(en)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.

1.ApplicationNumber: US-72192203-A
1.PublishNumber: US-2005191732-A1
2.Date Publish: 20050901
3.Inventor: POMPEJUS MARKUS
KROGER BURKHARD
SCHRODER HARTWIG
ZELDER OSKAR
HABERHAUER GREGOR

4.Inventor Harmonized: POMPEJUS MARKUS(DE)
KROGER BURKHARD(DE)
SCHRODER HARTWIG(DE)
ZELDER OSKAR(DE)
HABERHAUER GREGOR(DE)

5.Country: US
6.Claims:
(en)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.

7.Description:
(en)RELATED APPLICATIONS
This application claims priority to prior filed U.S. Provisional Patent Application Ser. No. 60/141,031, filed Jun. 25, 1999, U.S. Provisional Patent Application Ser. No. 60/143,694, filed Jul. 14, 2000, and U.S. Provisional Patent Application Ser. No. 60/151,778, filed Aug. 31, 1999. This application also claims priority to German Application No. 19931418.7, filed Jul. 8, 1999, German Application No. 19932124.8, filed Jul. 9, 1999, German Application No. 19932126.4, filed Jul. 9, 1999, German Application No. 19932127.2, filed Jul. 9, 1999, German Application No. 19932133.7, filed Jul. 9, 1999, German Application No. 19932207.4, filed Jul. 9, 1999, German Application No. 19932208.2, filed Jul. 9, 1999, German Application No. 19932225.2, filed Jul. 9, 1999, German Application No. 19932229.5, filed Jul. 9, 1999, German Application No. 19932914.1, filed Jul. 9, 1999, German Application No. 19933006.9, filed Jul. 9, 1999, German Application No. 19940765.7, filed Aug. 27, 1999, German Application No. 19940768.1, filed Aug. 27, 1999, German Application No. 19940831.9, filed Aug. 27, 1999, German Application No. 19940832.7, filed Aug. 27, 1999, German Application No. 19941385.1, filed Aug. 31, 1999, German Application No. 19941396.7, filed Aug. 31, 1999, and German Application No. 19942087.4, filed Sep. 3, 1999. The entire contents of all of the aforementioned applications are hereby expressly incorporated herein by this reference.


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.
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 rd edition, pages 578-590 (1988)). The ‘essential’ amino acids (histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine), so named because they are generally a nutritional requirement due to the complexity of their biosyntheses, are readily converted by simple biosynthetic pathways to the remaining 11 ‘nonessential’ amino acids (alanine, arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine). Higher animals do retain the ability to synthesize some of these amino acids, but the essential amino acids must be supplied from the diet in order for normal protein synthesis to occur.
Aside from their function in protein biosynthesis, these amino acids are interesting chemicals in their own right, and many have been found to have various applications in the food, feed, chemical, cosmetics, agriculture, and pharmaceutical industries. Lysine is an important amino acid in the nutrition not only of humans, but also of monogastric animals such as poultry and swine. Glutamate is most commonly used as a flavor additive (mono-sodium glutamate, MSG) and is widely used throughout the food industry, as are aspartate, phenylalanine, glycine, and cysteine. Glycine, L-methionine and tryptophan are all utilized in the pharmaceutical industry. Glutamine, valine, leucine, isoleucine, histidine, arginine, proline, serine and alanine are of use in both the pharmaceutical and cosmetics industries. Threonine, tryptophan, and D/L-methionine are common feed additives. (Leuchtenberger, W. (1996) Amino aids—technical production and use, p. 466-502 in Rehm et al. (eds.) Biotechnology vol. 6, chapter 14a, VCH: Weinheim). Additionally, these amino acids have been found to be useful as precursors for the synthesis of synthetic amino acids and proteins, such as N-acetylcysteine, S-carboxymethyl-L-cysteine, (S)-5-hydroxytryptophan, and others described in Ulmann's Encyclopedia of Industrial Chemistry, vol. A2, p. 57-97, VCH: Weinheim, 1985.
The biosynthesis of these natural amino acids in organisms capable of producing them, such as bacteria, has been well characterized (for review of bacterial amino acid biosynthesis and regulation thereof, see Umbarger, H. E. (1978) Ann. Rev. Biochem. 47: 533-606). Glutamate is synthesized by the reductive amination of α-ketoglutarate, an intermediate in the citric acid cycle. Glutamine, proline, and arginine are each subsequently produced from glutamate. The biosynthesis of serine is a three-step process beginning with 3-phosphoglycerate (an intermediate in glycolysis), and resulting in this amino acid after oxidation, transamination, and hydrolysis steps. Both cysteine and glycine are produced from serine; the former by the condensation of homocysteine with serine, and the latter by the transferal of the side-chain β-carbon atom to tetrahydrofolate, in a reaction catalyzed by serine transhydroxymethylase. Phenylalanine, and tyrosine are synthesized from the glycolytic and pentose phosphate pathway precursors erythrose 4-phosphate and phosphoenolpyruvate in a 9-step biosynthetic pathway that differ only at the final two steps after synthesis of prephenate. Tryptophan is also produced from these two initial molecules, but its synthesis is an 11-step pathway. Tyrosine may also be synthesized from phenylalanine, in a reaction catalyzed by phenylalanine hydroxylase. Alanine, valine, and leucine are all biosynthetic products of pyruvate, the final product of glycolysis. Aspartate is formed from oxaloacetate, an intermediate of the citric acid cycle. Asparagine, methionine, threonine, and lysine are each produced by the conversion of aspartate. Isoleucine is formed from threonine. A complex 9-step pathway results in the production of histidine from 5-phosphoribosyl-1-pyrophosphate, an activated sugar.
Amino acids in excess of the protein synthesis needs of the cell cannot be stored, and are instead degraded to provide intermediates for the major metabolic pathways of the cell (for review see Stryer, L. Biochemistry 3 rd ed. Ch. 21 “Amino Acid Degradation and the Urea Cycle” p. 495-516 (1988)). Although the cell is able to convert unwanted amino acids into useful metabolic intermediates, amino acid production is costly in terms of energy, precursor molecules, and the enzymes necessary to synthesize them. Thus it is not surprising that amino acid biosynthesis is regulated by feedback inhibition, in which the presence of a particular amino acid serves to slow or entirely stop its own production (for overview of feedback mechanisms in amino acid biosynthetic pathways, see Stryer, L. Biochemistry, 3 rd ed. Ch. 24: “Biosynthesis of Amino Acids and Heme” p. 575-600 (1988)). Thus, the output of any particular amino acid is limited by the amount of that amino acid present in the cell.
B. Vitamin, Cofactor, and Nutraceutical Metabolism and Uses
Vitamins, cofactors, and nutraceuticals comprise another group of molecules which the higher animals have lost the ability to synthesize and so must ingest, although they are readily synthesized by other organisms such as bacteria. These molecules are either bioactive substances themselves, or are precursors of biologically active substances which may serve as electron carriers or intermediates in a variety of metabolic pathways. Aside from their nutritive value, these compounds also have significant industrial value as coloring agents, antioxidants, and catalysts or other processing aids. (For an overview of the structure, activity, and industrial applications of these compounds, see, for example, Ullman's Encyclopedia of Industrial Chemistry, “Vitamins” vol. A27, p. 443-613, VCH: Weinheim, 1996.) The term “vitamin” is art-recognized, and includes nutrients which are required by an organism for normal functioning, but which that organism cannot synthesize by itself. The group of vitamins may encompass cofactors and nutraceutical compounds. The language “cofactor” includes nonproteinaceous compounds required for a normal enzymatic activity to occur. Such compounds may be organic or inorganic; the cofactor molecules of the invention are preferably organic. The term “nutraceutical” includes dietary supplements having health benefits in plants and animals, particularly humans. Examples of such molecules are vitamins, antioxidants, and also certain lipids (e.g., polyunsaturated fatty acids).
The biosynthesis of these molecules in organisms capable of producing them, such as bacteria, has been largely characterized (Ullman's Encyclopedia of Industrial Chemistry, “Vitamins” vol. A27, p. 443-613, VCH: Weinheim, 1996; Michal, G. (1999) Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, John Wiley & Sons; Ong, A. S., Niki, E. & Packer, L. (1995) “Nutrition, Lipids, Health, and Disease” Proceedings of the UNESCO/Confederation of Scientific and Technological Associations in Malaysia, and the Society for Free Radical Research—Asia, held Sep. 1-3, 1994 at Penang, Malaysia, AOCS Press: Champaign, Ill. X, 374 S).
Thiamin (vitamin B 1 ) is produced by the chemical coupling of pyrimidine and thiazole moieties. Riboflavin (vitamin B 2 ) is synthesized from guanosine-5′-triphosphate (GTP) and ribose-5′-phosphate. Riboflavin, in turn, is utilized for the synthesis of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). The family of compounds collectively termed ‘vitamin B 6 ’ (e.g., pyridoxine, pyridoxamine, pyridoxa-5′-phosphate, and the commercially used pyridoxin hydrochloride) are all derivatives of the common structural unit, 5-hydroxy-6-methylpyridine. Pantothenate (pantothenic acid, (R)-(+)-N-(2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)-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 B 5 ), pantetheine (and its derivatives) and coenzyme A.
Biotin biosynthesis from the precursor molecule pimeloyl-CoA in microorganisms has been studied in detail and several of the genes involved have been identified. Many of the corresponding proteins have been found to also be involved in Fe-cluster synthesis and are members of the nifS class of proteins. Lipoic acid is derived from octanoic acid, and serves as a coenzyme in energy metabolism, where it becomes part of the pyruvate dehydrogenase complex and the 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 B 12 ) and porphyrines belong to a group of chemicals characterized by a tetrapyrole ring system. The biosynthesis of vitamin B 12 is sufficiently complex that it has not yet been completely characterized, but many of the enzymes and substrates involved are now known. Nicotinic acid (nicotinate), and nicotinamide are pyridine derivatives which are also termed ‘niacin’. Niacin is the precursor of the important coenzymes NAD (nicotinamide adenine dinucleotide) and NADP (nicotinamide adenine dinucleotide phosphate) and their reduced forms.
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 B 6 , pantothenate, and biotin. Only Vitamin B 12 is produced solely by fermentation, due to the complexity of its synthesis. In vitro methodologies require significant inputs of materials and time, often at great cost.
C. Purine, Pyrimidine, Nucleoside and Nucleotide Metabolism and Uses
Purine and pyrimidine metabolism genes and their corresponding proteins are important targets for the therapy of tumor diseases and viral infections. The language “purine” or “pyrimidine” includes the nitrogenous bases which are constituents of nucleic acids, co-enzymes, and nucleotides. The term “nucleotide” includes the basic structural units of nucleic acid molecules, which are comprised of a nitrogenous base, a pentose sugar (in the case of RNA, the sugar is ribose; in the case of DNA, the sugar is D-deoxyribose), and phosphoric acid. The language “nucleoside” includes molecules which serve as precursors to nucleotides, but which are lacking the phosphoric acid moiety that nucleotides possess. By inhibiting the biosynthesis of these molecules, or their mobilization to form nucleic acid molecules, it is possible to inhibit RNA and DNA synthesis; by inhibiting this activity in a fashion targeted to cancerous cells, the ability of tumor cells to divide and replicate may be inhibited. Additionally, there are nucleotides which do not form nucleic acid molecules, but rather serve as energy stores (i.e., AMP) or as coenzymes (i.e., FAD and NAD).
Several publications have described the use of these chemicals for these medical indications, by influencing purine and/or pyrimidine metabolism (e.g. Christopherson, R. I. and Lyons, S. D. (1990) “Potent inhibitors of de novo pyrimidine and purine biosynthesis as chemotherapeutic agents.” Med. Res. Reviews 10: 505-548). Studies of enzymes involved in purine and pyrimidine metabolism have been focused on the development of new drugs which can be used, for example, as immunosuppressants or anti-proliferants (Smith, J. L., (1995) “Enzymes in nucleotide synthesis.” Curr. Opin. Struct. Biol. 5: 752-757; (1995) Biochem Soc. Transact. 23: 877-902). However, purine and pyrimidine bases, nucleosides and nucleotides have other utilities: as intermediates in the biosynthesis of several fine chemicals (e.g., thiamine, S-adenosyl-methionine, folates, or riboflavin), as energy carriers for the cell (e.g., ATP or GTP), and for chemicals themselves, commonly used as flavor enhancers (e.g., IMP or GMP) or for several medicinal applications (see, for example, Kuninaka, A. (1996) Nucleotides and Related Compounds in Biotechnology vol. 6, Rehm et al., eds. VCH: Weinheim, p. 561-612). Also, enzymes involved in purine, pyrimidine, nucleoside, or nucleotide metabolism are increasingly serving as targets against which chemicals for crop protection, including fungicides, herbicides and insecticides, are developed.
The metabolism of these compounds in bacteria has been characterized (for reviews see, for example, Zalkin, H. and Dixon, J. E. (1992) “de novo purine nucleotide biosynthesis”, in: Progress in Nucleic Acid Research and Molecular Biology, vol. 42, Academic Press:, p. 259-287; and Michal, G. (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., NH 4 Cl, (NH 4 ) 2 SO 4 , or NH 4 OH), nitrates, urea, amino acids, or complex nitrogen sources like corn steep liquor, soy bean flour, soy bean protein, yeast extract, meat extract, 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 th ed. 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/lon 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. 2 nd, 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., RXA02702, RXN02707, RXS02560, and RXC00110). 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 RXA02702, RXN02707, RXS02560, and RXC00110 are translations of the coding regions of the nucleotide sequence of nucleic acid molecules RXA02702, RXN02707, RXS02560, and RXC00110, 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:1, designated, as indicated on Table 1, as “F RXA02702”, is an F-designated gene, as are SEQ ID NOs: 9, 11, and 13 (designated on Table 1 as “F RXA02707”, “F RXA02708”, and “F RXA02709”, 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 36% identical to the nucleotide sequence designated RXA00009 (SEQ ID NO:85), a nucleotide sequence which is greater than and/or at least 40% identical to the nucleotide sequence designated RXA00277 (SEQ ID NO:91), and a nucleotide sequence which is greater than and/or at least 43% identical to the nucleotide sequence designated RXA00499 (SEQ ID NO:173). 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. 1 (RXA02702) comprises nucleotides 1 to 1458). 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 β-units, the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids. Res. 15: 6625-6641). The antisense nucleic acid molecule can also comprise a 2′-o-methylribonucleotide (Inoue et al. (1987) Nucleic Acids Res. 15: 6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215: 327-330).
In still another embodiment, an antisense nucleic acid of the invention is a ribozyme. Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334: 585-591)) can be used to catalytically cleave 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 (RXA02705) 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 λ P 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, pBdC1, and pET 11d (Studier et al., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 60-89; and Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: New York IBSN 0 444 904018). Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-lac fusion promoter. Target gene expression from the pET 11d vector relies on transcription from a T7 gn10-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gn1). This viral polymerase is supplied by host strains BL21 (DE3) or HMS174(DE3) from a resident % prophage harboring a T7 gn1 gene under the transcriptional control of the lacUV 5 promoter. For transformation of other varieties of bacteria, appropriate vectors may be selected. 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. 2 nd, ed, Cold Spring Harbor Laboratory , Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.
In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1: 268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43: 235-275), in particular promoters of T cell receptors (Winoto and Baltimore (1989) EMBO J. 8: 729-733) and immunoglobulins (Banerji et al. (1983) Cell 33: 729-740; Queen and Baltimore (1983) Cell 33: 741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle (1989) PNAS 86: 5473-5477), pancreas-specific promoters (Edlund et al. (1985) Science 230: 912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166). Developmentally-regulated promoters are also encompassed, for example the murine hox promoters (Kessel and Gruss (1990) Science 249: 374-379) and the α-fetoprotein promoter (Campes and Tilghman (1989) Genes Dev. 3: 537-546).
The invention further provides a recombinant expression vector comprising a DNA molecule of the invention cloned into the expression vector in an antisense orientation. That is, the DNA molecule is operatively linked to a regulatory sequence in a manner which allows for expression (by transcription of the DNA molecule) of an RNA molecule which is antisense to 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. 2 nd, 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,” DDT 2: 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 rd ed., 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 MgSO 4 ×7H 2 O, 10 ml/l KH 2 PO 4 solution (100 g/l, adjusted to pH 6.7 with KOH), 50 ml/l M12 concentrate (10 g/l (NH 4 ) 2 SO 4 , 1 g/l NaCl, 2 g/l MgSO 4 ×7H 2 O, 0.2 g/l CaCl 2 , 0.5 g/l yeast extract (Difco), 10 ml/l trace-elements-mix (200 mg/l FeSO 4 ×H 2 O, 10 mg/l ZnSO 4 ×7H 2 O, 3 mg/l MnCl 2 ×4H 2 O, 30 mg/l H 2 BO 3 20 mg/l CoCl 2 ×6H 2 O, 1 mg/l NiCl 2 ×6H 2 O, 3 mg/l Na 2 MoO 4 ×2H 2 O, 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 Schäfer, A et al. (1990) J. Bacteriol. 172: 1663-1666). It is also possible to transfer the shuttle vectors for C. glutamicum to E. coli by preparing plasmid DNA from C. glutamicum (using standard methods well-known in the art) and transforming it into E. coli . This transformation step can be performed using standard methods, but it is advantageous to use an Mcr-deficient E. coli strain, such as NM522 (Gough & Murray (1983) J. Mol. Biol. 166: 1-19).
Genes may be overexpressed in C. glutamicum strains using plasmids which comprise pCG1 (U.S. Pat. No. 4,617,267) or fragments thereof, and optionally the gene for kanamycin resistance from TN903 (Grindley, N. D. and Joyce, C. M. (1980) Proc. Natl. Acad. Sci. USA 77(12): 7176-7180). In addition, genes may be overexpressed in C. glutamicum strains using plasmid pSL109 (Lee, H.-S. and A. J. Sinskey (1994) J. Microbiol. Biotechnol. 4: 256-263).
Aside from the use of replicative plasmids, gene overexpression can also be achieved by integration into the genome. Genomic integration in C. glutamicum or other Corynebacterium or Brevibacterium species may be accomplished by well-known methods, such as homologous recombination with genomic region(s), restriction endonuclease mediated integration (REMI) (see, e.g., DE Patent 19823834), or through the use of transposons. It is also possible to modulate the activity of a gene of interest by modifying the regulatory regions (e.g., a promoter, a repressor, and/or an enhancer) by sequence modification, insertion, or deletion using site-directed methods (such as homologous recombination) or methods based on random events (such as transposon mutagenesis or REMI). Nucleic acid sequences which function as transcriptional terminators may also be inserted 3′ to the coding region of one or more genes of the invention; such terminators are well-known in the art and are described, for example, in Winnacker, E. L. (1987) From Genes to Clones—Introduction to Gene Technology. VCH: Weinheim.
EXAMPLE 6
Assessment of the Expression of the Mutant Protein
Observations of the activity of a mutated protein in a transformed host cell rely on the fact that the mutant protein is expressed in a similar fashion and in a similar quantity to that of the wild-type protein. A useful method to ascertain the level of transcription of the mutant gene (an indicator of the amount of mRNA available for translation to the gene product) is to perform a Northern blot (for reference see, for example, Ausubel et al. (1988) Current Protocols in Molecular Biology, Wiley: 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 NH 4 Cl or (NH 4 ) 2 SO 4 , NH 4 OH, nitrates, urea, amino acids or complex nitrogen sources like corn steep liquor, soy bean flour, soy bean protein, yeast extract, meat extract and others.
Inorganic salt compounds which may be included in the media include the chloride-, phosphorous- or sulfate-salts of calcium, magnesium, sodium, cobalt, molybdenum, potassium, manganese, zinc, copper and iron. Chelating compounds can be added to the medium to keep the metal ions in solution. Particularly useful chelating compounds include dihydroxyphenols, like catechol or protocatechuate, or organic acids, such as citric acid. It is typical for the media to also contain other growth factors, such as vitamins or growth promoters, examples of which include biotin, riboflavin, thiamin, folic acid, nicotinic acid, pantothenate and pyridoxin. 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 NH 4 OH during growth. If complex medium components such as yeast extract are utilized, the necessity for additional buffers may be reduced, due to the fact that many complex compounds have high buffer capacities. If a fermentor is utilized for culturing the micro-organisms, the pH can also be controlled using gaseous ammonia.
The incubation time is usually in a range from several hours to several days. This time is selected in order to permit the maximal amount of product to accumulate in the broth. The disclosed growth experiments can be carried out in a variety of vessels, such as microtiter plates, glass tubes, glass flasks or glass or metal fermentors of different sizes. 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 OD 600 of 0.5-1.5 using cells grown on agar plates, such as CM plates (10 g/l glucose, 2,5 g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeast extract, 5 g/l meat extract, 22 g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeast extract, 5 g/l meat extract, 22 g/l agar, pH 6.8 with 2M NaOH) that had been incubated at 30° C. Inoculation of the media is accomplished by either introduction of a saline suspension of C. glutamicum cells from CM plates or addition of a liquid preculture of this bacterium.
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 rd ed. Academic Press: New York; Bisswanger, H., (1994) Enzymkinetik, 2 nd ed. VCH: Weinheim (ISBN 3527300325); Bergmeyer, H. U., Bergmeyer, J., Graβl, M., eds. (1983-1986) Methods of Enzymatic Analysis, 3 rd ed., vol. I-XII, Verlag Chemie: Weinheim; and Ullmann's Encyclopedia of Industrial Chemistry (1987) vol. A9, “Enzymes”. VCH: Weinheim, p. 352-363.
The activity of proteins which bind to DNA can be measured by several well-established methods, such as DNA band-shift assays (also called gel retardation assays). The effect of such proteins on the expression of other molecules can be measured using reporter gene assays (such as that described in Kolmar, H. et al. (1995) EMBO J. 14: 3895-3904 and references cited therein). Reporter gene test systems are well known and established for applications in both pro- and eukaryotic cells, using enzymes such as beta-galactosidase, green fluorescent protein, and several others.
The determination of activity of membrane-transport proteins can be performed according to techniques such as those described in Gennis, R. B. (1989) “Pores, Channels and Transporters”, in Biomembranes, Molecular Structure and Function, Springer: Heidelberg, p. 85-137; 199-234; and 270-322.
EXAMPLE 9
Analysis of Impact of Mutant Protein on the Production of the Desired Product
The effect of the genetic modification in C. glutamicum on production of a desired compound (such as an amino acid) can be assessed by growing the modified microorganism under suitable conditions (such as those described above) and analyzing the medium and/or the cellular component for increased production of the desired product (i.e., an amino acid). Such analysis techniques are well known to one of ordinary skill in the art, and include spectroscopy, thin layer chromatography, staining methods of various kinds, enzymatic and microbiological methods, and analytical chromatography such as high performance liquid chromatography (see, for example, Ullman, Encyclopedia of Industrial Chemistry, vol. A2, p. 89-90 and p. 443-613, VCH: Weinheim (1985); Fallon, A. et al., (1987) “Applications of HPLC in Biochemistry” in: Laboratory Techniques in Biochemistry and Molecular Biology, vol. 17; Rehm et al. (1993) Biotechnology, vol. 3, Chapter III: “Product recovery and purification”, page 469-714, VCH: Weinheim; Belter, P. A. et al. (1988) Bioseparations: downstream processing for biotechnology, John Wiley and Sons; Kennedy, J. F. and Cabral, J. M. S. (1992) Recovery processes for biological materials, John Wiley and Sons; Shaeiwitz, J. A. and Henry, J. D. (1988) Biochemical separations, in: Ulmann's Encyclopedia of Industrial Chemistry, vol. B3, Chapter 11, page 1-27, VCH: Weinheim; and Dechow, F. J. (1989) Separation and purification techniques in biotechnology, Noyes Publications.)
In addition to the measurement of the final product of fermentation, it is also possible to analyze other components of the metabolic pathways utilized for the production of the desired compound, such as intermediates and side-products, to determine the overall efficiency of production of the compound. Analysis methods include measurements of nutrient levels in the medium (e.g., sugars, hydrocarbons, nitrogen sources, phosphate, and other ions), measurements of biomass composition and growth, analysis of the production of common metabolites of biosynthetic pathways, and measurement of gasses produced during fermentation. Standard methods for these measurements are outlined in Applied Microbial Physiology, A Practical Approach, P. M. Rhodes and P. F. Stanbury, eds., IRL Press, p. 103-129; 131-163; and 165-192 (ISBN: 0199635773) and references cited therein.
EXAMPLE 10
Purification of the Desired Product from C. Glutamicum Culture
Recovery of the desired product from the C. glutamicum cells or supernatant of the above-described culture can be performed by various methods well known in the art. If the desired product is not secreted from the cells, the cells can be harvested from the culture by low-speed centrifugation, the cells can be lysed by standard techniques, such as mechanical force or sonication. The cellular debris is removed by 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., 35 S-methionine, 35 S-cysteine, 14 C-labelled amino acids, 15 N-amino acids, 15 NO 3 or 15 NH 4 + or 13 C-labelled amino acids) 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 Identifi- ID ID cation NT NT NO NO Code Contig. Start Stop Function 1 2 RXA02702 GR00758 1572 115 UDP-N-ACETYLMURAMATE-ALANINE LIGASE (EC 6.3.2.8) 3 4 RXA02705 GR00758 5803 4388 UDP-N-ACETYLMURAMOYLALANINE-D-GLUTAMATE LIGASE (EC 6.3.2.9) 5 6 RXA01254 GR00365 3807 2539 UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE-2,6- DIAMINOPIMELATE LIGASE (EC 6.3.2.13) 7 8 RXN02707 VV0017 20110 18581 UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6- DIAMINOPIMELATE-D-ALANYL-D-ALANYL LIGASE 9 10 F RXA02707 GR00758 7264 6920 UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6- DIAMINOPIMELATE-D-ALANYL-D-ALANYL LIGASE (EC 6.3.2.15) 11 12 F RXA02708 GR00758 7694 7260 UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL-2,6- DIAMINOPIMELATE-D-ALANYL-D- ALANYL LIGASE (EC 6.3.2.15) 13 14 F RXA02709 GR00758 8451 7723 UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL- 2,6-DIAMINOPIMELATE-D-ALANYL-D- ALANYL LIGASE (EC 6.3.2.15) 15 16 RXA02710 GR00758 10035 8473 UDP-N-ACETYLMURAMOYLALANYL-D- GLUTAMATE-2,6-DIAMINOPIMELATE LIGASE (EC 6.3.2.13) 17 18 RXN00531 VV0079 19063 19557 FINE TANGLED PILI MAJOR SUBUNIT 19 20 RXA00944 GR00259 1573 602 NADPH DEHYDROGENASE 3 (EC 1.6.99.1) 21 22 RXS02560 VV0101 9922 10788 NADPH-FLAVIN OXIDOREDUCTASE (EC 1.6.99.—) 23 24 RXS03119 VV0098 86877 87008 SUPEROXIDE DISMUTASE [MN] (EC 1.15.1.1) 25 26 RXS03120 VV0098 87351 87476 SUPEROXIDE DISMUTASE [MN] (EC 1.15.1.1) Cell wall biosynthesis 27 28 RXA01430 GR00417 7458 6271 N-ACETYLMURAMOYL-L-ALANINE AMIDASE (EC 3.5.1.28) 29 30 RXA02641 GR00749 5097 3022 N-ACETYLMURAMOYL-L-ALANINE AMIDASE (EC 3.5.1.28) 31 32 RXA00135 GR00021 1709 2962 UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE (EC 2.5.1.7) 33 34 RXA02706 GR00758 6910 5813 PHOSPHO-N-ACETYLMURAMOYL-PENTAPEPTIDE- TRANSFERASE (EC 2.7.8.13) 35 36 RXA02411 GR00703 1845 997 GLUTAMATE RACEMASE (EC 5.1.1.3) 37 38 RXN01022 VV0143 4460 3381 D-ALANINE-D-ALANINE LIGASE (EC 6.3.2.4) 39 40 F RXA01022 GR00292 3 806 D-ALANINE-D-ALANINE LIGASE (EC 6.3.2.4) 41 42 RXA02703 GR00758 2698 1610 UDP-N-ACETYLGLUCOSAMINE—N-ACETYLMURAMYL- (PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE TRANSFERASE (EC 2.4.1.—) 43 44 RXA02711 GR00758 12273 10162 PENICILLIN-BINDING PROTEIN 2 45 46 RXA02859 GR10005 846 121 PENICILLIN-BINDING PROTEIN 5* PRECURSOR (D-ALANYL-D- ALANINE CARBOXYPEPTIDASE) (EC 3.4.16.4) 47 48 RXA00569 GR00152 3928 4953 PENICILLIN-BINDING PROTEIN 4 49 50 RXN03092 VV0054 10445 9561 PENICILLIN-BINDING PROTEIN 1A 51 52 F RXA00594 GR00158 3525 4457 PENICILLIN-BINDING PROTEIN 1A 53 54 RXA01828 GR00516 7736 6315 PENICILLIN-BINDING PROTEIN 3 55 56 RXA00612 GR00162 3 1187 PENICILLIN-BINDING PROTEIN 1A 57 58 RXA01510 GR00424 15370 16650 PENICILLIN-BINDING PROTEIN 4 PRECURSOR (PBP-4) (D-ALANYL- D-ALANINE CARBOXYPEPTIDASE) (EC 3.4.16.4)/D-ALANYL- D-ALANINE-ENDOPEPTIDASE (EC 3.4.99.—) 59 60 RXN01608 VV0139 3536 5374 PENICILLIN-BINDING PROTEIN 5 PRECURSOR 61 62 F RXA01608 GR00449 837 2675 (AL008883) penecillin binding protein [Mycobacterium tuberculosis] 63 64 RXA01270 GR00367 21652 20498 perosamine synthetase 65 66 RXN00549 VV0079 31746 33419 PENICILLIN-BINDING PROTEIN 1A 67 68 RXN00550 VV0079 33457 33777 PENICILLIN-BINDING PROTEIN 1A 69 70 RXN03091 VV0054 9515 8970 PENICILLIN-BINDING PROTEIN 1A 71 72 RXN03178 VV0334 921 121 PENICILLIN-BINDING PROTEIN 5* PRECURSOR (D- ALANYL-D-ALANINE CARBOXYPEPTIDASE) (EC 3.4.16.4) 73 74 F RXA02859 GR10005 846 121 PENICILLIN-BINDING PROTEIN 5* PRECURSOR (D- ALANYL-D-ALANINE CARBOXYPEPTIDASE) (EC 3.4.16.4) 75 76 RXN01267 VV0009 17895 16582 UDP-N-ACETYLGLUCOSAMINE 1-CARBOXYVINYLTRANSFERASE (EC 2.5.1.7) 77 78 RXN00045 VV0119 4409 5317 UDP-N-acetylglucosamine-2-epimerase (EC 5.1.3.14)/N- acetylmannosamine kinase (EC 2.7.1.60) Cell division 79 80 RXN02704 VV0017 16043 14355 CELL DIVISIN PROTEIN FTSW 81 82 F RXA02704 GR00758 4382 2694 CELL DIVISIN PROTEIN FTSW 83 84 RXA02722 GR00759 2729 1404 CELL DIVISION PROTEIN FTSZ 85 86 RXA00009 GR00002 1545 646 CELL DIVISION PROTEIN FTSX 87 88 RXA00010 GR00002 2248 1562 CELL DIVISION ATP-BINDING PROTEIN FTSE 89 90 RXA00143 GR00022 6328 4847 CELL DIVISION INHIBITOR 91 92 RXA00277 GR00043 1588 5 CELL DIVISION CONTROL PROTEIN 15 (EC 2.7.1.—) 93 94 RXA00857 GR00233 2 1291 CELL DIVISION PROTEIN FTSK 95 96 RXA01435 GR00418 2 871 CELL DIVISION CONTROL PROTEIN 15 (EC 2.7.1.—) 97 98 RXA01511 GR00424 16655 17596 CELL CYCLE PROTEIN MESJ 99 100 RXA01513 GR00424 18368 20926 CELL DIVISION PROTEIN FTSH (EC 3.4.24.—) 101 102 RXA02098 GR00630 4161 5906 CELL DIVISION PROTEIN FTSY 103 104 RXA02713 GR00758 14077 13067 Hypothetical Cell Division Protein mraW 105 106 RXN02723 VV0017 11745 11080 FTSQ 107 108 F RXA02723 GR00759 3460 2984 FTSQ 109 110 RXA01426 GR00417 2777 3403 GLUCOSE INHIBITED DIVISION PROTEIN B 111 112 RXA01428 GR00417 4495 5631 STAGE 0 SPORULATION PROTEIN J 113 114 RXA01640 GR00456 4661 1344 STAGE III SPORULATION PROTEIN E 115 116 RXA01829 GR00516 9058 7736 STAGE V SPORULATION PROTEIN E 117 118 RXA01427 GR00417 3512 4432 SOJ PROTEIN 119 120 RXN02973 VV0229 657 4 SOJ PROTEIN 121 122 F RXA01603 GR00447 14043 14663 SOJ PROTEIN 123 124 RXN00818 VV0054 28524 27685 INHIBITION OF MORPHOLOGICAL DIFFERENTIATION Proteolysis 125 126 RXN03028 VV0008 41156 43930 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA 127 128 F RXA02470 GR00715 2216 3196 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA 129 130 F RXA02471 GR00715 3159 4991 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA 131 132 RXN03094 VV0057 1794 43 CLPB PROTEIN 133 134 F RXA01668 GR00464 2205 3920 CLPB PROTEIN 135 136 RXN02937 VV0098 85783 85382 N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14) 137 138 RXN03077 VV0043 1729 2913 N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14) 139 140 F RXA02855 GR10002 1693 2877 N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC 3.5.1.14), hippurate hydrolase 141 142 RXN00982 VV0149 7596 6091 (L42758) proteinase [Streptomyces lividans] 143 144 F RXA00977 GR00275 1647 2660 (L42758) proteinase [Streptomyces lividans] 145 146 F RXA00982 GR00276 5194 4949 (L42758) proteinase [Streptomyces lividans] 147 148 RXN01181 VV0065 1 957 AMINOPEPTIDASE A/I (EC 3.4.11.1) 149 150 F RXA01181 GR00337 1 957 AMINOPEPTIDASE 151 152 RXN01014 VV0209 13328 10728 AMINOPEPTIDASE N (EC 3.4.11.2) 153 154 F RXA01014 GR00289 3 1580 AMINOPEPTIDASE N (EC 3.4.11.2) 155 156 F RXA01018 GR00290 2289 3152 AMINOPEPTIDASE N (EC 3.4.11.2) 157 158 RXN01046 VV0015 47863 49641 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA 159 160 RXN01974 VV0218 3793 5577 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA 161 162 RXN01120 VV0182 5678 4401 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX 163 164 F RXA01120 GR00310 2349 1072 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX 165 166 RXN00397 VV0025 3803 4603 XAA-PRO AMINOPEPTIDASE (EC 3.4.11.9) 167 168 RXN01868 VV0127 9980 11905 ZINC METALLOPROTEASE (EC 3.4.24.—) 169 170 F RXA01868 GR00534 1640 30 ZINC METALLOPROTEASE (EC 3.4.24.—) 171 172 F RXA01869 GR00534 1954 1652 ZINC METALLOPROTEASE (EC 3.4.24.—) 173 174 RXN00499 VV0086 8158 9438 PROLINE IMINOPEPTIDASE (EC 3.4.11.5) 175 176 F RXA00499 GR00125 3 959 PROLINE IMINOPEPTIDASE 177 178 RXN01277 VV0009 32155 34158 PROLYL ENDOPEPTIDASE (EC 3.4.21.26) 179 180 F RXA01277 GR00368 1738 50 PROLYL ENDOPEPTIDASE (EC 3.4.21.26) 181 182 RXN00675 VV0005 33258 34049 METHIONINE AMINOPEPTIDASE (EC 3.4.11.18) 183 184 F RXA00675 GR00178 2 484 METHIONINE AMINOPEPTIDASE (EC 3.4.11.18) 185 186 RXN00877 VV0099 2221 3885 PEPTIDYL-DIPEPTIDASE DCP (EC 3.4.15.5) 187 188 F RXA00877 GR00242 3 1067 PEPTIDYL-DIPEPTIDASE DCP (EC 3.4.15.5) 189 190 RXN01226 VV0064 4172 4711 PEPTIDYL-TRNA HYDROLASE (EC 3.1.1.29) 191 192 RXN01963 VV0200 689 6 Hypothetical Secretory Serine Protease (EC 3.4.21.—) 193 194 RXN00621 VV0135 5853 5071 PROTEASE II (EC 3.4.21.83) 195 196 F RXA00621 GR00163 4075 4857 PTRB periplasmic protease 197 198 RXN00622 VV0135 5150 3735 PROTEASE II (EC 3.4.21.83) 199 200 F RXA00622 GR00163 4778 6193 PTRB periplasmic protease 201 202 RXN02146 VV0300 14742 15368 PROTEIN P60 PRECURSOR 203 204 RXN03133 VV0127 39393 40076 HYDROGENASE 1 MATURATION PROTEASE (EC 3.4.—.—) 205 206 RXN02820 VV0131 4799 6109 GAMMA-GLUTAMYLTRANSPEPTIDASE (EC 2.3.2.2) 207 208 F RXA02820 GR00801 1 507 GAMMA-GLUTAMYLTRANSPEPTIDASE (EC 2.3.2.2) 209 210 F RXA02000 GR00589 3430 3933 GAMMA-GLUTAMYLTRANSPEPTIDASE (EC 2.3.2.2) 211 212 RXN02944 VV0169 12751 12074 GAMMA-GLUTAMYLTRANSPEPTIDASE PRECURSOR (EC 2.3.2.2) 213 214 RXS00197 VV0115 2733 1522 Membrane Spanning Protease 215 216 RXS01223 VV0064 7528 8139 PEPTIDYL-TRNA HYDROLASE (EC 3.1.1.29) 217 218 RXS01642 VV0005 49423 48182 Serine protease Enzymes in general 219 220 RXA01728 GR00489 2452 1478 BETA C-S LYASE (EC 3.—.—.—) PUTATIVE AMINOTRANSFERASE 221 222 RXA02214 GR00650 954 1562 Acetyltransferases 223 224 RXA02716 GR00758 16827 17387 Acetyltransferases 225 226 RXN01499 VV0008 7034 3213 ENTEROBACTIN SYNTHETASE COMPONENT F 227 228 FRXA01499 GR00424 7034 3213 Acetyltransferases (the isoleucine patch superfamily) 229 230 RXN00787 VV0321 3736 5637 D-AMINO ACID DEHYDROGENASE LARGE SUBUNIT (EC 1.4.99.1) 231 232 F RXA00787 GR00209 598 5 D-AMINO ACID DEHYDROGENASE LARGE SUBUNIT (EC 1.4.99.1) 233 234 F RXA00791 GR00210 831 4 D-AMINO ACID DEHYDROGENASE LARGE SUBUNIT (EC 1.4.99.1) 235 236 RXA01057 GR00296 7548 6046 D-AMINO ACID DEHYDROGENASE LARGE SUBUNIT (EC 1.4.99.1) 237 238 RXA01055 GR00296 4821 4720 D-AMINO ACID DEHYDROGENASE SMALL SUBUNIT (EC 1.4.99.1) 239 240 RXA01056 GR00296 5952 5053 D-AMINO ACID DEHYDROGENASE SMALL SUBUNIT (EC 1.4.99.1) 241 242 RXN02021 VV0160 2008 1061 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (EC 2.3.1.117) 243 244 RXS00949 quinate dehydrogenase (pyrroloquinoline-quinone) (EC 1.1.99.25) 245 246 RXS00004 VV0196 6930 6460 NITRILASE REGULATOR 247 248 RXS00166 VV0232 3650 4309 Methyltransferase 249 250 RXS00288 VV0079 14586 15596 QUINONE OXIDOREDUCTASE (EC 1.6.5.5) 251 252 RXS01114 VV0182 9118 10341 3-KETOACYL-COA THIOLASE (EC 2.3.1.16) 253 254 RXS01205 VV0268 893 363 UNDECAPRENYL-PHOSPHATE ALPHA-N- ACETYLGLUCOSAMINYLTRANSFERASE (EC 2.4.1.—) 255 256 RXS01269 VV0009 21430 20990 UNDECAPRENYL-PHOSPHATE GALACTOSEPHOSPHOTRANSFERASE (EC 2.7.8.6) 257 258 RXS01421 VV0122 16024 15638 ACYLTRANSFERASE (EC 2.3.1.—) 259 260 RXS01491 VV0139 36800 37450 DNA FOR L-PROLINE 3-HYDROXYLASE, COMPLETE CDS 261 262 RXS01572 VV0009 43945 44436 ALCOHOL DEHYDROGENASE (EC 1.1.1.1) 263 264 RXS02453 VV0107 7370 8122 ACETOIN(DIACETYL) REDUCTASE (EC 1.1.1.5) 265 266 RXS02474 VV0008 47021 46248 (S,S)-butane-2,3-diol dehydrogenase (EC 1.1.1.76) 267 268 RXS02485 VV0007 2359 3459 UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE (EC 1.1.1.158) 269 270 RXS02539 VV0057 17332 15815 ALDEHYDE DEHYDROGENASE (EC 1.2.1.3) 271 272 RXS02578 VV0098 7668 6565 ACYLTRANSFERASE 273 274 RXS02741 VV0074 5768 6733 QUINONE OXIDOREDUCTASE (EC 1.6.5.5) 275 276 RXS03061 VV0034 108 437 ALDEHYDE DEHYDROGENASE (EC 1.2.1.3) 277 278 RXS03150 VV0155 10678 10055 ALDEHYDE DEHYDROGENASE (EC 1.2.1.3) 279 280 RXS02554 Oxidoreductase (EC 1.1.1.—) 281 282 RXS03058 METHYLTRANSFERASE (EC 2.1.1.—) 283 284 RXS03218 CAFFEOYL-COA O-METHYLTRANSFERASE (EC 2.1.1.104) 285 286 F RXA01918 GR00549 4644 5057 CAFFEOYL-COA O-METHYLTRANSFERASE (EC 2.1.1.104) 287 288 RXC00110 VV0054 27517 26969 Protein involved in hydrolysis of epoxides 289 290 RXC01971 VV0105 4545 3715 Metal-Dependent Hydrolase Genes encoding enzymes for the metabolism of inorganic compounds Phosphate and Phosphonate metabolism 291 292 RXA02118 GR00636 2124 1783 PHNA PROTEIN 293 294 RXA00078 GR00012 6375 5962 PHNB PROTEIN 295 296 RXA02105 GR00632 294 4 PHNB PROTEIN 297 298 RXN00663 VV0142 10120 11493 PHOH PROTEIN HOMOLOG 299 300 F RXA00663 GR00173 1222 227 PHOH PROTEIN HOMOLOG 301 302 RXA00888 GR00242 14325 15341 PHOH PROTEIN HOMOLOG 303 304 RXA01437 GR00418 3932 2550 PHOSPHATE ACETYLTRANSFERASE (EC 2.3.1.8) 305 306 RXN00778 VV0103 18126 19250 PHOSPHATE-BINDING PERIPLASMIC PROTEIN PRECURSOR 307 308 F RXA00778 GR00205 9079 8246 PHOSPHATE-BINDING PERIPLASMIC PROTEIN PRECURSOR 309 310 RXA02497 GR00720 10059 10985 EXOPOLYPHOSPHATASE (EC 3.6.1.11) 311 312 RXA01477 GR00422 8469 10016 ALKALINE PHOSPHATASE D PRECURSOR (EC 3.1.3.1) 313 314 RXA01509 GR00424 15169 14696 INORGANIC PYROPHOSPHATASE (EC 3.6.1.1) 315 316 RXA00100 GR00014 9512 10111 DEDA PROTEIN, similar to alkaline phosphatase 317 318 RXA00615 GR00162 3355 2774 DEDA PROTEIN 319 320 RXN00250 VV0189 286 1032 DEDA PROTEIN - ALKALINE PHOSPHATASE LIKE PROTEIN 321 322 F RXA02010 GR00602 79 525 DEDA PROTEIN 323 324 RXA02120 GR00636 5021 4260 CARBOXYVINYL-CARBOXYPHOSPHONATE PHOSPHORYLMUTASE (EC 2.7.8.23) 325 326 RXS01000 VV0106 7252 6407 PHOSPHONATES TRANSPORT SYSTEM PERMEASE PROTEIN PHNE 327 328 RXS01002 VV0106 8858 8055 PHOSPHONATES TRANSPORT ATP-BINDING PROTEIN PHNC 329 330 RXS01003 VV0106 8055 7252 PHOSPHONATES TRANSPORT SYSTEM PERMEASE PROTEIN PHNE 331 332 RXS01902 VV0098 84095 83037 alkaline phosphatase Fe-Metabolism 333 334 RXA01967 GR00567 1848 706 FERRIC ENTEROCHELIN ESTERASE HOMOLOG 335 336 RXA00070 GR00011 3436 3867 FERRIC UPTAKE REGULATION PROTEIN 337 338 RXA01934 GR00555 7192 7749 FERRIPYOCHELIN BINDING PROTEIN 339 340 RXN01997 VV0084 33308 33793 FERRITIN 341 342 F RXA01997 GR00586 546 935 FERRITIN 343 344 RXA01082 GR00302 1486 827 IRON REPRESSOR 345 346 RXA01236 GR00358 2185 1241 IRON(III) DICITRATE-BINDING PERIPLASMIC PROTEIN PRECURSOR 347 348 RXA01354 GR00393 2692 1757 IRON(III) DICITRATE-BINDING PERIPLASMIC PROTEIN PRECURSOR 349 350 RXA01620 GR00451 2585 3532 IRON(III) DICITRATE-BINDING PERIPLASMIC PROTEIN PRECURSOR 351 352 RXA02052 GR00624 4586 3795 IRON(III) DICITRATE-BINDING PERIPLASMIC PROTEIN PRECURSOR 353 354 RXA00372 GR00078 1653 2729 PERIPLASMIC-IRON-BINDING PROTEIN SHIB 355 356 RXA00088 GR00013 4389 5402 FERRIC ANGUIBACTIN-BINDING PROTEIN PRECURSOR 357 358 RXS00156 VV0167 1342 2451 FERROCHELATASE (EC 4.99.1.1) 359 360 RXS00624 VV0135 2018 1332 FERROCHELATASE (EC 4.99.1.1) Modification and degradation of aromatic compounds 361 362 RXA00024 GR00003 938 1882 ARYL-ALCOHOL DEHYDROGENASE (NADP+) (EC 1.1.1.91) 363 364 RXA02526 GR00725 4109 5314 3-CARBOXY-CIS,CIS-MUCONATE CYCLOISOMERASE (EC 5.5.1.2) 365 366 RXN02813 VV0128 13120 14118 3-CARBOXY-CIS,CIS-MUCONATE CYCLOISOMERASE HOMOLOG (EC 5.5.1.2) 367 368 F RXA02813 GR00794 651 10 3-CARBOXY-CIS,CIS-MUCONATE CYCLOISOMERASE HOMOLOG (EC 5.5.1.2) 369 370 RXA01113 GR00307 1098 862 4-CARBOXYMUCONOLACTONE DECARBOXYLASE (EC 4.1.1.44) 371 372 RXA02126 GR00637 1556 1876 4-CARBOXYMUCONOLACTONE DECARBOXYLASE (EC 4.1.1.44) 373 374 RXA01465 GR00421 4121 2961 MUCONATE CYCLOISOMERASE (EC 5.5.1.1) 375 376 RXA02316 GR00665 9038 8025 MUCONATE CYCLOISOMERASE (EC 5.5.1.1) 377 378 RXA01464 GR00421 2945 2655 MUCONOLACTONE ISOMERASE (EC 5.3.3.4) 379 380 RXA02603 GR00742 7742 8737 4-HYDROXYBENZOATE OCTAPRENYLTRANSFERASE (EC 2.5.1.—) 381 382 RXN02839 VV0362 3 449 4-HYDROXYBENZOATE OCTAPRENYLTRANSFERASE (EC 2.5.1.—) 383 384 F RXA02839 GR00832 3 419 4-HYDROXYBENZOATE OCTAPRENYLTRANSFERASE (EC 2.5.1.—) 385 386 RXA01502 GR00424 8385 9617 BENZENE 1,2-DIOXYGENASE SYSTEM FERREDOXIN-NAD(+) REDUCTASE COMPONENT (EC 1.18.1.3) 387 388 RXA02828 GR00813 15 572 BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE III (EC 1.13.11.39) 389 390 RXA02064 GR00626 5223 4585 CAFFEOYL-COA O-METHYLTRANSFERASE (EC 2.1.1.104) 391 392 RXN00639 VV0128 7858 8712 CATECHOL 1,2-DIOXYGENASE (EC 1.13.11.1) 393 394 F RXA00639 GR00168 665 6 CATECHOL 1,2-DIOXYGENASE (EC 1.13.11.1) 395 396 RXN01653 VV0321 12867 11407 DIBENZOTHIOPHENE DESULFURIZATION ENZYME A 397 398 F RXA00797 GR00212 445 804 DIBENZOTHIOPHENE DESULFURIZATION ENZYME A 399 400 F RXA01653 GR00458 1909 971 DIBENZOTHIOPHENE DESULFURIZATION ENZYME A 401 402 RXN02530 VV0057 5469 6125 DIMETHYLANILINE MONOOXYGENASE (N-OXIDE FORMING) 1 (EC 1.14.13.8) 403 404 F RXA02530 GR00726 20 469 DIMETHYLANILINE MONOOXYGENASE (N-OXIDE FORMING) 1 (EC 1.14.13.8) 405 406 RXA02083 GR00629 1720 311 DIMETHYLANILINE MONOOXYGENASE (N-OXIDE FORMING) 2 (EC 1.14.13.8) 407 408 RXA00892 GR00243 2188 1295 PARANITROBENZYL ESTERASE (EC 3.1.1.—) 409 410 RXA02092 GR00629 12153 10516 PARANITROBENZYL ESTERASE (EC 3.1.1.—) 411 412 RXN00658 VV0083 15705 16397 PHENOL 2-MONOOXYGENASE (EC 1.14.13.7) 413 414 F RXA00658 GR00170 321 4 PHENOL 2 MONOOXYGENASE (EC 1.14.13.7) 415 416 RXA01385 GR00406 5320 3440 PHENOL 2 MONOOXYGENASE (EC 1.14.13.7) 417 418 RXN01461 VV0128 12414 13025 PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN (EC 1.13.11.3) 419 420 F RXA01461 GR00421 463 5 PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN (EC 1.13.11.3) 421 422 RXA01462 GR00421 1167 478 PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN (EC 1.13.11.3) 423 424 RXN00641 VV0128 7440 5950 TOLUATE 1,2-DIOXYGENASE ALPHA SUBUNIT (EC 1.14.12.—) 425 426 F RXA00640 GR00168 1083 1331 TOLUATE 1,2-DIOXYGENASE ALPHA SUBUNIT (EC 1.14.12.—) 427 428 F RXA00641 GR00168 1533 2573 TOLUATE 1,2-DIOXYGENASE ALPHA SUBUNIT (EC 1.14.12.—) 429 430 RXA00642 GR00168 2616 3107 TOLUATE 1,2-DIOXYGENASE BETA SUBUNIT (EC 1.14.12.—) 431 432 RXA00643 GR00168 3122 4657 TOLUATE 1,2-DIOXYGENASE ELECTRON TRANSFER COMPONENT 433 434 RXN01993 VV0182 16 1143 VANILLATE DEMETHYLASE (EC 1.14.—.—) 435 436 F RXA01993 GR00584 1 366 VANILLATE DEMETHYLASE (EC 1.14.—.—) 437 438 F RXA02012 GR00604 2 670 VANILLATE DEMETHYLASE (EC 1.14.—.—) 439 440 RXA01994 GR00584 373 1347 VANILLATE DEMETHYLASE OXIDOREDUCTASE (EC 1.—.—.—) 441 442 RXA02535 GR00726 6599 7753 XYLENE MONOOXYGENASE ELECTRON TRANSFER COMPONENT 443 444 RXA00964 GR00269 1575 451 1-hydroxy-2-naphthoate 1,2-dioxygenase (EC 1.13.11.38) 445 446 RXN01466 VV0019 7050 6091 ARYLESTERASE (EC 3.1.1.2) 447 448 F RXA01466 GR00422 826 5 ARYLESTERASE (EC 3.1.1.2) 449 450 RXN03036 VV0014 671 6 PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN (EC 1.13.11.3) 451 452 F RXA02895 GR10037 671 6 CHLOROCATECHOL 1,2-DIOXYGENASE (EC 1.13.11.1) 453 454 RXA02449 GR00710 1458 2360 hydroxyquinol 1,2-dioxygenase (EC 1.13.11.37) 455 456 RXN00178 VV0174 14670 15554 hydroxyquinol 1,2-dioxygenase (EC 1.13.11.37) 457 458 F RXA00178 GR00028 304 1188 HYDROXYQUINOL-1,2-DIOXYGENASE 459 460 RXA02111 GR00632 4310 5593 QUINOLINATE SYNTHETASE A 461 462 RXA00644 GR00168 4657 CIS-1,2-DIHYDROXYCYCLOHEXA-3,5-DIENE-1-CARBOXYLATE DEHYDROGENASE (EC 1.3.1.55) 463 464 RXN00177 VV0174 13589 14656 MALEYLACETATE REDUCTASE (EC 1.3.1.32) 465 466 F RXA00177 GR00028 3 290 MALEYLACETATE REDUCTASE (EC 1.3.1.32) metabolism of 2,4,5- trichlorophenoxyacetic acid 467 468 RXA02448 GR00710 340 1428 MALEYLACETATE REDUCTASE (EC 1.3.1.32) 469 470 RXA00048 GR00008 2185 527 3-(3-HYDROXYPHENYL) PROPIONATE HYDROXYLASE 471 472 RXA01126 GR00313 2 565 POSSIBLE 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMAERASE 473 474 RXA01117 GR00309 1713 973 SUCCINYL-COA:3-KETOACID-COENZYME A TRANSFERASE PRECURSOR (EC 2.8.3.5) 475 476 RXA00772 GR00205 2715 1210 SUCCINYL-COA:COENZYME A TRANSFERASE (EC 2.8.3.—) 477 478 RXA01288 GR00372 2018 1644 SUCCINYL-COA:COENZYME A TRANSFERASE (EC 2.8.3.—)






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;

Kobayashi, M. et al. “Cloning, sequencing, and characterization of the ftsZ


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;
Dipeptide-binding protein; adenine
Wehmeier, L. et al. “The role of the Corynebacterium glutamicum rel gene in


rel
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;
N-acetylglutamylphosphate reductase;


argB; argD;
ornithine acetyltransferase; N-


argF; argR;
acetylglutamate kinase; acetylornithine


argG; argH
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;
Chorismate synthase; shikimate kinase; 3-


aroB; 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



(incomplete i )
role in cell wall integrity:




A study with Corynebacterium glutamicum ,” J. Bacteriol.,




180(12): 3159-3165 (1998)

AJ007732
ppc; secG;
Phosphoenolpyruvate-carboxylase; ?; high


amt; ocd;
affinity ammonium uptake protein;


soxA
putative ornithine-cyclodecarboxylase;



sarcosine oxidase

AJ010319
ftsY, glnB,
Involved in cell division; PII protein;
Jakoby, M. et al. “Nitrogen regulation in Corynebacterium glutamicum ;


glnD; srp;
uridylyltransferase (uridylyl-removing
Isolation of genes involved in biochemical characterization of corresponding


amtP
enzmye); signal recognition particle; low
proteins,” FEMS Microbiol., 173(2): 303-310 (1999)



affinity ammonium uptake protein

AJ132968
cat
Chloramphenicol aceteyl transferase

AJ224946
mqo
L-malate: quinone oxidoreductase
Molenaar, D. et al. “Biochemical and genetic characterization of the




membrane-associated malate dehydrogenase (acceptor) from Corynebacterium




glutamicum ,” Eur. J. Biochem., 254(2): 395-403 (1998)

AJ238250
ndh
NADH dehydrogenase

AJ238703
porA
Porin
Lichtinger, T. et al. “Biochemical and biophysical characterization of the cell




wall porin of Corynebacterium glutamicum : The channel is formed by a low




molecular mass polypeptide,” Biochemistry, 37(43): 15024-15032 (1998)

D17429

Transposable element IS31831
Vertes, A. A. et al. “Isolation and characterization of IS31831, a transposable




element from Corynebacterium glutamicum ,” Mol. Microbiol., 11(4): 739-746




(1994)

D84102
odhA
2-oxoglutarate dehydrogenase
Usuda, Y. et al. “Molecular cloning of the Corynebacterium glutamicum




( Brevibacterium lactofermentum AJ12036) odhA gene encoding a novel type




of 2-oxoglutarate dehydrogenase,” Microbiology, 142: 3347-3354 (1996)

E01358
hdh; hk
Homoserine dehydrogenase; homoserine
Katsumata, R. et al. “Production of L-thereonine and L-isoleucine,” Patent: JP



kinase
1987232392-A 1 Oct. 12, 1987

E01359

Upstream of the start codon of homoserine
Katsumata, R. et al. “Production of L-thereonine and L-isoleucine,” Patent: JP



kinase gene
1987232392-A 2 Oct. 12, 1987

E01375

Tryptophan operon

E01376
trpL; trpE
Leader peptide; anthranilate synthase
Matsui, K. et al. “Tryptophan operon, peptide and protein coded thereby,




utilization of tryptophan operon gene expression and production of




tryptophan,” Patent: JP 1987244382-A 1 Oct. 24, 1987

E01377

Promoter and operator regions of
Matsui, K. et al. “Tryptophan operon, peptide and protein coded thereby,



tryptophan operon
utilization of tryptophan operon gene expression and production of




tryptophan,” Patent: JP 1987244382-A 1 Oct. 24, 1987

E03937

Biotin-synthase
Hatakeyama, K. et al. “DNA fragment containing gene capable of coding




biotin synthetase and its utilization,” Patent: JP 1992278088-A 1 Oct. 02, 1992

E04040

Diamino pelargonic acid aminotransferase
Kohama, K. et al. “Gene coding diaminopelargonic acid aminotransferase and




desthiobiotin synthetase and its utilization,” Patent: JP 1992330284-A 1




Nov. 18, 1992

E04041

Desthiobiotinsynthetase
Kohama, K. et al. “Gene coding diaminopelargonic acid aminotransferase and




desthiobiotin synthetase and its utilization,” Patent: JP 1992330284-A 1




Nov. 18, 1992

E04307

Flavum aspartase
Kurusu, Y. et al. “Gene DNA coding aspartase and utilization thereof,” Patent:




JP 1993030977-A 1 Feb. 09, 1993

E04376

Isocitric acid lyase
Katsumata, R. et al. “Gene manifestation controlling DNA,” Patent: JP




1993056782-A 3 Mar. 09, 1993

E04377

Isocitric acid lyase N-terminal fragment
Katsumata, R. et al. “Gene manifestation controlling DNA,” Patent: JP




1993056782-A 3 Mar. 09, 1993

E04484

Prephenate dehydratase
Sotouchi, N. et al. “Production of L-phenylalanine by fermentation,” Patent: JP




199307635 2-A 2 Mar. 30, 1993

E05108

Aspartokinase
Fugono, N. et al. “Gene DNA coding Aspartokinase and its use,” Patent: JP




1993184366-A 1 Jul. 27, 1993

E05112

Dihydro-dipichorinate synthetase
Hatakeyama, K. et al. “Gene DNA coding dihydrodipicolinic acid synthetase




and its use,” Patent: JP 1993184371-A 1 Jul. 27, 1993

E05776

Diaminopimelic acid dehydrogenase
Kobayashi, M. et al. “Gene DNA coding Diaminopimelic acid dehydrogenase




and its use,” Patent: JP 1993284970-A 1 Nov. 02, 1993

E05779

Threonine synthase
Kohama, K. et al. “Gene DNA coding threonine synthase and its use,” Patent:




JP 1993284972-A 1 Nov. 02, 1993

E06110

Prephenate dehydratase
Kikuchi, T. et al. “Production of L-phenylalanine by fermentation method,”




Patent: JP 1993344881-A 1 Dec. 27, 1993

E06111

Mutated Prephenate dehydratase
Kikuchi, T. et al. “Production of L-phenylalanine by fermentation method,”




Patent: JP 1993344881-A 1 Dec. 27, 1993

E06146

Acetohydroxy acid synthetase
Inui, M. et al. “Gene capable of coding Acetohydroxy acid synthetase and its




use,” Patent: JP 1993344893-A 1 Dec. 27, 1993

E06825

Aspartokinase
Sugimoto, M. et al. “Mutant aspartokinase gene,” patent: JP 1994062866-A 1




Mar. 08, 1994

E06826

Mutated aspartokinase alpha subunit
Sugimoto, M. et al. “Mutant aspartokinase gene,” patent: JP 1994062866-A 1




Mar. 08, 1994

E06827

Mutated aspartokinase alpha subunit
Sugimoto, M. et al. “Mutant aspartokinase gene,” patent: JP 1994062866-A 1




Mar. 08, 1994

E07701
secY

Honno, N. et al. “Gene DNA participating in integration of membraneous




protein to membrane,” Patent: JP 1994169780-A 1 Jun. 21, 1994

E08177

Aspartokinase
Sato, Y. et al. “Genetic DNA capable of coding Aspartokinase released from




feedback inhibition and its utilization,” Patent: JP 1994261766-A 1




Sep. 20, 1994

E08178,

Feedback inhibition-released
Sato, Y. et al. “Genetic DNA capable of coding Aspartokinase released from

E08179,

Aspartokinase
feedback inhibition and its utilization,” Patent: JP 1994261766-A 1

E08180,


Sep. 20, 1994

E08181,

E08182

E08232

Acetohydroxy-acid isomeroreductase
Inui, M. et al. “Gene DNA coding acetohydroxy acid isomeroreductase,”




Patent: JP 1994277067-A 1 Oct. 04, 1994

E08234
secE

Asai, Y. et al. “Gene DNA coding for translocation machinery of protein,”




Patent: JP 1994277073-A 1 Oct. 04, 1994

E08643

FT aminotransferase and desthiobiotin
Hatakeyama, K. et al. “DNA fragment having promoter function in



synthetase promoter region
coryneform bacterium ,” Patent: JP 1995031476-A 1 Feb. 03, 1995

E08646

Biotin synthetase
Hatakeyama, K. et al. “DNA fragment having promoter function in




coryneform bacterium ,” Patent: JP 1995031476-A 1 Feb. 03, 1995

E08649

Aspartase
Kohama, K. et al “DNA fragment having promoter function in coryneform




bacterium,” Patent: JP 1995031478-A 1 Feb. 03, 1995

E08900

Dihydrodipicolinate reductase
Madori, M. et al. “DNA fragment containing gene coding Dihydrodipicolinate




acid reductase and utilization thereof,” Patent: JP 1995075578-A 1




Mar. 20, 1995

E08901

Diaminopimelic acid decarboxylase
Madori, M. et al. “DNA fragment containing gene coding Diaminopimelic acid




decarboxylase and utilization thereof,” Patent: JP 1995075579-A 1




Mar. 20, 1995

E12594

Serine hydroxymethyltransferase
Hatakeyama, K. et al. “Production of L-trypophan,” Patent: JP 1997028391-A




1 Feb. 04, 1997

E12760,

transposase
Moriya, M. et al. “Amplification of gene using artificial transposon,” Patent:

E12759,


JP 1997070291-A Mar. 18, 1997

E12758

E12764

Arginyl-tRNA synthetase; diaminopimelic
Moriya, M. et al. “Amplification of gene using artificial transposon,” Patent:



acid decarboxylase
JP 1997070291-A Mar. 18, 1997

E12767

Dihydrodipicolinic acid synthetase
Moriya, M. et al. “Amplification of gene using artificial transposon,” Patent:




JP 1997070291-A Mar. 18, 1997

E12770

aspartokinase
Moriya, M. et al. “Amplification of gene using artificial transposon,” Patent:




JP 1997070291-A Mar. 18, 1997

E12773

Dihydrodipicolinic acid reductase
Moriya, M. et al. “Amplification of gene using artificial transposon,” Patent:




JP 1997070291-A Mar. 18, 1997

E13655

Glucose-6-phosphate dehydrogenase
Hatakeyama, K. et al. “Glucose-6-phosphate dehydrogenase and DNA capable




of coding the same,” Patent: JP 1997224661-A 1 Sep. 02, 1997

L01508
IlvA
Threonine dehydratase
Moeckel, B. et al. “Functional and structural analysis of the threonine




dehydratase of Corynebacterium glutamicum ,” J. Bacteriol., 174: 8065-8072




(1992)

L07603
EC 4.2.1.15
3-deoxy-D-arabinoheptulosonate-7-
Chen, C. et al. “The cloning and nucleotide sequence of Corynebacterium



phosphate synthase
glutamicum 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase gene,”




FEMS Microbiol. Lett., 107: 223-230 (1993)

L09232
IlvB; ilvN;
Acetohydroxy acid synthase large subunit;
Keilhauer, C. et al. “Isoleucine synthesis in Corynebacterium glutamicum :


ilvC
Acetohydroxy acid synthase small subunit;
molecular analysis of the ilvB-ilvN-ilvC operon,” J. Bacteriol., 175(17):



Acetohydroxy acid isomeroreductase
5595-5603 (1993)

L18874
PtsM
Phosphoenolpyruvate sugar
Fouet, A et al. “Bacillus subtilis sucrose-specific enzyme II of the



phosphotransferase
phosphotransferase system: expression in Escherichia coli and homology to




enzymes II from enteric bacteria,” PNAS USA, 84(24): 8773-8777




(1987); Lee, J. K. et al. “Nucleotide sequence of the gene encoding




the Corynebacterium glutamicum mannose enzyme II and




analyses of the deduced protein




sequence,” FEMS Microbiol. Lett., 119(1-2): 137-145 (1994)

L27123
aceB
Malate synthase
Lee, H-S. et al. “Molecular characterization of aceB, a gene encoding malate




synthase in Corynebacterium glutamicum ,” J. Microbiol. Biotechnol.,




4(4): 256-263 (1994)

L27126

Pyruvate kinase
Jetten, M. S. et al. “Structural and functional analysis of pyruvate kinase from




Corynebacterium glutamicum ,” Appl. Environ. Microbiol., 60(7): 2501-2507




(1994)

L28760
aceA
Isocitrate lyase

L35906
dtxr
Diphtheria toxin repressor
Oguiza, J. A. et al. “Molecular cloning, DNA sequence analysis, and




characterization of the Corynebacterium diphtheriae dtxR from Brevibacterium




lactofermentum ,” J. Bacteriol., 177(2): 465-467 (1995)

M13774

Prephenate dehydratase
Follettie, M. T. et al. “Molecular cloning and nucleotide sequence of the




Corynebacterium glutamicum pheA gene,” J. Bacteriol., 167: 695-702 (1986)

M16175
5S rRNA

Park, Y-H. et al. “Phylogenetic analysis of the coryneform bacteria by 56




rRNA sequences,” J. Bacteriol., 169: 1801-1806 (1987)

M16663
trpE
Anthranilate synthase, 5′ end
Sano, K. et al. “Structure and function of the trp operon control regions of




Brevibacterium lactofermentum , a glutamic-acid-producing bacterium,” Gene,




52: 191-200 (1987)

M16664
trpA
Tryptophan synthase, 3′end
Sano, K. et al. “Structure and function of the trp operon control regions of




Brevibacterium lactofermentum , a glutamic-acid-producing bacterium,” Gene,




52: 191-200 (1987)

M25819

Phosphoenolpyruvate carboxylase
O'Regan, M. et al. “Cloning and nucleotide sequence of the




Phosphoenolpyruvate carboxylase-coding gene of Corynebacterium




glutamicum ATCC13032,” Gene, 77(2): 237-251 (1989)

M85106

23S rRNA gene insertion sequence
Roller, C. et al. “Gram-positive bacteria with a high DNA G + C content are




characterized by a common insertion within their 23S rRNA genes,” J. Gen.




Microbiol., 138: 1167-1175 (1992)

M85107,

23S rRNA gene insertion sequence
Roller, C. et al. “Gram-positive bacteria with a high DNA G + C content are

M85108


characterized by a common insertion within their 23S rRNA genes,” J. Gen.




Microbiol., 138: 1167-1175 (1992)

M89931
aecD; brnQ;
Beta C-S lyase; branched-chain
Rossol, I. et al. “The Corynebacterium glutamicum aecD gene encodes a C-S


yhbw
amino acid
lyase with alpha, beta-elimination activity that degrades aminoethylcysteine,”



uptake carrier; hypothetical protein yhbw
J. Bacteriol., 174(9): 2968-2977 (1992); Tauch, A. et al. “Isoleucine uptake in




Corynebacterium glutamicum ATCC 13032 is directed by the brnQ gene




product,” Arch. Microbiol., 169(4): 303-312 (1998)

S59299
trp
Leader gene (promoter)
Herry, D. M. et al. “Cloning of the trp gene cluster from a tryptophan-




hyperproducing strain of Corynebacterium glutamicum : identification of a




mutation in the trp leader sequence,” Appl. Environ. Microbiol., 59(3):




791-799 (1993)

U11545
trpD
Anthranilate phosphoribosyltransferase
O'Gara, J. P. and Dunican, L. K. (1994) Complete nucleotide sequence of the




Corynebacterium glutamicum ATCC 21850 tpD gene.” Thesis, Microbiology




Department, University College Galway, Ireland.

U13922
cglIM;
Putative type II 5-cytosoine
Schafer, A. et al. “Cloning and characterization of a DNA region encoding a


cglIR; clgIIR
methyltransferase; putative type II
stress-sensitive restriction system from Corynebacterium glutamicum ATCC



restriction endonuclease; putative type I or
13032 and analysis of its role in intergeneric conjugation with Escherichia



type III restriction endonuclease
coli ,” J. Bacteriol., 176(23): 7309-7319 (1994); Schafer, A. et al. “The




Corynebacterium glutamicum cglIM gene encoding a 5-cytosine in an McrBC-




deficient Escherichia coli strain,” Gene, 203(2): 95-101 (1997)

U14965
recA

U31224
ppx

Ankri, S. et al. “Mutations in the Corynebacterium 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;
?; gamma glutamyl kinase; similar to D-
Ankri, S. et al. “Mutations in the Corynebacterium glutamicumproline


unkdh
isomer specific 2-hydroxyacid
biosynthetic pathway: A natural bypass of the proA step,” J. Bacteriol.,



dehydrogenases
178(15): 4412-4419 (1996)

U31281
bioB
Biotin synthase
Serebriiskii, I. G., “Two new members of the bio B superfamily: Cloning,




sequencing and expression of bio B genes of Methylobacillus flagellatum and




Corynebacterium glutamicum ,” Gene, 175: 15-22 (1996)

U35023
thtR; accBC
Thiosulfate sulfurtransferase; acyl CoA
Jager, W. et al. “A Corynebacterium glutamicum gene encoding a two-domain



carboxylase
protein similar to biotin carboxylases and biotin-carboxyl-carrier proteins,”




Arch. Microbiol., 166(2); 76-82 (1996)

U43535
cmr
Multidrug resistance protein
Jager, W. et al. “A Corynebacterium glutamicum gene conferring multidrug




resistance in the heterologous host Escherichia coli ,” J. Bacteriol.,




179(7): 2449-2451 (1997)

U43536
clpB
Heat shock ATP-binding protein

U53587
aphA-3
3′5″-aminoglycoside phosphotransferase

U89648

Corynebacterium glutamicum unidentified



sequence involved in histidine



biosynthesis, partial sequence

X04960
trpA; trpB;
Tryptophan operon
Matsui, K. et al. “Complete nucleotide and deduced amino acid sequences of


trpC; trpD;

the Brevibacterium lactofermentum tryptophan operon,” Nucleic Acids Res.,


trpE; trpG;

14(24): 10113-10114 (1986)


trpL

X07563
lys A
DAP decarboxylase
Yeh, P. et al. “Nucleic sequence of the lysA gene of Corynebacterium



(meso-diaminopimelate
glutamicum and possible mechanisms for modulation of its expression,” Mol.



decarboxylase, EC 4.1.1.20)
Gen. Genet., 212(1): 112-119 (1988)

X14234
EC 4.1.1.31
Phosphoenolpyruvate carboxylase
Eikmanns, B. J. et al. “The Phosphoenolpyruvate carboxylase gene of




Corynebacterium glutamicum : Molecular cloning, nucleotide sequence, and




expression,” Mol. Gen. Genet., 218(2): 330-339 (1989); Lepiniec, L. et al.




“Sorghum Phosphoenolpyruvate carboxylase gene family: structure, function




and molecular evolution,” Plant. Mol. Biol., 21 (3): 487-502 (1993)

X17313
fda
Fructose-bisphosphate aldolase
Von der Osten, C. H. et al. “Molecular cloning, nucleotide sequence and fine-




structural analysis of the Corynebacterium glutamicum fda gene: structural




comparison of C. glutamicum fructose-1,6-biphosphate aldolase to class I and




class II aldolases,” Mol. Microbiol.,

X53993
dapA
L-2,3-dihydrodipicolinate synthetase (EC
Bonnassie, S. et al. “Nucleic sequence of the dapA gene from



4.2.1.52)
Corynebacterium glutamicum ,” Nucleic Acids Res., 18(21): 6421 (1990)

X54223

AttB-related site
Cianciotto, N. et al. “DNA sequence homology between att B-related sites of




Corynebacterium diphtheriae , Corynebacterium ulcerans , Corynebacterium




glutamicum , and the attP site of lambdacorynephage,” FEMS. Microbiol,




Lett., 66: 299-302 (1990)

X54740
argS; lysA
Arginyl-tRNA synthetase;
Marcel, T. et al. “Nucleotide sequence and organization of the upstream region



Diaminopimelate decarboxylase
of the Corynebacterium glutamicum lysA gene,” Mol. Microbiol., 4(11):




1819-1830 (1990)

X55994
trpL; trpE
Putative leader peptide; anthranilate
Heery, D. M. et al. “Nucleotide sequence of the Corynebacterium glutamicum



synthase component 1
trpE gene,” Nucleic Acids Res., 18(23): 7138 (1990)

X56037
thrC
Threonine synthase
Han, K. S. et al. “The molecular structure of the Corynebacterium glutamicum




threonine synthase gene,” Mol. Microbiol., 4(10): 1693-1702 (1990)

X56075
attB-related
Attachment site
Cianciotto, N. et al. “DNA sequence homology between att B-related sites of


site

Corynebacterium diphtheriae , Corynebacterium ulcerans , Corynebacterium




glutamicum , and the attP site of lambdacorynephage,” FEMS. Microbiol,




Lett., 66: 299-302 (1990)

X57226
lysC-alpha;
Aspartokinase-alpha subunit;
Kalinowski, J. et al. “Genetic and biochemical analysis of the Aspartokinase


lysC-beta;
Aspartokinase-beta subunit; aspartate beta
from Corynebacterium glutamicum ,” Mol. Microbiol., 5(5):


asd
semialdehyde dehydrogenase
1197-1204 (1991); Kalinowski, J. et al.




“Aspartokinase genes lysC alpha and lysC beta overlap




and are adjacent to the aspertate beta-semialdehyde dehydrogenase gene asd in




Corynebacterium glutamicum ,” Mol. Gen. Genet., 224(3): 317-324 (1990)

X59403
gap; pgk; tpi
Glyceraldehyde-3-phosphate;
Eikmanns, B. J. “Identification, sequence analysis, and expression of a



phosphoglycerate kinase; triosephosphate
Corynebacterium glutamicum gene cluster encoding the three glycolytic



isomerase
enzymes glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate




kinase, and triosephosphate isomeras,” J. Bacteriol., 174(19): 6076-6086




(1992)

X59404
gdh
Glutamate dehydrogenase
Bormann, E. R. et al. “Molecular analysis of the Corynebacterium glutamicum




gdh gene encoding glutamate dehydrogenase,” Mol. Microbiol., 6(3): 317-326




(1992)

X60312
lysI
L-lysine permease
Seep-Feldhaus, A. H. et al. “Molecular analysis of the Corynebacterium




glutamicum lysI gene involved in lysine uptake,” Mol. Microbiol., 5(12):




2995-3005 (1991)

X66078
cop1
Ps1 protein
Joliff, G. et al. “Cloning and nucleotide sequence of the csp1 gene encoding




PS1, one of the two major secreted proteins of Corynebacterium glutamicum :




The deduced N-terminal region of PS1 is similar to the Mycobacterium antigen




85 complex,” Mol. Microbiol., 6(16): 2349-2362 (1992)

X66112
glt
Citrate synthase
Eikmanns, B. J. et al. “Cloning sequence, expression and transcriptional




analysis of the Corynebacterium glutamicum gltA gene encoding citrate




synthase,” Microbiol., 140: 1817-1828 (1994)

X67737
dapB
Dihydrodipicolinate reductase

X69103
csp2
Surface layer protein PS2
Peyret, J. L. et al. “Characterization of the cspB gene encoding PS2, an ordered




surface-layer protein in Corynebacterium glutamicum ,” Mol. Microbiol.,




9(1): 97-109 (1993)

X69104

IS3 related insertion element
Bonamy, C. et al. “Identification of IS1206, a Corynebacterium glutamicum




IS3-related insertion sequence and phylogenetic analysis,” Mol. Microbiol.,




14(3): 571-581 (1994)

X70959
leuA
Isopropylmalate synthase
Patek, M. et al. “Leucine synthesis in Corynebacterium glutamicum : enzyme




activities, structure of leuA, and effect of leuA inactivation on lysine




synthesis,” Appl. Environ. Microbiol., 60(1): 133-140 (1994)

X71489
icd
Isocitrate dehydrogenase (NADP+)
Eikmanns, B. J. et al. “Cloning sequence analysis, expression, and inactivation




of the Corynebacterium glutamicum icd gene encoding isocitrate




dehydrogenase and biochemical characterization of the enzyme,” J. Bacteriol.,




177(3): 774-782 (1995)

X72855
GDHA
Glutamate dehydrogenase (NADP+)

X75083,
mtrA
5-methyltryptophan resistance
Heery, D. M. et al. “A sequence from a tryptophan-hyperproducing strain of

X70584


Corynebacterium glutamicum encoding resistance to 5-methyltryptophan,”




Biochem. Biophys. Res. Commun., 201(3): 1255-1262 (1994)

X75085
recA

Fitzpatrick, R. et al. “Construction and characterization of recA mutant strains




of Corynebacterium glutamicum and Brevibacterium lactofermentum ,” Appl.




Microbiol. Biotechnol., 42(4): 575-580 (1994)

X75504
aceA; thiX
Partial Isocitrate lyase; ?
Reinscheid, D. J. et al. “Characterization of the isocitrate lyase gene from




Corynebacterium glutamicum and biochemical analysis of the enzyme,” J.




Bacteriol., 176(12): 3474-3483 (1994)

X76875

ATPase beta-subunit
Ludwig, W. et al. “Phylogenetic relationships of bacteria based on comparative




sequence analysis of elongation factor Tu and ATP-synthase beta-subunit




genes,” Antonie Van Leeuwenhoek, 64: 285-305 (1993)

X77034
tuf
Elongation factor Tu
Ludwig, W. et al. “Phylogenetic relationships of bacteria based on comparative




sequence analysis of elongation factor Tu and ATP-synthase beta-subunit




genes,” Antonie Van Leeuwenhoek, 64: 285-305 (1993)

X77384
recA

Billman-Jacobe, H. “Nucleotide sequence of a recA gene from




Corynebacterium glutamicum ,” DNA Seq., 4(6): 403-404 (1994)

X78491
aceB
Malate synthase
Reinscheid, D. J. et al. “Malate synthase from Corynebacterium glutamicum




pta-ack operon encoding phosphotransacetylase: sequence analysis,”




Microbiology, 140: 3099-3108 (1994)

X80629
16S rDNA
16S ribosomal RNA
Rainey, F. A. et al. “Phylogenetic analysis of the genera Rhodococcus and




Norcardia and evidence for the evolutionary origin of the genus Norcardia




from within the radiation of Rhodococcus species,” Microbiol., 141: 523-528




(1995)

X81191
gluA; gluB;
Glutamate uptake system
Kronemeyer, W. et al. “Structure of the gluABCD cluster encoding the


gluC; 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;
Acetylglutamate kinase; N-acetyl-gamma-
Sakanyan, V. et al. “Genes and enzymes of the acetyl cycle of arginine


argD; argF;
glutamyl-phosphate reductase;
biosynthesis in Corynebacterium glutamicum : enzyme evolution in the early


argJ
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;
3-methyl-2-oxobutanoate
Sahm, H. et al. “D-pantothenate synthesis in Corynebacterium glutamicum and


xylB
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;
UPD-N-acetylmuramate-alanine ligase;
Honrubia, M. P. et al. “Identification, characterization, and chromosomal


ftsQ/divD;
division initiation protein or cell division
organization of the ftsZ gene from Brevibacterium lactofermentum ,” Mol. Gen.


ftsZ
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;
Oguiza, J. A. et al. “A gene encoding arginyl-tRNA synthetase is located in the



diaminopimelate
upstream region of the lysA gene in Brevibacterium lactofermentum :



decarboxylase (partial)
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
orf1; 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)



1 A sequence for this gene was published in the indicated reference. However, the sequence obtained by the inventors of the present application is significantly longer than the published version. It is believed that the published version relied on an incorrect start codon, and thus represents only a fragment of the actual coding region.






































































































































































































































































































































































































































































































































































TABLE 3





Corynebacterium and Brevibacterium Strains Which May be Used in the Practice of the Invention












Genus
species
ATCC
FERM
NRRL
CECT
NCIMB
CBS
NCTC
DSMZ















Brevibacterium


ammoniagenes

21054









Brevibacterium


ammoniagenes

19350


Brevibacterium


ammoniagenes

19351


Brevibacterium


ammoniagenes

19352


Brevibacterium


ammoniagenes

19353


Brevibacterium


ammoniagenes

19354


Brevibacterium


ammoniagenes

19355


Brevibacterium


ammoniagenes

19356


Brevibacterium


ammoniagenes

21055


Brevibacterium


ammoniagenes

21077


Brevibacterium


ammoniagenes

21553


Brevibacterium


ammoniagenes

21580


Brevibacterium


ammoniagenes

39101


Brevibacterium


butanicum

21196


Brevibacterium


divaricatum

21792
P928


Brevibacterium


flavum

21474


Brevibacterium


flavum

21129


Brevibacterium


flavum

21518


Brevibacterium


flavum



B11474


Brevibacterium


flavum



B11472


Brevibacterium


flavum

21127


Brevibacterium


flavum

21128


Brevibacterium


flavum

21427


Brevibacterium


flavum

21475


Brevibacterium


flavum

21517


Brevibacterium


flavum

21528


Brevibacterium


flavum

21529


Brevibacterium


flavum



B11477


Brevibacterium


flavum



B11478


Brevibacterium


flavum

21127


Brevibacterium


flavum



B11474


Brevibacterium


healii

15527


Brevibacterium


ketoglutamicum

21004


Brevibacterium


ketoglutamicum

21089


Brevibacterium


ketosoreductum

21914


Brevibacterium


lactofermentum




70


Brevibacterium


lactofermentum




74


Brevibacterium


lactofermentum




77


Brevibacterium


lactofermentum

21798


Brevibacterium


lactofermentum

21799


Brevibacterium


lactofermentum

21800


Brevibacterium


lactofermentum

21801


Brevibacterium


lactofermentum



B11470


Brevibacterium


lactofermentum



B11471


Brevibacterium


lactofermentum

21086


Brevibacterium


lactofermentum

21420


Brevibacterium


lactofermentum

21086


Brevibacterium


lactofermentum

31269


Brevibacterium


linens

9174


Brevibacterium


linens

19391


Brevibacterium


linens

8377


Brevibacterium


paraffinolyticum





11160


Brevibacterium

spec.





717.73


Brevibacterium

spec.





717.73


Brevibacterium

spec.
14604


Brevibacterium

spec.
21860


Brevibacterium

spec.
21864


Brevibacterium

spec.
21865


Brevibacterium

spec.
21866


Brevibacterium

spec.
19240


Corynebacterium


acetoacidophilum

21476


Corynebacterium


acetoacidophilum

13870


Corynebacterium


acetoglutamicum



B11473


Corynebacterium


acetoglutamicum



B11475


Corynebacterium


acetoglutamicum

15806


Corynebacterium


acetoglutamicum

21491


Corynebacterium


acetoglutamicum

31270


Corynebacterium


acetophilum



B3671


Corynebacterium


ammoniagenes

6872





2399


Corynebacterium


ammoniagenes

15511


Corynebacterium


fujiokense

21496


Corynebacterium


glutamicum

14067


Corynebacterium


glutamicum

39137


Corynebacterium


glutamicum

21254


Corynebacterium


glutamicum

21255


Corynebacterium


glutamicum

31830


Corynebacterium


glutamicum

13032


Corynebacterium


glutamicum

14305


Corynebacterium


glutamicum

15455


Corynebacterium


glutamicum

13058


Corynebacterium


glutamicum

13059


Corynebacterium


glutamicum

13060


Corynebacterium


glutamicum

21492


Corynebacterium


glutamicum

21513


Corynebacterium


glutamicum

21526


Corynebacterium


glutamicum

21543


Corynebacterium


glutamicum

13287


Corynebacterium


glutamicum

21851


Corynebacterium


glutamicum

21253


Corynebacterium


glutamicum

21514


Corynebacterium


glutamicum

21516


Corynebacterium


glutamicum

21299


Corynebacterium


glutamicum

21300


Corynebacterium


glutamicum

39684


Corynebacterium


glutamicum

21488


Corynebacterium


glutamicum

21649


Corynebacterium


glutamicum

21650


Corynebacterium


glutamicum

19223


Corynebacterium


glutamicum

13869


Corynebacterium


glutamicum

21157


Corynebacterium


glutamicum

21158


Corynebacterium


glutamicum

21159


Corynebacterium


glutamicum

21355


Corynebacterium


glutamicum

31808


Corynebacterium


glutamicum

21674


Corynebacterium


glutamicum

21562


Corynebacterium


glutamicum

21563


Corynebacterium


glutamicum

21564


Corynebacterium


glutamicum

21565


Corynebacterium


glutamicum

21566


Corynebacterium


glutamicum

21567


Corynebacterium


glutamicum

21568


Corynebacterium


glutamicum

21569


Corynebacterium


glutamicum

21570


Corynebacterium


glutamicum

21571


Corynebacterium


glutamicum

21572


Corynebacterium


glutamicum

21573


Corynebacterium


glutamicum

21579


Corynebacterium


glutamicum

19049


Corynebacterium


glutamicum

19050


Corynebacterium


glutamicum

19051


Corynebacterium


glutamicum

19052


Corynebacterium


glutamicum

19053


Corynebacterium


glutamicum

19054


Corynebacterium


glutamicum

19055


Corynebacterium


glutamicum

19056


Corynebacterium


glutamicum

19057


Corynebacterium


glutamicum

19058


Corynebacterium


glutamicum

19059


Corynebacterium


glutamicum

19060


Corynebacterium


glutamicum

19185


Corynebacterium


glutamicum

13286


Corynebacterium


glutamicum

21515


Corynebacterium


glutamicum

21527


Corynebacterium


glutamicum

21544


Corynebacterium


glutamicum

21492


Corynebacterium


glutamicum



B8183


Corynebacterium


glutamicum



B8182


Corynebacterium


glutamicum



B12416


Corynebacterium


glutamicum



B12417


Corynebacterium


glutamicum



B12418


Corynebacterium


glutamicum



B11476


Corynebacterium


glutamicum

21608


Corynebacterium


lilium


P973


Corynebacterium


nitrilophilus

21419



11594


Corynebacterium

spec.

P4445


Corynebacterium

spec.

P4446


Corynebacterium

spec.
31088


Corynebacterium

spec.
31089


Corynebacterium

spec.
31090


Corynebacterium

spec.
31090


Corynebacterium

spec.
31090


Corynebacterium

spec.
15954






20145


Corynebacterium

spec.
21857


Corynebacterium

spec.
21862


Corynebacterium

spec.
21863



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

FERM: Fermentation Research Institute, Chiba, Japan

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

CECT: Coleccion Espanola de Cultivos Tipo, Valencia, Spain

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

CBS: Centraalbureau voor Schimmelcultures, Baarn, NL

NCTC: National Collection of Type Cultures, London, UK

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

For reference see Sugawara, H. et al. (1993) World directory of collections of cultures of microorganisms: Bacteria, fungi and yeasts (4 th edn), World federation for culture collections world data center on microorganisms, Saimata, Japen.
































































































































































































TABLE 4





ALIGNMENT RESULTS


















%









homo-


length





logy
Date of

ID #
(NT)
Genbank Hit
Length
Accession
Name of Genbank Hit
Source of Genbank Hit
(GAP)
Deposit













rxa00009
1023
GB_IN1: CELZK563
29655
U40061
Caenorhabditis elegans cosmid ZK563.

Caenorhabditis elegans

33,694
9-Nov-95



GB_IN1: CELZK563
29655
U40061
Caenorhabditis elegans cosmid ZK563.

Caenorhabditis elegans

36,040
9-Nov-95

rxa00010
810
GB_BA1: MTCY164
39150
Z95150
Mycobacterium tuberculosis H37Rv complete genome; segment 135/162.

Mycobacterium tuberculosis

38,442
19-Jun-98



GB_BA1: MTFTSX
4068
X70031
M. tuberculosis ftsX and ftsE (partial) genes.

Mycobacterium tuberculosis

63,158
06-MAR-1997



GB_BA1: SHGCPIR
107379
X86780
S. hygroscopicus gene cluster for polyketide immunosuppressant rapamycin.
Streptomyces hygroscopicus
38,875
16-Aug-96

rxa00024
1068
GB_HTG1: CEY113G7_31
10000
AL031113
Caenorhabditis elegans chromosome V clone Y113G7, *** SEQUENCING

Caenorhabditis elegans

36,217
12-Jan-99






IN PROGRESS ***, in unordered pieces.



GB_HTG1: CEY113G7_31
10000
AL031113
Caenorhabditis elegans chromosome V clone Y113G7, *** SEQUENCING

Caenorhabditis elegans

36,217
12-Jan-99






IN PROGRESS ***, in unordered pieces.



GB_PL2: ATF1C12
111945
AL022224
Arabidopsis thaliana DNA chromosome 4, BAC clone F1C12 (ESSA

Arabidopsis thaliana

35,824
20-Sep-99






project).

rxa00048
1782
GB_HTG3: AC008905
129915
AC008905
Homo sapiens chromosome 5 clone CITB-H1_2259l14, *** SEQUENCING

Homo sapiens

38,826
3-Aug-99






IN PROGRESS ***, 40 unordered pieces.



GB_HTG3: AC008905
129915
AC008905
Homo sapiens chromosome 5 clone CITB-H1_2259l14, *** SEQUENCING

Homo sapiens

38,826
3-Aug-99






IN PROGRESS ***, 40 unordered pieces.



GB_HTG3: AC008905
129915
AC008905
Homo sapiens chromosome 5 clone CITB-H1_2259l14, *** SEQUENCING

Homo sapiens

37,379
3-Aug-99






IN PROGRESS ***, 40 unordered pieces.

rxa00070
555
GB_BA2: BPEFUR
1003
L31851
Bordetella pertussis DNA repair protein (recN) gene, partial cds; iron

Bordetella pertussis

45,756
17-Apr-95






regulatory protein (fur) gene, complete cds.



GB_BA2: BPU11699
537
U11699
Bordetella pertussis ferric uptake regulator (fur) gene, complete cds.

Bordetella pertussis

47,119
14-Jan-95



GB_BA1: BTFURRECN
1106
Z48227
B. pertussis fur gene for ferric uptake regulator and partial recN gene.

Bordetella pertussis

45,756
10-Feb-95

rxa00078
537
GB_PR3: HUMCOL2A1Z3
1001
L10347
Human pro-alpha1 type II collagen (COL2A1) gene exons 1-54, complete

Homo sapiens

39,010
3-Aug-95






cds.



GB_HTG2: AC006721
135550
AC006721
Caenorhabditis elegans clone Y18H1, *** SEQUENCING IN PROGRESS

Caenorhabditis elegans

40,661
23-Feb-99






***, 5 unordered pieces.



GB_HTG2: AC006721
135550
AC006721
Caenorhabditis elegans clone Y18H1, *** SEQUENCING IN PROGRESS

Caenorhabditis elegans

40,661
23-Feb-99






***, 5 unordered pieces.

rxa00088
899
GB_RO: MMCGT6
3009
U48896
Mus musculus UDP-galactose: ceramide galactosyltransferase (Cgt) gene,

Mus musculus

35,455
1-Nov-96






exon 6 and complete cds.



GB_RO: MMCGT6
3009
U48896
Mus musculus UDP-galactose: ceramide galactosyltransferase (Cgt) gene,

Mus musculus

34,439
1-Nov-96






exon 6 and complete cds.

rxa00100
723
GB_PL1: CAC41C10
38874
AL033501
C. albicans cosmid Ca41C10.

Candida albicans

36,222
10-Nov-98



GB_PR4: AC007115
180821
AC007115
Homo sapiens chromosome 12 clone 917O5, complete sequence.

Homo sapiens

33,050
17-Aug-99



GB_PR4: AC007115
180821
AC007115
Homo sapiens chromosome 12 clone 917O5, complete sequence.

Homo sapiens

34,993
17-Aug-99

rxa00135
1377
GB_BA1: MTCY373
35516
Z73419
Mycobacterium tuberculosis H37Rv complete genome; segment 57/162.

Mycobacterium tuberculosis

60,639
17-Jun-98



GB_BA1: MLU15186
36241
U15186
Mycobacterium leprae cosmid L471.

Mycobacterium leprae

38,377
09-MAR-1995



GB_BA1: MTMURAGEN
1257
X96711
M. tuberculosis murA gene.

Mycobacterium tuberculosis

61,575
22-MAR-1996

rxa00143
1605
GB_PAT: I92051
1107
I92051
Sequence 18 from Patent US 5726299.
Unknown.
37,773
01-DEC-1998



GB_PAT: I78761
1107
I78761
Sequence 17 from patent US 5693781.
Unknown.
37,773
3-Apr-98



GB_BA1: MTCY28
40163
Z95890
Mycobacterium tuberculosis H37Rv complete genome; segment 79/162.

Mycobacterium tuberculosis

36,984
18-Jun-98

rxa00177
1191
GB_GSS14: AQ543786
345
AQ543786
RPCI-11-365L6.TV RPCI-11 Homo sapiens genomic clone RPCI-11-365L6,

Homo sapiens

38,551
19-MAY-1999






genomic survey sequence.



GB_PL2: AF017646
3394
AF017646
Schizosaccharomyces pombe TFIIH subunit p47 (tfh47) gene, complete

Schizosaccharomyces

38,122
17-MAR-1999






cds.
pombe



GB_PL1: SPCC1682
37404
AL031525
S. pombe chromosome III cosmid c1682.

Schizosaccharomyces

33,983
14-DEC-1998







pombe

rxa00178
1008
GB_BA1: AB016258
2260
AB016258
Arthrobacter sp. gene for maleylacetate reductase and hydroxyquinol 1,2-
Arthrobacter sp.
65,182
8-Sep-99






dioxygenase, partial and complete cds.



GB_BA1: CGPUTP
3791
Y09163
C. glutamicum putP gene.

Corynebacterium glutamicum

38,806
8-Sep-97



GB_STS: G05495
271
G05495
human STS WI-5918.

Homo sapiens

39,925
8-Jun-95

rxa00277
1684
GB_BA1: MTCY22G10
35420
Z84724
Mycobacterium tuberculosis H37Rv complete genome; segment 21/162.

Mycobacterium tuberculosis

39,976
17-Jun-98



GB_IN1: CELT03F1
38643
U88169
Caenorhabditis elegans cosmid T03F1.

Caenorhabditis elegans

35,127
7-Feb-97



GB_IN2: CELK02A2
38261
U23171
Caenorhabditis elegans cosmid K02A2.

Caenorhabditis elegans

36,166
21-MAY-1999

rxa00372
1200
GB_IN2: AC005452
79333
AC005452
Drosophila melanogaster , chromosome 2R, region 43B2-43C2, P1 clone

Drosophila melanogaster

37,006
26-Nov-98






DS07185, complete sequence.



GB_IN2: AC005452
79333
AC005452
Drosophila melanogaster , chromosome 2R, region 43B2-43C2, P1 clone

Drosophila melanogaster

34,907
26-Nov-98






DS07185, complete sequence.



GB_IN1: CELW03F8
34766
AF039041
Caenorhabditis elegans cosmid W03F8.

Caenorhabditis elegans

40,712
1-Jan-98

rxa00389
1683
GB_IN1: AB010703
772
AB010703
Theileria sp. gene for major piroplasm surface protein, partial cds, isolate
Theileria sp.
40,285
18-Apr-98






Kamphaeng Saen.



GB_BA1: LLU08911
619
U08911
Lactobacillus leichmannii putative D-alanine: D-alanine ligase (ddl) gene,

Lactobacillus leichmannii

40,194
16-Feb-96






partial cds.



GB_IN1: TPMS1
822
Z48740
T. parva Tpms1 gene for merozoite surface glycoprotein.

Theileria parva

38,902
15-MAY-1995

rxa00467
792
GB_PR4: DJ293M10
202267
AF111167
Homo sapiens jun dimerization protein gene, partial cds; cfos gene,

Homo sapiens

37,995
7-Apr-99






complete cds; and unknown gene.



GB_PR4: DJ293M10
202267
AF111167
Homo sapiens jun dimerization protein gene, partial cds; cfos gene,

Homo sapiens

36,639
7-Apr-99






complete cds; and unknown gene.



GB_IN1: CEW01C9
21493
Z49969
Caenorhabditis elegans cosmid W01C9, complete sequence.

Caenorhabditis elegans

37,980
23-Nov-98

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 IMAGE: 1917114

Homo sapiens

42,675
2-Feb-99






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

rxa00508
1206
GB_HTG2: AC007111
84245
AC007111
Homo sapiens chromosome 16 clone 1-8F, *** SEQUENCING IN

Homo sapiens

37,931
18-MAR-1999






PROGRESS ***, 2 ordered pieces.



GB_HTG2: AC007111
84245
AC007111
Homo sapiens chromosome 16 clone 1-8F, *** SEQUENCING IN

Homo sapiens

37,931
18-MAR-1999






PROGRESS ***, 2 ordered pieces.



GB_VI: AF141890
1791
AF141890
Columbid herpesvirus 1 DNA-dependent DNA polymerase gene, partial cds.
columbid herpesvirus 1
39,401
7-Jul-99

rxa00569
1149
GB_PAT: I15213
3728
I15213
Sequence 1 from patent US 5460951.
Unknown.
41,244
2-Apr-96



GB_PAT: E07353
3728
E07353
cDNA encoding bone-related carboxypeptidase-like protein, OSF-5.
Mus sp.
41,244
29-Sep-97



GB_HTG1: CEY70G10
152184
AL020987
Caenorhabditis elegans chromosome III clone Y70G10, *** SEQUENCING

Caenorhabditis elegans

34,148
12-DEC-1997






IN PROGRESS ***, in unordered pieces.

rxa00612
1077
GB_HTG2: AC005020
177756
AC005020
Homo sapiens clone GS259H13, *** SEQUENCING IN PROGRESS ***, 4

Homo sapiens

34,551
12-Jun-98






unordered pieces.



GB_HTG2: AC005020
177756
AC005020
Homo sapiens clone GS259H13, *** SEQUENCING IN PROGRESS ***, 4

Homo sapiens

34,551
12-Jun-98






unordered pieces.



GB_HTG2: AC005020
177756
AC005020
Homo sapiens clone GS259H13, *** SEQUENCING IN PROGRESS ***, 4

Homo sapiens

37,628
12-Jun-98






unordered pieces.

rxa00615
705
GB_GSS15: AQ622921
517
AQ622921
HS_5351_A1_A08_T7A RPCI-11 Human Male BAC Library Homo sapiens

Homo sapiens

38,254
16-Jun-99






genomic clone Plate = 927 Col = 15 Row = A, genomic survey sequence.



GB_GSS3: B36703
432
B36703
HS-1041-B1-B12-MR.abi CIT Human Genomic Sperm Library C Homo

Homo sapiens

44,981
17-OCT-1997






sapiens genomic clone Plate = CT 823 Col = 23 Row = D, genomic survey






sequence.



GB_EST25: AI245926
572
AI245926
qk33c08.x1 NCI_CGAP_Co8 Homo sapiens cDNA clone IMAGE: 1870766

Homo sapiens

38,902
28-Jan-99






3′ similar to SW: COPG_BOVIN P53620 COATOMER GAMMA SUBUNIT;,






mRNA sequence.

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 ***, 3

Homo sapiens

38,636
13-Aug-99






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 cds.

Trypanosoma brucei brucei

48,076
08-OCT-1999

rxa00639
978
GB_BA2: AF043741
1223
AF043741
Rhodococcus rhodochrous catechol 1,2-dioxygenase (catA) gene, complete

Rhodococcus rhodochrous

66,940
27-Aug-98






cds.



GB_BA1: D83237
1626
D83237
Rhodococcus erythropolis DNA for catechol 1,2-dioxgenase, complete cds.

Rhodococcus erythropolis

65,440
1-Sep-99



GB_BA1: ROX99622
7224
X99622
Rhodococcus opacus catR, catA, catB, catC genes and five ORFs.

Rhodococcus opacus

63,617
24-Sep-97

rxa00641
1614
GB_BA2: AF134348
5000
AF134348
Pseudomonas putida plasmid pDK1 toluate 1,2 dioxygenase subunit

Pseudomonas putida

59,863
20-MAY-1999






(xylX), toluate 1,2 dioxygenase subunit (xylY), and toluate 1,2 dioxygenase






subunit (xylZ) genes, complete cds; and 1,2-dihydroxycyclohexa-3,5-diene






carboxylate dehydrogenase (xylL) gene, partial cds.



GB_BA1: PWWXYL
9037
M64747
Pseudomonas putida plasmid pWW0 meta operon, 5′ genes.
Plasmid pWW0
59,588
26-Apr-93



GB_BA1: PCCBDABC
3548
X79076
P. cepacia ( 2CBS) cbdA, cbdB and cbdC genes.

Burkholderia cepacia

55,410
3-Apr-97

rxa00642
615
GB_BA2: AF134348
5000
AF134348
Pseudomonas putida plasmid pDK1 toluate 1,2 dioxygenase subunit (xylX),

Pseudomonas putida

60,920
20-MAY-1999






toluate 1,2 dioxygenase subunit (xylY), and toluate 1,2 dioxygenase subunit






(xylZ) genes, complete cds; and 1,2-dihydroxycyclohexa-3,5-diene






carboxylate dehydrogenase (xylL) gene, partial cds.



GB_BA1: PWWXYL
9037
M64747
Pseudomonas putida plasmid pWW0 meta operon, 5′ genes.
Plasmid pWW0
58,756
26-Apr-93



GB_GSS11: AQ274007
637
AQ274007
nbxb0032I07f CUGI Rice BAC Library Oryza sativa genomic clone

Oryza sativa

41,390
3-Nov-98






nbxb0032I07f, genomic survey sequence.

rxa00643
1659
GB_BA2: AF134348
5000
AF134348
Pseudomonas putida plasmid pDK1 toluate 1,2 dioxygenase subunit (xylX),

Pseudomonas putida

53,871
20-MAY-1999






toluate 1,2 dioxygenase subunit (xylY), and toluate 1,2 dioxygenase subunit






(xylZ) genes, complete cds; and 1,2-dihydroxycyclohexa-3,5-diene






carboxylate dehydrogenase (xylL) gene, partial cds.



GB_BA1: PWWXYL
9037
M64747
Pseudomonas putida plasmid pWW0 meta operon, 5′ genes.
Plasmid pWW0
52,603
26-Apr-93



GB_EST22: AI020666
328
AI020666
ua97f07.r1 Soares mouse mammary gland NbMMG Mus musculus cDNA

Mus musculus

43,865
16-Jun-98






clone IMAGE: 1365445 5′ similar to SW: DUS7_RAT Q63340 DUAL






SPECIFICITY PROTEIN PHOSPHATASE 7;, mRNA sequence.

rxa00644
951
GB_BA1: PWWXYL
9037
M64747
Pseudomonas putida plasmid pWW0 meta operon, 5′ genes.
Plasmid pWW0
55,626
26-Apr-93



GB_BA2: AF134348
5000
AF134348
Pseudomonas putida plasmid pDK1 toluate 1,2 dioxygenase subunit (xylX),

Pseudomonas putida

50,410
20-MAY-1999






toluate 1,2 dioxygenase subunit (xylY), and toluate 1,2 dioxygenase subunit






(xylZ) genes, complete cds; and 1,2-dihydroxycyclohexa-3,5-diene






carboxylate dehydrogenase (xylL) gene, partial cds.



GB_EST22: AI038396
438
AI038396
ox21g10.x1 Soares_fetal_liver_spleen_1NFLS_S1 Homo sapiens cDNA

Homo sapiens

40,138
28-Aug-98






clone IMAGE: 1657026 3′ similar to contains Alu repetitive element; contains






element L1 repetitive element;, mRNA sequence.

rxa00658
816
GB_EST16: C26090
414
C26090
C26090 Rice callus cDNA Oryza sativa cDNA clone C11617_1A, mRNA

Oryza sativa

40,636
6-Aug-97






sequence.



GB_EST16: C26090
414
C26090
C26090 Rice callus cDNA Oryza sativa cDNA clone C11617_1A, mRNA

Oryza sativa

38,406
6-Aug-97






sequence.

rxa00663
1497
GB_BA1: MTV017
67200
AL021897
Mycobacterium tuberculosis H37Rv complete genome; segment 48/162.

Mycobacterium tuberculosis

57,976
24-Jun-99



GB_BA1: MLCB1222
34714
AL049491
Mycobacterium leprae cosmid B1222.

Mycobacterium leprae

39,669
27-Aug-99



GB_HTG2: AC007482
155357
AC007482
Homo sapiens clone hRPK.56_A_1, *** SEQUENCING IN PROGRESS ***,

Homo sapiens

36,154
05-MAY-1999






6 unordered pieces.

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 clone

Drosophila melanogaster

35,531
27-OCT-1999






BACR48M05, complete sequence.

rxa00762
999
GB_HTG2: HSJ473J16
203460
AL109942
Homo sapiens chromosome 6 clone RP3-473J16 map q25.3-26, ***

Homo sapiens

37,295
03-DEC-1999






SEQUENCING IN PROGRESS ***, in unordered pieces.



GB_HTG2: HSJ473J16
203460
AL109942
Homo sapiens chromosome 6 clone RP3-473J16 map q25.3-26, ***

Homo sapiens

37,295
03-DEC-1999






SEQUENCING IN PROGRESS ***, in unordered pieces.



GB_PR2: HSU91327
129252
U91327
Human chromosome 12p15 BAC clone CIT987SK-99D8 complete

Homo sapiens

35,650
21-Aug-97






sequence.

rxa00772
1629
GB_BA2: AF010184
1494
AF010184
Pseudomonas aeruginosa coenzyme A transferase PsecoA (psecoA) gene,

Pseudomonas aeruginosa

56,472
18-Jul-98






complete cds.



GB_PAT: I92043
713
I92043
Sequence 10 from patent US 5726299.
Unknown.
92,701
01-DEC-1998



GB_PAT: I78754
713
I78754
Sequence 10 from patent US 5693781.
Unknown.
92,701
3-Apr-98

rxa00778
1248
GB_BA1: MTPST2GN
1347
Z48056
M. tuberculosis PstS-2 gene.

Mycobacterium tuberculosis

47,791
24-Apr-99



GB_BA1: D90907
132419
D90907
Synechocystis sp. PCC6803 complete genome, 9/27, 1056467-1188885.
Synechocystis sp.
35,536
7-Feb-99



GB_BA1: D90907
132419
D90907
Synechocystis sp. PCC6803 complete genome, 9/27, 1056467-1188885.
Synechocystis sp.
38,006
7-Feb-99

rxa00787
2025
GB_PL1: SCX11RA
36849
X91258
S. cerevisiae DNA from chromosome XII right arm including ACE2, CKI1,

Saccharomyces cerevisiae

36,122
13-OCT-1995






PDC5, SLS1, PUT1 and tRNA-Asp genes.



GB_PL2: YSCL9606
29154
U53881
Saccharomyces cerevisiae chromosome XII cosmid 9606.
Saccharomyces cerevisiae
36,122
25-OCT-1997



GB_PL1: SCX11RA
36849
X91258
S. cerevisiae DNA from chromosome XII right arm including ACE2, CKI1,

Saccharomyces cerevisiae

37,198
13-OCT-1995






PDC5, SLS1, PUT1 and tRNA-Asp genes.

rxa00792
1320
GB_PR4: AC004841
132072
AC004841
Homo sapiens PAC clone DJ0607J23 from 7q21.2-q31.1, complete

Homo sapiens

37,452
18-MAR-1999






sequence.



GB_HTG2: AC006706
180664
AC006706
Caenorhabditis elegans clone Y110A2, *** SEQUENCING IN PROGRESS

Caenorhabditis elegans

34,824
23-Feb-99






***, 4 unordered pieces.



GB_HTG2: AC006706
180664
AC006706
Caenorhabditis elegans clone Y110A2, *** SEQUENCING IN PROGRESS

Caenorhabditis elegans

34,824
23-Feb-99






***, 4 unordered pieces.

rxa00857
1313
GB_BA1: MTV002
56414
AL008967
Mycobacterium tuberculosis H37Rv complete genome; segment 122/162.

Mycobacterium tuberculosis

38,080
17-Jun-98



GB_BA1: MSGY154
40221
AD000002
Mycobacterium tuberculosis sequence from clone y154.

Mycobacterium tuberculosis

68,345
03-DEC-1996



GB_BA1: MLCB33
42224
Z94723
Mycobacterium leprae cosmid B33.

Mycobacterium leprae

38,824
24-Jun-97

rxa00877
1788
GB_PAT: I92050
567
I92050
Sequence 17 from patent US 5726299.
Unknown.
62,787
01-DEC-1998



GB_PAT: I78760
567
I78760
Sequence 16 from patent US 5693781.
Unknown.
62,787
3-Apr-98



GB_BA2: AE000426
10240
AE000426
Escherichia coli K-12 MG1655 section 316 of 400 of the complete genome.

Escherichia coli

36,456
12-Nov-98

rxa00888
1140
GB_BA1: MTCY27
27548
Z95208
Mycobacterium tuberculosis H37Rv complete genome; segment 104/162.

Mycobacterium tuberculosis

40,165
17-Jun-98



GB_BA1: U00016
42931
U00016
Mycobacterium leprae cosmid B1937.

Mycobacterium leprae

58,444
01-MAR-1994



GB_BA1: ECU82598
136742
U82598
Escherichia coli genomic sequence of minutes 9 to 12.

Escherichia coli

37,876
15-Jan-97

rxa00892
1017
GB_BA2: AE000817
13157
AE000817
Methanobacterium thermoautotrophicum from bases 251486 to 264642

Methanobacterium

36,710
15-Nov-97






(section 23 of 148) of the complete genome.
thermoautotrophicum



GB_EST29: AI620549
239
AI620549
tu95b07.x1 NCI_CGAP_Gas4 Homo sapiens cDNA clone IMAGE: 2258773

Homo sapiens

38,075
21-Apr-99






3′ similar to gb: X60708_rna1 DIPEPTIDYL PEPTIDASE IV (HUMAN);,






mRNA sequence.



GB_BA2: AE000817
13157
AE000817
Methanobacterium thermoautotrophicum from bases 251486 to 264642

Methanobacterium

35,650
15-Nov-97






(section 23 of 148) of the complete genome.
thermoautotrophicum

rxa00897
1128
GB_PR3: HS246D7
28011
AL031843
Human DNA sequence from clone 246D7 on chromosome 22q13.1-13.33.

Homo sapiens

38,724
23-Nov-99






Contains ESTs, a GSS and an STS, complete sequence.



GB_PR3: HSDJ185D5
24387
AL118498
Human DNA sequence from clone 185D5 on chromosome 22, complete

Homo sapiens

37,021
23-Nov-99






sequence.



GB_PR3: HS246D7
28011
AL031843
Human DNA sequence from clone 246D7 on chromosome 22q13.1-13.33.

Homo sapiens

36,054
23-Nov-99






Contains ESTs, a GSS and an STS, complete sequence.

rxa00944
1095
GB_BA1: ECU68759
1531
U68759
Enterobacter cloacae pentaerythritol tetranitrate reductase (onr) gene,

Enterobacter cloacae

43,041
14-DEC-1996






complete cds.



GB_PAT: A59288
1531
A59288
Sequence 1 from Patent WO9703201.
unidentified
43,041
06-MAR-1998



GB_EST23: AI099394
601
AI099394
ue32a09.y1 Sugano mouse liver mlia Mus musculus cDNA clone
Mus musculus
37,225
20-Aug-98






IMAGE: 1482040 5′ similar to gb: U21301 Mus musculus c-mer tyrosine






kinase receptor mRNA, complete (MOUSE);, mRNA sequence.

rxa00964
1248
GB_HTG6: AC009794
152794
AC009794
Homo sapiens chromosome 4 clone RP11-343C10 map 4, ***

Homo sapiens

34,762
03-DEC-1999






SEQUENCING IN PROGRESS ***, 33 unordered pieces.



GB_HTG6: AC009794
152794
AC009794
Homo sapiens chromosome 4 clone RP11-343C10 map 4, ***

Homo sapiens

35,708
03-DEC-1999






SEQUENCING IN PROGRESS ***, 33 unordered pieces.

rxa00982
1629
GB_BA1: BLARGS
2501
Z21501
B. lactofermentum argS and lysA genes for arginyl-tRNA synthetase and

Corynebacterium glutamicum

39,003
28-DEC-1993






diaminopimelate decarboxylase (partial).



GB_BA1: CGXLYSA
2344
X54740
Corynebacterium glutamicum argS-lysA operon gene for the upstream

Corynebacterium glutamicum

41,435
30-Jun-93






region of the arginyl-tRNA synthetase and diaminopimelate decarboxylase






(EC 4.1.1.20).



GB_PAT: E14508
3579
E14508
DNA encoding Brevibacterium diaminopimelic acid decarboxylase and

Corynebacterium glutamicum

40,566
28-Jul-99






arginyl-tRNA synthase.

rxa01014
2724
GB_BA1: MTV008
63033
AL021246
Mycobacterium tuberculosis H37Rv complete genome; segment 108/162.

Mycobacterium tuberculosis

56,167
17-Jun-98



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)

rxa01022
1203
GB_PAT: A68384
1080
A68384
Sequence 1 from Patent WO9748809.

Mycobacterium avium

56,913
06-MAY-1999



GB_BA2: AF077728
1346
AF077728
Mycobacterium smegmatis D-alanine: D-alanine ligase gene, complete cds.

Mycobacterium smegmatis

57,203
1-Jan-99

rxa01055

GB_BA1: MSGB1723CS
38477
L78825
Mycobacterium leprae cosmid B1723 DNA sequence.

Mycobacterium leprae

54,599
15-Jun-96

rxa01056
1023
GB_BA2: AE001715
11086
AE001715
Thermotoga maritima section 27 of 136 of the complete genome.

Thermotoga maritima

39,034
2-Jun-99



GB_EST38: AW046857
161
AW046857
UI-M-BH1-akl-a-04-0-UI.s1 NIH_BMAP_M_S2 Mus musculus cDNA clone

Mus musculus

45,963
18-Sep-99






UI-M-BH1-akl-a-04-0-UI 3′, mRNA sequence.



GB_EST38: AW049435
244
AW049435
UI-M-BH1-ams-b-01-0-UI.s1 NIH_BMAP_M_S2 Mus musculus cDNA clone

Mus musculus

40,984
18-Sep-99






UI-M-BH1-ams-b-01-0-UI 3′, mRNA sequence.

rxa01057
1626
GB_PL1: LPAJ5046
656
AJ225046
Lycopersicon peruvianum mRNA for Hsp20.1 protein.

Lycopersicon peruvianum

37,117
22-Jul-98



GB_PL2: SPAC806
22870
AL117212
S. pombe chromosome I cosmid c806.

Schizosaccharomyces

38,211
24-Nov-99








pombe




GB_PL2: SPAC806
22870
AL117212
S. pombe chromosome I cosmid c806.

Schizosaccharomyces

36,934
24-Nov-99








pombe


rxa01082
783
GB_BA2: AF112535
4363
AF112535
Corynebacterium glutamicum putative glutaredoxin NrdH (nrdH), NrdI (nrdI),

Corynebacterium glutamicum

99,794
5-Aug-99






and ribonucleotide reductase alpha-chain (nrdE) genes, complete cds.



GB_PL2: TAE237897
8020
AJ237897
Triticum aestivum sbe1 gene, exons 1-14.

Triticum aestivum

37,132
1-Nov-99



GB_PL2: AF076680
10499
AF076680
Aegilops tauschii starch branching enzyme-I (SBE-I) gene, complete cds.

Aegilops tauschii

38,651
14-MAY-1999

rxa01113
260
GB_VI: ASU02468
11424
U02468
African swine fever virus BA71V (A489R, A280R, A505R, A498R, A528R,
African swine fever virus
31,923
28-Apr-94






A506R, and A542R) genes, complete cds.



GB_VI: ASU18466
170101
U18466
African swine fever virus, complete genome.
African swine fever virus
31,923
22-Apr-95



GB_GSS5: AQ752779
1647
AQ752779
HS_5569_B1_D02_SP6 RPCI-11 Human Male BAC Library Homo sapiens

Homo sapiens

37,154
19-Jul-99






genomic clone Plate = 1145 Col = 3 Row = H, genomic survey sequence.

rxa01115
876
GB_BA1: AB014757
6057
AB014757
Pseudomonas sp. 61-3 genes for PhbR, acetoacetyl-CoA reductase, beta-
Pseudomonas sp. 61-3
40,850
26-DEC-1998






ketothiolase and PHB synthase, complete cds.



GB_IN2: DMU60591
5630
U60591
Drosophila melanogaster kuzbanian (kuz) mRNA, complete cds.

Drosophila melanogaster

37,326
10-Sep-96



GB_RO: MMMMP10
1744
Y13185
Mus musculus mRNA for stromelysin-2.
Mus musculus
35,877
14-Jan-98

rxa01116
735
GB_BA1: SC4C6
30941
AL079355
Streptomyces coelicolor cosmid 4C6.

Streptomyces coelicolor

40,616
21-Jun-99



GB_BA2: AF109386
6551
AF109386
Streptomyces sp. 2065 protocatechuaic acid catabolic gene cluster,
Streptomyces sp. 2065
64,099
06-DEC-1999






complete sequence.



GB_BA1: MTCY07A7
23967
Z95556
Mycobacterium tuberculosis H37Rv complete genome; segment 109/162.

Mycobacterium tuberculosis

41,716
17-Jun-98

rxa01117
864
GB_BA2: AF109386
6551
AF109386
Streptomyces sp. 2065 protocatechuaic acid catabolic gene cluster,
Streptomyces sp. 2065
62,116
06-DEC-1999






complete sequence.



GB_BA2: AF003947
5475
AF003947
Rhodococcus opacus succinyl CoA: 3-oxoadipate CoA transferase subunit

Rhodococcus opacus

36,712
12-MAR-1998






homolog (pcal') gene, partial cds, protocatechuate dioxygenase beta






subunit (pcaH), protocatechuate dioxygenase alpha subunit (pcaG), 3-






carboxy-cis,cis-muconate cycloisomerase homolog (pcaB), 3-oxoadipate






enol-lactone hydrolase/4-carboxymuconolactone decarboxylase (pcaL) and






PcaR (pcaR) genes, complete cds, and 3-oxoadipyl CoA thiolase homolog






(pcaF') gene, partial cds.



GB_BA1: XCLPSIJ
2578
Y11313
X. campestris lpsI, lpsJ, xanA genes and orfX.

Xanthomonas campestris

39,833
20-Jan-98

rxa01120
1401
GB_BA1: MTV008
63033
AL021246
Mycobacterium tuberculosis H37Rv complete genome; segment 108/162.

Mycobacterium tuberculosis

36,715
17-Jun-98



GB_BA1: CAJ10321
6710
AJ010321
Caulobacter crescentus partial tig gene and clpP, cicA, clpX, lon genes.

Caulobacter crescentus

63,311
01-OCT-1998



GB_BA2: AF150957
4440
AF150957
Azospirillum brasilense trigger factor (tig), heat-shock protein ClpP (clpP),

Azospirillum brasilense

60,613
7-Jun-99






and heat-shock protein ClpX (clpX) genes, complete cds; and Lon protease






(lon) gene, partial cds.

rxa01126
583
GB_HTG3: AC009199
66498
AC009199
Drosophila melanogaster chromosome 2 clone BACR10J23 (D1024) RPCI-

Drosophila melanogaster

35,294
20-Sep-99






98 10.J.23 map 37B-37B strain y; cn bw sp, *** SEQUENCING IN






PROGRESS ***, 79 unordered pieces.



GB_HTG3: AC009199
66498
AC009199
Drosophila melanogaster chromosome 2 clone BACR10J23 (D1024) RPCI-

Drosophila melanogaster

35,294
20-Sep-99






98 10.J.23 map 37B-37B strain y; cn bw sp, *** SEQUENCING IN






PROGRESS ***, 79 unordered pieces.



GB_PL1: AB016880
81284
AB016880
Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone: MTG10,

Arabidopsis thaliana

34,477
20-Nov-99






complete 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 98/162.

Mycobacterium tuberculosis

60,434
17-Jun-98



GB_BA1: SC5F7
40024
AL096872
Streptomyces coelicolor cosmid 5F7.

Streptomyces coelicolor

57,011
22-Jul-99






A3(2)

rxa01236
1068
GB_EST3: H01832
381
H01832
yj28c11.s1 Soares placenta Nb2HP Homo sapiens cDNA clone

Homo sapiens

41,406
19-Jun-95






IMAGE: 150068 3′, mRNA sequence.



GB_PR4: AC004850
105891
AC004850
Homo sapiens PAC clone DJ0665C04 from 7p14-p13, complete sequence.

Homo sapiens

37,428
26-Feb-99



GB_GSS11: AQ304150
528
AQ304150
HS_3208_A1_D12_T7 CIT Approved Human Genomic Sperm Library D

Homo sapiens

37,421
16-DEC-1998






Homo sapiens genomic clone Plate = 3208 Col = 23 Row = G, genomic survey






sequence.

rxa01254
1392
GB_BA1: MTV025
121125
AL022121
Mycobacterium tuberculosis H37Rv complete genome; segment 155/162.

Mycobacterium tuberculosis

58,315
24-Jun-99



GB_BA1: MSGB577COS
37770
L01263
M. leprae genomic dna sequence, cosmid b577.

Mycobacterium leprae

56,323
14-Jun-96



GB_BA1: MLCB2407
35615
AL023596
Mycobacterium leprae cosmid B2407.

Mycobacterium leprae

37,645
27-Aug-99

rxa01270
1278
GB_BA1: BSPX91182
345
X91182
Bacterial sp. partial 16S rRNA gene (clone group G10).
unidentified bacterium
41,228
15-Jul-96



GB_BA1: BSPJN12D
347
Z69277
Bacterial sp. partial 16S rRNA gene (clone group JN12d).
Bacteria
38,905
24-Jun-98



GB_EST7: W93397
545
W93397
zd95b03.s1 Soares_fetal_heart_NbHH19W Homo sapiens cDNA clone

Homo sapiens

40,516
25-Nov-96






IMAGE: 357197 3′, mRNA sequence.

rxa01277
2127
GB_PL2: AF111709
52684
AF111709
Oryza sativa subsp. indica Retrosat 1 retrotransposon and Ty3-Gypsy type
Oryza sativa subsp. indica
37,410
26-Apr-99






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 cDNA

Caenorhabditis elegans

36,890
19-Jun-97






clone cm5e4 5′, mRNA sequence.

rxa01288
498
GB_VI: S62819
3348
S62819
F2L = putative RNA polymerase-associated transcription factor . . . F4R =

40,471
25-Aug-93






type I orf virus topoisomerase homolog [orf virus OV, NZ2, host = sheep,






Genomic, 3 genes, 3348 nt].



GB_PR4: HUMCCLEC1
17079
AF077344
Homo sapiens cartilage-derived C-type lectin (CLECSF1) gene, exons 1

Homo sapiens

34,631
15-OCT-1999






and 2.



GB_PR4: HUMCCLEC1
17079
AF077344
Homo sapiens cartilage-derived C-type lectin (CLECSF1) gene, exons 1

Homo sapiens

39,300
15-OCT-1999






and 2.

rxa01354
1059
GB_PR1: D87675
301692
D87675
Homo sapiens DNA for amyloid precursor protein, complete cds.

Homo sapiens

37,984
22-Sep-97



GB_PR1: D87675
301692
D87675
Homo sapiens DNA for amyloid precursor protein, complete cds.

Homo sapiens

35,140
22-Sep-97



GB_RO: MMNUCLEO
11478
X07699
Mouse nucleolin gene.

Mus musculus

37,146
27-Aug-98

rxa01376
984
GB_BA1: MTCY71
42729
Z92771
Mycobacterium tuberculosis H37Rv complete genome; segment 141/162.

Mycobacterium tuberculosis

39,496
10-Feb-99



GB_BA1: ACCPSXM
2748
X81320
A. calcoaceticus epsX and epsM genes.

Acinetobacter calcoaceticus

40,353
19-OCT-1994



GB_BA2: ECU05248
1781
U05248
Escherichia coli polysialic acid gene cluster region 2 (neuD and neuB)

Escherichia coli

34,995
1-Feb-95






genes, complete cds.

rxa01385
2004
GB_BA1: FVBPENTA
2519
M98557
Flavobacterium sp. pentachlorophenol 4-monooxygenase gene, complete
Flavobacterium sp.
40,855
26-Apr-93






mRNA.



GB_PAT: I19994
2516
I19994
Sequence 2 from patent US 5512478.
Unknown.
40,855
07-OCT-1996



GB_BA2: AF059680
2410
AF059680
Sphingomonas sp. UG30 pentachlorophenol 4-monooxygenase (pcpB)
Sphingomonas sp. UG30
42,993
27-Apr-99






gene, complete cds; and pentachlorophenol 4-monooxygenase reductase






(pcpD) gene, partial cds.

rxa01426
750
GB_GSS3: B35912
313
B35912
HS-1031-A2-D02-MR.abi CIT Human Genomic Sperm Library C Homo

Homo sapiens

38,019
17-OCT-1997






sapiens genomic clone Plate = CT 811 Col = 4 Row = G, genomic survey






sequence.



GB_GSS1: FR0027767
497
AL020589
F. rubripes GSS sequence, clone 197B17aA3,

Fugu rubripes

35,814
10-DEC-1997






genomic survey sequence.



GB_GSS5: AQ774340
449
AQ774340
HS_3137_A2_E11_MR CIT Approved Human Genomic Sperm Library D

Homo sapiens

40,535
29-Jul-99






Homo sapiens genomic clone Plate = 3137 Col = 22 Row = I, genomic survey






sequence.

rxa01427
1044
GB_BA2: AF036766
3487
AF036766
Lactobacillus reuteri plasmid pTE15 replication-associated protein A (repA)

Lactobacillus reuteri

39,101
19-Feb-98






and replication-associated protein B (repB) genes, complete cds.



GB_PR4: AC007032
126803
AC007032
Homo sapiens clone NH0022N19, complete sequence.

Homo sapiens

34,180
17-Jul-99



GB_PR4: AC007032
126803
AC007032
Homo sapiens clone NH0022N19, complete sequence.

Homo sapiens

36,858
17-Jul-99

rxa01428
1260
GB_BA1: SCH24
41625
AL049826
Streptomyces coelicolor cosmid H24.

Streptomyces coelicolor

51,278
11-MAY-1999



GB_BA2: AF031590
6676
AF031590
Streptomyces coelicolor thioredoxin (trxA) gene, partial cds; SpoOJ-like, Soj-

Streptomyces coelicolor

39,389
20-Feb-98






like, GidB-like, Jag-like, inner membrane protein, and 9-10 kDa protein-like






genes, complete cds; RNase P protein (rnpA) gene, partial cds; and






unknown gene.



GB_BA1: SCTRXARNP
6676
Y16311
Streptomyces coelicolor trxA & rnpA genes & ORFs 205, 344, 255, 239,

Streptomyces coelicolor

39,389
18-DEC-1998






170, 341 & 124.

rxa01430
1311
GB_EST30: AI643302
254
AI643302
vI39b08.y1 Stratagene mouse skin (#937313) Mus musculus cDNA clone

Mus musculus

38,627
29-Apr-99






IMAGE: 974583 5′ similar to SW: 6PGD_HUMAN P52209 6-






PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING;,






mRNA sequence.



GB_EST34: AI788121
490
AI788121
ul17f02.y1 Sugano mouse embryo mewa Mus musculus cDNA clone

Mus musculus

40,583
2-Jul-99






IMAGE: 2087835 5′ similar to SW: 6PGD_HUMAN P52209 6-






PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING;,






mRNA sequence.



GB_EST16: AA560354
253
AA560354
vl39b08.r1 Stratagene mouse skin (#937313) Mus musculus cDNA clone

Mus musculus

42,544
18-Aug-97






IMAGE: 974583 5′ similar to TR: G984325 G984325






PHOSPHOGLUCONATE DEHYDROGENASE.;, mRNA sequence.

rxa01435
893
GB_EST22: AI069195
892
AI069195
mgae0005dF02f Magnaporthe grisea Appressorium Stage cDNA Library

Pyricularia grisea

40,964
09-DEC-1999






Pyricularia grisea cDNA clone mgae0005dF02f 5′, mRNA sequence.



GB_EST26: AI392390
574
AI392390
NCSC1B12T7 Subtracted Conidial Neurospora crassa cDNA clone SC1B12

Neurospora crassa

40,127
3-Feb-99






3′ similar to adenylate kinase 2 (ATP-AMP transphosphorylase), mRNA






sequence.



GB_HTG2: AC004845
140230
AC004845
Homo sapiens clone DJ0635O05, *** SEQUENCING IN PROGRESS ***, 7

Homo sapiens

36,437
12-Jun-98






unordered pieces.

rxa01437
1506
GB_BA1: CGPTAACKA
3657
X89084
C. glutamicum pta gene and ackA gene.

Corynebacterium glutamicum

100,000
23-MAR-1999



GB_BA1: MTCY22G10
35420
Z84724
Mycobacterium tuberculosis H37Rv complete genome; segment 21/162.

Mycobacterium tuberculosis

54,867
17-Jun-98



GB_HTG3: AC010254
114363
AC010254
Homo sapiens chromosome 5 clone CIT-HSPC_434O11, *** SEQUENCING

Homo sapiens

35,547
15-Sep-99






IN PROGRESS ***, 58 unordered pieces.

rxa01461
735
GB_BA2: AF003947
5475
AF003947
Rhodococcus opacus succinyl CoA: 3-oxoadipate CoA transferase subunit

Rhodococcus opacus

57,939
12-MAR-1998






homolog (pcal′) gene, partial cds, protocatechuate dioxygenase beta






subunit (pcaH), protocatechuate dioxygenase alpha subunit (pcaG), 3-






carboxy-cis, cis-muconate cycloisomerase homolog (pcaB), 3-oxoadipate






enol-lactone hydrolase/4-carboxymuconolactone decarboxylase (pcaL) and






PcaR (pcaR) genes, complete cds, and 3-oxoadipyl CoA thiolase homolog






(pcaF′) gene, partial cds.



GB_PR2: HSA535K18
182408
AL078638
Human DNA sequence from clone RP11-535K18 on chromosome

Homo sapiens

37,123
22-Nov-99






Xq26.2-27.1, complete sequence.



GB_EST33: AI764654
420
AI764654
UI-R-Y0-abw-e-02-0-UI.s2 UI-R-Y0 Rattus norvegicus cDNA clone UI-R-Y0-

Rattus norvegicus

35,885
25-Jun-99






abw-e-02-0-UI 3′, mRNA sequence.

rxa01462
813
GB_BA2: AF003947
5475
AF003947
Rhodococcus opacus succinyl CoA: 3-oxoadipate CoA transferase subunit

Rhodococcus opacus

66,667
12-MAR-1998






homolog (pcal′) gene, partial cds, protocatechuate dioxygenase beta






subunit (pcaH), protocatechuate dioxygenase alpha subunit (pcaG), 3-






carboxy-cis, cis-muconate cycloisomerase homolog (pcaB), 3-oxoadipate






enol-lactone hydrolase/4-carboxymuconolactone decarboxylase (pcaL)and






PcaR (pcaR) genes, complete cds, and 3-oxoadipyl CoA thiolase homolog






(pcaF′) gene, partial cds.



GB_BA1: SC4C6
30941
AL079355
Streptomyces coelicolor cosmid 4C6.

Streptomyces coelicolor

40,822
21-Jun-99



GB_BA2: AF109386
6551
AF109386
Streptomyces sp. 2065 protocatechuaic acid catabolic gene cluster,
Streptomyces sp. 2065
56,049
06-DEC-1999






complete sequence.

rxa01464
414
GB_BA1: AB009343
6342
AB009343
Frateuria sp. ANA-18 ORFR2, catBI, catCI, catAI and catD genes, complete
Frateuria sp. ANA-18
50,966
26-MAY-1999






cds.



GB_GSS10: AQ241375
284
AQ241375
CITBI-EI-2505O7.TF.1 CITBI-E1 Homo sapiens genomic clone 2505O7,

Homo sapiens

39,085
30-Sep-98






genomic survey sequence.



GB_HTG3: AC010363
174962
AC010363
Homo sapiens chromosome 5 clone CITB-H1_2039P12, *** SEQUENCING

Homo sapiens

35,784
15-Sep-99






IN PROGRESS ***, 43 unordered pieces.

rxa01465
1284
GB_BA1: ROX99622
7224
X99622
Rhodococcus opacus catR, catA, catB, catC genes and five ORFs.

Rhodococcus opacus

58,814
24-Sep-97



GB_BA1: D83237
1626
D83237
Rhodococcus erythropolis DNA for catechol 1,2-dioxgenase, complete cds.

Rhodococcus erythropolis

53,904
1-Sep-99



GB_EST9: AA119571
445
AA119571
mp68d04.r1 Soares 2NbMT Mus musculus cDNA clone IMAGE: 574375 5′

Mus musculus

39,551
17-Feb-97






similar to TR: G559375 G559375 RAS GTPASE-ACTIVATING PROTEIN.;,






mRNA sequence.

rxa01466
1083
GB_EST37: AI934978
425
AI934978
wd17b06.x1 Soares_NFL_T_GBC_S1 Homo sapiens cDNA clone

Homo sapiens

43,609
2-Sep-99






IMAGE: 2328371 3′, mRNA sequence.



GB_EST15: AA465729
289
AA465729
aa32g06.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 815002

Homo sapiens

41,115
13-Aug-97






3′, mRNA sequence.



GB_EST24: AI219091
633
AI219091
qg12a05.x1 Soares_placenta_8to9weeks_2NbHP8to9 W Homo sapiens

Homo sapiens

36,066
29-Nov-98






cDNA clone IMAGE: 1759280 3′ similar to TR: Q99988 Q99988 TGF-BETA






SUPERFAMILY PROTEIN. [1];, mRNA sequence.

rxa01477
1671
GB_BA2: CGU89648
1105
U89648
Corynebacterium glutamicum unidentified sequence involved in histidine

Corynebacterium glutamicum

49,726
30-MAR-1999






biosynthesis, partial sequence.



GB_EST21: AA919685
782
AA919685
vx11g06.r1 Soares 2NbMT Mus musculus cDNA clone IMAGE: 1264186 5′

Mus musculus

37,762
20-Apr-98






similar to gb: M73696 Murine Glvr-1 mRNA, complete cds (MOUSE);, mRNA






sequence.



GB_HTG2: HS1005F21
101795
AL078633

Homo sapiens chromosome 20 clone RP5-1005F21, *** SEQUENCING IN


Homo sapiens

38,371
30-Nov-99






PROGRESS ***, in unordered pieces.

rxa01499
3945
GB_PR4: AC006454
153201
AC006454
Homo sapiens clone DJ0852P06, complete sequence.

Homo sapiens

38,033
13-Aug-99



GB_BA1: LSLYSSYNT
4724
AC006454
Lysobacter sp. gene encoding synthetase.

Lysobacter

42,840
8-Jan-97



GB_PR4: AC006454
153201
AC006454
Homo sapiens clone DJ0852P06, complete sequence.

Homo sapiens

38,823
13-Aug-99

rxa01502
1356
GB_PAT: I92046
2203
I92046
Sequence 13 from patent US 5726299.
Unknown.
39,755
01-DEC-1998



GB_PAT: I78757
2203
I78757
Sequence 13 from patent US 5693781.
Unknown.
39,755
3-Apr-98



GB_BA1: MTCY359
36021
Z83859
Mycobacterium tuberculosis H37Rv complete genome; segment 84/162.

Mycobacterium tuberculosis

36,613
17-Jun-98

rxa01509
597
GB_BA1: SCE9
37730
AL049841
Streptomyces coelicolor cosmid E9.

Streptomyces coelicolor

60,637
19-MAY-1999



GB_BA1: MTY15C10
33050
Z95436
Mycobacterium tuberculosis H37Rv complete genome; segment 154/162.

Mycobacterium tuberculosis

59,296
17-Jun-98



GB_BA1: MLCB2548
38916
AL023093
Mycobacterium leprae cosmid B2548.

Mycobacterium leprae

59,764
27-Aug-99

rxa01510
1404
GB_GSS9: AQ129927
440
AQ129927
HS_2165_B1_D09_MR CIT Approved Human Genomic Sperm Library D

Homo sapiens

36,136
23-Sep-98






Homo sapiens genomic clone Plate = 2165 Col = 17 Row = H, genomic survey






sequence.



GB_BA2: AF016585
41097
AF016585
Streptomyces caelestis cytochrome P-450 hydroxylase homolog (nidi) gene,

Streptomyces caelestis

37,464
07-DEC-1997






partial cds; polyketide synthase modules 1 through 7 (nidA) genes,






complete cds; and N-methyltransferase homolog gene, partial cds.



GB_HTG4: AC010747
216500
AC010747
Homo sapiens chromosome unknown clone NH0555H09, WORKING

Homo sapiens

33,022
29-OCT-1999






DRAFT SEQUENCE, in unordered pieces.

rxa01511
1065
GB_BA1: BRLBIOBA
1647
D14084
Brevibacterium flavum gene for biotin synthetase, complete cds.

Corynebacterium glutamicum

40,283
3-Feb-99



GB_GSS3: B45213
358
B45213
HS-1060-B2-D07-MF.abi CIT Human Genomic Sperm Library C Homo

Homo sapiens

49,505
21-OCT-1997






sapiens genomic clone Plate = CT 782 Col = 14 Row = H, genomic survey






sequence.



GB_HTG4: AC010747
216500
AC010747
Homo sapiens chromosome unknown clone NH0555H09, WORKING

Homo sapiens

33,819
29-OCT-1999






DRAFT SEQUENCE, in unordered pieces.

rxa01513
2682
GB_BA1: MTCY7H7B
24244
Z95557
Mycobacterium tuberculosis H37Rv complete genome; segment 153/162.

Mycobacterium tuberculosis

40,354
18-Jun-98



GB_BA2: AF037269
2364
AF037269
Mycobacterium smegmatis cell division protein (FtsH) gene, complete cds.

Mycobacterium smegmatis

60,814
19-Aug-98



GB_BA1: MLCB2548
38916
AL023093
Mycobacterium leprae cosmid B2548.

Mycobacterium leprae

39,992
27-Aug-99

rxa01593
990
GB_BA1: U00012
33312
U00012
Mycobacterium leprae cosmid B1308.

Mycobacterium leprae

39,126
30-Jan-96



GB_IN1: CELF27E11
25700
AF016413
Caenorhabditis elegans cosmid F27E11.

Caenorhabditis elegans

34,227
2-Aug-97



GB_OV: DYGAGR
4354
L01423
Discopyge ommata (clone OL4) agrin mRNA, 3′ end cds.

Discopyge ommata

38,414
28-Apr-93

rxa01608
1962
GB_BA2: AF119150
18605
AF119150
Vibrio cholerae Rtx toxin gene cluster, complete cds.

Vibrio cholerae

36,919
21-MAR-1999



GB_BA2: AF119150
18605
AF119150
Vibrio cholerae Rtx toxin gene cluster, complete cds.

Vibrio cholerae

38,130
21-MAR-1999

rxa01620

rxa01640
3441
GB_PR3: HS52D1
148691
Z96811
Human DNA sequence from PAC 52D1 on chromosome Xq21. Contains CA

Homo sapiens

35,501
23-Nov-99






repeats, STS.



GB_BA2: AF079155
686
AF079155
Ralstonia eutropha phasin (phaP) mRNA, complete cds.

Ralstonia eutropha

40,497
6-Apr-99



GB_IN2: AF039570
1866
AF039570
Caenorhabditis elegans aryl hydrocarbon receptor ortholog AHR-1 (ahr-1)

Caenorhabditis elegans

39,699
04-OCT-1999






mRNA, complete cds.

rxa01653
1584
GB_HTG7: AC010997
187768
AC010997
Homo sapiens clone RP11-399K21, *** SEQUENCING IN PROGRESS ***,

Homo sapiens

34,516
08-DEC-1999






35 unordered pieces.



GB_HTG7: AC010997
187768
AC010997
Homo sapiens clone RP11-399K21, *** SEQUENCING IN PROGRESS ***,

Homo sapiens

36,177
08-DEC-1999






35 unordered pieces.



GB_VI: AF030154
34446
AF030154
Bovine adenovirus 3 complete genome.
bovine adenovirus type 3
40,345
27-Jan-99

rxa01716
509
GB_BA1: AB010645
16836
AB010645
Acetobacter xylinus genes for endoglucanase, cellulose synthase subunit

Acetobacter xylinus

34,783
13-Feb-99






ABCD and beta-glucosidase, complete cds.



GB_BA1: AB010645
16836
AB010645
Acetobacter xylinus genes for endoglucanase, cellulose synthase subunit

Acetobacter xylinus

37,598
13-Feb-99






ABCD and beta-glucosidase, complete cds.



GB_BA1: ABCBCSABCD
9540
M37202
A. xylinum bcs A, B, C and D genes, complete cds's.

Acetobacter xylinus

39,173
24-Apr-93

rxa01728
1098
GB_BA2: CORCSLYS
2821
M89931
Corynebacterium glutamicum beta C-S lyase (aecD) and branched-chain

Corynebacterium glutamicum

99,636
4-Jun-98






amino acid uptake carrier (brnQ) genes, complete cds, and hypothetical






protein Yhbw (yhbw) gene, partial cds.



GB_PL2: HAAP
931
X95952
H. annuus mRNA for aquaporin.

Helianthus annuus

39,231
14-Jul-99



GB_HTG1: CEY32F6
187816
AL008875
Caenorhabditis elegans chromosome V clone Y32F6, *** SEQUENCING IN

Caenorhabditis elegans

37,431
9-Nov-97






PROGRESS ***, in unordered pieces.

rxa01732
1173
GB_PR4: HUAC004125
194020
AC004125
Homo sapiens Chromosome 16 BAC clone CIT987SK-625P11, complete

Homo sapiens

35,345
23-Nov-99






sequence.



GB_PR4: HUAC004125
194020
AC004125
Homo sapiens Chromosome 16 BAC clone CIT987SK-625P11, complete

Homo sapiens

37,381
23-Nov-99






sequence.



GB_IN1: CER11A5
26671
Z83122
Caenorhabditis elegans cosmid R11A5, complete sequence.

Caenorhabditis elegans

36,140
2-Sep-99

rxa01810
1200
GB_EST28: AI499508
403
AI499508
to02d01.x1 NCI_CGAP_Ut2 Homo sapiens cDNA clone IMAGE: 2177857 3′

Homo sapiens

36,725
11-MAR-1999






similar to SW: NU4M_PANTR P03906 NADH-UBIQUINONE






OXIDOREDUCTASE CHAIN 4;, mRNA sequence.



GB_EST28: AI499508
403
AI499508
to02d01.x1 NCI_CGAP_Ut2 Homo sapiens cDNA clone IMAGE: 2177857 3′

Homo sapiens

38,264
11-MAR-1999






similar to SW: NU4M_PANTR P03906 NADH-UBIQUINONE






OXIDOREDUCTASE CHAIN 4;, mRNA sequence.

rxa01828
1545
GB_BA1: MLCB1770
37821
Z70722
Mycobacterium leprae cosmid B1770.

Mycobacterium leprae

36,411
29-Aug-97



GB_HTG2: AC008073
173144
AC008073
Homo sapiens clone NH0507M03, *** SEQUENCING IN PROGRESS ***, 3

Homo sapiens

36,310
17-Jul-99






unordered pieces.



GB_HTG2: AC008073
173144
AC008073
Homo sapiens clone NH0507M03, *** SEQUENCING IN PROGRESS ***, 3

Homo sapiens

36,310
17-Jul-99






unordered pieces.

rxa01829
1446
GB_IN1: AB018544
620
AB018544
Hydra magnipapillata mRNA for Hym-176 preprohormone, complete cds.

Hydra magnipapillata

34,855
6-Feb-99



GB_EST8: AA003136
450
AA003136
mg51e01.r1 Soares mouse embryo NbME13.5 14.5 Mus musculus cDNA

Mus musculus

42,202
19-Jul-96






clone IMAGE: 427320 5′ similar to gb: X07315 PLACENTAL PROTEIN 15






(HUMAN);, mRNA sequence.



GB_IN1: AB018544
620
AB018544
Hydra magnipapillata mRNA for Hym-176 preprohormone, complete cds.

Hydra magnipapillata

35,968
6-Feb-99

rxa01868
2049
GB_BA1: MTV033
21620
AL021928
Mycobacterium tuberculosis H37Rv complete genome; segment 11/162.

Mycobacterium tuberculosis

38,679
17-Jun-98



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

rxa01934
681
GB_PR4: DJ534K4
216387
AF109907
Homo sapiens S164 gene, partial cds; PS1 and hypothetical protein genes,

Homo sapiens

39,189
23-DEC-1998






complete cds; and S171 gene, partial cds.



GB_HTG2: AC006342
201618
AC006342
Homo sapiens clone DJ0054D12, *** SEQUENCING IN PROGRESS ***, 3

Homo sapiens

34,412
11-Jan-99






unordered pieces.



GB_HTG2: AC006342
201618
AC006342
Homo sapiens clone DJ0054D12, *** SEQUENCING IN PROGRESS ***, 3

Homo sapiens

34,412
11-Jan-99






unordered pieces.

rxa01967
1266
GB_IN2: AC005467
62091
AC005467
Drosophila melanogaster , chromosome 2R, region 48C1-48C2, P1 clone

Drosophila melanogaster

35,252
12-DEC-1998






DS00568, complete sequence.



GB_BA2: AE001678
13485
AE001678
Chlamydia pneumoniae section 94 of 103 of the complete genome.

Chlamydophila pneumoniae

35,203
08-MAR-1999



GB_IN2: AC005467
62091
AC005467
Drosophila melanogaster , chromosome 2R, region 48C1-48C2, P1 clone

Drosophila melanogaster

34,699
12-DEC-1998






DS00568, complete sequence.

rxa01993
1166
GB_BA1: PPVANAB
2864
Y14759
Pseudomonas putida vanA and vanB genes.

Pseudomonas putida

51,697
09-MAY-1998



GB_HTG2: AC006799
278007
AC006799
Caenorhabditis elegans clone Y51H7, *** SEQUENCING IN PROGRESS

Caenorhabditis elegans

38,455
23-Feb-99






***, 7 unordered pieces.



GB_HTG2: AC006799
278007
AC006799
Caenorhabditis elegans clone Y51H7, *** SEQUENCING IN PROGRESS

Caenorhabditis elegans

38,455
23-Feb-99






***, 7 unordered pieces.

rxa01994
1098
GB_HTG4: AC009961
231522
AC009961
Homo sapiens chromosome unknown clone NH0357L02, WORKING

Homo sapiens

35,576
29-OCT-1999






DRAFT SEQUENCE, in unordered pieces.



GB_HTG4: AC009961
231522
AC009961
Homo sapiens chromosome unknown clone NH0357L02, WORKING

Homo sapiens

35,576
29-OCT-1999






DRAFT SEQUENCE, in unordered pieces.



GB_HTG4: AC009961
231522
AC009961
Homo sapiens chromosome unknown clone NH0357L02, WORKING

Homo sapiens

35,472
29-OCT-1999






DRAFT SEQUENCE, in unordered pieces.

rxa01997
609
GB_BA2: AF112536
1798
AF112536
Corynebacterium glutamicum ribonucleotide reductase beta-chain (nrdF)

Corynebacterium glutamicum

37,719
5-Aug-99






gene, complete cds.



GB_BA1: SCH66
9153
AL049731
Streptomyces coelicolor cosmid H66.

Streptomyces coelicolor

38,655
29-Apr-99



GB_EST29: AI558691
598
AI558691
fb79c10.y1 Zebrafish WashU MPIMG EST Danio rerio cDNA 5′ similar to

Danio rerio

40,232
24-MAR-1999






SW: ATF3_HUMAN P18847 CYCLIC-AMP-DEPENDENT






TRANSCRIPTION FACTOR ATF-3;, mRNA sequence.

rxa02052
915
GB_EST3: R64206
453
R64206
yi18d08.r1 Soares placenta Nb2HP Homo sapiens cDNA clone

Homo sapiens

35,920
26-MAY-1995






IMAGE: 139599 5′, mRNA sequence.



GB_PR2: AC002540
70851
AC002540
Human BAC clone GS025M02 from 7q21-q22, complete sequence.

Homo sapiens

37,099
12-Sep-97



GB_GSS3: B55001
406
B55001
CIT-HSP-385H2. TRB CIT-HSP Homo sapiens genomic clone 385H2,

Homo sapiens

35,599
20-Jun-98






genomic survey sequence.

rxa02064
762
GB_PR4: AF135187
33016
AF135187
Homo sapiens interferon-induced protein p78 (MX1) gene, complete cds.

Homo sapiens

32,935
8-Jul-99



GB_PR3: AC005612
60904
AC005612
Homo sapiens chromosome 21, P1 clone LBL#8 (LBNL H8), complete

Homo sapiens

32,935
4-Sep-98






sequence.



GB_PR1: HUM8DC11Z
3949
L35666
Homo sapiens (subclone H8 10_f11 from P1 35 H5 C8) DNA sequence.

Homo sapiens

31,995
22-Aug-94

rxa02082
3010
GB_BA1: MSGB32CS
36404
L78818
Mycobacterium leprae cosmid B32 DNA sequence.

Mycobacterium leprae

50,604
15-Jun-96



GB_BA1: MTCY338
29372
Z74697
Mycobacterium tuberculosis H37Rv complete genome; segment 127/162.

Mycobacterium tuberculosis

38,113
17-Jun-98



GB_GSS10: AQ242118
766
AQ242118
3I23-4r Ochrobactrum anthropi BAC Library Ochrobactrum anthropi

Ochrobactrum anthropi

41,876
02-OCT-1998






genomic clone 3I23-4r, genomic survey sequence.

rxa02083
1533
GB_PR4: AC008055
196899
AC008055
Homo sapiens 12q22-103.4-106.5 BAC RPCI11-718L23 (Roswell Park

Homo sapiens

36,818
09-OCT-1999






Cancer Institute Human BAC Library) complete sequence.



GB_PL2: AC002292
120787
AC002292
Genomic sequence of Arabidopsis BAC F8A5, complete sequence.

Arabidopsis thaliana

37,517
02-OCT-1997



GB_PR4: AC008055
196899
AC008055
Homo sapiens 12q22-103.4-106.5 BAC RPCI11-718L23 (Roswell Park

Homo sapiens

35,563
09-OCT-1999






Cancer Institute Human BAC Library) complete sequence.

rxa02092
1761
GB_BA2: AF031929
2675
AF031929
Lactobacillus helveticus cochaperonin GroES and chaperonin GroEL genes,

Lactobacillus helveticus

36,149
8-Aug-98






complete cds; and DNA mismatch repair enzyme (hexA) gene, partial cds.



GB_HTG1: HSDJ34F7
129811
AL049547
Homo sapiens chromosome 6 clone RP1-34F7, *** SEQUENCING IN

Homo sapiens

37,587
23-Nov-99






PROGRESS ***, in unordered pieces.



GB_PR2: HSU24578
17488
U24578
Human RP1 and complement C4B precursor (C4B) genes, partial cds.

Homo sapiens

36,755
16-MAY-1996

rxa02098
1869
GB_BA1: CAJ10319
5368
AJ010319
Corynebacterium glutamicum amtP, gInB, gInD genes and partial ftsY and

Corynebacterium glutamicum

99,766
14-MAY-1999






srp genes.



GB_BA1: CAJ10319
5368
AJ010319
Corynebacterium glutamicum amtP, gInB, gInD genes and partial ftsY and

Corynebacterium glutamicum

36,983
14-MAY-1999






srp genes.

rxa02105
391
GB_EST17:
352
AA660065
EST00115 watermelon lambda zap express library Citrullus lanatus cDNA

Citrullus lanatus

37,231
10-Nov-97






clone WMLS233 5′ similar to translation initiation factor, mRNA sequence.



GB_GSS6: AQ839377
523
AQ839377
HS_4640_B2_F09_T7A CIT Approved Human Genomic Sperm Library D

Homo sapiens

37,500
30-Aug-99






Homo sapiens genomic clone Plate = 4640 Col = 18 Row = L, genomic survey






sequence.



GB_PL1: SPCC970
31438
AL031530
S. pombe chromosome III cosmid c970.

Schizosaccharomyces

38,268
07-MAY-1999








pombe


rxa02111
1407
GB_BA1: SC6G10
36734
AL049497
Streptomyces coelicolor cosmid 6G10.
Streptomyces coelicolor
50,791
24-MAR-1999



GB_BA1: U00010
41171
U00010
Mycobacterium leprae cosmid B1170.

Mycobacterium leprae

37,563
01-MAR-1994



GB_BA1: MTCY336
32437
Z95586
Mycobacterium tuberculosis H37Rv complete genome: segment 70/162.

Mycobacterium tuberculosis

39,504
24-Jun-99

rxa02118
465
GB_HTG2: AC007164
158320
AC007164
Homo sapiens clone NH0304A10, *** SEQUENCING IN PROGRESS ***, 3

Homo sapiens

38,377
23-Apr-99






unordered pieces.

rxa02120
885
GB_PL2: PUMCDC2A
1288
L34206
Petroselinum crispum protein kinase p34cdc2 (cdc2) mRNA, complete cds.

Petroselinum crispum

37,816
17-Feb-96



GB_GSS10: AQ214799
431
AQ214799
HS_3010_A2_G12_MR CIT Approved Human Genomic Sperm Library D

Homo sapiens

34,591
18-Sep-98






Homo sapiens genomic clone Plate = 3010 Col = 24 Row = M, genomic survey






sequence.



GB_PL2: PUMCDC2A
1288
L34206
Petroselinum crispum protein kinase p34cdc2 (cdc2) mRNA, complete cds.

Petroselinum crispum

36,541
17-Feb-96

rxa02126
444
GB_GSS4: AQ707596
485
AQ707596
HS_5560_B1_H08_SP6E RPCI-11 Human Male BAC Library Homo

Homo sapiens

38,482
7-Jul-99






sapiens genomic clone Plate = 1136 Col = 15 Row = P, genomic survey






sequence.



GB_GSS13: AQ494885
411
AQ494885
HS_5195_A1_B11_SP6E RPCI-11 Human Male BAC Library Homo

Homo sapiens

40,897
28-Apr-99






sapiens genomic clone Plate = 771 Col = 21 Row = C, genomic






survey sequence.



GB_GSS4: AQ707596
485
AQ707596
HS_5560_B1_H08_SP6E RPCI-11 Human Male BAC Library Homo

Homo sapiens

43,533
7-Jul-99






sapiens genomic clone Plate = 1136 Col = 15 Row = P, genomic survey






sequence.

rxa02148
1266
GB_HTG2: AC007905
100722
AC007905
Homo sapiens chromosome 16q24.3 clone PAC 754F23, *** SEQUENCING

Homo sapiens

36,051
24-Jun-99






IN PROGRESS ***, 33 unordered pieces.



GB_HTG2: AC007905
100722
AC007905
Homo sapiens chromosome 16q24.3 clone PAC 754F23, *** SEQUENCING

Homo sapiens

36,051
24-Jun-99






IN PROGRESS ***, 33 unordered pieces.



GB_HTG2: AC007905
100722
AC007905
Homo sapiens chromosome 16q24.3 clone PAC 754F23, *** SEQUENCING

Homo sapiens

35,402
24-Jun-99






IN PROGRESS ***, 33 unordered pieces.

rxa02214
732
GB_GSS13: AQ459868
402
AQ459868
HS_5116_A1_H04_SP6E RPCI-11 Human Male BAC Library Homo

Homo sapiens

43,035
23-Apr-99






sapiens genomic clone Plate = 692 Col = 7 Row = O, genomic survey






sequence.



GB_EST26: AU005050
790
AU005050
AU005050 Bombyx mori p50(Daizo) Bombyx mori cDNA clone ws30188,

Bombyx mori

45,902
19-Jan-99






mRNA sequence.



GB_PL2: F8K7
98581
AC007727
Arabidopsis thaliana chromosome 1 BAC F8K7 sequence, complete

Arabidopsis thaliana

37,155
29-Jun-99






sequence.

rxa02316
1137
GB_EST32: AI723424
600
AI723424
hcgls49.T7 Haemonchus contortus Intestinal mRNA Haemonchus contortus

Haemonchus contortus

35,953
10-Jun-99






cDNA clone hcgls49.T7 T7, mRNA sequence.



GB_PR4: AC000134
203300
AC000134
Homo sapiens Chromosome 11q13 BAC Clone 137c7, complete sequence.

Homo sapiens

37,030
06-MAY-1999



GB_STS: AF021124
575
AF021124
Homo sapiens trinucleotide repeat ctg-68, sequence tagged site.

Homo sapiens

41,913
3-Apr-98

rxa02384
831
GB_PL1: ATA224957
4081
AJ224957
Arabidopsis thaliana RGAL gene.

Arabidopsis thaliana

35,627
19-MAY-1998



GB_RO: AF022770
577
AF022770
Mus musculus peripherial benzodiazepine receptor associated protein

Mus musculus

39,652
24-Sep-97






(Pap7) mRNA, partial cds.



GB_GSS11: AQ258908
890
AQ258908
nbxb0021F23r CUGI Rice BAC Library Oryza sativa genomic clone

Oryza sativa

39,515
23-OCT-1998






nbxb0021F23r, genomic survey sequence.

rxa02411
972
GB_BA1: AB020624
1605
AB020624
Corynebacterium glutamicum murl gene for D-glutamate racemase,

Corynebacterium glutamicum

98,868
24-Jul-99






complete cds.



GB_EST18: AA733776
385
AA733776
vv03f03.r1 Stratagene mouse skin (#937313) Mus musculus cDNA clone

Mus musculus

43,864
7-Jan-98






IMAGE: 1210589 5′, mRNA sequence.



GB_EST38: AW033449
612
AW033449
EST277020 tomato callus, TAMU Lycopersicon esculentum cDNA clone

Lycopersicon esculentum

35,620
15-Sep-99






cLEC28F5, mRNA sequence.

rxa02448
1212
GB_BA1: AB016258
2260
AB016258
Arthrobacter sp. gene for maleylacetate reductase and hydroxyquinol 1,2-
Arthrobacter sp.
60,465
8-Sep-99






dioxygenase, partial and complete cds.



GB_EST37: AW014148
553
AW014148
UI-H-BI0-aaj-c-04-0-UI.s1 NCI_CGAP_Sub1 Homo sapiens cDNA clone

Homo sapiens

44,560
10-Sep-99






IMAGE: 2709487 3′, mRNA sequence.



GB_EST14: AA432042
543
AA432042
zw80f01.r1 Soares_testis_NHT Homo sapiens cDNA clone IMAGE: 782521

Homo sapiens

36,522
22-MAY-1997






5′ similar to WP: T12A7.1 CE06433;, mRNA sequence.

rxa02449
1026
GB_BA1: AB016258
2260
AB016258
Arthrobacter sp. gene for maleylacetate reductase and hydroxyquinol 1,2-
Arthrobacter sp.
66,244
8-Sep-99






dioxygenase, partial and complete cds.



GB_BA1: CGPUTP
3791
Y09163
C. glutamicum putP gene.

Corynebacterium glutamicum

39,899
8-Sep-97



GB_BA1: AB016258
2260
AB016258
Arthrobacter sp. gene for maleylacetate reductase and hydroxyquinol 1,2-
Arthrobacter sp.
70,410
8-Sep-99






dioxygenase, partial and complete cds.

rxa02497
1050
GB_BA2: CGU31224
422
U31224
Corynebacterium glutamicum (ppx) gene, partial cds.

Corynebacterium glutamicum

96,445
2-Aug-96



GB_BA1: MTCY20G9
37218
Z77162
Mycobacterium tuberculosis H37Rv complete genome; segment 25/162.

Mycobacterium tuberculosis

59,429
17-Jun-98



GB_BA1: SCE7
16911
AL049819
Streptomyces coelicolor cosmid E7.

Streptomyces coelicolor

39,510
10-MAY-1999

rxa02526
1329
GB_GSS10: AQ240233
483
AQ240233
CIT-HSP-2385F9.TR.1 CIT-HSP Homo sapiens genomic clone 2385F9,

Homo sapiens

42,475
30-Sep-98






genomic survey sequence.



GB_OV: S48556
195
S48556
{tandem repeat P1 monomer} [ Cacatua galerita = sulfur-crested cockatoo,

Cacatua galerita

50,515
08-MAY-1993






Genomic, 195 nt].



GB_PR2: HSM801056
2555
AL117532
Homo sapiens mRNA; cDNA DKFZp434E192 (from clone DKFZp434E192).

Homo sapiens

39,116
15-Sep-99

rxa02530
780
GB_PR3: HSJ753D10
97912
AL049651
Human DNA sequence from clone 753D10 on chromosome 20 Contains

Homo sapiens

34,248
23-Nov-99






genes for SSTR4(somatostatin receptor 4) and THBD(thrombomodulin),






ESTs, STSs, GSSs and CpG islands, complete sequence.



GB_EST33: AI782764
661
AI782764
EST263643 tomato susceptible, Cornell Lycopersicon esculentum cDNA

Lycopersicon esculentum

35,385
29-Jun-99






clone cLES20B10, mRNA sequence.



GB_GSS9: AQ121479
521
AQ121479
HS_3084_A2_B02_MF CIT Approved Human Genomic Sperm Library D

Homo sapiens

38,689
22-Sep-98






Homo sapiens genomic clone Plate = 3084 Col = 4 Row = C, genomic survey






sequence.

rxa02535
1278
GB_HTG3: AC008710
146065
AC008710
Homo sapiens chromosome 5 clone CIT978SKB_7E3, *** SEQUENCING

Homo sapiens

35,799
3-Aug-99






IN PROGRESS ***, 39 unordered pieces.



GB_HTG3: AC008710
146065
AC008710
Homo sapiens chromosome 5 clone CIT978SKB_7E3, *** SEQUENCING

Homo sapiens

35,799
3-Aug-99






IN PROGRESS ***, 39 unordered pieces.



GB_HTG3: AC008710
146065
AC008710
Homo sapiens chromosome 5 clone CIT978SKB_7E3, *** SEQUENCING

Homo sapiens

34,886
3-Aug-99






IN PROGRESS ***, 39 unordered pieces.

rxa02603
1119
GB_BA1: MTV026
23740
AL022076
Mycobacterium tuberculosis H37Rv complete genome; segment 157/162.

Mycobacterium tuberculosis

37,975
24-Jun-99



GB_IN2: AC005714
177740
AC005714
Drosophila melanogaster , chromosome 2R, region 58D4-58E2, BAC clone

Drosophila melanogaster

41,226
01-MAY-1999






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.

rxa02641

rxa02651
1053
GB_BA1: MTCY48
35377
Z74020
Mycobacterium tuberculosis H37Rv complete genome; segment 69/162.

Mycobacterium tuberculosis

62,678
17-Jun-98



GB_BA1: SC4A10
43147
AL109663
Streptomyces coelicolor cosmid 4A10.

Streptomyces coelicolor

39,109
5-Aug-99







A3(2)



GB_BA1: MLCL458
43839
AL049478
Mycobacterium leprae cosmid L458.

Mycobacterium leprae

62,753
27-Aug-99

rxa02674
1575
GB_BA2: PPU96338
5276
U96338
Pseudomonas putida NCIMB 9866 plasmid pRA4000 p-cresol degradative

Pseudomonas putida

58,095
13-MAY-1999






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.



GB_BA1: SCE9
37730
AL049841
Streptomyces coelicolor cosmid E9.

Streptomyces coelicolor

38,544
19-MAY-1999



GB_BA2: PPU96339
4464
U96339
Pseudomonas putida NCIMB 9869 plasmid pRA500 p-cresol degradative

Pseudomonas putida

70,588
13-MAY-1999






pathway genes, p-hydroxybenzaldehyde dehydrogenase (pchA) gene,






partial cds, and p-cresol methylhydroxylase, cytochrome subunit (pchC),






unknown (pchX), p-cresol methylhydroxylase, flavoprotein subunit (pchF),






protocatechuate-3,4-dioxygenase, beta subunit (pcaH) and protocatechuate-






3,4-dioxygenase, alpha subunit (pcaG) genes, complete cds.

rxa02702
1581
GB_BA1: AB015023
2291
AB015023
Corynebacterium glutamicum genes for MurC and FtsQ, complete cds.

Corynebacterium glutamicum

99,365
6-Feb-99



GB_BA1: AB003132
4116
AB003132
Corynebacterium glutamicum gene for MurC, FtsQ, FtsZ, complete cds.

Corynebacterium glutamicum

99,317
4-Aug-97



GB_BA1: BLFTSZ
5546
Y08964
B. lactofermentum murC, ftsQ or divD & ftsZ genes.

Corynebacterium glutamicum

99,296
08-OCT-1998

rxa02703
1212
GB_BA1: AB015023
2291
AB015023
Corynebacterium glutamicum genes for MurC and FtsQ, complete cds.

Corynebacterium glutamicum

97,468
6-Feb-99



GB_PL2: VFAMACTRA
1879
Y09591
V. faba mRNA for amino acid transporter.

Vicia faba

38,915
02-DEC-1999



GB_PAT: E05047
966
E05047
DNA encoding recombinant monoglyceride lipase.
Bacillus sp.
37,158
29-Sep-97

rxa02704
1812
GB_BA1: MTCY270
37586
Z95388
Mycobacterium tuberculosis H37Rv complete genome; segment 96/162.

Mycobacterium tuberculosis

37,946
10-Feb-99



GB_BA2: AE000961
18765
AE000961
Archaeoglobus fulgidus section 146 of 172 of the complete genome.

Archaeoglobus fulgidus

38,521
15-DEC-1997



GB_BA1: MTCY270
37586
Z95388
Mycobacterium tuberculosis H37Rv complete genome; segment 96/162.

Mycobacterium tuberculosis

37,850
10-Feb-99

rxa02705
1539
GB_PAT: I26124
6911
I26124
Sequence 4 from patent US 5556776.
Unknown.
97,619
07-OCT-1996



EM_PAT: E11760
6911
E11760
Base sequence of sucrase gene.

Corynebacterium glutamicum

97,619
08-OCT-1997









(Rel. 52,









Created)



GB_BA1: SC4A10
43147
AL109663
Streptomyces coelicolor cosmid 4A10.

Streptomyces coelicolor

37,856
5-Aug-99







A3(2)

rxa02706
1221
GB_PAT: I26124
6911
I26124
Sequence 4 from patent US 5556776.
Unknown.
98,605
07-OCT-1996



EM_PAT: E11760
6911
E11760
Base sequence of sucrase gene.

Corynebacterium glutamicum

98,605
08-OCT-1997









(Rel. 52,









Created)



GB_BA1: MTCY270
37586
Z95388
Mycobacterium tuberculosis H37Rv complete genome; segment 96/162.

Mycobacterium tuberculosis

34,868
10-Feb-99

rxa02707
1653
EM_PAT: E11760
6911
E11760
Base sequence of sucrase gene.

Corynebacterium glutamicum

98,547
08-OCT-1997









(Rel. 52,









Created)



GB_PAT: I26124
6911
I26124
Sequence 4 from patent US 5556776.
Unknown.
98,547
07-OCT-1996



GB_BA1: MLCB268
38859
AL022602
Mycobacterium leprae cosmid B268.

Mycobacterium leprae

37,815
27-Aug-99

rxa02710
1686
EM_PAT: E11760
6911
E11760
Base sequence of sucrase gene

Corynebacterium glutamicum

52,124
08-OCT-1997









(Rel. 52,









Created)



GB_PAT: I26124
6911
I26124
Sequence 4 from patent US 5556776.
Unknown.
52,124
07-OCT-1996



GB_GSS13: AQ484169
515
AQ484169
RPCI-11-264A12.TV RPCI-11 Homo sapiens genomic clone RPCI-11-

Homo sapiens

40,856
24-Apr-99






264A12, genomic survey sequence.

rxa02711
2235
GB_BA2: XCU45994
1203
U45994
Xanthomonas campestris pv. campestris insertion sequence IS1404.
Xanthomonas campestris pv.
39,061
29-Jan-99







campestris



GB_BA2: XCU77781
4160
U77781
Xanthomonas campestris pv. amaranthicola Xaml DNA methyltransferase
Xanthomonas campestris pv.
39,551
9-Feb-99






(xamlM) gene, complete cds; insertion sequence IS1389 and unknown
amaranthicola






genes.



GB_BA2: AF108355
1222
AF108355
Xanthomonas campestris pv. amaranthicola insertion sequence IS1389-B
Xanthomonas campestris pv.
40,281
09-MAR-1999






unknown genes.
amaranthicola

rxa02713
1134
GB_BA1: MTCY270
37586
Z95388
Mycobacterium tuberculosis H37Rv complete genome; segment 96/162.

Mycobacterium tuberculosis

38,669
10-Feb-99



GB_PR1: D31907
599
D31907
Homo sapiens gene for zinc regulatory factor, partial cds.

Homo sapiens

36,396
7-Feb-99



GB_PR1: HSMTFMR
3302
X78710
H. sapiens MTF-1 mRNA for metal-regulatory transcription factor.

Homo sapiens

37,243
1-Aug-94

rxa02716
684
GB_PR3: AC002347
134977
AC002347
Homo sapiens chromosome 17, clone 297N7, complete sequence.

Homo sapiens

36,282
3-Feb-98



GB_PR3: HS310J6
87942
AL035593
Human DNA sequence from clone 310J6 on chromosome 6q22.1-22.3.

Homo sapiens

37,291
23-Nov-99






Contains part of a novel gene, ESTs, STSs and GSSs, complete sequence.



GB_HTG3: AC011509
111353
AC011509
Homo sapiens chromosome 19 clone CITB-H1_2189E23, ***

Homo sapiens

37,407
07-OCT-1999






SEQUENCING IN PROGRESS ***, 35 unordered pieces.

rxa02722
1449
GB_BA1: BLFTSZ
5546
Y08964
B. lactofermentum murC, ftsQ or divD & ftsZ genes.

Corynebacterium glutamicum

99,652
08-OCT-1998



GB_BA1: AB003132
4116
AB003132
Corynebacterium glutamicum gene for MurC, FtsQ, FtsZ, complete cds.

Corynebacterium glutamicum

98,535
4-Aug-97



GB_PAT: E17182
1125
E17182
Brevibacterium flavum ftsQ gene complete cds.

Corynebacterium glutamicum

97,235
28-Jul-99

rxa02723
789
GB_BA1: AB015023
2291
AB015023
Corynebacterium glutamicum genes for MurC and FtsQ, complete cds.

Corynebacterium glutamicum

99,113
6-Feb-99



GB_BA1: BLFTSZ
5546
Y08964
B. lactofermentum murC, ftsQ or divD & ftsZ genes.

Corynebacterium glutamicum

99,113
08-OCT-1998



GB_BA1: AB003132
4116
AB003132
Corynebacterium glutamicum gene for MurC, FtsQ, FtsZ, complete cds.

Corynebacterium glutamicum

99,113
4-Aug-97

rxa02813
1108
GB_HTG3: AC009658
171795
AC009658
Homo sapiens chromosome 15 clone 344_A_16 map 15, *** SEQUENCING

Homo sapiens

34,622
01-OCT-1999






IN PROGRESS ***, 29 unordered pieces.



GB_HTG3: AC009658
171795
AC009658
Homo sapiens chromosome 15 clone 344_A_16 map 15, *** SEQUENCING

Homo sapiens

34,622
01-OCT-1999






IN PROGRESS ***, 29 unordered pieces.



GB_RO: MMU65079
2300
U65079
Mus musculus actin-binding protein (ENC-1) mRNA, complete cds.

Mus musculus

35,013
29-Jul-97

rxa02820
1411
GB_BA1: BFU64514
3837
U64514
Bacillus firmus dppABC operon, dipeptide transporter protein dppA gene,

Bacillus firmus

36,859
1-Feb-97






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 NaCl

Mesembryanthemum

35,770
21-Jul-99






treatment Mesembryanthemum crystallinum cDNA clone L30-944 5′ similar

crystallinum







to 60S ribosomal protein L36 (AC004684)[ Arabidopsis thaliana ], mRNA






sequence.

rxa02828
572
GB_BA1: MTCY10H4
39160
Z80233
Mycobacterium tuberculosis H37Rv complete genome; segment 2/162.

Mycobacterium tuberculosis

39,823
17-Jun-98



GB_BA1: MTORIREP
8400
X92504
M. tuberculosis origin of replication and genes rnpA, rpmH, dnaA, dnaN,

Mycobacterium tuberculosis

39,823
26-Aug-97






recF.



GB_RO: RATENDOGLY
3906
L37380
Rat apical endosomal glycoprotein mRNA, complete cds.

Rattus norvegicus

38,704
20-Apr-95

rxa02839
470
GB_BA2: ECOUW89
176195
U00006
E. coli chromosomal region from 89.2 to 92.8 minutes.

Escherichia coli

99,362
17-DEC-1993



GB_BA2: AE000477
11314
AE000477
Escherichia coli K-12 MG1655 section 367 of 400 of the complete genome.

Escherichia coli

99,787
12-Nov-98



GB_BA1: ECOPLSB
3865
K00127
E. coli plsB and dgk genes coding for sn-glycerol-3-phosphate

Escherichia coli

33,761
28-Feb-94






acyltransferase and diglyceride kinase.

rxs03218