,092 02-MAR-1998
    similar to TR: G976083 G976083 HISTONE H2A RELATED.;, mRNA sequence.
    GB_PR4: AC005377 102311 AC005377 Homo sapiens PAC clone DJ1136G02 from 7q32-q34, complete sequence. Homo sapiens 37,811 28-Apr-99
    rxa01629 1635 GB_BA1: CGPROPGEN 2936 Y12537 C. glutamicum proP gene. Corynebacterium 100,000 17-Nov-98
    glutamicum
    GB_BA1: CGPROPGEN 2936 Y12537 C. glutamicum proP gene. Corynebacterium 100,000 17-Nov-98
    glutamicum
    GB_PR4: AF191071 88481 AF191071 Homo sapiens chromosome 8 clone BAC 388D06, complete sequence. Homo sapiens 35,612 11-OCT-1999
    rxa01644 1401 GB_BA1: MSGB577COS 37770 L01263 M. leprae genomic dna sequence, cosmid b577. Mycobacterium leprae 55,604 14-Jun-96
    GB_BA1: MLCB2407 35615 AL023596 Mycobacterium leprae cosmid B2407. Mycobacterium leprae 36,416 27-Aug-99
    GB_BA1: MTV025 121125 AL022121 Mycobacterium tuberculosis H37Rv complete genome; segment 155/162. Mycobacterium 55,844 24-Jun-99
    tuberculosis
    rxa01667 1329 GB_BA1: CGU43536 3464 U43536 Corynebacterium glutamicum heat shock, ATP-binding protein (clpB) gene, complete Corynebacterium 100,000 13-MAR-1997
    cds. glutamicum
    GB_HTG4: AC009841 164434 AC009841 Drosophila melanogaster chromosome 3L/77E1 clone RPCI98-13F11, *** Drosophila melanogaster 33,205 16-OCT-1999
    SEQUENCING IN PROGRESS ***, 70 unordered pieces.
    GB_HTG4: AC009841 164434 AC009841 Drosophila melanogaster chromosome 3L/77E1 clone RPCI98-13F11, *** Drosophila melanogaster 33,205 16-OCT-1999
    SEQUENCING IN PROGRESS ***, 70 unordered pieces.
    rxa01722 1848 GB_GSS1: FR0022586 522 AL015452 F. rubripes GSS sequence, clone 077P23aB10, genomic survey sequence. Fugu rubripes 40,192 10-DEC-1997
    GB_GSS1: FR0022584 485 AL015450 F. rubripes GSS sequence, clone 077P23aB11, genomic survey sequence. Fugu rubripes 35,876 10-DEC-1997
    GB_IN1: CET26H2 37569 Z82055 Caenorhabditis elegans cosmid T26H2, complete sequence. Caenorhabditis elegans 34,759 19-Nov-99
    rxa01727 1401 GB_BA2: CORCSLYS 2821 M89931 Corynebacterium glutamicum beta C-S lyase (aecD) and branched-chain amino acid Corynebacterium 99,929 4-Jun-98
    uptake carrier (brnQ) genes, complete cds, and hypothetical protein Yhbw (yhbw) glutamicum
    gene, partial cds.
    GB_HTG6: AC011037 167849 AC011037 Homo sapiens clone RP11-7F18, WORKING DRAFT SEQUENCE, 19 unordered Homo sapiens 36,903 30-Nov-99
    pieces.
    GB_HTG6: AC011037 167849 AC011037 Homo sapiens clone RP11-7F18, WORKING DRAFT SEQUENCE, 19 unordered Homo sapiens 35,642 30-Nov-99
    pieces.
    rxa01737 1182 GB_BA1: SCGD3 33779 AL096822 Streptomyces coelicolor cosmid GD3. Streptomyces coelicolor 38,054 8-Jul-99
    GB_HTG1: CNS01DSB 222193 AL121768 Homo sapiens chromosome 14 clone R-976B16, *** SEQUENCING IN PROGRESS Homo sapiens 35,147 05-OCT-1999
    ***, in ordered pieces.
    GB_HTG1: CNS01DSB 222193 AL121768 Homo sapiens chromosome 14 clone R-976B16, *** SEQUENCING IN PROGRESS Homo sapiens 35,147 05-OCT-1999
    ***, in ordered pieces.
    rxa01762 1659 GB_BA1: MTCI28 36300 Z97050 Mycobacterium tuberculosis H37Rv complete genome; segment 10/162. Mycobacterium 49,574 23-Jun-98
    tuberculosis
    GB_BA1: SC6G10 36734 AL049497 Streptomyces coelicolor cosmid 6G10. Streptomyces coelicolor 44,049 24-MAR-1999
    GB_BA1: SCE29 26477 AL035707 Streptomyces coelicolor cosmid E29. Streptomyces coelicolor 40,246 12-MAR-1999
    rxa01764 1056 GB_PL2: SPAC343 42947 AL109739 S. pombe chromosome I cosmid c343. Schizosaccharomyces 37,084 6-Sep-99
    pombe
    GB_PL2: SPAC343 42947 AL109739 S. pombe chromosome I cosmid c343. Schizosaccharomyces 34,890 6-Sep-99
    pombe
    rxa01801 1140 GB_EST38: AW066306 334 AW066306 687009D03.y1 687 Early embryo from Delaware Zea mays cDNA, mRNA Zea mays 46,108 12-OCT-1999
    sequence.
    GB_GSS13: AQ484750 375 AQ484750 RPCI-11-248N4.TV RPCI-11 Homo sapiens genomic clone RPCI-11-248N4, Homo sapiens 32,000 24-Apr-99
    genomic survey sequence.
    GB_GSS13: AQ489971 252 AQ489971 RPCI-11-247N23.TV RPCI-11 Homo sapiens genomic clone RPCI-11-247N23, Homo sapiens 36,111 24-Apr-99
    genomic survey sequence.
    rxa01823 900 GB_BA1: SCI51 40745 AL109848 Streptomyces coelicolor cosmid I51. Streptomyces coelicolor 35,779 16-Aug-99
    A3(2)
    GB_BA1: ECU82598 136742 U82598 Escherichia coli genomic sequence of minutes 9 to 12. Escherichia coli 39,211 15-Jan-97
    GB_BA1: BSUB0018 209510 Z99121 Bacillus subtilis complete genome (section 18 of 21): from 3399551 to 3609060. Bacillus subtilis 36,999 26-Nov-97
    rxa01853 675 GB_BA1: MTCY227 35946 Z77724 Mycobacterium tuberculosis H37Rv complete genome; segment 114/162. Mycobacterium 37,612 17-Jun-98
    tuberculosis
    GB_HTG3: AC010189 265962 AC010189 Homo sapiens clone RPCI11-296K13, *** SEQUENCING IN PROGRESS ***, 80 Homo sapiens 39,006 16-Sep-99
    unordered pieces.
    GB_HTG3: AC010189 265962 AC010189 Homo sapiens clone RPCI11-296K13, *** SEQUENCING IN PROGRESS ***, 80 Homo sapiens 39,006 16-Sep-99
    unordered pieces.
    rxa01881 558 GB_HTG4: AC011117 148447 AC011117 Homo sapiens chromosome 4 clone 173_C_09 map 4, *** SEQUENCING IN Homo sapiens 39,130 14-OCT-1999
    PROGRESS ***, 10 ordered pieces.
    GB_HTG4: AC011117 148447 AC011117 Homo sapiens chromosome 4 clone 173_C_09 map 4, *** SEQUENCING IN Homo sapiens 39,130 14-OCT-1999
    PROGRESS ***, 10 ordered pieces.
    GB_BA1: MTCY2B12 20431 Z81011 Mycobacterium tuberculosis H37Rv complete genome; segment 61/162. Mycobacterium 37,893 18-Jun-98
    tuberculosis
    rxa01894 978 GB_BA1: MTCY274 39991 Z74024 Mycobacterium tuberculosis H37Rv complete genome; segment 126/162. Mycobacterium 37,229 19-Jun-98
    tuberculosis
    GB_IN1: CELF46H5 38886 U41543 Caenorhabditis elegans cosmid F46H5. Caenorhabditis elegans 38,525 29-Nov-96
    GB_HTG3: AC009204 115633 AC009204 Drosophila melanogaster chromosome 2 clone BACR03E19 (D1033) RPCI-98 Drosophila melanogaster 31,579 18-Aug-99
    03.E.19 map 36E-37C strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 94
    unordered pieces.
    rxa01897 666 GB_HTG1: CEY48B6 293827 AL021151 Caenorhabditis elegans chromosome II clone Y48B6, *** SEQUENCING IN Caenorhabditis elegans 34,703 1-Apr-99
    PROGRESS ***, in unordered pieces.
    GB_HTG1: CEY48B6 293827 AL021151 Caenorhabditis elegans chromosome II clone Y48B6, *** SEQUENCING IN Caenorhabditis elegans 34,703 1-Apr-99
    PROGRESS ***, in unordered pieces.
    GB_HTG1: CEY53F4_2 110000 Z92860 Caenorhabditis elegans chromosome II clone Y53F4, *** SEQUENCING IN Caenorhabditis elegans 33,333 15-Oct-99
    PROGRESS ***, in unordered pieces.
    rxa01946 1298 GB_BA1: MTV007 32806 AL021184 Mycobacterium tuberculosis H37Rv complete genome; segment 64/162. Mycobacterium 65,560 17-Jun-98
    tuberculosis
    GB_BA1: SC5F2A 40105 AL049587 Streptomyces coelicolor cosmid 5F2A. Streptomyces coelicolor 50,648 24-MAY-1999
    GB_BA1: SCARD1GN 2321 X84374 S. capreolus ard1 gene. Streptomyces capreolus 44,973 23-Aug-95
    rxa01980 756 GB_PL2: AC008262 99698 AC008262 Genomic sequence for Arabidopsis thaliana BAC F4N2 from chromosome I, Arabidopsis thaliana 35,310 21-Aug-99
    complete sequence.
    GB_PL1: AB013388 73428 AB013388 Arabidopsis thaliana genomic DNA, chromosome 5, TAC clone: K19E1, complete Arabidopsis thaliana 35,505 20-Nov-99
    sequence.
    GB_PL1: AB013388 73428 AB013388 Arabidopsis thaliana genomic DNA, chromosome 5, TAC clone: K19E1, complete Arabidopsis thaliana 39,973 20-Nov-99
    sequence.
    rxa01983 630 GB_HTG4: AC006467 175695 AC006467 Drosophila melanogaster chromosome 2 clone BACR03L08 (D532) RPCI-98 03.L.8 Drosophila melanogaster 36,672 27-OCT-1999
    map 40A-40C strain y; cn bw sp, *** SEQUENCING IN
    PROGRESS ***, 9 unordered pieces.
    GB_HTG4: AC006467 175695 AC006467 Drosophila melanogaster chromosome 2 clone BACR03L08 (D532) RPCI-98 03.L.8 Drosophila melanogaster 36,672 27-OCT-1999
    map 40A-40C strain y; cn bw sp, *** SEQUENCING IN
    PROGRESS ***, 9 unordered pieces.
    GB_HTG4: AC006467 175695 AC006467 Drosophila melanogaster chromosome 2 clone BACR03L08 (D532) RPCI-98 03.L.8 Drosophila melanogaster 32,367 27-OCT-1999
    map 40A-40C strain y; cn bw sp, *** SEQUENCING IN PROGRESSo ***, 9
    unordered pieces.
    rxa02020 1111 GB_BA1: CGDNAAROP 2612 X85965 C. glutamicum ORF3 and aroP gene. Corynebacterium 100,000 30-Nov-97
    glutamicum
    GB_PAT: A58887 1612 A58887 Sequence 1 from Patent WO9701637. unidentified 100,000 06-MAR-1998
    GB_BA1: STYCARABA 4378 M95047 Salmonella typhimurium transport protein, complete cds, and transfer RNA-Arg. Salmonella typhimurium 50,547 13-MAR-1996
    rxa02029 1437 GB_HTG2: AC003023 104768 AC003023 Homo sapiens chromosome 11 clone pDJ363p2, *** SEQUENCING IN PROGRESS Homo sapiens 35,820 21-OCT-1997
    ****, 22 unordered pieces.
    GB_HTG2: AC003023 104768 AC003023 Homo sapiens chromosome 11 clone pDJ363p2, *** SEQUENCING IN PROGRESS Homo sapiens 35,820 21-OCT-1997
    ***, 22 unordered pieces.
    GB_HTG2: HS118B18 104729 AL034344 Homo sapiens chromosome 6 clone RP1-118B18 map p24.1-25.3, *** Homo sapiens 34,355 03-DEC-1999
    SEQUENCING IN PROGRESS ***, in unordered pieces.
    rxa02030 1509 GB_PR4: AC007695 63247 AC007695 Homo sapiens 12q24 BAC RPCI11-124N23 (Roswell Park Cancer Institute Human Homo sapiens 38,681 1-Sep-99
    BAC Library) complete sequence.
    GB_PR4: AC006464 99908 AC006464 Homo sapiens BAC clone NH0436C12 from 2, complete sequence. Homo sapiens 35,445 22-OCT-1999
    GB_PR4: AC006464 99908 AC006464 Homo sapiens BAC clone NH0436C12 from 2, complete sequence. Homo sapiens 35,968 22-OCT-1999
    rxa02073 1653 GB_BA1: CGGDHA 2037 X72855 C. glutamicum GDHA gene. Corynebacterium 39,655 24-MAY-1993
    glutamicum
    GB_BA1: CGGDH 2037 X59404 Corynebacterium glutamicum, gdh gen for glutamate dehydrogenase. Corynebacterium 44,444 30-Jul-99
    glutamicum
    GB_BA2: SC2H4 25970 AL031514 Streptomyces coelicolor cosmid 2H4. Streptomyces coelicolor 38,452 19-OCT-1999
    A3(2)
    rxa02074
    rxa02095 1527 GB_EST18: AA703380 471 AA703380 zj12b06.s1 Soares_fetal_liver_spleen_1NFLS_S1 Home sapiens cDNA clone Home sapiens 36,518 24-DEC-1997
    IMAGE: 450035 3′ similar to contains LTR5.t3 LTR5 repetitive element:, mRNA
    sequence.
    GB_HTG6: AC009769 122911 AC009769 Homo sapiens chromosome 8 clone RP11-202I12 map 8, LOW-PASS SEQUENCE Homo sapiens 35,473 07-DEC-1999
    SAMPLING.
    GB_EST7: W70175 436 W70175 zd52c02.r1 Soares_fetal_heart_NbHH19W Homo sapiens cDNA clone Homo sapiens 34,174 16-OCT-1996
    IMAGE: 344258 5′ similar to contains LTR5.b2 LTR5 repetitive element;, mRNA
    sequence.
    rxa02099 373 GB_BA1: CAJ10319 5368 AJ010319 Corynebacterium glutamicum amtP, glnB, glnD genes and partial ftsY and srp genes. Corynebacterium 100,000 14-MAY-1999
    glutamicum
    GB_HTG3: AC011509 111353 AC011509 Homo sapiens chromosome 19 clone CITB-H1_2189E23, *** SEQUENCING IN Homo sapiens 33,423 07-OCT-1999
    PROGRESS ***, 35 unordered pieces.
    GB_HTG3: AC011509 111353 AC011509 Homo sapiens chromosome 19 clone CITB-H1_2189E23, *** SEQUENCING IN Homo sapiens 33,423 07-OCT-1999
    PROGRESS ***, 35 unordered pieces.
    rxa02115 1197 GB_HTG5: AC010126 175986 AC010126 Homo sapiens clone GS502B02, *** SEQUENCING IN PROGRESS ***, Homo sapiens 36,717 13-Nov-99
    3 unordered pieces.
    GB_HTG5: AC010126 175986 AC010126 Homo sapiens clone GS502B02, *** SEQUENCING IN PROGRESS ***, Homo sapiens 36,092 13-Nov-99
    3 unordered pieces.
    GB_PR1: HUMHM145 2214 D10925 Human mRNA for HM145. Homo sapiens 39,171 3-Feb-99
    rxa02128 1818 GB_BA1: MTCY190 34150 Z70283 Mycobacterium tuberculosis H37Rv complete genome; segment 98/162. Mycobacterium 38,682 17-Jun-98
    tuberculosis
    GB_BA1: MTCY190 34150 Z70283 Mycobacterium tuberculosis H37Rv complete genome; segment 98/162. Mycobacterium 35,746 17-Jun-98
    tuberculosis
    GB_GSS10: AQ161109 738 AQ161109 nbxb0006D03r CUGI Rice BAC Library Oryza sativa genomic clone nbxb0006D03r, Oryza sativa 38,482 12-Sep-98
    genomic survey sequence.
    rxa02133 329 GB_BA2: MPAE000058 28530 AE000058 Mycoplasma pneumoniae section 58 of 63 of the complete genome. Mycoplasma pneumoniae 32,317 18-Nov-96
    GB_HTG4: AC008308 151373 AC008308 Drosophila melanogaster chromosome 3 clone BACR10M16 (D743) RPCI-98 Drosophila melanogaster 34,579 20-OCT-1999
    10.M.16 map 93C-93D strain y; cn bw sp,
    *** SEQUENCING IN PROGRESS ***, 186 unordered pieces.
    GB_HTG4: AC008308 151373 AC008308 Drosophila melanogaster chromosome 3 clone BACR10M16 (D743) RPCI-98 Drosophila melanogaster 34,579 20-OCT-1999
    10.M.16 map 93C-93D strain y; cn bw sp,
    *** SEQUENCING IN PROGRESS ***, 186 unordered pieces.
    rxa02150 924 GB_EST37: AW012260 358 AW012260 um06e09.y1 Sugano mouse kidney mkia Mus musculus cDNA clone Mus musculus 39,385 10-Sep-99
    IMAGE: 2182312 5′ similar to SW: AMPL_BOVIN P00727 CYTOSOL
    AMINOPEPTIDASE;, mRNA sequence.
    GB_GSS3: B87734 389 B87734 RPCI11-30D24.TP RPCI-11 Homo sapiens genomic clone RPCI-11-30D24, genomic Homo sapiens 37,629 9-Apr-99
    survey sequence.
    GB_PR4: AC005042 192218 AC005042 Homo sapiens clone NH0552E01, complete sequence. Homo sapiens 36,901 14-Jan-99
    rxa02171 1776 GB_BA2: AF010496 189370 AF010496 Rhodobacter capsulatus strain SB1003, partial genome. Rhodobacter capsulatus 53,714 12-MAY-1998
    GB_EST24: AI170522 367 AI170522 EST216450 Normalized rat lung, Bento Soares Rattus sp. cDNA clone RLUCO75 3′ Rattus sp. 44,186 20-Jan-99
    end, mRNA sequence.
    GB_PL1: PHVDLECA 1441 K03288 P. vulgaris phytohemagglutinin gene encoding erythroagglutinating Phaseolus vulgaris 39,103 27-Apr-93
    phytohemagglutinin (PHA-E), complete cds.
    rxa02173 1575 GB_BA1: CGGLTG 3013 X66112 C. glutamicum glt gene for citrate synthase and ORF. Corynebacterium 44,118 17-Feb-95
    glutamicum
    GB_BA1: CGGLTG 3013 X66112 C. glutamicum glt gene for citrate synthase and ORF. Corynebacterium 36,189 17-Feb-95
    glutamicum
    GB_BA2: AE000104 10146 AE000104 Rhizobium sp. NGR234 plasmid pNGR234a, section 41 of 46 of the complete Rhizobium sp. NGR234 38,487 12-DEC-1997
    plasmid sequence.
    rxa02224 1920 GB_BA2: CXU21300 8990 U21300 Corynebacterium striatum hypothetical protein YbhB gene, partial cds; ABC Corynebacterium 37,264 9-Apr-99
    transporter TetB (tetB), ABC transporter TetA (tetA), transposase, 23S rRNA striatum
    methyltransferase, and transposase genes, complete cds; and unknown
    genes.
    GB_HTG3: AC009185 87184 AC009185 Homo sapiens chromosome 5 clone CIT-HSPC_248O19, *** SEQUENCING IN Homo sapiens 36,459 07-OCT-1999
    PROGRESS ***, 2 ordered pieces.
    GB_HTG3: AC009185 87184 AC009185 Homo sapiens chromosome 5 clone CIT-HSPC_248O19, *** SEQUENCING IN Homo sapiens 36,459 07-OCT-1999
    PROGRESS ***, 2 ordered pieces.
    rxa02225 905 GB_BA2: MPAE000058 28530 AE000058 Mycoplasma pneumoniae section 58 of 63 of the complete genome. Mycoplasma pneumoniae 35,498 18-Nov-96
    GB_EST26: AI337275 618 AI337275 tb96h11.x1 NCI_CGAP_Co16 Homo sapiens cDNA clone IMAGE: Homo sapiens 35,589 18-MAR-1999
    2062245 3′ similar to TR: Q15392 Q15392 ORF, COMPLETE CDS.;,
    mRNA sequence.
    GB_EST26: AI337275 618 AI337275 tb96h11.x1 NCI_CGAP_Co16 Homo sapiens cDNA clone IMAGE: Homo sapiens 42,786 18-MAR-1999
    2062245 3′ similar to TR: Q15392 Q15392 ORF, COMPLETE CDS.;,
    mRNA sequence.
    rxa02233 1410 GB_BA1: ERWPNLB 1291 M65057 Erwinia carotovora pectin lyase (pnl) gene, complete cds. Erwinia carotovora 37,780 26-Apr-93
    GB_EST30: AV021947 313 AV021947 AV021947 Mus musculus 18-day embryo C57BL/6J Mus musculus cDNA clone Mus musculus 39,423 28-Aug-99
    1190024M23, mRNA sequence.
    GB_EST33: AV087117 251 AV087117 AV087117 Mus musculus tongue C57BL/6J adult Mus musculus cDNA clone Mus musculus 47,410 25-Jun-99
    2310028C15, mRNA sequence.
    rxa02253 1050 GB_EST11: AA250210 532 AA250210 mx79g10.r1 Soares mouse NML Mus musculus cDNA clone IMAGE: 692610 5′ Mus musculus 36,136 12-MAR-1997
    similar to TR: E236517 E236517 F44G4.1;, mRNA sequence.
    GB_EST11: AA250210 532 AA250210 mx79g10.r1 Soares mouse NML Mus musculus cDNA clone IMAGE: 692610 5′ Mus musculus 36,202 12-MAR-1997
    similar to TR: E236517 E236517 F44G4.1;, mRNA sequence.
    rxa02261 1479 GB_BA1: CGL007732 4460 AJ007732 Corynebacterium glutamicum 3′ ppc gene, secG gene, amt gene, ocd gene and 5′ Corynebacterium 100,000 7-Jan-99
    soxA gene. glutamicum
    GB_BA1: CGAMTGENE 2028 X93513 C. glutamicum amt gene. Corynebacterium 100,000 29-MAY-1996
    glutamicum
    GB_BA1: CORPEPC 4885 M25819 C. glutamicum phosphoenolpyruvate carboxylase gene, complete cds. Corynebacterium 100,000 15-DEC-1995
    glutamicum
    rxa02268 1023 GB_PL2: AF087130 3478 AF087130 Neurospora crassa siderophore regulation protein (sre) gene, complete cds. Neurospora crassa 39,268 22-OCT-1998
    GB_EST30: AI663709 408 AI663709 ud47a06.y1 Soares mouse mammary gland NbMMG Mus musculus cDNA clone Mus musculus 41,523 10-MAY-1999
    IMAGE: 1449010 5′ similar to TR: O75585 O75585 MITOGEN- AND STRESS-
    ACTIVATED PROTEIN KINASE-2;, mRNA sequence.
    GB_RO: AF074714 3120 AF074714 Mus musculus mitogen- and stress-activated protein kinase-2 (mMSK2) mRNA, Mus musculus 38,347 24-OCT-1998
    complete cds.
    rxa02269 1095 GB_GSS4: AQ742825 847 AQ742825 HS_5482_B2_A04_T7A RPCI-11 Human Male BAC Library Homo sapiens Homo sapiens 37,703 16-Jul-99
    genomic clone Plate = 1058 Col = 8 Row = B, genomic survey sequence.
    GB_HTG3: AC009293 162944 AC009293 Homo sapiens chromosome 18 clone 53_I_06 map 18, *** SEQUENCING IN Homo sapiens 37,006 13-Aug-99
    PROGRESS ***, 15 unordered pieces.
    GB_HTG3: AC009293 162944 AC009293 Homo sapiens chromosome 18 clone 53_I_06 map 18, *** SEQUENCING IN Homo sapiens 37,006 13-Aug-99
    PROGRESS ***, 15 unordered pieces.
    rxa02309 1173 GB_BA1: MTY25D10 40838 Z95558 Mycobacterium tuberculosis H37Rv complete genome; segment 28/162. Mycobacterium 52,344 17-Jun-98
    tuberculosis
    GB_BA1: MSGY224 40051 AD000004 Mycobacterium tuberculosis sequence from clone y224. Mycobacterium 52,344 03-DEC-1996
    tuberculosis
    GB_HTG2: AC007163 186618 AC007163 Homo sapiens clone NH0091M05, *** SEQUENCING IN PROGRESS ***, 1 Homo sapiens 37,263 23-Apr-99
    unordered pieces.
    rxa02310 1386 GB_BA1: MTY25D10 40838 Z95558 Mycobacterium tuberculosis H37Rv complete genome; segment 28/162. Mycobacterium 36,861 17-Jun-98
    tuberculosis
    GB_BA1: MSGY224 40051 AD000004 Mycobacterium tuberculosis sequence from clone y224. Mycobacterium 36,861 03-DEC-1996
    tuberculosis
    GB_PR3: HS279N11 169998 Z98255 Human DNA sequence from PAC 279N11 on chromosome Xq11.2-13.3. Homo sapiens 34,516 23-Nov-99
    rxa02321 1752 GB_BA1: AB018531 4961 AB018531 Corynebacterium glutamicum dtsR1 and dtsR2 genes, complete cds. Corynebacterium 99,030 19-OCT-1998
    glutamicum
    GB_PAT: E17019 4961 E17019 Brevibacterium lactofermentum dtsR and dtsR2 genes. Corynebacterium 98,973 28-Jul-99
    glutamicum
    GB_BA1: AB018530 2855 AB018530 Corynebacterium glutamicum dtsR gene, complete cds. Corynebacterium 99,030 19-OCT-1998
    glutamicum
    rxa02335 1896 GB_BA1: CGU35023 3195 U35023 Corynebacterium glutamicum thiosulfate sulfurtransferase (thtR) gene, partial cds, Corynebacterium 99,947 16-Jan-97
    acyl CoA carboxylase (accBC) gene, complete cds. glutamicum
    GB_BA1: U00012 33312 U00012 Mycobacterium leprae cosmid B1308. Mycobacterium leprae 40,247 30-Jan-96
    GB_BA1: MTCY71 42729 Z92771 Mycobacterium tuberculosis H37Rv complete genome; segment 141/162. Mycobacterium 67,568 10-Feb-99
    tuberculosis
    rxa02364 750 GB_BA1: AP000006 319000 AP000006 Pyrococcus horikoshii OT3 genomic DNA, 1166001-1485000 nt. position (6/7). Pyrococcus horikoshii 36,130 8-Feb-99
    GB_BA1: AP000006 319000 AP000006 Pyrococcus horikoshii OT3 genomic DNA, 1166001-1485000 nt. position (6/7). Pyrococcus horikoshii 34,543 8-Feb-99
    rxa02372 2010 GB_HTG3: AC011461 100974 AC011461 Homo sapiens chromosome 19 clone CIT-HSPC_429L19, *** SEQUENCING IN Homo sapiens 36,138 07-OCT-1999
    PROGRESS ***, 4 ordered pieces.
    GB_HTG3: AC011461 100974 AC011461 Homo sapiens chromosome 19 clone CIT-HSPC_429L19, *** SEQUENCING IN Homo sapiens 36,138 07-OCT-1999
    PROGRESS ***, 4 ordered pieces.
    GB_EST21: AA992021 279 AA992021 ot36c01.s1 Soares_testis_NHT Homo sapiens cDNA clone IMAGE: 1618848 3′, Homo sapiens 41,219 3-Jun-98
    mRNA sequence.
    rxa02397 1119 GB_HTG4: AC009273 76175 AC009273 Arabidopsis thaliana chromosome 1 clone T1N6, *** SEQUENCING IN PROGRESS Arabidopsis thaliana 38,566 12-OCT-1999
    ***, 2 ordered pieces.
    GB_HTG4: AC009273 76175 AC009273 Arabidopsis thaliana chromosome 1 clone T1N6, *** SEQUENCING IN PROGRESS Arabidopsis thaliana 38,566 12-OCT-1999
    ***, 2 ordered pieces.
    GB_BA1: D90826 19493 D90826 E. coli genomic DNA, Kohara clone #335(40.9-41.3 min.). Escherichia coli 39,600 21-MAR-1997
    rxa02424 723 GB_EST13: AA334108 275 AA334108 EST38262 Embryo, 9 week Homo sapiens cDNA 5′ end, mRNA sequence. Homo sapiens 38,603 21-Apr-97
    GB_PR3: AC005224 166687 AC005224 Homo sapiens chromosome 17, clone hRPK.214_O_1, complete sequence. Homo sapiens 36,111 14-Aug-98
    GB_PR3: AC005224 166687 AC005224 Homo sapiens chromosome 17, clone hRPK.214_O_1, complete sequence. Homo sapiens 33,427 14-Aug-98
    rxa02426 1656 GB_PAT: A06664 1350 A06664 B. stearothermophilus lct gene. Bacillus 39,936 29-Jul-93
    stearothermophilus
    GB_PAT: A04115 1361 A04115 B. stearothermophilus recombinant lct gene. synthetic construct 40,042 17-Feb-97
    GB_BA1: BACLDHL 1361 M14788 B. stearothermophilus lct gene encoding L-lactate dehydrogenase, complete cds. Bacillus 40,338 26-Apr-93
    stearothermophilus
    rxa02487 1827 GB_BA2: AF007101 32870 AF007101 Streptomyces hygroscopicus putative pteridine-dependent dioxygenase, PKS Streptomyces 43,298 13-Jan-98
    modules 1, 2, 3 and 4, and putative regulatory protein genes, complete cds and hygroscopicus
    putative hydroxylase gene, partial cds.
    GB_BA1: MTCI364 29540 Z93777 Mycobacterium tuberculosis H37Rv complete genome; segment 52/162. Mycobacterium 44,352 17-Jun-98
    tuberculosis
    GB_BA2: AF119621 15986 AF119621 Pseudomonas abietaniphila BKME-9 Ditl (ditl), dioxygenase DitA oxygenase Pseudomonas 43,611 28-Apr-99
    component small subunit (ditA2), dioxygenase DitA oxygenase component large abietaniphila
    subunit (ditA1), DitH (ditH), DitG (ditG), DitF (ditF), DitR (ditR), DitE (ditE), DitD
    (ditD), aromatic diterpenoid extradiol ring-cleavage dioygenase (ditC), DitB (ditB),
    and dioxygenase DitA ferredoxin component (ditA3) genes, complete cds; and
    unknown genes.
    rxa02511 780 GB_PR4: AC002470 235395 AC002470 Homo sapiens Chromosome 22q11.2 BAC Clone b135h6 in BCRL2-GGT Region, Homo sapiens 37,971 30-Nov-99
    complete sequence.
    GB_PR4: AC002472 147100 AC002472 Homo sapiens Chromosome 22q11.2 PAC Clone p_n5 in BCRL2-GGT Region, Homo sapiens 38,239 13-Sep-99
    complete sequence.
    GB_EST34: AI806938 118 AI806938 wf24b07.x1 Soares_NFL_T_GBC_S1 Homo sapiens cDNA clone IMAGE: Homo sapiens 38,983 7-Jul-99
    2356501 3′ similar to SW: PLZF_HUMAN Q05516 ZINC FINGER PROTEIN
    PLZF;, mRNA sequence.
    rxa02512 1086 GB_BA1: MTCY1A10 25949 Z95387 Mycobacterium tuberculosis H37Rv complete genome; segment 117/162. Mycobacterium 37,407 17-Jun-98
    tuberculosis
    GB_BA1: MLCL581 36225 Z96801 Mycobacterium leprae cosmid L581. Mycobacterium leprae 43,193 24-Jun-97
    GB_OV: GGU43396 2738 U43396 Gallus gallus tropomyosin receptor kinase A (ctrkA) mRNA, complete cds. Gallus gallus 38,789 18-Jan-96
    rxa02527 1452 GB_BA2: AF008220 220060 AF008220 Bacillus subtilis rrnB-dnaB genomic region. Bacillus subtilis 37,395 4-Feb-98
    GB_BA2: AF008220 220060 AF008220 Bacillus subtilis rrnB-dnaB genomic region. Bacillus subtilis 36,218 4-Feb-98
    GB_HTG2: AC005861 112369 AC005861 Arabidopsis thaliana clone F23B24, *** SEQUENCING IN PROGRESS ***, 6 Arabidopsis thaliana 38,407 29-Apr-99
    unordered pieces.
    rxa02547 2262 GB_PL1: AB006530 7344 AB006530 Citrullus lanatus Sat gene for serine acetyltransferase, complete cds and 5′-flanking Citrullus lanatus 35,449 20-Aug-97
    region.
    GB_PL1: CNASA 5729 D85624 Citrullus vulgaris serine acetyltransferase (Sat) DNA, complete cds. Citrullus lanatus 35,449 6-Feb-99
    GB_PL1: AB006530 7344 AB006530 Citrullus lanatus Sat gene for serine acetyltransferase, complete cds and 5′-flanking Citrullus lanatus 34,646 20-Aug-97
    region.
    rxa02566 1332 GB_EST32: AI727189 619 AI727189 BNLGHI7498 Six-day Cotton fiber Gossypium hirsutum cDNA 5′ similar to Gossypium hirsutum 35,099 11-Jun-99
    (AB020715) KIAA0908 protein [Homo sapiens], mRNA sequence.
    GB_BA1: CGPUTP 3791 Y09163 C. glutamicum putP gene. Corynebacterium 38,562 8-Sep-97
    glutamicum
    GB_PL2: SPAC13G6 33481 Z54308 S. pombe chromosome I cosmid c13G6. Schizosaccharomyces 35,774 18-OCT-1999
    pombe
    rxa02571 1152 GB_BA1: CGU43535 2531 U43535 Corynebacterium glutamicum multidrug resistance protein (cmr) gene, complete cds. Corynebacterium 41,872 9-Apr-97
    glutamicum
    GB_EST35: AI857385 488 AI857385 wl55e03.x1 NCI_CGAP_Brn25 Homo sapiens cDNA clone IMAGE: 2428828 3′, Homo sapiens 39,139 26-Aug-99
    mRNA sequence.
    GB_BA1: CGU43535 2531 U43535 Corynebacterium glutamicum multidrug resistance protein (cmr) gene, complete cds. Corynebacterium 38,552 9-Apr-97
    glutamicum
    rxa02578 1227 GB_PL1: AB016871 79109 AB016871 Arabldopsis thaliana genomic DNA, chromosome 5, TAC clone: K16L22, complete Arabidopsis thaliana 34,213 20-Nov-99
    sequence.
    GB_PL1: AB025602 55790 AB025602 Arabidopsis thaliana genomic DNA, chromosome 5, BAC clone: F14A1, complete Arabidopsis thaliana 36,461 20-Nov-99
    sequence.
    GB_IN1: CELF36H9 35985 AF016668 Caenorhabditis elegans cosmid F36H9. Caenorhabditis elegans 35,977 8-Aug-97
    rxa02581 1983 GB_BA1: MTV005 37840 AL010186 Mycobacterium tuberculosis H37Rv complete genome; segment 51/162. Mycobacterium 38,517 17-Jun-98
    tuberculosis
    GB_BA1: MTV005 37840 AL010186 Mycobacterium tuberculosis H37Rv complete genome; segment 51/162. Mycobacterium 39,173 17-Jun-98
    tuberculosis
    rxa02582 4953 GB_BA1: MTV026 23740 AL022076 Mycobacterium tuberculosis H37Rv complete genome; segment 157/162. Mycobacterium 38,548 24-Jun-99
    tuberculosis
    GB_BA1: MTCY338 29372 Z74697 Mycobacterium tuberculosis H37Rv complete genome; segment 127/162. Mycobacterium 46,263 17-Jun-98
    tuberculosis
    GB_BA1: SEERYABS 20444 X62569 S. erythraea eryA gene for 6-deoxyerythronolyde B synthase II & III. Saccharopolyspora 45,053 28-Feb-92
    erythraea
    rxa02583 1671 GB_BA2: AF113605 1593 AF113605 Streptomyces coelicolor proplonyl-CoA carboxylase complex B subunit (pccB) gene, Streptomyces coelicolor 58,397 08-DEC-1999
    complete cds.
    GB_BA1: SC1C2 42210 AL031124 Streptomyces coelicolor cosmid 1C2. Streptomyces coelicolor 52.916 15-Jan-99
    GB_BA1: AB018531 4961 AB018531 Corynebacterium glutamicum dtsR1 and dtsR2 genes, complete cds. Corynebacterium 58,809 19-OCT-1998
    glutamicum
    rxa02599 600 GB_BA1: AEMML 2585 X99639 Ralstonia eutropha mmlH, mmlI & mmlJ genes. Ralstonia eutropha 35,264 22-Jan-98
    GB_EST15: AA508926 422 AA508926 MBAFCW1C08T3 Brugia malayi adult female cDNA (SAW96MLW-BmAF) Brugia Brugia malayi 43,377 8-Jul-97
    malayi cDNA clone AFCW1C08 5′, mRNA sequence.
    GB_BA1: AEMML 2585 X99639 Ralstonia eutropha mmlH, mmlI & mmlJ genes. Ralstonia eutropha 41,148 22-Jan-98
    rxa02634 1734 GB_BA1: SYNPOO 1964 X17439 Synechocystis ndhC, psbG genes for NDH-C, PSII-G and ORF157. Synechocystis PCC6803 38,145 10-Feb-99
    GB_GSS9: AQ101527 184 AQ101527 HS_2265_A1_E11_MF CIT Approved Human Genomic Sperm Library D Homo Homo sapiens 38,798 27-Aug-98
    sapiens genomic clone Plate = 2265 Col = 21 Row = l, genomic survey sequence.
    GB_IN1: MNE133341 399 AJ133341 Melarhaphe neritoides partial caM gene, exons 1-2. Melarhaphe neritoides 39,098 2-Jun-99
    rxa02638 999 GB_BA2 AE001756 10938 AE001756 Thermotoga maritima section 68 of 136 of the complete genome. Thermotoga maritima 40,104 2-Jun-99
    GB_GSS12: AQ423878 689 AQ423878 CITBI-E1-2575E20.TF CITBI-E1 Homo sapiens genomic clone 2575E20, genomic Homo sapiens 36,451 23-MAR-1999
    survey sequence.
    GB_HTG2: AC006765 274498 AC006765 Caenorhabditis elegans clone Y43H11, *** SEQUENCING IN PROGRESS***, 7 Caenorhabditis elegans 39,072 23-Feb-99
    unordered pieces.
    rxa02659 335 GB_EST36: AI900317 436 AI900317 sc04a02.y1 Gm-c1012 Glycine max cDNA clone GENOME SYSTEMS CLONE Glycine max 41,566 06-DEC-1999
    ID: Gm-c1012-1155 5′ similar to SW: PRS6_SOLTU P54778 26S PROTEASE
    REGULATORY SUBUNIT 6B HOMOLOG.;, mRNA sequence.
    GB_GSS12: AQ342831 683 AQ342831 RPCI11-122K17.TJ RPCI-11 Homo sapiens genomic clone RPCI-11-122K17, Homo sapiens 34,762 07-MAY-1999
    genomic survey sequence.
    GB_EST36: AI900856 779 AI900856 sb95c11.y1 Gm-c1012 Glycine max cDNA clone GENOME SYSTEMS CLONE ID: Glycine max 39,063 06-DEC-1999
    Gm-c1012-429 5′ similar to SW: PRS6_SOLTU P54778 26S PROTEASE
    REGULATORY SUBUNIT 6B HOMOLOG.;, mRNA sequence.
    rxa02676 1512 GB_IN2: CELB0213 39134 AF039050 Caenorhabditis elegans cosmid B0213. Caenorhabditis elegans 35,814 2-Jun-99
    GB_GSS1: CNS00PZB 364 AL085157 Arabidopsis thaliana genome survey sequence SP6 end of BAC F10D11 of IGF Arabidopsis thaliana 38,462 28-Jun-99
    library from strain Columbia of Arabidopsis thaliana, genomic survey sequence.
    GB_RO: RNITPR2R 10708 X61677 Rat ITPR2 gene for type 2 inositol triphosphate receptor. Rattus norvegicus 37,543 21-OCT-1991
    rxa02677 882 GB_RO: D89728 5002 D89728 Mus musculus mRNA for LOK, complete cds. Mus musculus 38,829 7-Feb-99
    GB_GSS8: AQ062004 362 AQ062004 CIT-HSP-2346O14, TR CIT-HSP Homo sapiens genomic clone 2346O14, genomic Homo sapiens 36,565 31-Jul-98
    survey sequence.
    GB_GSS14: AQ555818 462 AQ555818 HS_5230_B1_G06_SP6E RPCI-11 Human Male BAC Library Homo sapiens Homo sapiens 36,534 29-MAY-1999
    genomic clone Plate = 806 Col = 11 Row = N, genomic survey sequence.
    rxa02691 930 GB_IN1: DME9736 7411 AJ009736 Drosophila melanogaster idefix retroelement: gag, pol and env genes, partial. Drosophila melanogaster 36,522 19-Jan-99
    GB_PR4: AC004801 193561 AC004801 Homo sapiens 12q13.1 PAC RPCI1-228P16 (Roswell Park Cancer Institute Human Homo sapiens 39,341 2-Feb-99
    PAC Library) complete sequence.
    GB_PR4: AC004801 193561 AC004801 Homo sapiens 12q13.1 PAC RPCI1-228P16 (Roswell Park Cancer Institute Human Homo sapiens 37,037 2-Feb-99
    PAC Library) complete sequence.
    rxa02718 1170 GB_EST34: AV132028 258 AV132028 AV132028 Mus musculus C57BL/6J 11-day embryo Mus musculus cDNA clone Mus musculus 43,529 1-Jul-99
    2700087F01, mRNA sequence.
    GB_GSS10: AQ240654 452 AQ240654 CIT-HSP-2385D24.TFB.1 CIT-HSP Homo sapiens genomic clone 2385D24, genomic Homo sapiens 40,044 30-Sep-98
    survey sequence.
    GB_GSS11: AQ309500 576 AQ309500 CIT-HSP-2384D24.TFD CIT-HSP Homo sapiens genomic clone 2384D24, genomic Homo sapiens 38,869 22-DEC-1998
    survey sequence.
    rxa02749 999 GB_BA2: AF086791 37867 AF086791 Zymomonas mobilis strain ZM4 clone 67E10 carbamoylphosphate synthetase small Zymomonas mobilis 39,024 4-Nov-98
    subunit (carA), carbamoylphosphate synthetase large subunit (carB), transcription
    elongation factor (greA), enolase (eno), pyruvate dehydrogenase alpha
    subunit (pdhA), pyruvate dehydrogenase beta subunit (pdhB), ribonuclease H (mh),
    homoserine kinase homolog, alcohol dehydrogenase II (adhB), and
    excinuclease ABC subunit A (uvrA) genes, complete cds; and unknown genes.
    GB_BA1: SYCSLRB 146271 D64000 Synechocystis sp. PCC6803 complete genome, 19/27, 2392729-2538999. Synechocystis sp. 34,573 13-Feb-99
    GB_BA2: AE001306 13316 AE001306 Chlamydia trachomatis section 33 of 87 of the complete genome. Chlamydia trachomatis 38,940 2-Sep-98
    rxa02767 906 GB_BA2: AF126953 1638 AF126953 Corynebacterium glutamicum cystathionine gamma-synthase (metB) gene, complete Corynebacterium 100,000 10-Sep-99
    cds. glutamicum
    GB_BA1: SCI5 6661 AL079332 Streptomyces coelicolor cosmid I5. Streptomyces coelicolor 37,486 16-Jun-99
    GB_PR3: HS90L6 190837 Z97353 Human DNA sequence from clone 90L6 on chromosome 22q11.21-11.23. Contains Homo sapiens 34,149 23-Nov-99
    an RPL15 (60S Ribosomal Protein L15) pseudogene, ESTs, STSs and GSSs,
    complete sequence.
    rxa02792 876 GB_BA2: AF099015 5000 AF099015 Streptomyces coelicolor strain A3(2) integrase (int), Fe-containing superoxide Streptomyces coelicolor 36,721 1-Jun-99
    dismutase II (sodF2), Fe uptake system permease (ftrE), and Fe uptake system
    integral membrane protein (ftrD) genes, complete cds.
    GB_BA1: ECOUW93 338534 U14003 Escherichia coli K-12 chromosomal region from 92.8 to 00.1 minutes. Escherichia coli 38,787 17-Apr-96
    GB_HTG3: AC011361 186148 AC011361 Homo sapiens chromosome 5 clone CIT-HSPC_482N19, *** SEQUENCING IN Homo sapiens 43,577 06-OCT-1999
    PROGRESS ***, 69 unordered pieces.
    rxa02794 1197 GB_PR4: AC005998 96556 AC005998 Homo sapiens clone DJ0622E21, complete sequence. Homo sapiens 37,298 29-Jul-99
    GB_PR4: AC006008 57554 AC006008 Homo sapiens clone DJ0820A21, complete sequence. Homo sapiens 36,638 17-Jun-99
    GB_PR3: HSDJ73H14 95556 AL080272 Human DNA sequence from clone 73H14 on chromosome Xq26.3-28, complete Homo sapiens 39,726 23-Nov-99
    sequence.
    rxa02809 375 GB_RO: MUSSPCTLT 3172 M22527 Mouse cytotoxic T lymphocyte-specific serine protease CCPII gene, complete cds. Mus musculus 47,518 19-Jan-96
    GB_RO: MUSGRC 894 M18459 Mouse granzyme C serine esterase mRNA, complete cds. Mus musculus 44,939 12-Jun-93
    GB_RO: RNU57062 880 U57062 Rattus norvegicus natural killer cell protease 4 (RNKP-4) mRNA, complete cds. Rattus norvegicus 41,554 31-Jul-96
    rxa02811 484 GB_GSS6: AQ832862 476 AQ832862 HS_5261_A2_E10_SP6E RPCI-11 Human Male BAC Library Homo sapiens Homo sapiens 35,610 27-Aug-99
    genomic clone Plate = 837 Col = 20 Row = I, genomic survey sequence.
    GB_GSS5: AQ784593 515 AQ784593 HS_3248_A2_F02_T7C CIT Approved Human Genomic Sperm Library D Homo Homo sapiens 38,956 3-Aug-99
    sapiens genomic clone Plate = 3248 Col = 4 Row = K, genomic survey sequence.
    GB_GSS13: AQ473140 397 AQ473140 CITBI-E1-2589G6.TF CITBI-E1 Homo sapiens genomic clone 2589G6, genomic Homo sapiens 34,761 23-Apr-99
    survey sequence.
    rxa02836 678 GB_EST18: AA696785 316 AA696785 GM08392.5prime GM Drosophila melanogaster ovary BlueScript Drosophila Drosophila melanogaster 40,604 28-Nov-98
    melanogaster cDNA clone GM08392 5prime, mRNA sequence.
    GB_EST18: AA696785 316 AA696785 GM08392.5prime GM Drosophila melanogaster ovary BlueScript Drosophila Drosophila melanogaster 38,281 28-Nov-98
    melanogaster cDNA clone GM08392 5prime, mRNA sequence.
    rxs03212 1452 GB_BA1: CGBETPGEN 2339 X93514 C. glutamicum betP gene. Corynebacterium 99,931 8-Sep-97
    glutamicum
    GB_BA1: SC5F2A 40105 AL049587 Streptomyces coelicolor cosmid 5F2A. Streptomyces coelicolor 57,557 24-MAY-1999
    A3(2)
    GB_BA2: AF008220 220060 AF008220 Bacillus subtilis rrnB-dnaB genomic region. Bacillus subtilis 40,000 4-Feb-98
    rxs03220 725 GB_PL1: CKHUP2 2353 X66855 C. kessleri HUP2 mRNA. Chlorella kessleri 45,328 17-Feb-97
    GB_EST38: AW048153 383 AW048153 UI-M-BH1-alq-h-05-0-UI.s1 NIH_BMAP_M_S2 Mus musculus cDNA Mus musculus 41,758 18-Sep-99
    clone UI-M-BH1-alq-h-05-0-UI 3′, mRNA sequence.
    GB_PL1: CKHUP2 2353 X66855 C. kessleri HUP2 mRNA. Chlorella kessleri 38,106 17-Feb-97

Claims (20)

1. An isolated nucleic acid molecule selected from the group consisting of
a) an isolated nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:77, or a complement thereof;
b) an isolated nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence of SEQ ID NO:78, or a complement thereof;
c) an isolated nucleic acid molecule which encodes a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NO:78, or a complement thereof;
d) an isolated nucleic acid molecule comprising a nucleotide sequence which is at least 50% identical to the entire nucleotide sequence of SEQ ID NO:77, or a complement thereof; and
e) an isolated nucleic acid molecule comprising a fragment of at least 15 contiguous nucleotides of the nucleotide sequence of SEQ ID NO:77, or a complement thereof.
2. An isolated nucleic acid molecule comprising the nucleic acid molecule of claim 1 and a nucleotide sequence encoding a heterologous polypeptide.
3. A vector comprising the nucleic acid molecule of claim 1.
4. The vector of claim 3, which is an expression vector.
5. A host cell transfected with the expression vector of claim 4.
6. The host cell of claim 5, wherein said cell is a microorganism.
7. The host cell of claim 6, wherein said cell-belongs to the genus Corynebacterium or Brevibacterium.
8. A method of producing a polypeptide comprising culturing the host cell of claim 5 in an appropriate culture medium to, thereby, produce the polypeptide.
9. A method for producing a fine chemical, comprising culturing the cell of claim 5 such that the fine chemical is produced.
10. The method of claim 9, wherein said method further comprises the step of recovering the fine chemical from said culture.
11. The method of claim 9, wherein said cell belongs to the genus Corynebacterium or Brevibacterium.
12. The method of claim 9, wherein said cell is selected from the group consisting of Corynebacterium glutamicum, Corynebacterium herculis, Corynebacterium, lilium, Corynebacterium acetoacidophilum, Corynebacterium acetoglutamicum, Corynebacterium acetophilum, Corynebacterium ammoniagenes, Corynebacterium fujiokense, Corynebacterium nitrilophilus, Brevibacterium ammoniagenes, Brevibacterium butanicum, Brevibacterium divaricatum, Brevibacterium flavum, Brevibacterium healii, Brevibacterium ketoglutamicum, Brevibacterium ketosoreductum, Brevibacterium lactofermentum, Brevibacterium linens, Brevibacterium paraffinolyticum, and those strains set forth in Table 3.
13. The method of claim 9, wherein expression of the nucleic acid molecule from said vector results in modulation of production of said fine chemical.
14. The method of claim 9, wherein said fine chemical is selected from the group consisting of organic acids, proteinogenic and nonproteinogenic amino acids, purine and pyrimidine bases, nucleosides, nucleotides, lipids, saturated and unsaturated fatty acids, diols, carbohydrates, aromatic compounds, vitamins, cofactors, polyketides, and enzymes.
15. The method of claim 9, wherein said fine chemical is an amino acid selected from the group consisting of lysine, glutamate, glutamine, alanine, aspartate, glycine, serine, threonine, methionine, cysteine, valine, leucine, isoleucine, arginine, proline, histidine, tyrosine, phenylalanine, and tryptophan.
16. An isolated polypeptide selected from the group consisting of
a) an isolated polypeptide comprising the amino acid sequence of SEQ ID NO:78;
b) an isolated polypeptide comprising a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NO:78;
c) an isolated polypeptide which is encoded by a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:77;
d) an isolated polypeptide which is encoded by a nucleic acid molecule comprising a nucleotide sequence which is at least 50% identical to the entire nucleotide sequence of SEQ ID NO:77;
e) an isolated polypeptide comprising an amino acid sequence which is at least 50% identical to the entire amino acid sequence of SEQ ID NO:78; and
f) an isolated polypeptide comprising a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NO:78, wherein said polypeptide fragment maintains a biological activity of the polypeptide comprising the amino sequence.
17. The isolated polypeptide of claim 16, further comprising heterologous amino acid sequences.
18. A method for diagnosing the presence or activity of Corynebacterium diphtheriae in a subject, comprising detecting the presence of at least one of the nucleic acid molecules of claim 1, thereby diagnosing the presence or activity of Corynebacterium diphtheriae in the subject.
19. A method for diagnosing the presence or activity of Corynebacterium diphtheriae in a subject, comprising detecting the presence of at least one of the polypeptide molecules of claim 16, thereby diagnosing the presence or activity of Corynebacterium diphtheriae in the subject.
20. A host cell comprising a nucleic acid molecule selected from the group consisting of
a) the nucleic acid molecule of SEQ ID NO:77, wherein the nucleic acid molecule is disrupted by at least one technique selected from the group consisting of a point mutation, a truncation, an inversion, a deletion, an addition, a substitution and homologous recombination;
b) the nucleic acid molecule of SEQ ID NO:77, wherein the nucleic acid molecule comprises one or more nucleic acid modifications as compared to the sequence of SEQ ID NO:77, wherein the modification is selected from the group consisting of a point mutation, a truncation, an inversion, a deletion, an addition and a substitution; and
c) the nucleic acid molecule of SEQ ID NO:77, wherein the regulatory region of the nucleic acid molecule is modified relative to the wild-type regulatory region of the molecule by at least one technique selected from the group consisting of a point mutation, a truncation, an inversion, a deletion, an addition, a substitution and homologous recombination.
US11/507,094 1999-06-25 2006-08-18 Corynebacterium glutamicum genes encoding proteins involved in membrane synthesis and membrane transport Abandoned US20070111230A1 (en)

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