US20070111232A1

US20070111232A1 - Corynebacterium glutamicum genes encoding proteins involved in homeostasis and adaptation

Info

Publication number: US20070111232A1
Application number: US11/512,384
Authority: US
Inventors: Markus Pompejus; Burkhard Kroger; Hartwig Schroder; Oskar Zelder; Gregor Haberhauer
Original assignee: BASF SE
Current assignee: BASF SE
Priority date: 1999-06-25
Filing date: 2006-08-29
Publication date: 2007-05-17
Also published as: US6831165B1; US20050277115A1

Abstract

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

Description

RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No. 10/454,437, filed Jun. 4, 2003 which is a continuation of U.S. application Ser. No. 09/602,777, filed Jun. 23, 2000, now U.S. Pat. No. 6,831,165, issued Dec. 14, 2004, which claims priority to prior filed U.S. Provisional Patent Application Ser. No. 60/141,031, filed Jun. 25, 1999. This application also claims priority to prior filed German Patent Application No. 19931636.8, filed Jul. 8, 1999, German Patent Application No. 19932125.6, filed Jul. 9, 1999, German Patent Application No. 19932126.4, filed Jul. 9, 1999, German Patent Application No. 19932127.2, filed Jul. 9, 1999, German Patent Application No. 19932128.0, filed Jul. 9, 1999, German Patent Application No. 19932129.9, filed Jul. 9, 1999, German Patent Application No. 19932226.0, filed Jul. 9, 1999, German Patent Application No. 19932920.6, filed Jul. 14, 1999, German Patent Application No. 19932922.2, filed Jul. 14, 1999, German Patent Application No. 19932924.9, filed Jul. 14, 1999, German Patent Application No. 19932928.1, filed Jul. 14, 1999, German Patent Application No. 19932930.3, filed Jul. 14, 1999, German Patent Application No. 19932933.8, filed Jul. 14, 1999, German Patent Application No. 19932935.4, filed Jul. 14, 1999, German Patent Application No. 19932973.7, filed Jul. 14, 1999, German Patent Application No. 19933002.6, filed Jul. 14, 1999, German Patent Application No. 19933003.4, 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. 19941378.9, filed Aug. 31, 1999, German Patent Application No. 19941379.7, filed Aug. 31, 1999, German Patent Application No. 19941390.8, filed Aug. 31, 1999, German Patent Application No. 19941391.6, filed Aug. 31, 1999, and German Patent Application No. 19942088.2, filed Sep. 3, 1999. The entire contents of each of the aforementioned 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 “seqlistcorrected” (1.45 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” (430 KB) and “Appendix B” (151 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 homeostasis and adaptation (HA) 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 HA 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 HA nucleic acids of the invention, or modification of the sequence of the HA 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 HA 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 HA 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. The HA proteins encoded by the novel nucleic acid molecules of the invention are capable of, for example, performing a function involved in the maintenance of homeostasis in C. glutamicum, or in the ability of this microorganism to adapt to different environmental conditions. 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 HA 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. For example, by engineering enzymes which modify or degrade aromatic or aliphatic compounds such that these enzymes are increased or decreased in activity or number, it may be possible to modulate the production of one or more fine chemicals which are the modification or degradation products of these compounds. Similarly, enzymes involved in the metabolism of inorganic compounds provide key molecules (e.g. phosphorous, sulfur, and nitrogen molecules) for the biosynthesis of such fine chemicals as amino acids, vitamins, and nucleic acids. By altering the activity or number of these enzymes in C. glutamicum, it may be possible to increase the conversion of these inorganic compounds (or to use alternate inorganic compounds) to thus permit improved rates of incorporation of inorganic atoms into these fine chemicals. Genetic engineering of C. glutamicum enzymes involved in general cellular processes may also directly improve fine chemical production, since many of these enzymes directly modify fine chemicals (e.g., amino acids) or the enzymes which are involved in fine chemical synthesis or secretion. Modulation of the activity or number of cellular proteases may also have a direct effect on fine chemical production, since many proteases may degrade fine chemicals or enzymes involved in fine chemical production or breakdown.
Further, the aforementioned enzymes which participate in aromatic/aliphatic compound modification or degradation, general biocatalysis, inorganic compound metabolism or proteolysis are each themselves fine chemicals, desirable for their activity in various in vitro industrial applications. By altering the number of copies of the gene for one or more of these enzymes in C. glutamicum it may be possible to increase the number of these proteins produced by the cell, thereby increasing the potential yield or efficiency of production of these proteins from large-scale C. glutamicum or related bacterial cultures.
The alteration of an HA protein of the invention may also indirectly affect the yield, production, and/or efficiency of production of a fine chemical from a C. glutamicum strain incorporating such an altered protein. For example, by modulating the activity and/or number of those proteins involved in the construction or rearrangement of the cell wall, it may be possible to modify the structure of the cell wall itself such that the cell is able to better withstand the mechanical and other stresses present during large-scale fermentative culture. Also, large-scale growth of C. glutamicum requires significant cell wall production. Modulation of the activity or number of cell wall biosynthetic or degradative enzymes may allow more rapid rates of cell wall biosynthesis, which in turn may permit increased growth rates of this microorganism in culture and thereby increase the number of cells producing the desired fine chemical.
By modifying the HA enzymes of the invention, one may also indirectly impact the yield, production, or efficiency of production of one or more fine chemicals from C. glutamicum. For example, many of the general enzymes in C. glutamicum may have a significant impact on global cellular processes (e.g., regulatory processes) which in turn have a significant effect on fine chemical metabolism. Similarly, proteases, enzymes which modify or degrade possibly toxic aromatic or aliphatic compounds, and enzymes which promote the metabolism of inorganic compounds all serve to increase the viability of C. glutamicum. The proteases aid in the selective removal of misfolded or misregulated proteins, such as those that might occur under the relatively stressful environmental conditions encountered during large-scale fermentor culture. By altering these proteins, it may be possible to further enhance this activity and to improve the viability of C. glutamicum in culture. The aromatic/aliphatic modification or degradation proteins not only serve to detoxify these waste compounds (which may be encountered as impurities in culture medium or as waste products from cells themselves), but also to permit the cells to utilize alternate carbon sources if the optimal carbon source is limiting in the culture. By increasing their number and/or activity, the survival of C. glutamicum cells in culture may be enhanced. The inorganic metabolism proteins of the invention supply the cell with inorganic molecules required for all protein and nucleotide (among others) synthesis, and thus are critical for the overall viability of the cell. An increase in the number of viable cells producing one or more desired fine chemicals in large-scale culture should result in a concomitant increase in the yield, production, and/or efficiency of production of the fine chemical in the culture.
The invention provides novel nucleic acid molecules which encode proteins, referred to herein as HA proteins, which are capable of, for example, performing a function involved in the maintenance of homeostasis in C. glutamicum, or of participating in the ability of this microorganism to adapt to different environmental conditions. Nucleic acid molecules encoding an HA protein are referred to herein as HA nucleic acid molecules. In a preferred embodiment, an HA protein participates in C. glutamicum cell wall biosynthesis or rearrangements, metabolism of inorganic compounds, modification or degradation of aromatic or aliphatic compounds, or possesses a C. glutamicum enzymatic or proteolytic activity. 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 HA protein or biologically active portions thereof, as well as nucleic acid fragments suitable as primers or hybridization probes for the detection or amplification of HA-encoding nucleic acids (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 HA proteins of the present invention also preferably possess at least one of the HA 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 HA activity. Preferably, the protein or portion thereof encoded by the nucleic acid molecule maintains the ability to participate in the maintenance of homeostasis in C. glutamicum, or to perform a function involved in the adaptation of this microorganism to different environmental conditions. 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 HA 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 repair or recombination of DNA, in the transposition of genetic material, in gene expression (i.e., the processes of transcription or translation), in protein folding, or in protein secretion in Corynebacterium glutamicum, 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 HA 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 HA protein by culturing the host cell in a suitable medium. The HA 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 HA 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 HA sequence as a transgene. In another embodiment, an endogenous HA gene within the genome of the microorganism has been altered, e.g., functionally disrupted, by homologous recombination with an altered HA gene. In another embodiment, an endogenous or introduced HA gene in a microorganism has been altered by one or more point mutations, deletions, or inversions, but still encodes a functional HA protein. In still another embodiment, one or more of the regulatory regions (e.g., a promoter, repressor, or inducer) of an HA gene in a microorganism has been altered (e.g., by deletion, truncation, inversion, or point mutation) such that the expression of the HA 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 HA protein or a portion, e.g., a biologically active portion, thereof. In a preferred embodiment, the isolated HA protein or portion thereof can participate in the maintenance of homeostasis in C. glutamicum, or can perform a function involved in the adaptation of this microorganism to different environmental conditions. In another preferred embodiment, the isolated HA 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 maintenance of homeostasis in C. glutamicum, or to perform a function involved in the adaptation of this microorganism to different environmental conditions.
The invention also provides an isolated preparation of an HA protein. In preferred embodiments, the HA 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 HA 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 maintenance of homeostasis in C. glutamicum, or to perform a function involved in the adaptation of this microorganism to different environmental conditions, or has one or more of the activities set forth in Table 1.
Alternatively, the isolated HA 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 HA proteins also have one or more of the HA bioactivities described herein.
The HA polypeptide, or a biologically active portion thereof, can be operatively linked to a non-HA polypeptide to form a fusion protein. In preferred embodiments, this fusion protein has an activity which differs from that of the HA protein alone. In other preferred embodiments, this fusion protein participates in the maintenance of homeostasis in C. glutamicum, or performs a function involved in the adaptation of this microorganism to different environmental conditions. 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 HA protein, either by interacting with the protein itself or a substrate or binding partner of the HA protein, or by modulating the transcription or translation of an HA 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 HA 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 HA 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 HA protein activity or HA 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 processes involved in cell wall biosynthesis or rearrangements, metabolism of inorganic compounds, modification or degradation of aromatic or aliphatic compounds, or enzymatic or proteolytic activities. The agent which modulates HA protein activity can be an agent which stimulates HA protein activity or HA nucleic acid expression. Examples of agents which stimulate HA protein activity or HA nucleic acid expression include small molecules, active HA proteins, and nucleic acids encoding HA proteins that have been introduced into the cell. Examples of agents which inhibit HA activity or expression include small molecules and antisense HA 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 HA 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 HA nucleic acid and protein molecules which are involved in C. glutamicum cell wall biosynthesis or rearrangements, metabolism of inorganic compounds, modification or degradation of aromatic or aliphatic compounds, or that have a C. glutamicum enzymatic or proteolytic activity. 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 activity of a protein involved in the production of a fine chemical (e.g., an enzyme) has a direct impact on the yield, production, and/or efficiency of production of a fine chemical from the modified C. glutamicum), or 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 activity or number of copies of a C. glutamicum aromatic or aliphatic modification or degradation protein results in an increase in the viability of C. glutamicum cells, which in turn permits increased production in a large-scale culture setting). 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 Sep. 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, 3^rdedition, 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^rded. 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, 3^rded. 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 Sep. 1-3, 1994 at Penang, Malaysia, AOCS Press: Champaign, Ill. 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 B₁₂is 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 B₁₂is 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. (1999) “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. Maintenance of Homeostasis in C. glutamicum and Environmental Adaptation
The metabolic and other biochemical processes by which cells function are sensitive to environmental conditions such as temperature, pressure, solute concentration, and availability of oxygen. When one or more such environmental condition is perturbed or altered in a fashion that is incompatible with the normal functioning of these cellular processes, the cell must act to maintain an intracellular environment which will permit them to occur despite the hostile extracellular environment. Gram positive bacterial cells, such as C. glutamicum cells, have a number of mechanisms by which internal homeostasis may be maintained despite unfavorable extracellular conditions. These include a cell wall, proteins which are able to degrade possibly toxic aromatic and aliphatic compounds, mechanisms of proteolysis whereby misfolded or misregulated proteins may be rapidly destroyed, and catalysts which permit intracellular reactions to occur which would not normally take place under the conditions optimal for bacterial growth.
Aside from merely surviving in a hostile environment, bacterial cells (e.g. C. glutamicum cells) are also frequently able to adapt such that they are able to take advantage of such conditions. For example, cells in an environment lacking desired carbon sources may be able to adapt to growth on a less-suitable carbon source. Also, cells may be able to utilize less desirable inorganic compounds when the commonly utilized ones are unavailable. C. glutamicum cells possess a number of genes which permit them to adapt to utilize inorganic and organic molecules which they would normally not encounter under optimal growth conditions as nutrients and precursors for metabolism. Aspects of cellular processes involved in homeostasis and adaptation are further explicated below.
A. Modification and Degradation of Aromatic and Aliphatic Compounds
Bacterial cells are routinely exposed to a variety of aromatic and aliphatic compounds in nature. Aromatic compounds are organic molecules having a cyclic ring structure, while aliphatic compounds are organic molecules having open chain structures rather than ring structures. Such compounds may arise as by-products of industrial processes (e.g., benzene or toluene), but may also be produced by certain microorganisms (e.g., alcohols). Many of these compounds are toxic to cells, particularly the aromatic compounds, which are highly reactive due to the high-energy ring structure. Thus, certain bacteria have developed mechanisms by which they are able to modify or degrade these compounds such that they are no longer hazardous to the cell. Cells may possess enzymes that are able to, for example, hydroxylate, isomerize, or methylate aromatic or aliphatic compounds such that they are either rendered less toxic, or such that the modified form is able to be processed by standard cellular waste and degradation pathways. Also, cells may possess enzymes which are able to specifically degrade one or more such potentially hazardous substance, thereby protecting the cell. Principles and examples of these types of modification and degradation processes in bacteria are described in several publications, e.g., Sahm, H. (1999) “Procaryotes in Industrial Production” in Lengeler, J. W. et al., eds. Biology of the Procaryotes, Thieme Verlag: Stuttgart; and Schlegel, H. G. (1992) Allgemeine Mikrobiologie, Thieme: Stuttgart).
Aside from simply inactivating hazardous aromatic or aliphatic compounds, many bacteria have evolved to be able to utilize these compounds as carbon sources for continued metabolism when the preferred carbon sources of the cell are not available. For example, Pseudomonas strains able to utilize toluene, benzene, and 1,10-dichlorodecane as carbon sources are known (Chang, B. V. et al. (1997) Chemosphere 35(12): 2807-2815; Wischnak, C. et al. (1998) Appl. Environ. Microbiol. 64(9): 3507-3511; Churchill, S. A. et al. (1999) Appl. Environ. Microbiol. 65(2): 549-552). There are similar examples from many other bacterial species which are known in the art.
The ability of certain bacteria to modify or degrade aromatic and aliphatic compounds has begun to be exploited. Petroleum is a complex mixture of chemicals which includes aliphatic molecules and aromatic compounds. By applying bacteria having the ability to degrade or modify these toxic compounds to an oil spill, for example, it is possible to eliminate much of the environmental damage with high efficiency and low cost (see, for example, Smith, M. R. (1990) “The biodegradation of aromatic hydrocarbons by bacteria” Biodegradation 1(2-3): 191-206; and Suyama, T. et al. (1998) “Bacterial isolates degrading aliphatic polycarbonates,” FEMS Microbiol. Lett. 161(2): 255-261).
B. Metabolism of Inorganic Compounds
Cells (e.g., bacterial cells) contain large quantities of different molecules, such as water, inorganic ions, and organic substances (e.g., proteins, sugars, and other macromolecules). The bulk of the mass of a typical cell consists of only 4 types of atoms: carbon, oxygen, hydrogen, and nitrogen. Although they represent a smaller percentage of the content of a cell, inorganic substances are equally as important to the proper functioning of the cell. Such molecules include phosphorous, sulfur, calcium, magnesium, iron, zinc, manganese, copper, molybdenum, tungsten, and cobalt. Many of these compounds are critical for the construction of important molecules, such as nucleotides (phosphorous) and amino acids (nitrogen and sulfur). Others of these inorganic ions serve as cofactors for enzymic reactions or contribute to osmotic pressure. All such molecules must be taken up by the bacterium from the surrounding environment.
For each of these inorganic compounds it is desirable for the bacterium to take up the form which can be most readily used by the standard metabolic machinery of the cell. However, the bacterium may encounter environments in which these preferred forms are not readily available. In order to survive under these circumstances, it is important for bacteria to have additional biochemical mechanisms which are able to convert less metabolically active but readily available forms of these inorganic compounds to ones which may be used in cellular metabolism. Bacteria frequently possess a number of genes encoding enzymes for this purpose, which are not expressed unless the desired inorganic species are not available. Thus, these genes for the metabolism of various inorganic compounds serve as another tool which bacteria may use to adapt to suboptimal environmental conditions.
After carbon, the most important element in the cell is nitrogen. A typical bacterial cell contains between 12-15% nitrogen. It is a constituent of amino acids and nucleotides, as well as many other important molecules in the cell. Further, nitrogen may serve as a substitute for oxygen as a terminal electron acceptor in energy metabolism. Good sources of nitrogen include many organic and inorganic compounds, such ammonia gas or ammonia salts (e.g., NH₄Cl, (NH₄)₂SO₄, or NH₄OH), nitrates, urea, amino acids, or complex nitrogen sources like corn steep liquor, soy bean flour, soy bean protein, yeast extract, meat extract, etc. Ammonia nitrogen is fixed by the action of particular enzymes: glutamate dehydrogenase, glutamine synthase, and glutamine-2-oxoglutarate aminotransferase. The transfer of amino-nitrogen from one organic molecule to another is accomplished by the aminotransferases, a class of enzymes which transfer one amino group from an alpha-amino acid to an alpha-keto acid. Nitrate may be reduced via nitrate reductase, nitrite reductase, and further redox enzymes until it is converted to molecular nitrogen or ammonia, which may be readily utilized by the cell in standard metabolic pathways.
Phosphorous is typically found intracellularly in both organic and inorganic forms, and may be taken up by the cell in either of these forms as well, though most microorganisms preferentially take up inorganic phosphate. The conversion of organic phosphate to a form which the cell can utilize requires the action of phosphatases (e.g., phytases, which hydrolyze phyate-yielding phosphate and inositol derivatives). Phosphate is a key element in the synthesis of nucleic acids, and also has a significant role in cellular energy metabolism (e.g., in the synthesis of ATP, ADP, and AMP).
Sulfur is a requirement for the synthesis of amino acids (e.g., methionine and cysteine), vitamins (e.g., thiamine, biotin, and lipoic acid) and iron sulfur proteins. Bacteria obtain sulfur primarily from inorganic sulfate, though thiosulfate, sulfite, and sulfide are also commonly utilized. Under conditions where these compounds may not be readily available, many bacteria express genes which enable them to utilize sulfonate compounds such as 2-aminosulfonate (taurine) (Kertesz, M. A. (1993) “Proteins induced by sulfate limitation in Escherichia coli, Pseudomonas putida, or Staphylococcus aureus.” J. Bacteriol. 175: 1187-1190).
Other inorganic atoms, e.g., metal or calcium ions, are also critical for the viability of cells. Iron, for example, plays a key role in redox reactions and is a cofactor of iron-sulfur proteins, heme proteins, and cytochromes. The uptake of iron into bacterial cells may be accomplished by the action of siderophores, chelating agents which bind extracellular iron ions and translocate them to the interior of the cell. For reference on the metabolism of iron and other inorganic compounds, see: Lengeler et al. (1999) Biology of Prokaryotes, Thieme Verlag: Stuttgart; Neidhardt, F. C. et al., eds. Escherichia coli and Salmonella. ASM Press: Washington, D.C.; Sonenshein, A. L. et al., eds. (199?) Bacillus subtilis and Other Gram-Positive Bacteria, ASM Press: Washington, D.C.; Voet, D. and Voet, J. G. (1992) Biochemie, VCH: Weinheim; Brock, T. D. and Madigan, M. T. (1991) Biology of Microorgansisms, 6^thed. Prentice Hall: Englewood Cliffs, p. 267-269; Rhodes, P. M. and Stanbury, P. F. Applied Microbial Physiology—A Practical Approach, Oxford Univ. Press: Oxford.
C. Enzymes and Proteolysis
The intracellular conditions for which bacteria such as C. glutamicum are optimized are frequently not conditions under which many biochemical reactions would normally take place. In order to make such reactions proceed under physiological conditions, cells utilize enzymes. Enzymes are proteinaceous biological catalysts, spatially orienting reacting molecules or providing a specialized environment such that the energy barrier to a biochemical reaction is lowered. Different enzymes catalyze different reactions, and each enzyme may be the subject of transcriptional, translational, or posttranslational regulation such that the reaction will only take place under appropriate conditions and at specified times. Enzymes may contribute to the degradation (e.g., the proteases), synthesis (e.g., the synthases), or modification (e.g., transferases or isomerases) of compounds, all of which enable the production of necessary compounds within the cell. This, in turn, contributes to the maintenance of cellular homeostasis.
However, the fact that enzymes are optimized for activity under the physiological conditions at which the bacterium is most viable means that when environmental conditions are perturbed, there is a significant possibility that enzyme activity will also be perturbed. For example, changes in temperature may result in aberrantly folded proteins, and the same is true for changes of pH—protein folding is largely dependent on electrostatic and hydrophobic interactions of amino acids within the polypeptide chain, so any alteration to the charges on individual amino acids (as might be brought about by a change in cellular pH) may have a profound effect on the ability of the protein to correctly fold. Changes in temperature effectively change the amount of kinetic energy that the polypeptide molecule possesses, which affects the ability of the polypeptide to settle into a correctly folded, energetically stable configuration. Misfolded proteins may be harmful to the cell for two reasons. First, the aberrantly folded protein may have a similarly aberrant activity, or no activity whatsoever. Second, misfolded proteins may lack the conformational regions necessary for proper regulation by other cellular systems and thus may continue to be active but in an uncontrolled fashion.
The cell has a mechanism by which misfolded enzymes and regulatory proteins may be rapidly destroyed before any damage occurs to the cell: proteolysis. Proteins such as those of the la/Ion family and those of the Clp family specifically recognize and degrade misfolded proteins (see, e.g., Sherman, M. Y., Goldberg, A. L. (1999) EXS 77: 57-78 and references therein and Porankiewicz J. (1999) Molec. Microbiol. 32(3): 449-58, and references therein; Neidhardt, F. C., et al. (1996) E. coli and Salmonella, ASM Press: Washington, D.C. and references therein; and Pritchard, G. G., and Coolbear, T. (1993) FEMS Microbiol. Rev. 12(1-3): 179-206 and references therein). These enzymes bind to misfolded or unfolded proteins and degrade them in an ATP-dependent manner. Proteolysis thus serves as an important mechanism employed by the cell to prevent damage to normal cellular functions upon environmental changes, and it further permits cells to survive under conditions and in environments which would otherwise be toxic due to misregulated and/or aberrant enzyme or regulatory activity.
Proteolysis also has important functions in the cell under optimal environmental conditions. Within normal metabolic processes, proteases aid in the hydrolysis of peptide bonds, in the catabolism of complex molecules to provide necessary degradation products, and in protein modification. Secreted proteases play an important role in the catabolism of external nutrients even prior to the entry of these compounds into the cell. Further, proteolytic activity itself may serve regulatory functions; sporulation in B. subtilis and cell cycle progression in Caulobacter spp. are known to be regulated by key proteolytic events in each of these species (Gottesman, S. (1999) Curr. Opin. Microbiol. 2(2): 142-147). Thus, proteolytic processes are key for cellular survival under both suboptimal and optimal environmental conditions, and contribute to the overall maintenance of homeostasis in cells.
D. Cell Wall Production and Rearrangements
While the biochemical machinery of the cell may be able to readily adapt to different and possibly unfavorable environments, cells still require a general mechanism by which they may be protected from the environment. For many bacteria, the cell wall affords such protection, and also plays roles in adhesion, cell growth and division, and transport of desired solutes and waste materials.
In order to function, cells require intracellular concentrations of metabolites and other molecules that are substantially higher than those of the surrounding media. Since these metabolites are largely prevented from leaving the cell due to the presence of the hydrophobic membrane, the tendency of the system is for water molecules to enter the cell from the external medium such that the interior concentrations of solutes match the exterior concentrations. Water molecules are readily able to cross the cellular membrane, and this membrane is not able to withstand the resulting swelling and pressure, which may lead to osmotic lysis of the cell. The rigidity of the cell wall greatly improves the ability of the cell to tolerate these pressures, and offers a further barrier to the unwanted diffusion of these metabolites and desired solutes from the cell. Similarly, the cell wall also serves to prevent unwanted material from entering the cell.
The cell wall also participates in a number of other cellular processes, such as adhesion and cell growth and division. Due to the fact that the cell wall completely surrounds the cell, any interaction of the cell with its surroundings must be mediated by the cell wall. Thus, the cell wall must participate in any adherence of the cell to other cells and to desired surfaces. Further, the cell cannot grow or divide without concomitant changes in the cell wall. Since the protection that the wall affords requires its presence during growth, morphogenesis and multiplication, one of the key steps in cell division is cell wall synthesis within the cell such that a new cell divides from the old. Thus, frequently cell wall biosynthesis is regulated in tandem with cell growth and cell division (see, e.g., Sonenshein, A. L. et al, eds. (1993) Bacillus subtilis and Other Gram-Positive Bacteria, ASM: Washington, D.C.).
The structure of the cell wall varies between gram-positive and gram-negative bacteria. However, in both types, the fundamental structural unit of the wall remains similar: an overlapping lattice of two polysaccharides, N-acetyl glucosamine (NAG) and N-acetyl muramic acid (NAM) which are cross-linked by amino acids (most commonly L-alanine, D-glutamate, diaminopimelic acid, and D-alanine), termed ‘peptidoglycan’. The processes involved in the synthesis of the cell wall are known (see, e.g., Michal, G., ed. (1999) Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, Wiley: New York).
In gram-negative bacteria, the inner cellular membrane is coated by a single-layered peptidoglycan (approximately 10 nm thick), termed the murein-sacculus. This peptidoglycan structure is very rigid, and its structure determines the shape of the organism. The outer surface of the murein-sacculus is covered with an outer membrane, containing porins and other membrane proteins, phospholipids, and lipopolysaccharides. To maintain a tight association with the outer membrane, the gram-negative cell wall also has interspersed lipid molecules which serve to anchor it to the surrounding membrane.
In gram-positive bacteria, such as Corynebacterium glutamicum, the cytoplasmic membrane is covered by a multi-layered peptidoglycan, which ranges from 20-80 nm in thickness (see, e.g., Lengeler et al. (1999) Biology of Prokaryotes Thieme Verlag: Stuttgart, p. 913-918, p. 875-899, and p. 88-109 and references therein). The gram-positive cell wall also contains teichoic acid, a polymer of glycerol or ribitol linked through phosphate groups. Teichoic acid is also able to associate with amino acids, and forms covalent bonds with muramic acid. Also present in the cell wall may be lipoteichoic acids and teichuronic acids. If present, cellular surface structures such as flagella or capsules will be anchored in this layer as well.
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 HA nucleic acid and protein molecules, which participate in the maintenance of homeostasis in C. glutamicum, or which perform a function involved in the adaptation of this microorganism to different environmental conditions. In one embodiment, the HA molecules participate in C. glutamicum cell wall biosynthesis or rearrangements, in the metabolism of inorganic compounds, in the modification or degradation of aromatic or aliphatic compounds, or have an enzymatic or proteolytic activity. In a preferred embodiment, the activity of the HA molecules of the present invention with regard to C. glutamicum cell wall biosynthesis or rearrangements, metabolism of inorganic compounds, modification or degradation of aromatic or aliphatic compounds, or enzymatic or proteolytic activity has an impact on the production of a desired fine chemical by this organism. In a particularly preferred embodiment, the HA molecules of the invention are modulated in activity, such that the C. glutamicum cellular processes in which the HA molecules participate (e.g., C. glutamicum cell wall biosynthesis or rearrangements, metabolism of inorganic compounds, modification or degradation of aromatic or aliphatic compounds, or enzymatic or proteolytic activity) are also altered in activity, resulting either directly or indirectly in a modulation of the yield, production, and/or efficiency of production of a desired fine chemical by C. glutamicum.
The language, “HA protein” or “HA polypeptide” includes proteins which participate in a number of cellular processes related to C. glutamicum homeostasis or the ability of C. glutamicum cells to adapt to unfavorable environmental conditions. For example, an HA protein may be involved in C. glutamicum cell wall biosynthesis or rearrangements, in the metabolism of inorganic compounds in C. glutamicum, in the modification or degradation of aromatic or aliphatic compounds in C. glutamicum, or have a C. glutamicum enzymatic or proteolytic activity. Examples of HA proteins include those encoded by the HA genes set forth in Table 1 and Appendix A. The terms “HA gene” or “HA nucleic acid sequence” include nucleic acid sequences encoding an HA protein, which consist of a coding region and also corresponding untranslated 5′ and 3′ sequence regions. Examples of HA 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. The term “homeostasis” is art-recognized and includes all of the mechanisms utilized by a cell to maintain a constant intracellular environment despite the prevailing extracellular environmental conditions. A non-limiting example of such processes is the utilization of a cell wall to prevent osmotic lysis due to high intracellular solute concentrations. The term “adaptation” or “adaptation to an environmental condition” is art-recognized and includes mechanisms utilized by the cell to render the cell able to survive under nonpreferred environmental conditions (generally speaking, those environmental conditions in which one or more favored nutrients are absent, or in which an environmental condition such as temperature, pH, osmolarity, oxygen percentage and the like fall outside of the optimal survival range of the cell). Many cells, including C. glutamicum cells, possess genes encoding proteins which are expressed under such environmental conditions and which permit continued growth in such suboptimal conditions.
In another embodiment, the HA 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 HA 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. For example, by engineering enzymes which modify or degrade aromatic or aliphatic compounds such that these enzymes are increased or decreased in activity or number, it may be possible to modulate the production of one or more fine chemicals which are the modification or degradation products of these compounds. Similarly, enzymes involved in the metabolism of inorganic compounds provide key molecules (e.g. phosphorous, sulfur, and nitrogen molecules) for the biosynthesis of such fine chemicals as amino acids, vitamins, and nucleic acids. By altering the activity or number of these enzymes in C. glutamicum, it may be possible to increase the conversion of these inorganic compounds (or to use alternate inorganic compounds) to thus permit improved rates of incorporation of inorganic atoms into these fine chemicals. Genetic engineering of C. glutamicum enzymes involved in general cellular processes may also directly improve fine chemical production, since many of these enzymes directly modify fine chemicals (e.g., amino acids) or the enzymes which are involved in fine chemical synthesis or secretion. Modulation of the activity or number of cellular proteases may also have a direct effect on fine chemical production, since many proteases may degrade fine chemicals or enzymes involved in fine chemical production or breakdown.
Further, the aforementioned enzymes which participate in aromatic/aliphatic compound modification or degradation, general biocatalysis, inorganic compound metabolism or proteolysis are each themselves fine chemicals, desirable for their activity in various in vitro industrial applications. By altering the number of copies of the gene for one or more of these enzymes in C. glutamicum it may be possible to increase the number of these proteins produced by the cell, thereby increasing the potential yield or efficiency of production of these proteins from large-scale C. glutamicum or related bacterial cultures.
The alteration of an HA protein of the invention may also indirectly affect the yield, production, and/or efficiency of production of a fine chemical from a C. glutamicum strain incorporating such an altered protein. For example, by modulating the activity and/or number of those proteins involved in the construction or rearrangement of the cell wall, it may be possible to modify the structure of the cell wall itself such that the cell is able to better withstand the mechanical and other stresses present during large-scale fermentative culture. Also, large-scale growth of C. glutamicum requires significant cell wall production. Modulation of the activity or number of cell wall biosynthetic or degradative enzymes may allow more rapid rates of cell wall biosynthesis, which in turn may permit increased growth rates of this microorganism in culture and thereby increase the number of cells producing the desired fine chemical.
By modifying the HA enzymes of the invention, one may also indirectly impact the yield, production, or efficiency of production of one or more fine chemicals from C. glutamicum. For example, many of the general enzymes in C. glutamicum may have a significant impact on global cellular processes (e.g., regulatory processes) which in turn have a significant effect on fine chemical metabolism. Similarly, proteases, enzymes which modify or degrade possibly toxic aromatic or aliphatic compounds, and enzymes which promote the metabolism of inorganic compounds all serve to increase the viability of C. glutamicum. The proteases aid in the selective removal of misfolded or misregulated proteins, such as those that might occur under the relatively stressful environmental conditions encountered during large-scale fermentor culture. By altering these proteins, it may be possible to further enhance this activity and to improve the viability of C. glutamicum in culture. The aromatic/aliphatic modification or degradation proteins not only serve to detoxify these waste compounds (which may be encountered as impurities in culture medium or as waste products from cells themselves), but also to permit the cells to utilize alternate carbon sources if the optimal carbon source is limiting in the culture. By increasing their number and/or activity, the survival of C. glutamicum cells in culture may be enhanced. The inorganic metabolism proteins of the invention supply the cell with inorganic molecules required for all protein and nucleotide (among others) synthesis, and thus are critical for the overall viability of the cell. An increase in the number of viable cells producing one or more desired fine chemicals in large-scale culture should result in a concomitant increase in the yield, production, and/or efficiency of production of the fine chemical in the 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 HA DNAs and the predicted amino acid sequences of the C. glutamicum HA 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 that participate in C. glutamicum cell wall biosynthesis or rearrangements, metabolism of inorganic compounds, modification or degradation of aromatic or aliphatic compounds, or that have a C. glutamicum enzymatic or proteolytic activity.
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 HA protein or a biologically active portion or fragment thereof of the invention can participate in the maintenance of homeostasis in C. glutamicum, or can perform a function involved in the adaptation of this microorganism to different environmental conditions, 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 HA 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 HA-encoding nucleic acid (e.g., HA 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 HA 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 HA 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 HA 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 HA DNAs of the invention. This DNA comprises sequences encoding HA 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., RXA02458, RXN00249, RXS00153, or RXC00963). 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 RXA02458, RXN00249, RXS00153, and RXC00963 are translations of the coding regions of the nucleotide sequences of nucleic acid molecules RXA02458, RXN00249, RXS00153, and RXC00963, 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.
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:5, designated, as indicated on Table 1, as “F RXA00249”, is an F-designated gene, as are SEQ ID NOs: 11, 15, and 33 (designated on Table 1 as “F RXA02264”, “F RXA02274”, and “F RXA00675”, 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 HA protein. The nucleotide sequences determined from the cloning of the HA genes from C. glutamicum allows for the generation of probes and primers designed for use in identifying and/or cloning HA homologues in other cell types and organisms, as well as HA 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 HA homologues. Probes based on the HA 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 HA protein, such as by measuring a level of an HA-encoding nucleic acid in a sample of cells, e.g., detecting HA mRNA levels or determining whether a genomic HA 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 maintenance of homeostasis in C. glutamicum, or to perform a function involved in the adaptation of this microorganism to different environmental conditions. 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 maintenance of homeostasis in C. glutamicum, or to perform a function involved in the adaptation of this microorganism to different environmental conditions. Proteins involved in C. glutamicum cell wall biosynthesis or rearrangements, metabolism of inorganic compounds, modification or degradation of aromatic or aliphatic compounds, or that have a C. glutamicum enzymatic or proteolytic activity, 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 HA protein” contributes either directly or indirectly to the yield, production, and/or efficiency of production of one or more fine chemicals. Examples of HA 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 HA nucleic acid molecules of the invention are preferably biologically active portions of one of the HA proteins. As used herein, the term “biologically active portion of an HA protein” is intended to include a portion, e.g., a domain/motif, of an HA protein that can participate in the maintenance of homeostasis in C. glutamicum, or that can perform a function involved in the adaptation of this microorganism to different environmental conditions, or has an activity as set forth in Table 1. To determine whether an HA protein or a biologically active portion thereof can participate in C. glutamicum cell wall biosynthesis or rearrangements, metabolism of inorganic compounds, modification or degradation of aromatic or aliphatic compounds, or has a C. glutamicum enzymatic or proteolytic activity, 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 HA protein can be prepared by isolating a portion of one of the sequences in Appendix B, expressing the encoded portion of the HA protein or peptide (e.g., by recombinant expression in vitro) and assessing the activity of the encoded portion of the HA 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 HA 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 39% identical to the nucleotide sequence designated RXA00471 (SEQ ID NO:293), a nucleotide sequence which is greater than and/or at least 41% identical to the nucleotide sequence designated RXA00500 (SEQ ID NO:143), and a nucleotide sequence which is greater than and/or at least 35% identical to the nucleotide sequence designated RXA00502 (SEQ ID NO:147). 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 HA nucleotide sequences shown in Appendix A, it will be appreciated by those of ordinary skill in the art that DNA sequence polymorphisms that lead to changes in the amino acid sequences of HA proteins may exist within a population (e.g., the C. glutamicum population). Such genetic polymorphism in the HA 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 HA protein, preferably a C. glutamicum HA protein. Such natural variations can typically result in 1-5% variance in the nucleotide sequence of the HA gene. Any and all such nucleotide variations and resulting amino acid polymorphisms in HA that are the result of natural variation and that do not alter the functional activity of HA 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 HA DNA of the invention can be isolated based on their homology to the C. glutamicum HA 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 HA protein.
In addition to naturally-occurring variants of the HA 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 HA protein, without altering the functional ability of the HA 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 HA proteins (Appendix B) without altering the activity of said HA protein, whereas an “essential” amino acid residue is required for HA protein activity. Other amino acid residues, however, (e.g., those that are not conserved or only semi-conserved in the domain having HA activity) may not be essential for activity and thus are likely to be amenable to alteration without altering HA activity.
Accordingly, another aspect of the invention pertains to nucleic acid molecules encoding HA proteins that contain changes in amino acid residues that are not essential for HA activity. Such HA proteins differ in amino acid sequence from a sequence contained in Appendix B yet retain at least one of the HA 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 participating in the maintenance of homeostasis in C. glutamicum, or of performing a function involved in the adaptation of this microorganism to different environmental conditions, or has one or more of the 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 HA 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 HA 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 HA coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for an HA activity described herein to identify mutants that retain HA 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 HA 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 DNA 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 HA 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 HA 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. 3 (RXN00249) comprises nucleotides 1 to 957). In another embodiment, the antisense nucleic acid molecule is antisense to a “noncoding region” of the coding strand of a nucleotide sequence encoding HA. 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 HA 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 HA mRNA, but more preferably is an oligonucleotide which is antisense to only a portion of the coding or noncoding region of HA mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of HA 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-N-6-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 HA 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 P-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 HA mRNA transcripts to thereby inhibit translation of HA mRNA. A ribozyme having specificity for an HA-encoding nucleic acid can be designed based upon the nucleotide sequence of an HA DNA molecule disclosed herein (i.e., SEQ ID NO. 3 (RXN00249) 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 HA-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, HA 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, HA gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of an HA nucleotide sequence (e.g., an HA promoter and/or enhancers) to form triple helical structures that prevent transcription of an HA 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 HA 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 are 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-, lacI^q, T7-, T5-, T3-, gal-, trc-, ara-, SP6—, arny, SPO2, λ-P_R- or λP_L, 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 those 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., HA proteins, mutant forms of HA proteins, fusion proteins, etc.).
The recombinant expression vectors of the invention can be designed for expression of HA proteins in prokaryotic or eukaryotic cells. For example, HA 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 HA 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 HA 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, pBdCl, 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 gn1). 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: New York 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 HA 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: New York (IBSN 0 444 904018).
Alternatively, the HA 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., Sf 9 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 HA 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”, Nucl. Acid. Res. 12: 8711-8721, and include pLGV23, pGHlac+, pBIN19, pAK2004, and pDH51 (Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: New York 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 (Baneiji 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 HA 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 HA 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 those 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 HA 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 HA gene into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the HA gene. Preferably, this HA gene is a Corynebacterium glutamicum HA 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 HA 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 HA 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 HA protein). In the homologous recombination vector, the altered portion of the HA gene is flanked at its 5′ and 3′ ends by additional nucleic acid of the HA gene to allow for homologous recombination to occur between the exogenous HA gene carried by the vector and an endogenous HA gene in a microorganism. The additional flanking HA 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 HA gene has homologously recombined with the endogenous HA 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 HA gene on a vector placing it under control of the lac operon permits expression of the HA gene only in the presence of IPTG. Such regulatory systems are well known in the art.
In another embodiment, an endogenous HA 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 HA gene in a host cell has been altered by one or more point mutations, deletions, or inversions, but still encodes a functional HA protein. In still another embodiment, one or more of the regulatory regions (e.g., a promoter, repressor, or inducer) of an HA gene in a microorganism has been altered (e.g., by deletion, truncation, inversion, or point mutation) such that the expression of the HA gene is modulated. One of ordinary skill in the art will appreciate that host cells containing more than one of the described HA 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 HA protein. Accordingly, the invention further provides methods for producing HA 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 HA protein has been introduced, or into which genome has been introduced a gene encoding a wild-type or altered HA protein) in a suitable medium until HA protein is produced. In another embodiment, the method further comprises isolating HA proteins from the medium or the host cell.
C. Isolated HA Proteins
Another aspect of the invention pertains to isolated HA 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 HA 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 HA protein having less than about 30% (by dry weight) of non-HA protein (also referred to herein as a “contaminating protein”), more preferably less than about 20% of non-HA protein, still more preferably less than about 10% of non-HA protein, and most preferably less than about 5% non-HA protein. When the HA 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 HA 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 HA protein having less than about 30% (by dry weight) of chemical precursors or non-HA chemicals, more preferably less than about 20% chemical precursors or non-HA chemicals, still more preferably less than about 10% chemical precursors or non-HA chemicals, and most preferably less than about 5% chemical precursors or non-HA chemicals. In preferred embodiments, isolated proteins or biologically active portions thereof lack contaminating proteins from the same organism from which the HA protein is derived. Typically, such proteins are produced by recombinant expression of, for example, a C. glutamicum HA protein in a microorganism such as C. glutamicum.
An isolated HA protein or a portion thereof of the invention can participate in the repair or recombination of DNA, in the transposition of genetic material, in gene expression (i.e., the processes of transcription or translation), in protein folding, or in protein secretion in Corynebacterium glutamicum, 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 to participate in the maintenance of homeostasis in C. glutamicum, or to perform a function involved in the adaptation of this microorganism to different environmental conditions. The portion of the protein is preferably a biologically active portion as described herein. In another preferred embodiment, an HA protein of the invention has an amino acid sequence shown in Appendix B. In yet another preferred embodiment, the HA 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 HA 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 HA proteins of the present invention also preferably possess at least one of the HA activities described herein. For example, a preferred HA 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 maintenance of homeostasis in C. glutamicum, or can perform a function involved in the adaptation of this microorganism to different environmental conditions, or which has one or more of the activities set forth in Table 1.
In other embodiments, the HA 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 HA 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 HA 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 HA protein include peptides comprising amino acid sequences derived from the amino acid sequence of an HA protein, e.g., the an amino acid sequence shown in Appendix B or the amino acid sequence of a protein homologous to an HA protein, which include fewer amino acids than a full length HA protein or the full length protein which is homologous to an HA protein, and exhibit at least one activity of an HA 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 HA 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 HA protein include one or more selected domains/motifs or portions thereof having biological activity.
HA 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 HA protein is expressed in the host cell. The HA protein can then be isolated from the cells by an appropriate purification scheme using standard protein purification techniques. Alternative to recombinant expression, an HA protein, polypeptide, or peptide can be synthesized chemically using standard peptide synthesis techniques. Moreover, native HA protein can be isolated from cells (e.g., endothelial cells), for example using an anti-HA antibody, which can be produced by standard techniques utilizing an HA protein or fragment thereof of this invention.
The invention also provides HA chimeric or fusion proteins. As used herein, an HA “chimeric protein” or “fusion protein” comprises an HA polypeptide operatively linked to a non-HA polypeptide. An “HA polypeptide” refers to a polypeptide having an amino acid sequence corresponding to an HA protein, whereas a “non-HA polypeptide” refers to a polypeptide having an amino acid sequence corresponding to a protein which is not substantially homologous to the HA protein, e.g., a protein which is different from the HA 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 HA polypeptide and the non-HA polypeptide are fused in-frame to each other. The non-HA polypeptide can be fused to the N-terminus or C-terminus of the HA polypeptide. For example, in one embodiment the fusion protein is a GST-HA fusion protein in which the HA sequences are fused to the C-terminus of the GST sequences. Such fusion proteins can facilitate the purification of recombinant HA proteins. In another embodiment, the fusion protein is an HA 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 HA protein can be increased through use of a heterologous signal sequence.
Preferably, an HA 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 HA-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the HA protein.
Homologues of the HA protein can be generated by mutagenesis, e.g., discrete point mutation or truncation of the HA protein. As used herein, the term “homologue” refers to a variant form of the HA protein which acts as an agonist or antagonist of the activity of the HA protein. An agonist of the HA protein can retain substantially the same, or a subset, of the biological activities of the HA protein. An antagonist of the HA protein can inhibit one or more of the activities of the naturally occurring form of the HA protein, by, for example, competitively binding to a downstream or upstream member of a biochemical cascade which includes the HA protein, by binding to a target molecule with which the HA protein interacts, such that no functional interaction is possible, or by binding directly to the HA protein and inhibiting its normal activity.
In an alternative embodiment, homologues of the HA protein can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants, of the HA protein for HA protein agonist or antagonist activity. In one embodiment, a variegated library of HA variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library. A variegated library of HA variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential HA sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display) containing the set of HA sequences therein. There are a variety of methods which can be used to produce libraries of potential HA 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 HA 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 HA protein coding can be used to generate a variegated population of HA fragments for screening and subsequent selection of homologues of an HA protein. In one embodiment, a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of an HA 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 HA 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 HA 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 HA 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 HA 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 HA protein regions required for function; modulation of an HA protein activity; modulation of the metabolism of one or more inorganic compounds; modulation of the modification or degradation of one or more aromatic or aliphatic compounds; modulation of cell wall synthesis or rearrangements; modulation of enzyme activity or proteolysis; and modulation of cellular production of a desired compound, such as a fine chemical.
The HA 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 HA nucleic acid molecules of the invention are also useful for evolutionary and protein structural studies. The processes involved in adaptation and the maintenance of homeostasis in which the molecules of the invention participate are utilized by a wide variety of species; 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 HA nucleic acid molecules of the invention may result in the production of HA proteins having functional differences from the wild-type HA 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 HA protein, either by interacting with the protein itself or a substrate or binding partner of the HA protein, or by modulating the transcription or translation of an HA nucleic acid molecule of the invention. In such methods, a microorganism expressing one or more HA 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 HA protein is assessed.
The modulation of activity or number of HA proteins involved in cell wall biosynthesis or rearrangements may impact the production, yield, and/or efficiency of production of one or more fine chemicals from C. glutamicum cells. For example, by altering the activity of these proteins, it may be possible to modulate the structure or thickness of the cell wall. The cell wall serves in large measure as a protective device against osmotic lysis and external sources of injury; by modifying the cell wall it may be possible to increase the ability of C. glutamicum to withstand the mechanical and shear force stresses encountered by this microorganism during large-scale fermentor culture. Further, each C. glutamicum cell is surrounded by a thick cell wall, and thus, a significant portion of the biomass present in large scale culture consists of cell wall. By increasing the rate at which the cell wall is synthesized or by activating cell wall synthesis (through genetic engineering of the HA cell wall proteins of the invention) it may be possible to improve the growth rate of the microorganism. Similarly, by decreasing the activity or number of proteins involved in the degradation of cell wall or by decreasing the repression of cell wall biosynthesis, an overall increase in cell wall production may be achieved. An increase in the number of viable C. glutamicum cells (as may be accomplished by any of the foregoing described protein alterations) should result in increased numbers of cells producing the desired fine chemical in large-scale fermentor culture, which should permit increased yields or efficiency of production of these compounds from the culture.
The modulation of activity or number of C. glutamicum HA proteins that participate in the modification or degradation of aromatic or aliphatic compounds may also have direct or indirect impacts on the production of one or more fine chemicals from these cells. Certain aromatic or aliphatic modification or degradation products are desirable fine chemicals (e.g., organic acids or modified aromatic and aliphatic compounds); thus, by modifying the enzymes which perform these modifications (e.g., hydroxylation, methylation, or isomerization) or degradation reactions, it may be possible to increase the yields of these desired compounds. Similarly, by decreasing the activity or number of proteins involved in pathways which further degrade the modified or breakdown products of the aforementioned reactions it may be possible to improve the yields of these fine chemicals from C. glutamicum cells in culture.
These aromatic and aliphatic modification and degradative enzymes are themselves fine chemicals. In purified form, these enzymes may be used to degrade aromatic and aliphatic compounds (e.g., toxic chemicals such as petroleum products), either for the bioremediation of polluted sites, for the engineered decomposition of wastes, or for the large-scale and economically feasible production of desired modified aromatic or aliphatic compounds or their breakdown products, some of which may be conveniently used as carbon or energy sources for other fine chemical-producing compounds in culture (see, e.g., Faber, K. (1995) Biotransformations in Organic Chemistry, Springer: Berlin and references therein; and Roberts, S. M., ed. (1992-1996) Preparative Biotransformations, Wiley: Chichester, and references therein). By genetically altering these proteins such that their regulation by other cellular mechanisms is lessened or abolished, it may be possible to increase the overall number or activity of these proteins, thereby improving not only the yield of these fine chemicals but also the activity of these harvested proteins.
The modification of these aromatic and aliphatic modifying and degradation enzymes may also have an indirect effect on the production of one or more fine chemical. Many aromatic and aliphatic compounds (such as those that may be encountered as impurities in culture media or as waste products from cellular metabolism) are toxic to cells; by modifying and/or degrading these compounds such that they may be readily removed or destroyed, cellular viability should be increased. Further, these enzymes may modify or degrade these compounds in such a manner that the resulting products may enter the normal carbon metabolism pathways of the cell, thus rendering the cell able to use these compounds as alternate carbon or energy sources. In large-scale culture situations, when there may be limiting amounts of optimal carbon sources, these enzymes provide a method by which cells may continue to grow and divide using aromatic or aliphatic compounds as nutrients. In either case, the resulting increase in the number of C. glutamicum cells in the culture producing the desired fine chemical should in turn result in increased yields or efficiency of production of the fine chemical(s).
Modifications in activity or number of HA proteins involved in the metabolism of inorganic compounds may also directly or indirectly affect the production of one or more fine chemicals from C. glutamicum or related bacterial cultures. For example, many desirable fine chemicals, such as nucleic acids, amino acids, cofactors and vitamins (e.g., thiamine, biotin, and lipoic acid) cannot be synthesized without inorganic molecules such as phosphorous, nitrate, sulfate, and iron. The inorganic metabolism proteins of the invention permit the cell to obtain these molecules from a variety of inorganic compounds and to divert them into various fine chemical biosynthetic pathways. Therefore, by increasing the activity or number of enzymes involved in the metabolism of these inorganic compounds, it may be possible to increase the supply of these possibly limiting inorganic molecules, thereby directly increasing the production or efficiency of production of various fine chemicals from C. glutamicum cells containing such altered proteins. Modification of the activity or number of inorganic metabolism enzymes of the invention may also render C. glutamicum able to better utilize limited inorganic compound supplies, or to utilize nonoptimal inorganic compounds to synthesize amino acids, vitamins, cofactors, or nucleic acids, all of which are necessary for continued growth and replication of the cell. By improving the viability of these cells in large-scale culture, the number of C. glutamicum cells producing one or more fine chemicals in the culture may also be increased, in turn increasing the yields or efficiency of production of one or more fine chemicals.
C. glutamicum enzymes for general processes are themselves desirable fine chemicals. The specific properties of enzymes (i.e., regio- and stereospecificity, among others) make them useful catalysts for chemical reactions in vitro. Either whole C. glutamicum cells may be incubated with an appropriate substrate such that the desired product is produced by enzymes in the cell, or the desired enzymes may be overproduced and purified from C. glutamicum cultures (or those of a related bacterium) and subsequently utilized in in vitro reactions in an industrial setting (either in solution or immobilized on a suitable immobile phase). In either situation, the enzyme can either be a natural C. glutamicum protein, or it may be mutagenized to have an altered activity; typical industrial uses for such enzymes include as catalysts in the chemical industry (e.g., for synthetic organic chemistry) as food additives, as feed components, for fruit processing, for leather preparation, in detergents, in analysis and medicine, and in the textile industry (see, e.g., Yamada, H. (1993) “Microbial reactions for the production of useful organic compounds,” Chimica 47: 5-10; Roberts, S. M. (1998) Preparative biotransformations: the employment of enzymes and whole-cells in synthetic chemistry,” J. Chem. Soc. Perkin Trans. 1: 157-169; Zaks, A. and Dodds, D. R. (1997) “Application of biocatalysis and biotransformations to the synthesis of pharmaceuticals,” DDT2: 513-531; Roberts, S. M. and Williamson, N. M. (1997) “The use of enzymes for the preparation of biologically active natural products and analogues in optically active form,” Curr. Organ. Chemistry 1:1-20; Faber, K. (1995) Biotransformations in Organic Chemistry, Springer: Berlin; Roberts, S. M., ed. (1992-96) Preparative Biotransformations, Wiley: Chichester; Cheetham, P. S. J. (1995) “The applications of enzymes in industry” in: Handbook of Enzyme Biotechnology, 3^rded., Wiseman, A., ed., Elis: Horwood, p. 419-552; and Ullmann's Encyclopedia of Industrial Chemistry (1987), vol. A9, Enzymes, p. 390-457). Thus, by increasing the activity or number of these enzymes, it may be possible to also increase the ability of the cell to convert supplied substrates to desired products, or to overproduce these enzymes for increased yields in large-scale culture. Further, by mutagenizing these proteins it may be possible to remove feedback inhibition or other repressive cellular regulatory controls such that greater numbers of these enzymes may be produced and activated by the cell, thereby leading to greater yields, production, or efficiency of production of these fine chemical proteins from large-scale cultures. Further, manipulation of these enzymes may alter the activity of one or more C. glutamicum metabolic pathways, such as those for the biosynthesis or secretion of one or more fine chemicals.
Mutagenesis of the proteolytic enzymes of the invention such that they are altered in activity or number may also directly or indirectly affect the yield, production, and/or efficiency of production of one or more fine chemicals from C. glutamicum. For example, by increasing the activity or number of these proteins, it may be possible to increase the ability of the bacterium to survive in large-scale culture, due to an increased ability of the cell to rapidly degrade proteins misfolded in response to the high temperatures, nonoptimal pH, and other stresses encountered during fermentor culture. Increased numbers of cells in these cultures may result in increased yields or efficiency of production of one or more desired fine chemicals, due to the relatively larger number of cells producing these compounds in the culture. Also, C. glutamicum cells possess multiple cell-surface proteases which serve to break down external nutrients into molecules which may be more readily incorporated by the cells as carbon/energy sources or nutrients of other kinds. An increase in activity or number of these enzymes may improve this turnover and increase the levels of available nutrients, thereby improving cell growth or production. Thus, modifications of the proteases of the invention may indirectly impact C. glutamicum fine chemical production.
A more direct impact on fine chemical production in response to the modification of one or more of the proteases of the invention may occur when these proteases are involved in the production or degradation of a desired fine chemical. By decreasing the activity of a protease which degrades a fine chemical or a protein involved in the synthesis of a fine chemical it may be possible to increase the levels of that fine chemical (due to the decreased degradation or increased synthesis of the compound). Similarly, by increasing the activity of a protease which degrades a compound to result in a fine chemical or a protein involved in the degradation of a fine chemical, a similar result should be achieved: increased levels of the desired fine chemical from C. glutamicum cells containing these engineered proteins.
The aforementioned mutagenesis strategies for HA 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 HA 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 product produced by 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 MgSO₄x7H₂O, 10 ml/l KH₂PO₄solution (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 MgSO₄x7H₂O, 0.2 g/l CaCl₂, 0.5 g/l yeast extract (Difco), 10 ml/l trace-elements-mix (200 mg/l FeSO₄xH₂O, 10 mg/l ZnSO₄x7H₂O, 3 mg/l MnCl₂x4H₂O, 30 mg/l H₃BO₃20 mg/l CoCl₂x6H₂O, 1 mg/l NiCl₂x6H₂O, 3 mg/l Na₂MoO₄x2H₂O, 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-I 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 Schafer, 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: New York), 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: New York). 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 NH₄Cl 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 OD₆₀₀of 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, 3^rded. Academic Press: New York; Bisswanger, H., (1994) Enzymkinetik, 2^nded. VCH: Weinheim (ISBN 3527300325); Bergmeyer, H. U., Bergmeyer, J., Graβ1, M., eds. (1983-1986) Methods of Enzymatic Analysis, 3^rded., 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 centrifugation, 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: New York (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 HA 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 HA 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 PAM120 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, ¹⁵NO₃or 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	Identification
ID NO	ID NO	Code	Contig.	NT Start	NT Stop	Function

1	2	RXA02548	GR00727	3	293	SULFATE ADENYLATE TRANSFERASE SUBUNIT 2 (EC 2.7.7.4)
3	4	RXN00249	VV0057	36825	35869	ADENYLYLSULFATE KINASE (EC 2.7.1.25)
5	6	F RXA00249	GR00037	8837	7884	ADENYLYLSULFATE KINASE (EC 2.7.1.25)
7	8	RXA01073	GR00300	1274	2104	NH(3)-DEPENDENT NAD(+) SYNTHETASE (EC 6.3.5.1)

Urease

9	10	RXN02913	VV0020	8998	8513	UREASE BETA SUBUNIT (EC 3.5.1.5)
11	12	F RXA02264	GR00655	123	4	UREASE ALPHA SUBUNIT (EC 3.5.1.5)
13	14	RXN02274	VV0020	8509	6800	UREASE ALPHA SUBUNIT (EC 3.5.1.5)
15	16	F RXA02274	GR00656	3	1604	UREASE ALPHA SUBUNIT (EC 3.5.1.5)
17	18	RXA02265	GR00655	452	153	UREASE GAMMA SUBUNIT (EC 3.5.1.5)
19	20	RXA02278	GR00656	3420	4268	UREASE OPERON URED PROTEIN
21	22	RXA02275	GR00656	1632	2102	UREASE ACCESSORY PROTEIN UREE
23	24	RXA02276	GR00656	2105	2782	UREASE ACCESSORY PROTEIN UREF
25	26	RXA02277	GR00656	2802	3416	UREASE ACCESSORY PROTEIN UREG
27	28	RXA02603	GR00742	7742	8737	4-HYDROXYBENZOATE OCTAPRENYLTRANSFERASE (EC 2.5.1.—)
29	30	RXA01385	GR00406	5320	3440	PHENOL 2 MONOOXYGENASE (EC 1.14.13.7)

Proteolysis

31	32	RXN00675	VV0005	33258	34049	METHIONINE AMINOPEPTIDASE (EC 3.4.11.18)
33	34	F RXA00675	GR00178	2	484	METHIONINE AMINOPEPTIDASE (EC 3.4.11.18)
35	36	RXA01609	GR00449	2740	3612	METHIONINE AMINOPEPTIDASE (EC 3.4.11.18)
37	38	RXA01358	GR00393	5337	6857	ATP-DEPENDENT PROTEASE LA (EC 3.4.21.53)
39	40	RXA01458	GR00420	3225	2176	ATP-DEPENDENT PROTEASE LA (EC 3.4.21.53)
41	42	RXA01654	GR00459	986	1981	(AL022121) putative alkaline serine protease [Mycobacterium tuberculosis]
43	44	RXN01868	VV0127	9980	11905	ZINC METALLOPROTEASE (EC 3.4.24.—)
45	46	F RXA01868	GR00534	1640	30	ZINC METALLOPROTEASE (EC 3.4.24.—)
47	48	F RXA01869	GR00534	1954	1652	ZINC METALLOPROTEASE (EC 3.4.24.—)
49	50	RXN03028	VV0008	41156	43930	ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA
51	52	F RXA02470	GR00715	2216	3196	ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA
53	54	F RXA02471	GR00715	3159	4991	ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA
55	56	RXA02630	GR00748	2654	1332	(AL021999) putative serine protease [Mycobacterium tuberculosis]
57	58	RXA02834	GR00823	3	497	ATPases with chaperone activity, ATP-dependent protease subunit
59	60	RXA00112	GR00016	3687	2497	PROBABLE PERIPLASMIC SERINE PROTEASE DO-LIKE PRECURSOR
61	62	RXA00566	GR00152	742	137	ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC
						SUBUNIT (EC 3.4.21.92)
63	64	RXA00567	GR00152	1388	798	ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC
						SUBUNIT (EC 3.4.21.92)
65	66	RXN03094	VV0057	1794	43	CLPB PROTEIN
67	68	F RXA01668	GR00464	2205	3920	CLPB PROTEIN
69	70	RXN01120	VV0182	5678	4401	ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX
71	72	F RXA01120	GR00310	2349	1072	ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX
73	74	RXA00744	GR00202	10722	9781	Periplasmic serine proteases
75	76	RXA00844	GR00228	3620	4453	Hypothetical Secretory Serine Protease (EC 3.4.21.—)
77	78	RXA01151	GR00324	862	5	ATP-dependent Zn proteases
79	80	RXA02317	GR00665	9664	9053	PEPTIDASE E (EC 3.4.—.—)
81	82	RXA02644	GR00751	767	117	XAA-PRO DIPEPTIDASE (EC 3.4.13.9)
83	84	RXN02820	VV0131	4799	6109	GAMMA-GLUTAMYLTRANSPEPTIDASE (EC 2.3.2.2)
85	86	F RXA02820	GR00801	1	507	GAMMA-GLUTAMYLTRANSPEPTIDASE (EC 2.3.2.2)
87	88	F RXA02000	GR00589	3430	3933	GAMMA-GLUTAMYLTRANSPEPTIDASE (EC 2.3.2.2)
89	90	RXN03178	VV0334	921	121	PENICILLIN-BINDING PROTEIN 5* PRECURSOR
						(D-ALANYL-D-ALANINE CARBOXYPEPTIDASE) (EC 3.4.16.4)
91	92	F RXA02859	GR10005	846	121	PENICILLIN-BINDING PROTEIN 5* PRECURSOR
						(D-ALANYL-D-ALANINE CARBOXYPEPTIDASE) (EC 3.4.16.4)
93	94	RXA00137	GR00022	738	1826	XAA-PRO AMINOPEPTIDASE (EC 3.4.11.9)
95	96	RXN00499	VV0086	8158	9438	PROLINE IMINOPEPTIDASE (EC 3.4.11.5)
97	98	F RXA00499	GR00125	3	959	PROLINE IMINOPEPTIDASE
99	100	RXN00877	VV0099	2221	3885	PEPTIDYL-DIPEPTIDASE DCP (EC 3.4.15.5)
101	102	F RXA00877	GR00242	3	1067	PEPTIDYL-DIPEPTIDASE DCP (EC 3.4.15.5)
103	104	RXN01014	VV0209	13328	10728	AMINOPEPTIDASE N (EC 3.4.11.2)
105	106	F RXA01014	GR00289	3	1580	AMINOPEPTIDASE N (EC 3.4.11.2)
107	108	F RXA01018	GR00290	2289	3152	AMINOPEPTIDASE N (EC 3.4.11.2)
109	110	RXA01147	GR00323	1353	94	VACUOLAR AMINOPEPTIDASE I PRECURSOR (EC 3.4.11.1)
111	112	RXA01161	GR00329	1253	117	XAA-PRO AMINOPEPTIDASE (EC 3.4.11.9)
113	114	RXN01181	VV0065	1	957	AMINOPEPTIDASE A/I (EC 3.4.11.1)
115	116	F RXA01181	GR00337	1	957	AMINOPEPTIDASE
117	118	RXN01277	VV0009	32155	34158	PROLYL ENDOPEPTIDASE (EC 3.4.21.26)
119	120	F RXA01277	GR00368	1738	50	PROLYL ENDOPEPTIDASE (EC 3.4.21.26)
121	122	RXA01914	GR00548	125	550	AMINOPEPTIDASE
123	124	RXA02048	GR00624	207	1580	AMINOPEPTIDASE N (EC 3.4.11.2)
125	126	RXN00621	VV0135	5853	5071	PROTEASE II (EC 3.4.21.83)
127	128	F RXA00621	GR00163	4075	4857	PTRB periplasmic protease
129	130	RXN00622	VV0135	5150	3735	PROTEASE II (EC 3.4.21.83)
131	132	F RXA00622	GR00163	4778	6193	PTRB periplasmic protease
133	134	RXN00982	VV0149	7596	6091	(L42758) proteinase [Streptomyces lividans]
135	136	F RXA00977	GR00275	1647	2660	(L42758) proteinase [Streptomyces lividans]
137	138	F RXA00982	GR00276	5194	4949	(L42758) proteinase [Streptomyces lividans]
139	140	RXA00152	GR00023	7175	5880	HFLC PROTEIN (EC 3.4.—.—)
141	142	RXA02558	GR00731	4939	3965	HFLC PROTEIN (EC 3.4.—.—)
143	144	RXA00500	GR00125	969	1643	O-SIALOGLYCOPROTEIN ENDOPEPTIDASE (EC 3.4.24.57)
145	146	RXA00501	GR00125	1643	2149	O-SIALOGLYCOPROTEIN ENDOPEPTIDASE (EC 3.4.24.57)
147	148	RXA00502	GR00125	2156	3187	O-SIALOGLYCOPROTEIN ENDOPEPTIDASE (EC 3.4.24.57)

Enzymes in general

149	150	RXN02589	VV0098	16346	17110	Hypothetical Methyltransferase (EC 2.1.1.—)
151	152	F RXA02589	GR00741	13804	13040	Predicted S-adenosylmethionine-dependent methyltransferase
153	154	RXA00226	GR00032	26836	26012	SAM-dependent methyltransferases
155	156	RXN01885	VV0184	2004	2804	Hypothetical Methyltransferase (EC 2.1.1.—)
157	158	F RXA01885	GR00539	1589	2389	SAM-dependent methyltransferases
159	160	RXA02592	GR00741	18477	17707	SAM-dependent methyltransferases
161	162	RXN01795	VV0093	722	1318	MODIFIKATION METHYLASE (EC 2.1.1.73)
163	164	F RXA01795	GR00507	706	1140	MODIFICATION METHYLASE (EC 2.1.1.73)
165	166	RXA01214	GR00351	1640	3130	LACCASE 1 PRECURSOR (EC 1.10.3.2)
167	168	RXA01250	GR00364	592	5	LACCASE 1 PRECURSOR (EC 1.10.3.2)
169	170	RXA02477	GR00715	10581	11201	CARBONIC ANHYDRASE (EC 4.2.1.1)
171	172	RXN00833	GR00225	374	6	THIOL PEROXIDASE (EC 1.11.1.—)
173	174	F RXA00833	GR00225	374	6	THIOL PEROXIDASE (EC 1.11.1.—)
175	176	RXA01224	GR00354	4186	5208	2-NITROPROPANE DIOXYGENASE (EC 1.13.11.32)
177	178	RXA01182	GR00337	1363	971	Hypothetical Oxidoreductase
179	180	RXA02531	GR00726	1226	1936	Hypothetical Oxidoreductase
181	182	RXN00689	VV0005	22416	20926	BETAINE-ALDEHYDE DEHYDROGENASE PRECURSOR (EC 1.2.1.8)
183	184	F RXA00689	GR00180	1401	775	BETAINE-ALDEHYDE DEHYDROGENASE PRECURSOR (EC 1.2.1.8)
185	186	RXN03128	VV0120	3	857	MORPHINE 6-DEHYDROGENASE (EC 1.1.1.218)
187	188	F RXA02192	GR00643	2	523	MORPHINE 6-DEHYDROGENASE (EC 1.1.1.218)
189	190	RXA02351	GR00679	132	1070	NITRILOTRIACETATE MONOOXYGENASE
						COMPONENT A (EC 1.14.13.—)
191	192	RXN00905	VV0238	8075	8875	N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14)
193	194	F RXA00905	GR00247	2	694	N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14)
195	196	RXA00906	GR00247	630	1133	N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14)
197	198	RXA00907	GR00247	1143	1265	N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14)
199	200	RXA02101	GR00631	3104	1842	N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14)
201	202	RXN02565	VV0154	14299	13034	N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14)
203	204	F RXA02565	GR00733	1	342	N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14)
205	206	F RXA02567	GR00734	3	740	N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14)
207	208	RXN03077	VV0043	1729	2913	N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14)
209	210	F RXA02855	GR10002	1693	2877	N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14),
						hippurate hydrolase
211	212	RXA00026	GR00003	3657	5042	Hypothetical Amidohydrolase (EC 3.5.1.—)
213	214	RXA01971	GR00569	963	133	Hypothetical Metal-Dependent Hydrolase
215	216	RXA01802	GR00509	3461	4291	Predicted hydrolases (HAD superfamily)
217	218	RXN00866	VV0258	3557	4522	Predicted Zn-dependent hydrolases
219	220	F RXA00866	GR00236	3555	4499	Predicted Zn-dependent hydrolases
221	222	RXA02410	GR00703	792	127	Predicted Zn-dependent hydrolases
223	224	RXA00961	GR00267	2	433	SALICYLATE HYDROXYLASE (EC 1.14.13.1)
225	226	RXA00111	GR00016	930	1922	SOLUBLE EPOXIDE HYDROLASE (SEH) (EC 3.3.2.3)
227	228	RXA01932	GR00555	6479	5583	ACETYL-HYDROLASE (EC 3.1.1.—)
229	230	RXA02574	GR00739	833	1840	PUTATIVE SECRETED HYDROLASE
231	232	RXN00983	VV0231	1796	321	SIALIDASE PRECURSOR (EC 3.2.1.18)
233	234	F RXA00983	GR00278	1200	4	SIALIDASE PRECURSOR (EC 3.2.1.18)
235	236	RXA00984	GR00278	1716	1300	SIALIDASE PRECURSOR (EC 3.2.1.18)
237	238	RXN02513	VV0193	737	6	SIALIDASE PRECURSOR (EC 3.2.1.18)
239	240	F RXA02513	GR00722	93	824	SIALIDASE PRECURSOR (EC 3.2.1.18)
241	242	RXA00903	GR00246	637	5	Putative epimerase
243	244	RXA01224	GR00354	4186	5208	2-NITROPROPANE DIOXYGENASE (EC 1.13.11.32)
245	246	RXA01571	GR00438	1360	1959	ALCOHOL DEHYDROGENASE (EC 1.1.1.1)
247	248	RXN02478	VV0119	7564	6350	SIALIDASE PRECURSOR (EC 3.2.1.18)
249	250	RXN00343	VV0125	1118	6	3-OXOSTEROID 1-DEHYDROGENASE (EC 1.3.99.4)
251	252	RXN01555	VV0135	29820	28861	3-OXOSTEROID 1-DEHYDROGENASE (EC 1.3.99.4)
253	254	RXN01166	VV0117	18142	16838	EXTRACELLULAR LIPASE PRECURSOR (EC 3.1.1.3)
255	256	RXN02001	VV0326	630	1787	N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14)
257	258	RXN03145	VV0142	7561	7115	4-OXALOCROTONATE TAUTOMERASE (EC 5.3.2.—)
259	260	RXN01466	VV0019	7050	6091	ARYLESTERASE (EC 3.1.1.2)
261	262	RXN01145	VV0077	7538	6525	KETOL-ACID REDUCTOISOMERASE (EC 1.1.1.86)
263	264	RXN03088	VV0052	3431	3817	Hypothetical Methyltransferase (EC 2.1.1.—)
265	266	RXN02952	VV0320	1032	1547	PUTATIVE REDUCTASE
267	268	RXN00513	VV0092	1573	653	CARBOXYVINYL-CARBOXYPHOSPHONATE
						PHOSPHORYLMUTASE (EC 2.7.8.23)
269	270	RXN01152	VV0136	1740	907	PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE (EC 2.1.1.77)
271	272	RXN00787	VV0321	3736	5637	D-AMINO ACID DEHYDROGENASE LARGE SUBUNIT (EC 1.4.99.1)

N-metabolism

273	274	RXN01302	VV0148	2837	2385	NITRATE REDUCTASE ALPHA CHAIN (EC 1.7.99.4)
275	276	F RXA01302	GR00376	370	5	NITRATE REDUCTASE ALPHA CHAIN (EC 1.7.99.4)
277	278	RXN01308	VV0148	2406	4	NITRATE REDUCTASE ALPHA CHAIN (EC 1.7.99.4)
279	280	F RXA01307	GR00377	686	6	NITRATE REDUCTASE ALPHA CHAIN (EC 1.7.99.4)
281	282	F RXA01308	GR00378	1211	6	NITRATE REDUCTASE ALPHA CHAIN (EC 1.7.99.4)
283	284	RXN01309	VV0158	1	801	NITRATE REDUCTASE ALPHA CHAIN (EC 1.7.99.4)
285	286	F RXA01309	GR00379	719	51	NITRATE REDUCTASE ALPHA CHAIN (EC 1.7.99.4)
287	288	RXA02017	GR00610	1731	1048	NITRATE REDUCTASE ALPHA CHAIN (EC 1.7.99.4)
289	290	RXA02018	GR00610	2788	1739	NITRATE REDUCTASE BETA CHAIN (EC 1.7.99.4)
291	292	RXA02016	GR00610	1036	260	NITRATE REDUCTASE GAMMA CHAIN (EC 1.7.99.4)
293	294	RXA00471	GR00119	2997	3686	NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL
295	296	RXA00133	GR00021	201	1013	NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARP
297	298	RXA00650	GR00169	4017	3382	NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARP
299	300	RXA01189	GR00339	2545	1937	NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARP
301	302	RXA01607	GR00449	123	752	NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARP
303	304	RXN00470	VV0086	27401	28669	NITRATE/NITRITE SENSOR PROTEIN NARX (EC 2.7.3.—)
305	306	F RXA00470	GR00119	1752	2951	NITRATE/NITRITE SENSOR PROTEIN NARX (EC 2.7.3.—)
307	308	RXA00756	GR00203	2932	1937	N UTILIZATION SUBSTANCE PROTEIN A
309	310	RXA00139	GR00022	2514	3224	N UTILIZATION SUBSTANCE PROTEIN B
311	312	RXA01303	GR00376	1724	390	NITRITE EXTRUSION PROTEIN
313	314	RXA01412	GR00412	620	417	NITROGEN FIXATION PROTEIN FIXI (PROBABLE E1-E2 TYPE
						CATION ATPASE) (EC 3.6.1.—)
315	316	RXA00773	GR00205	3208	4350	NITROGEN REGULATION PROTEIN NIFR3
317	318	RXA02746	GR00764	1	267	NITROGEN REGULATORY PROTEIN P-II
319	320	RXA02745	GR00763	15350	14472	NODULATION ATP-BINDING PROTEIN I
321	322	RXN00820	VV0054	19455	19817	NODULATION PROTEIN N
323	324	F RXA00820	GR00221	1007	1369	NODULATION PROTEIN N
325	326	RXA01059	GR00296	8782	9390	OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE (EC 1.—.—.—)
327	328	RXN01386	VV0008	39246	38317	NITRILASE REGULATOR
329	330	RXN00073	VV0154	2369	687	FERREDOXIN-NITRITE REDUCTASE (EC 1.7.7.1)
331	332	RXN03131	VV0127	276	4	RHIZOPINE CATABOLISM PROTEIN MOCC
333	334	RXS00153	VV0167	4195	4620	NODULATION PROTEIN

Urease

Phosphate and Phosphonate metabolism

335	336	RXN01716	VV0319	3259	2774	EXOPOLYPHOSPHATASE (EC 3.6.1.11)
337	338	RXN02972	VV0319	2763	2353	EXOPOLYPHOSPHATASE (EC 3.6.1.11)
339	340	RXN00663	VV0142	10120	11493	PHOH PROTEIN HOMOLOG
341	342	RXN00778	VV0103	18126	19250	PHOSPHATE-BINDING PERIPLASMIC PROTEIN PRECURSOR
343	344	RXN00250	VV0189	286	1032	DEDA PROTEIN - ALKALINE PHOSPHATASE LIKE PROTEIN

Sulfate metabolism

345	346	RXA00072	GR00012	446	6	PHOSPHOADENOSINE PHOSPHOSULFATE REDUCTASE (EC 1.8.99.4)
347	348	RXA00793	GR00211	1469	2644	SULFATE STARVATION-INDUCED PROTEIN 6
349	350	RXA01192	GR00342	161	733	SULFATE STARVATION-INDUCED PROTEIN 6
351	352	RXA00715	GR00188	2120	2914	THIOSULFATE SULFURTRANSFERASE (EC 2.8.1.1)
353	354	RXA01664	GR00463	1306	485	THIOSULFATE SULFURTRANSFERASE (EC 2.8.1.1)
355	356	RXN02334	VV0141	7939	7217	THIOSULFATE SULFURTRANSFERASE (EC 2.8.1.1)
357	358	F RXA02334	GR00672	2	355	THIOSULFATE SULFURTRANSFERASE (EC 2.8.1.1)

Fe-Metabolism

359	360	RXN01499	VV0008	7034	3213	ENTEROBACTIN SYNTHETASE COMPONENT F
361	362	RXN01997	VV0084	33308	33793	FERRITIN

Mg Metabolism

363	364	RXA01848	GR00524	1532	789	MAGNESIUM-CHELATASE SUBUNIT CHLI
365	366	RXN01849	VV0139	16415	17515	MAGNESIUM-CHELATASE SUBUNIT CHLI
367	368	F RXA01849	GR00524	2004	1555	MAGNESIUM-CHELATASE SUBUNIT CHLI
369	370	F RXA01691	GR00474	570	4	MAGNESIUM-CHELATASE SUBUNIT CHLI
371	372	RXN00665	VV0252	135	635	MG2+/CITRATE COMPLEX SECONDARY TRANSPORTER

Modification and degradation of aromatic compounds

373	374	RXN03026	VV0007	28635	28901	3-DEHYDROQUINATE DEHYDRATASE (EC 4.2.1.10)
375	376	RXN02908	VV0025	8507	8247	O-SUCCINYLBENZOIC ACID—COA LIGASE (EC 6.2.1.26)
377	378	RXN03000	VV0235	570	4	SALICYLATE HYDROXYLASE (EC 1.14.13.1)
379	380	RXN03036	VV0014	671	6	PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN (EC 1.13.11.3)
381	382	RXN02974	VV0229	12631	12437	4-NITROPHENYLPHOSPHATASE (EC 3.1.3.41)
383	384	RXN00393	VV0025	7241	6348	1,4-DIHYDROXY-2-NAPHTHOATE
						OCTAPRENYLTRANSFERASE (EC 2.5.—.—)
385	386	RXN00948	VV0107	4266	5384	12-oxophytodienoate reductase (EC 1.3.1.42)
387	388	RXN01923	VV0020	3384	4133	2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE
						HYDROLASE (EC 3.7.1.—)
389	390	RXN00398	VV0025	14633	13884	2-PYRONE-4,6-DICARBOXYLATE LACTONASE (EC 3.1.1.57)
391	392	RXN02813	VV0128	13120	14118	3-CARBOXY-CIS,CIS-MUCONATE CYCLOISOMERASE
						HOMOLOG (EC 5.5.1.2)
393	394	RXN00136	VV0134	13373	14467	3-DEHYDROQUINATE SYNTHASE (EC 4.6.1.3)
395	396	RXN02508	VV0007	26733	28586	3-DEHYDROSHIKIMATE DEHYDRATASE (EC 4.2.1.—)
397	398	RXN02839	VV0362	3	449	4-HYDROXYBENZOATE OCTAPRENYLTRANSFERASE (EC 2.5.1.—)
399	400	RXN00639	VV0128	7858	8712	CATECHOL 1,2-DIOXYGENASE (EC 1.13.11.1)
401	402	RXN02530	VV0057	5469	6125	DIMETHYLANILINE MONOOXYGENASE
						(N-OXIDE FORMING) 1 (EC 1.14.13.8)
403	404	RXN00434	VV0112	12078	11212	QUINONE OXIDOREDUCTASE (EC 1.6.5.5)
405	406	RXN01619	VV0050	24649	23675	QUINONE OXIDOREDUCTASE (EC 1.6.5.5)
407	408	RXN01842	VV0234	1615	2532	QUINONE OXIDOREDUCTASE (EC 1.6.5.5)
409	410	RXN00641	VV0128	7440	5950	TOLUATE 1,2-DIOXYGENASE ALPHA SUBUNIT (EC 1.14.12.—)
411	412	RXN01993	VV0182	16	1143	VANILLATE DEMETHYLASE (EC 1.14.—.—)
413	414	RXN00658	VV0083	15705	16397	PHENOL 2-MONOOXYGENASE (EC 1.14.13.7)
415	416	RXN00178	VV0174	14670	15554	hydroxyquinol 1,2-dioxygenase (EC 1.13.11.37)
417	418	RXN01461	VV0128	12414	13025	PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN (EC 1.13.11.3)
419	420	RXN01653	VV0321	12867	11407	DIBENZOTHIOPHENE DESULFURIZATION ENZYME A
421	422	RXN02053	VV0009	39448	40026	DRGA PROTEIN
423	424	RXN00177	VV0174	13589	14656	MALEYLACETATE REDUCTASE (EC 1.3.1.32)
425	426	RXC00963	VV0249	1816	2652	PROTEIN involved in degradation of aromatic compounds

Modification and degradation of aliphatic compounds

427	428	RXN00299	VV0176	43379	42402	ALKANAL MONOOXYGENASE ALPHA CHAIN (EC 1.14.14.3)
429	430	F RXA00299	GR00048	7376	6633	ALKANAL MONOOXYGENASE ALPHA CHAIN (EC 1.14.14.3)
431	432	RXA00332	GR00057	16086	15385	ALKANAL MONOOXYGENASE ALPHA CHAIN (EC 1.14.14.3)
433	434	RXA01838	GR00519	2	820	ALKANAL MONOOXYGENASE ALPHA CHAIN (EC 1.14.14.3)
435	436	RXA02643	GR00750	1603	560	ALKANAL MONOOXYGENASE ALPHA CHAIN (EC 1.14.14.3)
437	438	RXA01933	GR00555	6590	7192	2-HALOALKANOIC ACID DEHALOGENASE I (EC 3.8.1.2)
439	440	RXA02351	GR00679	132	1070	NITRILOTRIACETATE MONOOXYGENASE
						COMPONENT A (EC 1.14.13.—)

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
		phosphoribosyltransferase; GTP	(p)ppGpp metabolism,” Microbiology, 144: 1853-1862 (1998)
		pyrophosphokinase
AF041436	argR	Arginine repressor
AF045998	impA	Inositol monophosphate phosphatase
AF048764	argH	Argininosuccinate lyase
AF049897	argC; argJ; argB; argD; argF;	N-acetylglutamylphosphate reductase;
	argR; argG; argH	ornithine acetyltransferase; N-
		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
		proline	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)
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;	Involved in cell division; PII protein;	Jakoby, M. et al. “Nitrogen regulation in Corynebacterium glutamicum;
	amtP	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
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E04377		Isocitric acid lyase N-terminal fragment	Katsumata, R. et al. “Gene manifestation controlling DNA,” Patent: JP
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E04484		Prephenate dehydratase	Sotouchi, N. et al. “Production of L-phenylalanine by fermentation,” Patent: JP
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E05108		Aspartokinase	Fugono, N. et al. “Gene DNA coding Aspartokinase and its use,” Patent: JP
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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
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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
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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
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L07603	EC 4.2.1.15	3-deoxy-D-arabinoheptulosonate-7-	Chen, C. et al. “The cloning and nucleotide sequence of Corynebacterium
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L09232	IlvB; ilvN; ilvC	Acetohydroxy acid synthase large subunit;	Keilhauer, C. et al. “Isoleucine synthesis in Corynebacterium glutamicum:
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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.
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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
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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.
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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
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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
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			Corynebacterium glutamicum cglIM gene encoding a 5-cytosine in an McrBC-
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U14965	recA
U31224	ppx		Ankri, S. et al. “Mutations in the Corynebacterium glutamicumproline
			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 glutamicumproline
			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 glutamicumproline
		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.,
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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;	Tryptophan operon	Matsui, K. et al. “Complete nucleotide and deduced amino acid sequences of
	trpE; trpG; trpL		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.
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X14234	EC 4.1.1.31	Phosphoenolpyruvate carboxylase	Eikmanns, B. J. et al. “The Phosphoenolpyruvate carboxylase gene of
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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.
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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,
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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
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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
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			(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
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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.
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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.
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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.
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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 glutamicumproline 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
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	keto glutamicum	21004
Brevibacterium	keto glutamicum	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	aceto glutamicum			B11473
Corynebacterium	aceto glutamicum			B11475
Corynebacterium	aceto glutamicum	15806
Corynebacterium	aceto glutamicum	21491
Corynebacterium	aceto glutamicum	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 (4^thedn), 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

rxa00026	1509	GB_RO: MMHC310M6	158405	AF109906	Mus musculus MHC class III region RD gene, partial cds; Bf, C2, G9A,	Mus musculus	38,003	10-DEC-1998
					NG22, G9, HSP70, HSP70, HSC70t, and smRNP genes, complete
					cds; G7A gene, partial cds; and unknown genes.
		GB_HTG2: AC007029	119007	AC007029	Homo sapiens clone DJ0855F16, *** SEQUENCING IN PROGRESS	Homo sapiens	37,943	7-Apr-99
					***, 1 unordered pieces.
		GB_HTG2: AC007029	119007	AC007029	Homo sapiens clone DJ0855F16, *** SEQUENCING IN PROGRESS	Homo sapiens	37,943	7-Apr-99
					***, 1 unordered pieces.
rxa00072
rxa00111	1116	GB_BA1: SAUSIGA	2748	M94370	Stigmatella aurantiaca sigma factor (sigA) gene, complete cds.	Stigmatella aurantiaca	40,435	16-Aug-94
		GB_BA1: SC5B8	28500	AL022374	Streptomyces coelicolor cosmid 5B8.	Streptomyces coelicolor	40,090	22-Apr-98
		GB_BA2: AE001767	9086	AE001767	Thermotoga maritima section 79 of 136 of the complete genome.	Thermotoga maritima	35,091	2-Jun-99
rxa00112	1314	GB_EST35: AU075536	418	AU075536	AU075536 Rice shoot Oryza sativa cDNA clone S0028_2Z, mRNA	Oryza sativa	39,423	7-Jul-99
					sequence.
		GB_GSS9: AQ157585	647	AQ157585	nbxb0009B16r CUGI Rice BAC Library Oryza sativa genomic clone	Oryza sativa	40,867	12-Sep-98
					nbxb0009B16r, genomic survey sequence.
		GB_GSS14: AQ510314	542	AQ510314	nbxb0095O05f CUGI Rice BAC Library Oryza sativa genomic clone	Oryza sativa	39,372	04-MAY-1999
					nbxb0095O05f, genomic survey sequence.
rxa00133	936	GB_BA1: SC2G5	38404	AL035478	Streptomyces coelicolor cosmid 2G5.	Streptomyces coelicolor	41,170	11-Jun-99
		GB_EST7: W64291	515	W64291	md98h12.r1 Soares mouse embryo NbME13.5 14.5 Mus musculus	Mus musculus	35,306	10-Jun-96
					cDNA clone IMAGE: 386087 5′ similar to gb: L26528 Mus musculus
					Rab11b mRNA, complete cds (MOUSE);, mRNA sequence.
		GB_PR3: AC005624	39594	AC005624	Homo sapiens chromosome 19, cosmid R30017, complete sequence.	Homo sapiens	39,054	6-Sep-98
rxa00137	1212	GB_BA2: AF124600	4115	AF124600	Corynebacterium glutamicum chorismate synthase (aroC), shikimate	Corynebacterium	99,867	04-MAY-1999
					kinase (aroK), and 3-dehydroquinate synthase (aroB) genes, complete	glutamicum
					cds; and putative cytoplasmic peptidase (pepQ) gene, partial cds.
		GB_BA1: MTCY159	33818	Z83863	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	40,959	17-Jun-98
					111/162.	tuberculosis
		GB_BA1: MT3DEHQ	3437	X59509	M. tuberculosis, genes for 3-dehydroquinate synthase and 3-	Mycobacterium	52,583	30-Jun-93
					dehydroquinase.	tuberculosis
rxa00139	834	GB_BA1: BLELONP	738	X99289	B. lactofermentum gene encoding elongation factor P.	Corynebacterium	100,000	1-Nov-97
						glutamicum
		GB_PL1: SPAC24C9	38666	Z98601	S. pombe chromosome I cosmid c24C9.	Schizosaccharomyces	35,230	24-Feb-99
						pombe
		GB_HTG1: CEY102A5_1	110000	Z99711	Caenorhabditis elegans chromosome V clone Y102A5, ***	Caenorhabditis elegans	37,775	Z99711
					SEQUENCING IN PROGRESS ***, in unordered pieces.
rxa00152	1419	GB_BA1: MTCY277	38300	Z79701	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	58,500	17-Jun-98
					65/162.	tuberculosis
		GB_BA1: MSGY456	37316	AD000001	Mycobacterium tuberculosis sequence from clone y456.	Mycobacterium	38,913	03-DEC-1996
						tuberculosis
		GB_BA2: AF002133	15437	AF002133	Mycobacterium avium strain GIR10 transcriptional regulator (mav81)	Mycobacterium avium	64,009	26-MAR-1998
					gene, partial cds, aconitase (acn), invasin 1 (inv1), invasin 2 (inv2),
					transcriptional regulator (moxR), ketoacyl-reductase (fabG), enoyl-
					reductase (inhA) and ferrochelatase (mav272) genes, complete cds.
rxa00226	948	GB_PR3: AC005756	43299	AC005756	Homo sapiens chromosome 19, fosmid 39347, complete sequence.	Homo sapiens	36,209	02-OCT-1998
		GB_GSS5: AQ818463	413	AQ818463	HS_5250_A2_B08_SP6E RPCI-11 Human Male BAC Library Homo	Homo sapiens	37,288	26-Aug-99
					sapiens genomic clone Plate = 826 Col = 16 Row = C, genomic survey
					sequence.
		GB_GSS5: AQ782337	832	AQ782337	HS_3184_B1_H12_T7C CIT Approved Human Genomic Sperm	Homo sapiens	35,917	2-Aug-99
					Library D Homo sapiens genomic clone Plate = 3184 Col = 23 Row = P,
					genomic survey sequence.
rxa00249	980	GB_BA2: AF035608	3614	AF035608	Pseudomonas aeruginosa ATP sulfurylase small subunit (cysD) and	Pseudomonas aeruginosa	50,205	1-Jun-98
					ATP sulfurylase GTP-binding subunit/APS kinase (cysN) genes,
					complete cds.
		GB_BA1: AB017641	17101	AB017641	Micromonospora griseorubida gene for polyketide synthase, complete	Micromonospora	40,266	2-Apr-99
					cds.	griseorubida
		GB_BA2: AF002133	15437	AF002133	Mycobacterium avium strain GIR10 transcriptional regulator (mav81)	Mycobacterium avium	38,429	26-MAR-1998
					gene, partial cds, aconitase (acn), invasin 1 (inv1), invasin 2 (inv2),
					transcriptional regulator (moxR), ketoacyl-reductase (fabG), enoyl-
					reductase (inhA) and ferrochelatase (mav272) genes, complete cds.
rxa00299	1101	GB_BA2: CORCSLYS	2821	M89931	Corynebacterium glutamicum beta C-S lyase (aecD) and branched-	Corynebacterium	100,000	4-Jun-98
					chain amino acid uptake carrier (brnQ) genes, complete cds, and	glutamicum
					hypothetical protein Yhbw (yhbw) gene, partial cds.
		GB_BA1: CGECTP	2719	AJ001436	Corynebacterium glutamicum ectP gene.	Corynebacterium	41,143	20-Nov-98
						glutamicum
		GB_BA2: AF181035	5922	AF181035	Rhodobacter sphaeroides glycogen utilization operon, complete	Rhodobacter sphaeroides	36,701	7-Sep-99
					sequence.
rxa00332	825	GB_BA1: CGTHRC	3120	X56037	Corynebacterium glutamicum thrC gene for threonine synthase (EC	Corynebacterium	37,730	17-Jun-97
					4.2.99.2).	glutamicum
		GB_PAT: I09078	3146	I09078	Sequence 4 from Patent WO 8809819.	Unknown.	38,700	02-DEC-1994
		GB_PR3: HSJ333B15	73666	AL109954	Human DNA sequence from clone 333B15 on chromosome 20,	Homo sapiens	37,203	23-Nov-99
					complete sequence.
rxa00470	1392	GB_PL2: DCPCNAM	865	X62977	D. carota mRNA for proliferating cell nuclear antigen (PCNA).	Daucus carota	37,914	30-Sep-99
		GB_PL2: AC006267	101644	AC006267	Arabidopsis thaliana BAC F9M13 from chromosome IV near 21.5 cM,	Arabidopsis thaliana	36,158	27-Apr-99
					complete sequence.
		GB_BA1: TT10SARNA	721	Y15063	Thermus thermophilus 10Sa RNA gene.	Thermus thermophilus	39,494	18-Aug-98
rxa00471	813	GB_BA1: SERERYAA	11219	M63676	S. erythraea first ORF of eryA gene, complete cds.	Saccharopolyspora	38,781	26-Apr-93
						erythraea
		GB_PAT: AR049367	11219	AR049367	Sequence 1 from patent U.S. Pat. No. 5824513.	Unknown.	38,781	29-Sep-99
		GB_BA1: SERERYAA	11219	M63676	S. erythraea first ORF of eryA gene, complete cds.	Saccharopolyspora	38,205	26-Apr-93
						erythraea
rxa00499	1404	GB_PR4: AC007206	42732	AC007206	Homo sapiens chromosome 19, cosmid R27370, complete sequence.	Homo sapiens	34,982	4-Apr-99
		GB_EST26: AI344735	462	AI344735	qp05a10.x1 NCI_CGAP_Kid5 Homo sapiens cDNA clone	Homo sapiens	42,675	2-Feb-99
					IMAGE: 1917114 3′ similar to gb: M15800 T-LYMPHOCYTE
					MATURATION-ASSOCIATED PROTEIN (HUMAN);, mRNA
					sequence.
		GB_PR4: AC006479	161837	AC006479	Homo sapiens clone DJ1051J04, complete sequence.	Homo sapiens	38,462	11-Nov-99
rxa00500	798	GB_PR4: AC006111	190825	AC006111	Homo sapiens chromosome 16 clone RPCI-11_461A8, complete	Homo sapiens	40,736	3-Jul-99
					sequence.
		GB_HTG2: AF128834	196589	AF128834	Homo sapiens chromosome 8 clone BAC 57G24 map 8p12, ***	Homo sapiens	34,062	28-Feb-99
					SEQUENCING IN PROGRESS ***, in unordered pieces.
		GB_HTG2: AF128834	196589	AF128834	Homo sapiens chromosome 8 clone BAC 57G24 map 8p12, ***	Homo sapiens	34,062	28-Feb-99
					SEQUENCING IN PROGRESS ***, in unordered pieces.
rxa00501	630	GB_BA1: D86429	5925	D86429	Saccharopolyspora rectivirgula gene for beta-galactosidase, complete	Saccharopolyspora	53,871	09-DEC-1998
					cds.	rectivirgula
		GB_HTG1: HS1099D15	1301	AL035456	Homo sapiens chromosome 20 clone RP5-1099D15, ***	Homo sapiens	33,546	23-Nov-99
					SEQUENCING IN PROGRESS ***, in unordered pieces.
		GB_HTG1: HS1099D15	1301	AL035456	Homo sapiens chromosome 20 clone RP5-1099D15, ***	Homo sapiens	33,546	23-Nov-99
					SEQUENCING IN PROGRESS ***, in unordered pieces.
rxa00502	1155	GB_BA2: U00015	42325	U00015	Mycobacterium leprae cosmid B1620.	Mycobacterium leprae	34,783	01-MAR-1994
		GB_BA1: U00020	36947	U00020	Mycobacterium leprae cosmid B229.	Mycobacterium leprae	34,900	01-MAR-1994
		GB_HTG1: HS179I15	210672	Z84464	Homo sapiens chromosome 13 clone 179I15, *** SEQUENCING IN	Homo sapiens	32,898	22-Jan-97
					PROGRESS ***, in unordered pieces.
rxa00566	729	GB_BA1: MTV008	63033	AL021246	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	37,011	17-Jun-98
					108/162.	tuberculosis
		GB_BA2: AF071885	2188	AF071885	Streptomyces coelicolor ATP-dependent Clp protease proteolytic	Streptomyces coelicolor	62,963	29-Jun-99
					subunit 1 (clpP1) and ATP-dependent Clp protease proteolytic subunit
					2 (clpP2) genes, complete cds; and ATP-dependent Clp
					protease ATP-binding subunit Clpx (clpX) gene, partial cds.
		GB_BA2: AF013216	15742	AF013216	Myxococcus xanthus Dog (dog), isocitrate lyase (icl), Mls (mls), Ufo	Myxococcus xanthus	54,683	28-Jan-98
					(ufo), fumarate hydratase (fhy), and proteosome major subunit (clpP)
					genes, complete cds; and acyl-CoA oxidase (aco) gene, partial cds.
rxa00567	714	GB_BA1: MTV008	63033	AL021246	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	42,090	17-Jun-98
					108/162.	tuberculosis
		GB_BA1: CGBPHI16	962	Y12472	C. glutamicum DNA, attachment site bacteriophage Phi-16.	Corynebacterium	40,000	05-MAR-1999
						glutamicum
		GB_BA1: ECOCLPPA	1236	J05534	Escherichia coli ATP-dependent clp protease proteolytic component	Escherichia coli	52,119	26-Apr-93
					(clpP) gene, complete cds.
rxa00621	906	GB_EST1: D36491	360	D36491	CELK033GYF Yuji Kohara unpublished cDNA Caenorhabditis elegans	Caenorhabditis elegans	40,390	8-Aug-94
					cDNA clone yk33g11 5′, mRNA sequence.
		GB_IN2: CELC16A3	34968	U41534	Caenorhabditis elegans cosmid C16A3.	Caenorhabditis elegans	35,477	18-MAY-1999
		GB_HTG3: AC009311	160198	AC009311	Homo sapiens clone NH0311L03, *** SEQUENCING IN PROGRESS	Homo sapiens	38,636	13-Aug-99
					***, 3 unordered pieces.
rxa00622	1539	GB_BA1: AB004795	3039	AB004795	Pseudomonas sp. gene for dipeptidyl aminopeptidase, complete cds.	Pseudomonas sp.	54,721	5-Feb-99
		GB_BA1: MBOPII	2392	D38405	Moraxella lacunata gene for protease II, complete cds.	Moraxella lacunata	50,167	8-Feb-99
		GB_IN2: AF078916	2960	AF078916	Trypanosoma brucei brucei oligopeptidase B (opb) gene, complete	Trypanosoma brucei	48,076	08-OCT-1999
					cds.	brucei
rxa00650	759	GB_BA2: AF161327	2021	AF161327	Corynebacterium diphtheriae histidine kinase ChrS (chrS) and	Corynebacterium	51,319	9-Sep-99
					response regulator ChrA (chrA) genes, complete cds.	diphtheriae
		GB_PL2: ATAC006533	99188	AC006533	Arabidopsis thaliana chromosome II BAC F20M17 genomic sequence,	Arabidopsis thaliana	38,051	26-MAY-1999
					complete sequence.
		GB_PL2: ATAC006533	99188	AC006533	Arabidopsis thaliana chromosome II BAC F20M17 genomic sequence,	Arabidopsis thaliana	35,403	26-MAY-1999
					complete sequence.
rxa00675	915	GB_BA1: SC3C8	33095	AL023861	Streptomyces coelicolor cosmid 3C8.	Streptomyces coelicolor	36,836	15-Jan-99
		GB_PR3: AC005736	215441	AC005736	Homo sapiens chromosome 16, BAC clone 462G18 (LANL), complete	Homo sapiens	42,027	01-OCT-1998
					sequence.
		GB_IN2: AC005719	188357	AC005719	Drosophila melanogaster, chromosome 2L, region 38A5-38B4, BAC	Drosophila melanogaster	35,531	27-OCT-1999
					clone BACR48M05, complete sequence.
rxa00689	1614	GB_PAT: E07294	2975	E07294	genomic DNA encoding dehydrogenase of Bacillus	Bacillus	45,677	29-Sep-97
					stearothermophilus.	stearothermophilus
		GB_BA1: BACALDHT	1975	D13846	B. stearothermophilus aldhT gene for aldehyde dehydrogenase,	Bacillus	45,677	20-Feb-99
					complete cds.	stearothermophilus
		GB_BA2: PPU96338	5276	U96338	Pseudomonas putida NCIMB 9866 plasmid pRA4000 p-cresol	Pseudomonas putida	44,317	13-MAY-1999
					degradative pathway genes, p-hydroxybenzaldehyde dehydrogenase
					(pchA), p-cresol methylhydroxylase, cytochrome subunit precursor
					(pchC), unknown (pchX) and p-cresol methylhydroxylase, flavoprotein
					subunit (pchF) genes, complete cds.
rxa00715	918	GB_EST30: AI647104	218	AI647104	vn15c01.y1 Stratagene mouse heart (#937316) Mus musculus cDNA	Mus musculus	58,511	29-Apr-99
					clone IMAGE: 1021248 5′, mRNA sequence.
		GB_EST17: AA636159	447	AA636159	vn15c01.r1 Stratagene mouse heart (#937316) Mus musculus cDNA	Mus musculus	41,195	22-OCT-1997
					clone IMAGE: 1021248 5′, mRNA sequence.
		GB_EST10: AA184468	583	AA184468	mt52h05.r1 Stratagene mouse embryonic carcinoma (#937317) Mus	Mus musculus	40,426	12-Feb-97
					musculus cDNA clone IMAGE: 633561 5′ similar to gb: D10918 Mouse
					mRNA for ubiquitin like protein, partial sequence (MOUSE);, mRNA
					sequence.
rxa00744	1065	GB_HTG3: AC009855	167592	AC009855	Homo sapiens clone 1_C_5, * SEQUENCING IN PROGRESS *,	Homo sapiens	36,673	3-Sep-99
					13 unordered pieces.
		GB_HTG3: AC009855	167592	AC009855	Homo sapiens clone 1_C_5, * SEQUENCING IN PROGRESS *,	Homo sapiens	36,673	3-Sep-99
					13 unordered pieces.
		GB_PR4: AC005082	169739	AC005082	Homo sapiens clone RG271G13, complete sequence.	Homo sapiens	39,557	8-Sep-99
rxa00756	1119	GB_BA1: MLCB596	38426	AL035472	Mycobacterium leprae cosmid B596.	Mycobacterium leprae	54,562	27-Aug-99
		GB_GSS12: AQ368028	652	AQ368028	toxb0001N11rCUGI Tomato BAC Library Lycopersicon esculentum	Lycopersicon esculentum	42,657	5-Feb-99
					genomic clone toxb0001N11r, genomic survey sequence.
		GB_HTG3: AC008067	151242	AC008067	Homo sapiens clone NH0303104, *** SEQUENCING IN PROGRESS	Homo sapiens	37,239	8-Sep-99
					***, 2 unordered pieces.
rxa00773	1266	GB_BA1: MLU15182	40123	U15182	Mycobacterium leprae cosmid B2266.	Mycobacterium leprae	36,616	09-MAR-1995
		GB_BA1: MSGL611CS	37769	L78822	Mycobacterium leprae cosmid L611 DNA sequence.	Mycobacterium leprae	35,714	15-Jun-96
		GB_GSS14: AQ578181	728	AQ578181	nbxb0083P08r CUGI Rice BAC Library Oryza sativa genomic clone	Oryza sativa	39,246	2-Jun-99
					nbxb0083P08r, genomic survey sequence.
rxa00793	1299	GB_GSS5: AQ769737	519	AQ769737	HS_3160_A2_G04_T7C CIT Approved Human Genomic Sperm	Homo sapiens	37,765	28-Jul-99
					Library D Homo sapiens genomic clone Plate = 3160 Col = 8 Row = M,
					genomic survey sequence.
		GB_BA1: RTU08434	2400	U08434	Rhizobium trifolii orotate phosphoribosyltransferase (pyrE) and	Rhizobium trifolii	40,700	16-Apr-97
					fructokinase (frk) genes, complete cds.
		GB_EST31: F33810	243	F33810	HSPD27491 HM3 Homo sapiens cDNA clone s3000041E12, mRNA	Homo sapiens	41,564	13-MAY-1999
					sequence.
rxa00820	486	GB_PR4: AC005868	96180	AC005868	Homo sapiens 12q24.2 PAC RPCI5-944M2 (Roswell Park Cancer	Homo sapiens	32,298	27-Feb-99
					Institute Human PAC Library) complete sequence.
		GB_EST8: AA000903	396	AA000903	mg38b04.r1 Soares mouse embryo NbME13.5 14.5 Mus musculus	Mus musculus	42,045	18-Jul-96
					cDNA clone IMAGE: 426031 5′, mRNA sequence.
		GB_EST25: AI317789	696	AI317789	uj20g09.y1 Sugano mouse embryo mewa Mus musculus cDNA clone	Mus musculus	38,557	17-DEC-1998
					IMAGE: 1920544 5′ similar to WP: C13C4.5 CE08130 SUGAR
					TRANSPORTER;, mRNA sequence.
rxa00833	618	GB_PH: BPH6589	41489	AJ006589	Bacteriophage phi-C31 complete genome.	Bacteriophage phi-C31	41,806	29-Apr-99
		GB_HTG2: AC006887	215801	AC006887	Caenorhabditis elegans clone Y59H11, *** SEQUENCING IN	Caenorhabditis elegans	35,798	24-Feb-99
					PROGRESS ***, 3 unordered pieces.
		GB_HTG2: AC006887	215801	AC006887	Caenorhabditis elegans clone Y59H11, *** SEQUENCING IN	Caenorhabditis elegans	35,798	24-Feb-99
					PROGRESS ***, 3 unordered pieces.
rxa00844	957	GB_GSS15: AQ605195	459	AQ605195	HS_2136_B1_C12_T7C CIT Approved Human Genomic Sperm	Homo sapiens	38,074	10-Jun-99
					Library D Homo sapiens genomic clone Plate = 2136 Col = 23 Row = F,
					genomic survey sequence.
		GB_HTG1: CNS00M8S	214599	AL079302	Homo sapiens chromosome 14 clone R-1089B7, *** SEQUENCING	Homo sapiens	38,120	15-OCT-1999
					IN PROGRESS ***, in ordered pieces.
		GB_HTG1: CNS00M8S	214599	AL079302	Homo sapiens chromosome 14 clone R-1089B7, *** SEQUENCING	Homo sapiens	38,120	15-OCT-1999
					IN PROGRESS ***, in ordered pieces.
rxa00866	1066	GB_BA1: CGORF4GEN	2398	X95649	C. glutamicum ORF4 gene.	Corynebacterium	99,273	10-MAR-1998
						glutamicum
		GB_BA1: BLDAPAB	3572	Z21502	B. lactofermentum dapA and dapB genes for dihydrodipicolinate	Corynebacterium	99,301	16-Aug-93
					synthase and dihydrodipicolinate reductase.	glutamicum
		GB_PAT: E14517	1411	E14517	DNA encoding Brevibacterium dihydrodipicolinic acid reductase.	Corynebacterium	99,659	28-Jul-99
						glutamicum
rxa00877	1788	GB_PAT: I92050	567	I92050	Sequence 17 from patent U.S. Pat. No. 5726299.	Unknown.	62,787	01-DEC-1998
		GB_PAT: I78760	567	I78760	Sequence 16 from patent U.S. Pat. No. 5693781.	Unknown.	62,787	3-Apr-98
		GB_BA2: AE000426	10240	AE000426	Escherichia coli K-12 MG1655 section 316 of 400 of the complete	Escherichia coli	36,456	12-Nov-98
					genome.
rxa00903	733	GB_BA2: AE001598	11136	AE001598	Chlamydia pneumoniae section 14 of 103 of the complete genome.	Chlamydophila	32,782	08-MAR-1999
						pneumoniae
		GB_PL2: AF079370	2897	AF079370	Kluyveromyces lactis invertase (INV1) gene, complete cds.	Kluyveromyces lactis	35,849	4-Aug-99
		GB_BA2: AE001598	11136	AE001598	Chlamydia pneumoniae section 14 of 103 of the complete genome.	Chlamydophila	40,138	08-MAR-1999
						pneumoniae
rxa00905	924	GB_PR2: HSQ15C24	73192	AJ239325	Homo sapiens chromosome 21 from cosmids LLNLc116 1C16 and	Homo sapiens	35,076	28-Sep-99
					LLNLc116 15C24 map 21q22.3 region D21S171-LA161, complete
					sequence.
		GB_GSS4: AQ691923	446	AQ691923	HS_5400_B2_G04_SP6E RPCI-11 Human Male BAC Library Homo	Homo sapiens	33,500	6-Jul-99
					sapiens genomic clone Plate = 976 Col = 8 Row = N, genomic survey
					sequence.
		GB_EST37: AI967802	479	AI967802	Ljirnpest12-930-d6 Ljirnp Lambda HybriZap two-hybrid library Lotus	Lotus japonicus	41,127	24-Aug-99
					japonicus cDNA clone LP930-12-d6 5′ similar to 60S ribosomal protein
					L7A, mRNA sequence.
rxa00906	627	GB_PAT: I78750	588	I78750	Sequence 6 from patent U.S. Pat. No. 5693781.	Unknown.	97,071	3-Apr-98
		GB_PAT: I92039	588	I92039	Sequence 6 from patent U.S. Pat. No. 5726299.	Unknown.	97,071	01-DEC-1998
		GB_PR3: HS929C8	139190	AL020994	Human DNA sequence from clone 929C8 on chromosome 22q12.1-12.3	Homo sapiens	39,016	23-Nov-99
					Contains CA repeat, GSS, STS, complete sequence.
rxa00907	246	GB_PAT: I78750	588	I78750	Sequence 6 from patent U.S. Pat. No. 5693781.	Unknown.	97,561	3-Apr-98
		GB_PAT: I92039	588	I92039	Sequence 6 from patent U.S. Pat. No. 5726299.	Unknown.	97,561	01-DEC-1998
		GB_PAT: I78750	588	I78750	Sequence 6 from patent U.S. Pat. No. 5693781.	Unknown.	37,222	3-Apr-98
rxa00961	455	GB_BA1: AB032799	9077	AB032799	Chromobacterium violaceum violacein biosynthetic gene cluster (vio	Chromobacterium	39,868	02-OCT-1999
					A, vio B, vio C, vio D), complete cds.	violaceum
		GB_BA2: AF172851	10094	AF172851	Chromobacterium violaceum violacein biosynthetic gene cluster,	Chromobacterium	42,760	30-Aug-99
					complete sequence.	violaceum
		GB_BA1: AB032799	9077	AB032799	Chromobacterium violaceum violacein biosynthetic gene cluster (vio	Chromobacterium	39,551	02-OCT-1999
					A, vio B, vio C, vio D), complete cds.	violaceum
rxa00982	1629	GB_BA1: BLARGS	2501	Z21501	B. lactofermentum argS and lysA genes for arginyl-tRNA synthetase	Corynebacterium	39,003	28-DEC-1993
					and diaminopimelate decarboxylase (partial).	glutamicum
		GB_BA1: CGXLYSA	2344	X54740	Corynebacterium glutamicum argS-lysA operon gene for the upstream	Corynebacterium	41,435	30-Jun-93
					region of the arginyl-tRNA synthetase and diaminopimelate	glutamicum
					decarboxylase (EC 4.1.1.20).
		GB_PAT: E14508	3579	E14508	DNA encoding Brevibacterium diaminopimelic acid decarboxylase and	Corynebacterium	40,566	28-Jul-99
					arginyl-tRNA synthase.	glutamicum
rxa00983	1599	GB_HTG2: AC008152	24000	AC008152	Leishmania major chromosome 35 clone L7936 strain Friedlin, ***	Leishmania major	38,658	28-Jul-99
					SEQUENCING IN PROGRESS ***, 4 unordered pieces.
		GB_HTG2: AC008152	24000	AC008152	Leishmania major chromosome 35 clone L7936 strain Friedlin, ***	Leishmania major	38,658	28-Jul-99
					SEQUENCING IN PROGRESS ***, 4 unordered pieces.
		GB_HTG3: AC008648	87249	AC008648	Homo sapiens chromosome 5 clone CIT978SKB_186E14, ***	Homo sapiens	36,102	3-Aug-99
					SEQUENCING IN PROGRESS ***, 22 unordered pieces.
rxa00984	440	GB_BA1: MVINED	3098	D01045	Micromonospora viridifaciens DNA for nedR protein and	Micromonospora	59,226	2-Feb-99
					neuraminidase, complete cds.	viridifaciens
		GB_PAT: E02375	1881	E02375	Neuraminidase gene.	Micromonospora	59,226	29-Sep-97
						viridifaciens
		GB_PR4: HUAC004513	101311	AC004513	Homo sapiens Chromosome 16 BAC clone CIT987SK-A-926E7,	Homo sapiens	41,204	23-Nov-99
					complete sequence.
rxa01014	2724	GB_BA1: MTV008	63033	AL021246	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	56,167	17-Jun-98
					108/162.	tuberculosis
		GB_BA1: STMAMPEPN	2849	L23172	Streptomyces lividans aminopeptidase N gene, complete cds.	Streptomyces lividans	57,067	18-MAY-1994
		GB_BA1: SC7H2	42655	AL109732	Streptomyces coelicolor cosmid 7H2.	Streptomyces coelicolor	37,551	2-Aug-99
						A3(2)
rxa01059	732	GB_HTG3: AC008154	172241	AC008154	Homo sapiens chromosome 7, * SEQUENCING IN PROGRESS *,	Homo sapiens	39,499	8-Sep-99
					26 unordered pieces.
		GB_HTG3: AC008154	172241	AC008154	Homo sapiens chromosome 7, * SEQUENCING IN PROGRESS *,	Homo sapiens	39,499	8-Sep-99
					26 unordered pieces.
		GB_EST32: AI756574	299	AI756574	ea02f10.y1 Eimeria M5-6 Merozoite stage Eimeria tenella cDNA 5′,	Eimeria tenella	37,793	23-Jun-99
					mRNA sequence.
rxa01073	954	GB_BA1: BACOUTB	1004	M15811	Bacillus subtilis outB gene encoding a sporulation protein, complete	Bacillus subtilis	53,723	26-Apr-93
					cds.
		GB_PR4: AC007938	167237	AC007938	Homo sapiens clone UWGC: djs201 from 7q31, complete sequence.	Homo sapiens	34,322	1-Jul-99
		GB_PL2: ATAC006282	92577	AC006282	Arabidopsis thaliana chromosome II BAC F13K3 genomic sequence,	Arabidopsis thaliana	36,181	13-MAR-1999
					complete sequence.
rxa01120	1401	GB_BA1: MTV008	63033	AL021246	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	36,715	17-Jun-98
					108/162.	tuberculosis
		GB_BA1: CAJ10321	6710	AJ010321	Caulobacter crescentus partial tig gene and clpP, cicA, clpX, lon	Caulobacter crescentus	63,311	01-OCT-1998
					genes.
		GB_BA2: AF150957	4440	AF150957	Azospirillum brasilense trigger factor (tig), heat-shock protein ClpP	Azospirillum brasilense	60,613	7-Jun-99
					(clpP), and heat-shock protein ClpX (clpX) genes, complete cds; and
					Lon protease (lon) gene, partial cds.
rxa01147	1383	GB_PR3: HS408N23	97916	Z98048	Human DNA sequence from PAC 408N23 on chromosome 22q13.	Homo sapiens	34,567	23-Nov-99
					Contains HIP, HSC70-INTERACTING PROTEIN (PROGESTERONE
					RECEPTOR-ASSOCIATED P48 PROTEIN), ESTs and STS.
		GB_BA2: AE001227	26849	AE001227	Treponema pallidum section 43 of 87 of the complete genome.	Treponema pallidum	37,564	16-Jul-98
		GB_PR3: HS408N23	97916	Z98048	Human DNA sequence from PAC 408N23 on chromosome 22q13.	Homo sapiens	34,911	23-Nov-99
					Contains HIP, HSC70-INTERACTING PROTEIN (PROGESTERONE
					RECEPTOR-ASSOCIATED P48 PROTEIN), ESTs and STS.
rxa01151	958	GB_BA1: MTCY261	27322	Z97559	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	38,789	17-Jun-98
					95/162.	tuberculosis
		GB_HTG4: AC009849	114993	AC009849	Drosophila melanogaster chromosome 2 clone BACR07H08 (D864)	Drosophila melanogaster	39,213	25-OCT-1999
					RPCI-98 07.H.8 map 31B-31C strain y; cn bw sp, *** SEQUENCING
					IN PROGRESS ***, 55 unordered pieces.
		GB_HTG4: AC009849	114993	AC009849	Drosophila melanogaster chromosome 2 clone BACR07H08 (D864)	Drosophila melanogaster	39,213	25-OCT-1999
					RPCI-98 07.H.8 map 31B-31C strain y; cn bw sp, *** SEQUENCING
					IN PROGRESS ***, 55 unordered pieces.
rxa01161	1260	GB_BA2: AF176799	2943	AF176799	Lactobacillus pentosus PepQ (pepQ) and catabolite control protein A	Lactobacillus pentosus	37,043	5-Sep-99
					(ccpA) genes, complete cds.
		GB_BA2: AF012084	3082	AF012084	Lactobacillus helveticus prolidase (pepQ) gene, complete cds.	Lactobacillus helveticus	46,796	1-Jul-98
		GB_EST32: AI728955	611	AI728955	BNLGHi12114 Six-day Cotton fiber Gossypium hirsutum cDNA 5′	Gossypium hirsutum	37,647	11-Jun-99
					similar to (AC004481) putative permease [Arabidopsis thaliana],
					mRNA sequence.
rxa01181	980	GB_BA1: MLCB22	40281	Z98741	Mycobacterium leprae cosmid B22.	Mycobacterium leprae	61,570	22-Aug-97
		GB_BA1: MTCY190	34150	Z70283	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	60,434	17-Jun-98
					98/162.	tuberculosis
		GB_BA1: SC5F7	40024	AL096872	Streptomyces coelicolor cosmid 5F7.	Streptomyces coelicolor	57,011	22-Jul-99
						A3(2)
rxa01182	516	GB_HTG1: CEY116A8_2	110000	Z98858	Caenorhabditis elegans chromosome IV clone Y116A8, ***	Caenorhabditis elegans	34,843	26-Oct-99
					SEQUENCING IN PROGRESS ***, in unordered pieces.
		GB_HTG1: CEY116A8_2	110000	Z98858	Caenorhabditis elegans chromosome IV clone Y116A8, ***	Caenorhabditis elegans	34,843	26-Oct-99
					SEQUENCING IN PROGRESS ***, in unordered pieces.
		GB_IN1: CEY116A8C	260341	AL117204	Caenorhabditis elegans cosmid Y116A8C, complete sequence.	Caenorhabditis elegans	34,843	19-Nov-99
rxa01189	732	GB_BA1: D90915	130001	D90915	Synechocystis sp. PCC6803 complete genome, 17/27, 2137259-2267259.	Synechocystis sp.	36,538	7-Feb-99
		GB_BA1: D90915	130001	D90915	Synechocystis sp. PCC6803 complete genome, 17/27, 2137259-2267259.	Synechocystis sp.	34,512	7-Feb-99
		GB_HTG3: AC010515	41038	AC010515	Homo sapiens chromosome 19 clone LLNL-R_249H9, ***	Homo sapiens	33,564	15-Sep-99
					SEQUENCING IN PROGRESS ***, 31 unordered pieces.
rxa01192	681	GB_OM: CFP180RRC	5425	X87224	Canis familiaris mRNA for ribosome receptor, p180.	Canis familiaris	41,229	22-Jan-99
		GB_OM: CFP180RRC	5425	X87224	Canis familiaris mRNA for ribosome receptor, p180.	Canis familiaris	38,187	22-Jan-99
rxa01214	1614	GB_IN1: CEY47D3A	199814	AL117202	Caenorhabditis elegans cosmid Y47D3A, complete sequence.	Caenorhabditis elegans	36,604	19-Nov-99
		GB_PR4: AC006039	176257	AC006039	Homo sapiens clone NH0319F03, complete sequence.	Homo sapiens	34,984	05-MAY-1999
		GB_PR4: AC006039	176257	AC006039	Homo sapiens clone NH0319F03, complete sequence.	Homo sapiens	35,951	05-MAY-1999
rxa01224	1146	GB_EST22: AI070047	479	AI070047	UI-R-C1-In-f-08-0-UI.s1 UI-R-C1 Rattus norvegicus cDNA clone UI-R-	Rattus norvegicus	36,975	5-Jul-99
					C1-In-f-08-0-UI 3′, mRNA sequence.
		GB_RO: S75965	625	S75965	THP = Tamm-Horsfall protein {promoter} [rats, Genomic, 625 nt].	Rattus sp.	34,400	27-Jul-95
		GB_EST5: H96951	459	H96951	yu01g03.r1 Soares_pineal_gland_N3HPG Homo sapiens cDNA clone	Homo sapiens	32,969	11-DEC-1995
					IMAGE: 232564 5′, mRNA sequence.
rxa01250	588	GB_PL1: NEULCCB	2656	M18334	N. crassa (strain TS) laccase gene, complete cds.	Neurospora crassa	44,330	03-MAY-1994
		GB_OV: MTRACOMPL	16714	Y16884	Rhea americana complete mitochondrial genome.	Mitochondrion Rhea	35,094	19-Jul-99
						americana
		GB_OV: AF090339	16704	AF090339	Rhea americana mitochondrion, complete genome.	Mitochondrion Rhea	35,094	27-MAY-1999
						americana
rxa01277	2127	GB_PL2: AF111709	52684	AF111709	Oryza sativa subsp. indica Retrosat 1 retrotransposon and Ty3-Gypsy	Oryza sativa subsp. indica	37,410	26-Apr-99
					type Retrosat 2 retrotransposon, complete sequences; and unknown
					genes.
		GB_IN1: CELZC250	34372	AF003383	Caenorhabditis elegans cosmid ZC250.	Caenorhabditis elegans	35,506	14-MAY-1997
		GB_EST1: Z14808	331	Z14808	CEL5E4 Chris Martin sorted cDNA library Caenorhabditis elegans	Caenorhabditis elegans	36,890	19-Jun-97
					cDNA clone cm5e4 5′, mRNA sequence.
rxa01302	576	GB_BA1: MTCI65	34331	Z95584	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	59,298	17-Jun-98
					50/162.	tuberculosis
		GB_BA1: MSGY348	40056	AD000020	Mycobacterium tuberculosis sequence from clone y348.	Mycobacterium	59,227	10-DEC-1996
						tuberculosis
		GB_BA1: SC5C7	41906	AL031515	Streptomyces coelicolor cosmid 5C7.	Streptomyces coelicolor	39,261	7-Sep-98
rxa01303	1458	GB_BA1: TTAJ5043	837	AJ225043	Thermus thermophilus partial narK gene.	Thermus thermophilus	55,245	18-Jun-98
		GB_PL2: AC010675	84723	AC010675	Arabidopsis thaliana chromosome I BAC T17F3 genomic sequence,	Arabidopsis thaliana	37,058	11-Nov-99
					complete sequence.
		GB_GSS9: AQ170862	518	AQ170862	HS_3165_B2_F03_T7 CIT Approved Human Genomic Sperm Library	Homo sapiens	38,610	17-OCT-1998
					D Homo sapiens genomic clone Plate = 3165 Col = 6 Row = L, genomic
					survey sequence.
rxa01308	2503	GB_BA1: D90757	17621	D90757	Escherichia coli genomic DNA. (27.3-27.7 min).	Escherichia coli	55,445	7-Feb-99
		GB_BA1: D90787	15942	D90787	E. coli genomic DNA, Kohara clone #276(33.0-33.3 min.).	Escherichia coli	36,815	29-MAY-1997
		GB_BA1: D90758	13860	D90758	Escherichia coli genomic DNA. (27.6-27.9 min).	Escherichia coli	54,942	7-Feb-99
rxa01309	824	GB_BA1: SCJ12	35302	AL109989	Streptomyces coelicolor cosmid J12.	Streptomyces coelicolor	62,423	24-Aug-99
						A3(2)
		GB_BA1: BSNARYWI	12450	Z49884	B. subtilis nar[G, H, I, J, K], ywi[C, D, E] and argS genes.	Bacillus subtilis	57,447	24-Jun-98
		GB_BA1: BSUB0020	212150	Z99123	Bacillus subtilis complete genome (section 20 of 21): from 3798401 to	Bacillus subtilis	37,129	26-Nov-97
					4010550.
rxa01358	1644	GB_GSS11: AQ260413	453	AQ260413	CITBI-E1-2510B12.TF CITBI-E1 Homo sapiens genomic clone	Homo sapiens	41,531	24-OCT-1998
					2510B12, genomic survey sequence.
		GB_EST20: AA840582	326	AA840582	vw77h07.r1 Stratagene mouse heart (#937316) Mus musculus cDNA	Mus musculus	42,901	27-Feb-98
					clone IMAGE: 1261021 5′ similar to gb: J04181 Mouse A-X actin
					mRNA, complete cds (MOUSE);, mRNA sequence.
		GB_PAT: A39944	3836	A39944	Sequence 1 from Patent WO9421807.	unidentified	38,764	05-MAR-1997
rxa01385	2004	GB_BA1: FVBPENTA	2519	M98557	Flavobacterium sp. pentachlorophenol 4-monooxygenase gene,	Flavobacterium sp.	40,855	26-Apr-93
					complete mRNA.
		GB_PAT: I19994	2516	I19994	Sequence 2 from patent U.S. Pat. No. 5512478.	Unknown.	40,855	07-OCT-1996
		GB_BA2: AF059680	2410	AF059680	Sphingomonas sp. UG30 pentachlorophenol 4-monooxygenase	Sphingomonas sp. UG30	42,993	27-Apr-99
					(pcpB) gene, complete cds; and pentachlorophenol 4-monooxygenase
					reductase (pcpD) gene, partial cds.
rxa01412	327	GB_GSS12: AQ332469	459	AQ332469	HS_5003_A1_H08_SP6E RPCI11 Human Male BAC Library Homo	Homo sapiens	38,208	06-MAR-1999
					sapiens genomic clone Plate = 579 Col = 15 Row = O, genomic survey
					sequence.
		GB_EST27: AA998532	453	AA998532	UI-R-C0-ic-d-11-0-UI.s1 UI-R-C0 Rattus norvegicus cDNA clone UI-R-	Rattus norvegicus	39,336	09-MAR-1999
					C0-ic-d-11-0-UI 3′, mRNA sequence.
		GB_HTG1: HSA342D11	178183	AL121748	Homo sapiens chromosome 10 clone RP11-342D11, ***	Homo sapiens	40,550	23-Nov-99
					SEQUENCING IN PROGRESS ***, in unordered pieces.
rxa01458	1173	GB_BA2: AE000745	15085	AE000745	Aquifex aeolicus section 77 of 109 of the complete genome.	Aquifex aeolicus	37,694	25-MAR-1998
		GB_BA2: AE000745	15085	AE000745	Aquifex aeolicus section 77 of 109 of the complete genome.	Aquifex aeolicus	35,567	25-MAR-1998
rxa01571	723	GB_BA1: AB011413	12070	AB011413	Streptomyces griseus genes for Orf2, Orf3, Orf4, Orf5, AfsA, Orf8,	Streptomyces griseus	57,500	7-Aug-98
					partial and complete cds.
		GB_BA1: AB011413	12070	AB011413	Streptomyces griseus genes for Orf2, Orf3, Orf4, Orf5, AfsA, Orf8,	Streptomyces griseus	35,655	7-Aug-98
					partial and complete cds.
rxa01607	753	GB_PR4: AC005005	133893	AC005005	Homo sapiens PAC clone DJ412A9 from 22, complete sequence.	Homo sapiens	38,399	02-MAR-1999
		GB_HTG3: AC008257	109187	AC008257	Drosophila melanogaster chromosome 2 clone BACR08A11 (D916)	Drosophila melanogaster	33,741	08-OCT-1999
					RPCI-98 08.A.11 map 42A-42A strain y; cn bw sp, *** SEQUENCING
					IN PROGRESS ***, 93 unordered pieces.
		GB_HTG3: AC008257	109187	AC008257	Drosophila melanogaster chromosome 2 clone BACR08A11 (D916)	Drosophila melanogaster	33,741	08-OCT-1999
					RPCI-98 08.A.11 map 42A-42A strain y; cn bw sp, *** SEQUENCING
					IN PROGRESS ***, 93 unordered pieces.
rxa01609	996	GB_BA1: MTV003	13246	AL008883	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	39,369	17-Jun-98
					125/162.	tuberculosis
		GB_BA1: MSGB1529CS	36985	L78824	Mycobacterium leprae cosmid B1529 DNA sequence.	Mycobacterium leprae	60,624	15-Jun-96
		GB_BA1: AB024601	14807	AB024601	Pseudomonas aeruginosa dapD gene for tetrahydrodipicolinate N-	Pseudomonas aeruginosa	41,603	12-MAR-1999
					succinyletransferase, complete cds, strain PAO1.
rxa01654	1119	GB_GSS4: AQ704352	532	AQ704352	HS_2147_A2_H04_MR CIT Approved Human Genomic Sperm	Homo sapiens	37,838	7-Jul-99
					Library D Homo sapiens genomic clone Plate = 2147 Col = 8 Row = O,
					genomic survey sequence.
		GB_RO: MMAE000663	250611	AE000663	Mus musculus TCR beta locus from bases 1 to 250611 (section 1 of	Mus musculus	35,799	4-Sep-97
					3) of the complete sequence.
		GB_EST23: AI158428	511	AI158428	ud24f12.r1 Soares 2NbMT Mus musculus cDNA clone	Mus musculus	41,337	30-Sep-98
					IMAGE: 1446863 5′, mRNA sequence.
rxa01664	945	GB_OV: AF026198	63155	AF026198	Fugu rubripes neural cell adhesion molecule L1 homolog (L1-CAM)	Fugu rubripes	35,187	02-MAY-1998
					gene, complete cds; putative protein 1 (PUT1) gene, partial cds;
					mitosis-specific chromosome segregation protein SMC1 homolog
					(SMC1) gene, complete cds; and calcium channel alpha-1 subunit
					homolog (CCA1) and putative protein 2 (PUT2) genes, partial cds,
					complete sequence.
		GB_PR3: AC004466	122186	AC004466	Homo sapiens 12q13.1 PAC RPCI5-1057I20 (Roswell Park Cancer	Homo sapiens	37,382	17-Sep-98
					Institute Human PAC library) complete sequence.
		GB_PR3: AC004466	122186	AC004466	Homo sapiens 12q13.1 PAC RPCI5-1057I20 (Roswell Park Cancer	Homo sapiens	37,325	17-Sep-98
					Institute Human PAC library) complete sequence.
rxa01795	720	GB_BA2: CGU13922	4412	U13922	Corynebacterium glutamicum putative type II 5-cytosoine	Corynebacterium	99,444	3-Feb-98
					methyltransferase (cgIIM) and putative type II restriction endonuclease	glutamicum
					(cgIIR) and putative type I or type III restriction endonuclease (clgIIR)
					genes, complete cds.
		GB_BA1: S86113	1044	S86113	ORF 1 [Neisseria gonorrhoeae, Genomic, 1044 nt].	Neisseria gonorrhoeae	58,320	07-MAY-1993
		GB_PAT: I22080	850	I22080	Sequence 1 from patent U.S. Pat. No. 5525717.	Unknown.	57,722	07-OCT-1996
rxa01802	954	GB_BA2: AE001519	14062	AE001519	Helicobacter pylori, strain J99 section 80 of 132 of the complete	Helicobacter pylori J99	33,510	20-Jan-99
					genome.
		GB_GSS5: AQ774071	552	AQ774071	HS_2269_B1_C10_T7C CIT Approved Human Genomic Sperm	Homo sapiens	37,967	29-Jul-99
					Library D Homo sapiens genomic clone Plate = 2269 Col = 19 Row = F,
					genomic survey sequence.
		GB_PR4: AC007459	40907	AC007459	Homo sapiens chromosome 16 clone 306C6, complete sequence.	Homo sapiens	39,140	04-MAY-1999
rxa01838	842	GB_BA1: SCE15	26440	AL049707	Streptomyces coelicolor cosmid E15.	Streptomyces coelicolor	36,297	22-Apr-99
		GB_HTG3: AC009545	165042	AC009545	Homo sapiens chromosome 11 clone 131_J_04 map 11, ***	Homo sapiens	37,651	01-OCT-1999
					SEQUENCING IN PROGRESS ***, 8 unordered pieces.
		GB_HTG3: AC009545	165042	AC009545	Homo sapiens chromosome 11 clone 131_J_04 map 11, ***	Homo sapiens	37,651	01-OCT-1999
					SEQUENCING IN PROGRESS ***, 8 unordered pieces.
rxa01848	867	GB_BA1: MTCY24A1	20270	Z95207	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	38,270	17-Jun-98
					124/162.	tuberculosis
		GB_EST21: C89252	587	C89252	C89252 Mouse early blastocyst cDNA Mus musculus cDNA clone	Mus musculus	37,219	28-MAY-1998
					01B00061JC08, mRNA sequence.
		GB_EST14: AA423340	457	AA423340	ve39d04.r1 Soares mouse mammary gland NbMMG Mus musculus	Mus musculus	38,377	16-OCT-1997
					cDNA clone IMAGE: 820519 5′, mRNA sequence.
rxa01849	1224	GB_BA1: MTCY24A1	20270	Z95207	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	39,950	17-Jun-98
					124/162.	tuberculosis
		GB_BA2: RCPHSYNG	45959	Z11165	R. capsulatus complete photosynthesis gene cluster.	Rhodobacter capsulatus	37,344	2-Sep-99
		GB_BA1: RSP010302	40707	AJ010302	Rhodobacter sphaeroides photosynthetic gene cluster.	Rhodobacter sphaeroides	40,898	27-Aug-99
rxa01868	2049	GB_BA1: MTV033	21620	AL021928	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	38,679	17-Jun-98
					11/162.	tuberculosis
		GB_BA1: MLCL622	42498	Z95398	Mycobacterium leprae cosmid L622.	Mycobacterium leprae	38,911	24-Jun-97
		GB_BA1: MSGB983CS	36788	L78828	Mycobacterium leprae cosmid B983 DNA sequence.	Mycobacterium leprae	38,933	15-Jun-96
rxa01885	924	GB_BA1: MTCY1A10	25949	Z95387	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	51,094	17-Jun-98
					117/162.	tuberculosis
		GB_PR3: HSU220B11	41247	Z69908	Human DNA sequence from cosmid cU220B11, between markers	Homo sapiens	39,038	23-Nov-99
					DXS6791 and DXS8038 on chromosome X.
		GB_BA1: PDU17435	993	U17435	Paracoccus denitrificans Fnr-like transcriptional activator (nnr) gene,	Paracoccus denitrificans	39,390	19-Jul-95
					complete cds.
rxa01914	526	GB_PR3: AC005796	43843	AC005796	Homo sapiens chromosome 19, cosmid R31408, complete sequence.	Homo sapiens	34,961	06-OCT-1998
		GB_PR3: HS390C10	114231	AL008721	Homo sapiens DNA sequence from BAC 390C10 on chromosome	Homo sapiens	39,600	23-Nov-99
					22q11.21-12.1. Contains an Immunoglobulin LIKE gene and a
					pseudogene similar to Beta Crystallin. Contains ESTs, STSs, GSSs
					and taga and tat repeat polymorphisms, complete sequence.
		GB_PR3: AC005796	43843	AC005796	Homo sapiens chromosome 19, cosmid R31408, complete sequence.	Homo sapiens	37,725	06-OCT-1998
rxa01932	1020	GB_PR3: AC003025	112309	AC003025	Human Chromosome 11p12.2 PAC clone pDJ466a11, complete	Homo sapiens	35,585	23-Jul-98
					sequence.
		GB_GSS3: B78728	312	B78728	CIT-HSP-431E3.TV CIT-HSP Homo sapiens genomic clone 431E3,	Homo sapiens	38,907	25-Jun-98
					genomic survey sequence.
		GB_PR3: AC003025	112309	AC003025	Human Chromosome 11p12.2 PAC clone pDJ466a11, complete	Homo sapiens	35,859	23-Jul-98
					sequence.
rxa01933	726	GB_HTG1: HS74O16	169401	AL110119	Homo sapiens chromosome 21 clone RPCIP704O1674 map 21q21,	Homo sapiens	35,302	27-Aug-99
					* SEQUENCING IN PROGRESS *, in unordered pieces.
		GB_HTG1: HS74O16	169401	AL110119	Homo sapiens chromosome 21 clone RPCIP704O1674 map 21q21,	Homo sapiens	35,302	27-Aug-99
					* SEQUENCING IN PROGRESS *, in unordered pieces.
		GB_PR4: AC006032	170282	AC006032	Homo sapiens BAC clone NH0115E20 from Y, complete sequence.	Homo sapiens	37,640	27-Feb-99
rxa01971	954	GB_HTG3: AC008230	108469	AC008230	Drosophila melanogaster chromosome 2 clone BACR17I17 (D934)	Drosophila melanogaster	35,466	10-Aug-99
					RPCI-98 17.I.17 map 53A-53C strain y; cn bw sp, *** SEQUENCING
					IN PROGRESS ***, 108 unordered pieces.
		GB_HTG3: AC008230	108469	AC008230	Drosophila melanogaster chromosome 2 clone BACR17I17 (D934)	Drosophila melanogaster	35,466	10-Aug-99
					RPCI-98 17.I.17 map 53A-53C strain y; cn bw sp, *** SEQUENCING
					IN PROGRESS***, 108 unordered pieces.
		GB_PR3: AF064860	165382	AF064860	Homo sapiens chromosome 21q22.3 PAC 70I24, complete sequence.	Homo sapiens	39,716	2-Jun-98
rxa02016	900	GB_EST2: D48846	459	D48846	RICS15292A Rice green shoot Oryza sativa cDNA, mRNA sequence.	Oryza sativa	37,118	2-Aug-95
		GB_GSS10: AQ195886	595	AQ195886	RPCI11-66O13.TJ RPCI-11 Homo sapiens genomic clone RPCI-11-	Homo sapiens	41,000	20-Apr-99
					66O13, genomic survey sequence.
		GB_GSS10: AQ195886	595	AQ195886	RPCI11-66O13.TJ RPCI-11 Homo sapiens genomic clone RPCI-11-	Homo sapiens	34,790	20-Apr-99
					66O13, genomic survey sequence.
rxa02017	807	GB_EST20: AA855266	406	AA855266	vw70b08.r1 Stratagene mouse heart (#937316) Mus musculus cDNA	Mus musculus	42,638	06-MAR-1998
					clone IMAGE: 1260279 5′, mRNA sequence.
		GB_EST20: AA855266	406	AA855266	vw70b08.r1 Stratagene mouse heart (#937316) Mus musculus cDNA	Mus musculus	37,183	06-MAR-1998
					clone IMAGE: 1260279 5′, mRNA sequence.
rxa02018	1073	GB_BA1: SC5C7	41906	AL031515	Streptomyces coelicolor cosmid 5C7.	Streptomyces coelicolor	41,732	7-Sep-98
		GB_BA1: MTCI65	34331	Z95584	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	62,395	17-Jun-98
					50/162.	tuberculosis
		GB_BA1: SCJ12	35302	AL109989	Streptomyces coelicolor cosmid J12.	Streptomyces coelicolor	61,603	24-Aug-99
						A3(2)
rxa02048	1497	GB_PAT: E15823	2323	E15823	DNA encoding cell surface protein from Corynebacterium	Corynebacterium	53,942	28-Jul-99
					ammoniagenes.	ammoniagenes
		GB_OM: SSAMPTDN	3387	Z29522	S. scrofa mRNA for aminopeptidase N.	Sus scrofa	42,672	26-Sep-94
		GB_OV: D87992	3181	D87992	Gallus gallus mRNA for aminopeptidase Ey, complete cds.	Gallus gallus	41,554	5-Jun-99
rxa02101	1386	GB_BA1: AP000064	247695	AP000064	Aeropyrum pernix genomic DNA, section 7/7.	Aeropyrum pernix	39,882	22-Jun-99
		GB_PL2: ATAC006587	79262	AC006587	Arabidopsis thaliana chromosome II BAC T17D12 genomic sequence,	Arabidopsis thaliana	38,490	23-MAR-1999
					complete sequence.
		GB_PL2: ATAC006587	79262	AC006587	Arabidopsis thaliana chromosome II BAC T17D12 genomic sequence,	Arabidopsis thaliana	34,863	23-MAR-1999
					complete sequence.
rxa02265	423	GB_BA2: AF120718	4137	AF120718	Lactobacillus fermentum urease operon, partial sequence.	Lactobacillus fermentum	56,265	31-MAR-1999
		GB_PAT: E03531	2896	E03531	DNA sequence coding for acid urease.	Lactobacillus fermentum	56,265	29-Sep-97
		GB_BA1: LBAAURE	2896	D10605	L. fermentum gene for acid urease.	Lactobacillus fermentum	56,265	2-Feb-99
rxa02276	801	GB_GSS10: AQ242920	451	AQ242920	HS_2061_A1_E08_MR CIT Approved Human Genomic Sperm	Homo sapiens	37,916	03-OCT-1998
					Library D Homo sapiens genomic clone Plate = 2061 Col = 15 Row = I,
					genomic survey sequence.
		GB_IN1: SLMMTPMF	14503	D29637	Physarum polycephalum mitochondrial DNA.	Mitochondrion Physarum	40,335	12-MAY-1999
						polycephalum
		GB_IN2: AF012249	5542	AF012249	Physarum polycephalum strain aux2-S region of mitochondria derived	Mitochondrion Physarum	40,335	08-MAY-1998
					from mF plasmid, including URFA′, URFC, URFD, URFE, URFF, and	polycephalum
					URFG genes, complete cds, and URFH gene, partial cds.
rxa02277	738	GB_BA2: AF048784	681	AF048784	Actinomyces naeslundii urease accessory protein (ureG) gene,	Actinomyces naeslundii	66,814	9-Feb-99
					complete cds.
		GB_BA2: AF056321	5482	AF056321	Actinomyces naeslundii urease gamma subunit UreA (ureA), urease	Actinomyces naeslundii	63,686	9-Feb-99
					beta subunit UreB (ureB), urease alpha subunit UreC (ureC), urease
					accessory protein UreE (ureE), urease accessory protein UreF
					(ureF), urease accessory protein UreG (ureG), and urease accessory
					protein UreD (ureD) genes, complete cds.
		GB_BA2: SSU35248	5773	U35248	Streptococcus salivarius ure cluster nickel transporter homolog (urel)	Streptococcus salivarius	61,931	26-Jan-96
					gene, partial cds, and urease beta subunit (ureA), gamma subunit
					(ureB), alpha subunit (ureC), and accessory proteins (ureE), (ureF),
					(ureG), and (ureD) genes, complete cds.
rxa02278	972	GB_GSS3: B49054	543	B49054	RPCI11-4I13.TV RPCI-11 Homo sapiens genomic clone RPCI-11-	Homo sapiens	39,161	8-Apr-99
					4I13, genomic survey sequence.
		GB_PL1: PMCMSGI	3363	L27092	Pneumocystis carinii B-cell receptor (msgl) gene, 3′ end.	Pneumocystis carinii	39,819	26-Sep-94
		GB_PL2: AF038556	12792	AF038556	Pneumocystis carinii f. sp. hominis variant regions of major surface	Pneumocystis carinii f. sp.	33,832	10-Sep-98
					glycoproteins (msg1, msg3, msg4) genes, partial cds.	hominis
rxa02317	735	GB_GSS8: AQ051031	914	AQ051031	nbxb0004dG10r CUGI Rice BAC Library Oryza sativa genomic clone	Oryza sativa	32,299	24-MAR-1999
					nbxb0004N20r, genomic survey sequence.
		GB_GSS8: AQ051031	914	AQ051031	nbxb0004dG10r CUGI Rice BAC Library Oryza sativa genomic clone	Oryza sativa	34,573	24-MAR-1999
					nbxb0004N20r, genomic survey sequence.
rxa02334	746	GB_BA1: CGU35023	3195	U35023	Corynebacterium glutamicum thiosulfate sulfurtransferase (thtR) gene,	Corynebacterium	100,000	16-Jan-97
					partial cds, acyl CoA carboxylase (accBC) gene, complete cds.	glutamicum
		GB_BA1: MTCY71	42729	Z92771	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	60,380	10-Feb-99
					141/162.	tuberculosis
		GB_BA1: U00012	33312	U00012	Mycobacterium leprae cosmid B1308.	Mycobacterium leprae	37,660	30-Jan-96
rxa02351	1039	GB_HTG2: HS225E12	126464	AL031772	Homo sapiens chromosome 6 clone RP1-225E12 map q24, ***	Homo sapiens	35,973	03-DEC-1999
					SEQUENCING IN PROGRESS ***, in unordered pieces.
		GB_HTG2: HS225E12	126464	AL031772	Homo sapiens chromosome 6 clone RP1-225E12 map q24, ***	Homo sapiens	35,973	03-DEC-1999
					SEQUENCING IN PROGRESS ***, in unordered pieces.
		GB_HTG2: HS225E12	126464	AL031772	Homo sapiens chromosome 6 clone RP1-225E12 map q24, ***	Homo sapiens	36,992	03-DEC-1999
					SEQUENCING IN PROGRESS ***, in unordered pieces.
rxa02410	789	GB_BA1: AB020624	1605	AB020624	Corynebacterium glutamicum murl gene for D-glutamate racemase,	Corynebacterium	99,227	24-Jul-99
					complete cds.	glutamicum
		GB_EST4: H51527	294	H51527	yo33b09.s1 Soares adult brain N2b4HB55Y Homo sapiens cDNA	Homo sapiens	40,411	18-Sep-95
					clone IMAGE: 179705 3′, mRNA sequence.
		GB_GSS1: CNS003CM	1101	AL064136	Drosophila melanogaster genome survey sequence T7 end of BAC #	Drosophila melanogaster	37,674	3-Jun-99
					BACR08C19 of RPCI-98 library from Drosophila melanogaster (fruit
					fly), genomic survey sequence.
rxa02477	744	GB_HTG4: AC010054	130191	AC010054	Drosophila melanogaster chromosome 3L/74E2 clone RPCI98-15E10,	Drosophila melanogaster	37,466	16-OCT-1999
					* SEQUENCING IN PROGRESS *, 70 unordered pieces.
		GB_HTG4: AC010054	130191	AC010054	Drosophila melanogaster chromosome 3L/74E2 clone RPCI98-15E10,	Drosophila melanogaster	37,466	16-OCT-1999
					* SEQUENCING IN PROGRESS *, 70 unordered pieces.
		GB_HTG4: AC009375	137069	AC009375	Drosophila melanogaster chromosome 3L/75A1 clone RPCI98-44L18,	Drosophila melanogaster	39,118	16-OCT-1999
					* SEQUENCING IN PROGRESS *, 59 unordered pieces.
rxa02513	832	GB_BA1: MTER260	373	X92572	M. terrae gene for 32 kDa protein (partial).	Mycobacterium terrae	42,895	15-Jan-98
		GB_PL1: AB019229	84294	AB019229	Arabidopsis thaliana genomic DNA, chromosome 3, P1 clone:	Arabidopsis thaliana	36,084	20-Nov-99
					MDC16, complete sequence.
		GB_PL1: AB019229	84294	AB019229	Arabidopsis thaliana genomic DNA, chromosome 3, P1 clone:	Arabidopsis thaliana	35,244	20-Nov-99
					MDC16, complete sequence.
rxa02531	834	GB_BA1: CGLATTB	271	X89850	C. glutamicum DNA for attB region.	Corynebacterium	40,590	8-Aug-96
						glutamicum
		GB_EST11: AA239557	423	AA239557	mv25f04.r1 GuayWoodford Beier mouse kidney day 0 Mus musculus	Mus musculus	38,760	12-MAR-1997
					cDNA clone IMAGE: 656095 5′ similar to gb: X52634 Murine tlm
					oncogene for tlm protein (MOUSE);, mRNA sequence.
		GB_BA1: RSPYPPCL	6500	AJ002398	Rhodobacter sphaeroides pyp and pcl genes, and orfA, orfB, orfC,	Rhodobacter sphaeroides	37,091	17-DEC-1998
					orfD, orfE, orfF.
rxa02548	314	GB_BA2: AF127374	63734	AF127374	Streptomyces lavendulae LinA homolog, cytochrome P450	Streptomyces lavendulae	66,242	27-MAY-1999
					hydroxylase ORF4, cytochrome P450 hydroxylase ORF3, MitT (mitT),
					MitS (mitS), MitR (mitR), MitQ (mitQ), MitP (mitP), MitO (mitO), MitN
					(mitN), MitM (mitM), MitL (mitL), MitK (mitK), MitJ (mitJ), MitI (mitI),
					MitH (mitH), MitG (mitG), MitF (mitF), MitE (mitE), MitD (mitD), MitC
					(mitC), MitB (mitB), MitA (mitA), MmcA (mmcA), MmcB (mmcB),
					MmcC (mmcC), MmcD (mmcD), MmcE (mmcE), MmcF (mmcF),
					MmcG (mmcG), MmcH (mmcH), MmcI (mmcI), MmcJ (mmcJ), MmcK
					(mmcK), MmcL (mmcL), MmcM (mmcM), MmcN (mmcN), MmcO
					(mmcO), Mrd (mrd), MmcP (mmcP), MmcQ (mmcQ), MmcR (mmcR),
					MmcS (mmcS), MmcT (mmcT), MmcU (mmcU), MmcV (mmcV), Mct
					(mct), MmcW (mmcW), MmcX (mmcX), and MmcY (mmcY) genes,
					complete cds; and unknown genes.
		GB_BA2: AF127374	63734	AF127374	Streptomyces lavendulae LinA homolog, cytochrome P450	Streptomyces lavendulae	38,411	27-MAY-1999
					hydroxylase ORF4, cytochrome P450 hydroxylase ORF3, MitT (mitT),
					MitS (mitS), MitR (mitR), MitQ (mitQ), MitP (mitP), MitO (mitO), MitN
					(mitN), MitM (mitM), MitL (mitL), MitK (mitK), MitJ (mitJ), MitI (mitI),
					MitH (mitH), MitG (mitG), MitF (mitF), MitE (mitE), MitD (mitD), MitC
					(mitC), MitB (mitB), MitA (mitA), MmcA (mmcA), MmcB (mmcB),
					MmcC (mmcC), MmcD (mmcD), MmcE (mmcE), MmcF (mmcF),
					MmcG (mmcG), MmcH (mmcH), MmcI (mmcI), MmcJ (mmcJ), MmcK
					(mmcK), MmcL (mmcL), MmcM (mmcM), MmcN (mmcN), MmcO
					(mmcO), Mrd (mrd), MmcP (mmcP), MmcQ (mmcQ), MmcR (mmcR),
					MmcS (mmcS), MmcT (mmcT), MmcU (mmcU), MmcV (mmcV), Mct
					(mct), MmcW (mmcW), MmcX (mmcX), and MmcY (mmcY) genes,
					complete cds; and unknown genes.
		GB_GSS4: AQ741886	742	AQ741886	HS_5569_B2_B02_SP6 RPCI-11 Human Male BAC Library Homo	Homo sapiens	38,907	16-Jul-99
					sapiens genomic clone Plate = 1145 Col = 4 Row = D, genomic survey
					sequence.
rxa02558	1098	GB_EST18: AA567307	741	AA567307	HL01004.5prime HL Drosophila melanogaster head BlueScript	Drosophila melanogaster	38,736	28-Nov-98
					Drosophila melanogaster cDNA clone HL01004 5prime, mRNA
					sequence.
		GB_EST27: AI402394	630	AI402394	GH21610.5prime GH Drosophila melanogaster head pOT2 Drosophila	Drosophila melanogaster	41,308	8-Feb-99
					melanogaster cDNA clone GH21610 5prime, mRNA sequence.
		GB_GSS10: AQ237646	715	AQ237646	RPCI11-61I9.TJB RPCI-11 Homo sapiens genomic clone RPCI-11-	Homo sapiens	44,340	21-Apr-99
					61I9, genomic survey sequence.
rxa02565	1389	GB_EST32: AI726448	562	AI726448	BNLGHi5854 Six-day Cotton fiber Gossypium hirsutum cDNA 5′	Gossypium hirsutum	37,003	11-Jun-99
					similar to (U53418) UDP-glucose dehydrogenase [Glycine max],
					mRNA sequence.
		GB_EST32: AI726198	608	AI726198	BNLGHi5243 Six-day Cotton fiber Gossypium hirsutum cDNA 5′	Gossypium hirsutum	40,925	11-Jun-99
					similar to (U53418) UDP-glucose dehydrogenase [Glycine max],
					mRNA sequence.
		GB_PR4: AC002992	154848	AC002992	Homo sapiens chromosome Y, clone 203M13, complete sequence.	Homo sapiens	38,039	13-OCT-1999
rxa02574	1131	GB_EST4: H29653	415	H29653	ym58f01.r1 Soares infant brain 1NIB Homo sapiens cDNA clone	Homo sapiens	39,036	17-Jul-95
					IMAGE: 52678 5′ similar to SP: OXDD_BOVIN P31228 D-ASPARTATE
					OXIDASE;, mRNA sequence.
		GB_PR3: HSDJ261K5	131974	AL050350	Human DNA sequence from clone 261K5 on chromosome 6q21-22.1.	Homo sapiens	35,957	23-Nov-99
					Contains the 3′ part of the gene for a novel organic cation transporter
					(BAC ORF RG331P03), the DDO gene for D-aspartate oxidase (EC
					1.4.3.1), ESTs, STSs, GSSs and two putative CpG islands, complete
					sequence.
		GB_EST2: R20147	494	R20147	yg18h02.r1 Soares infant brain 1NIB Homo sapiens cDNA clone	Homo sapiens	36,437	17-Apr-95
					IMAGE: 32866 5′ similar to SP: OXDD_BOVIN P31228 D-ASPARTATE
					OXIDASE;, mRNA sequence.
rxa02589	888	GB_HTG1: CEY6E2	186306	Z96799	Caenorhabditis elegans chromosome V clone Y6E2, ***	Caenorhabditis elegans	37,979	02-OCT-1997
					SEQUENCING IN PROGRESS ***, in unordered pieces.
		GB_HTG1: CEY6E2	186306	Z96799	Caenorhabditis elegans chromosome V clone Y6E2, ***	Caenorhabditis elegans	37,979	02-OCT-1997
					SEQUENCING IN PROGRESS ***, in unordered pieces.
		GB_HTG3: AC011690	72277	AC011690	Homo sapiens clone 17_E_13, LOW-PASS SEQUENCE SAMPLING.	Homo sapiens	35,814	10-OCT-1999
rxa02592	894	GB_BA1: MSGB983CS	36788	L78828	Mycobacterium leprae cosmid B983 DNA sequence.	Mycobacterium leprae	53,235	15-Jun-96
		GB_GSS9: AQ170723	487	AQ170723	HS_2270_B2_F05_MR CIT Approved Human Genomic Sperm Library	Homo sapiens	39,666	16-OCT-1998
					D Homo sapiens genomic clone Plate = 2270 Col = 10 Row = L, genomic
					survey sequence.
		GB_GSS12: AQ349397	791	AQ349397	RPCI11-118H16.TJ RPCI-11 Homo sapiens genomic clone RPCI-11-	Homo sapiens	34,204	07-MAY-1999
					118H16, genomic survey sequence.
rxa02603	1119	GB_BA1: MTV026	23740	AL022076	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	37,975	24-Jun-99
					157/162.	tuberculosis
		GB_IN2: AC005714	177740	AC005714	Drosophila melanogaster, chromosome 2R, region 58D4-58E2, BAC	Drosophila melanogaster	41,226	01-MAY-1999
					clone BACR48M13, complete sequence.
		GB_EST19: AA775050	218	AA775050	ac76e10.s1 Stratagene lung (#937210) Homo sapiens cDNA clone	Homo sapiens	40,826	5-Feb-98
					IMAGE: 868554 3′ similar to gb: Y00371_rna1 HEAT SHOCK
					COGNATE 71 KD PROTEIN (HUMAN);, mRNA sequence.
rxa02630	1446	GB_BA1: MLCL373	37304	AL035500	Mycobacterium leprae cosmid L373.	Mycobacterium leprae	49,015	27-Aug-99
		GB_BA1: MTV044	16150	AL021999	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	49,192	17-Jun-98
					45/162.	tuberculosis
		GB_BA1: MLU15180	38675	U15180	Mycobacterium leprae cosmid B1756.	Mycobacterium leprae	45,621	09-MAR-1995
rxa02643	1167	GB_EST37: AI950576	308	AI950576	wx52e08.x1 NCI_CGAP_Lu28 Homo sapiens cDNA clone	Homo sapiens	40,909	6-Sep-99
					IMAGE: 2547302 3′, mRNA sequence.
		GB_EST37: AI950576	308	AI950576	wx52e08.x1 NCI_CGAP_Lu28 Homo sapiens cDNA clone	Homo sapiens	40,288	6-Sep-99
					IMAGE: 2547302 3′, mRNA sequence.
rxa02644	774	GB_EST34: AV149547	302	AV149547	AV149547 Mus musculus C57BL/6J 10-11 day embryo Mus musculus	Mus musculus	38,627	5-Jul-99
					cDNA clone 2810489D03, mRNA sequence.
		GB_EST35: AV156221	271	AV156221	AV156221 Mus musculus head C57BL/6J 12-day embryo Mus	Mus musculus	33,990	7-Jul-99
					musculus cDNA clone 3000001C24, mRNA sequence.
		GB_EST32: AV054919	274	AV054919	AV054919 Mus musculus pancreas C57BL/6J adult Mus musculus	Mus musculus	36,585	23-Jun-99
					cDNA clone 1810033C08, mRNA sequence.
rxa02745	902	GB_BA1: MTV007	32806	AL021184	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	39,298	17-Jun-98
					64/162.	tuberculosis
		GB_BA2: AF027770	30683	AF027770	Mycobacterium smegmatis FxbA (fxbA) gene, partial cds; FxbB (fxbB),	Mycobacterium smegmatis	55,125	03-DEC-1998
					FxbC (fxbC), and FxuD (fxtD) genes, complete cds; and unknown
					genes.
		GB_BA2: SAU43537	3938	U43537	Streptomyces argillaceus mithramycin resistance determinant, ATP-	Streptomyces argillaceus	46,868	5-Sep-96
					binding protein (mtrA) and membrane protein (mtrB) genes, complete
					cds.
rxa02746	290	GB_BA1: CAJ10319	5368	AJ010319	Corynebacterium glutamicum amtP, glnB, glnD genes and partial ftsY	Corynebacterium	100,000	14-MAY-1999
					and srp genes.	glutamicum
		GB_BA1: MTCY338	29372	Z74697	Mycobacterium tuberculosis H37Rv complete genome; segment	Mycobacterium	39,785	17-Jun-98
					127/162.	tuberculosis
		GB_HTG3: AC008733	216140	AC008733	Homo sapiens chromosome 19 clone CITB-E1_2525J15, ***	Homo sapiens	35,688	3-Aug-99
					SEQUENCING IN PROGRESS ***, 72 unordered pieces.
rxa02820	1411	GB_BA1: BFU64514	3837	U64514	Bacillus firmus dppABC operon, dipeptide transporter protein dppA	Bacillus firmus	36,859	1-Feb-97
					gene, partial cds, and dipeptide transporter proteins dppB and dppC
					genes, complete cds.
		GB_IN1: CET04C10	20958	Z69885	Caenorhabditis elegans cosmid T04C10, complete sequence.	Caenorhabditis elegans	35,934	2-Sep-99
		GB_EST35: AI823090	720	AI823090	L30-944T3 Ice plant Lambda Uni-Zap XR expression library, 30 hours	Mesembryanthemum	35,770	21-Jul-99
					NaCl treatment Mesembryanthemum crystallinum cDNA clone L30-	crystallinum
					944 5′ similar to 60S ribosomal protein L36 (AC004684)[Arabidopsis
					thaliana], mRNA sequence.
rxa02834	518	GB_BA1: CJY13333	3315	Y13333	Campylobacter jejuni clpB gene.	Campylobacter jejuni	53,400	12-Apr-99
		GB_BA2: AF065404	181654	AF065404	Bacillus anthracis virulence plasmid PX01, complete sequence.	Bacillus anthracis	45,168	20-OCT-1999
		GB_PL2: AC006601	110684	AC006601	Arabidopsis thaliana chromosome V map near 60.5 cM, complete	Arabidopsis thaliana	36,680	22-Feb-99
					sequence.

Claims

1. An isolated polypeptide selected from the group consisting of:

a) an isolated polypeptide comprising the amino acid sequence of SEQ ID NO:2;

b) an isolated polypeptide comprising a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NO:2;

c) an isolated polypeptide which is encoded by a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:1;

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:1;

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:2; and

f) an isolated polypeptide comprising a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NO:2, wherein said polypeptide fragment maintains a biological activity of the polypeptide comprising the amino sequence.

2. The isolated polypeptide of claim 1, further comprising heterologous amino acid sequences.

3. The isolated polypeptide of claim 1, wherein the polypeptide has a sulfate adenylate transferase subunit 2 activity.

4. A method for producing a fine chemical, comprising culturing a recombinant host cell capable of expressing the polypeptide of claim 1.

5. The method of claim 4, wherein said method further comprises the step of recovering the fine chemical from said culture.

6. The method of claim 4, wherein said cell belongs to the genus Corynebacterium or Brevibacterium.

7. The method of claim 4, 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.

8. The method of claim 4, wherein expression of the polypeptide results in modulation of production of said fine chemical.

9. The method of claim 4, 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.

10. The method of claim 4, wherein said fine chemical is an amino acid.

11. The method of claim 10, wherein the amino acid is 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.

12. 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 1 thereby diagnosing the presence or activity of Corynebacterium diphtheriae in the subject.