# Patent

## Title
Nucleotide sequences coding for proteins involved in the biosynthesis of L-serine, an improved method for the microbial production of L-serine and a genetically modified microorganism suitable therefor

## Abstract

The present invention relates to nucleotide sequences of coryneform bacteria, coding for proteins involved in the bio-synthesis of L-serine and to methods for the isolation thereof. The invention further relates to an improved method for the production of L-serine. In addition, the present invention relates to the use of L-serine in the food, animal feed and/or pharmaceutical industries or in human medicine.

## Background
This is a c-i-p application of international application PCT/EP01/02283 filed Mar. 1, 2001 and claiming the priority of German applications 100 09 799.5 filed Mar. 1, 2000 AND 100 44 831 3 filed Sep. 11, 2000.


BACKGROUND OF THE INVENTION
The present invention relates to nucleotide sequences of coryneform bacteria, coding for proteins involved in the bio-synthesis of L-serine and to an improved method for the microbial production of L-serine and to a genetically modified microorganism suitable therefor. The present invention further comprises the use of L-serine and/or secondary products thereof in the food, animal feed and/or pharmaceutical industries and/or in human medicine.
In recent years, amino acids such as L-glutamate, L-lysine or branched-chain L-amino acids have increasingly become the focus of economic interest. This is equally true for the amino acid L-serine which serves not only as a precursor for the synthesis of the aliphatic amino acids L-glycine or L-cysteine but also for the production of L-tryptophan from indole and L-serine. To this end, the amino acid L-serine is regarded to have an increasingly economic potential, in particular in the food, animal feed and pharmaceutical industries and also in many areas of human medicine.
Numerous methods for the microbial production of L-serine have been described in the literature. In addition, fermentations of coryneform bacteria for the production of L-serine are already known. Thus, for example, a Corynebacterium glyciniphilum strain is capable of forming L-serine from glycine and carbohydrates (Kubota K., Kageyama K., Shiro T., and Okumura S., (1971), Journal of General Applications in Microbiology, 17: 167–168; Kubota K., Kageyama K., Maeyashiki I., Yamada K., and Okumura S., (1972), Journal of General Applications in Microbiology 18: 365). Here, the enzyme L-serine hydroxymethyltransferase is involved in converting glycine to L-serine (Kubota K. and Yokozeki K., (1989), Journal of Fermentation and Bioengineering, 67(6): 387–390). Furthermore, the bacterial strains used exhibit a reduced serine degradation which can be attributed to a reduction in the activity of the enzyme L-serine dehydratase (Kubota K., Kageyama K., Shiro T. and Okumura S., (1971) Journal of General Applications in Microbiology, 17: 167–168; Kubota K., (1985), Agricultural Biological Chemistry, 49: 7–12).
Furthermore, the fermentative production of L-serine from methanol and glycine with the aid of methylotrophic bacteria, for example of the genus Hyphomicrobium, is described in Izumi Y., Yoshida T., Miyazaki S. S., Mitsunaga T., Ohshiro T., Shiamo M., Miyata A. and Tanabe T., (1993), Applied Microbiology and Biotechnology, 39: 427–432.
In the aforementioned cases, however, formation of the amino acid L-serine starting from carbohydrates requires the addition of the amino acid glycine as a precursor.
Furthermore, methods for fermentation of coryneform bacteria which are capable of producing L-serine directly from carbohydrates without addition of further precursors are already known. Thus, for example, Yoshida H. and Nakayama K., (1974), Nihon-Nogei-Kagakukaishi 48: 201–208 describe bacterial strains of the genus Corynebacterium and, in particular, of the species Corynebacterium glutamicum, which have been obtained by random mutagenesis and which are distinguished, inter alia, by a resistance to the L-serine analogs serine hydroxamate and β-chloroalanine. This causes, inter alia, the metabolic flow to be able to flow increasingly in the direction of L-serine biosynthesis, since the activity of the corresponding enzymes is less inhibited by the final product.
EP 0 931 833 discloses bacterial strains of the species Brevibacterium flavum which were likewise obtained by random mutagenesis and which therefore have defective serine degradation. In addition, the strains described there have a modified serA gene which codes for a feedback-insensitive 3-phosphoglycerate dehydrogenase. These strains additionally contain the genes serB and serC which originate from the heterologous organism Escherichia coli and which code for the enzymes phosphoserine phosphatase and phosphoserine aminotransferase, respectively. The system described here thus has a high complexity with respect to the multiplicity of additionally introduced, partially heterologous, gene structures, combined with a genetic uncertainty of the bacterial strains with respect to the initially mentioned random mutagenesis. This holds the risk of a relatively high instability of such bacterial strains during the course of a large-scale production process. It has further been described that the bacterial strains illustrated here only achieve an increase in L-serine production by a factor of 2 to 5, at most. The reason for this may be, inter alia, a suboptimal expression of heterologous genes.
Another disadvantage of heterologous systems is the low acceptance of foreign DNA-containing systems, in particular for the production of medically and pharmacologically relevant substances and of substances relevant to food.
Besides the biosynthesis of economically interesting L-amino acids such as, for example, L-serine, secretion of these metabolic products into the culture medium is also crucially important for the yield of L-serine in the final product. This export may be unspecific due to diffusion or actively mediated by membrane transport systems, as described, for example, for the amino acids L-isoleucine or L-lysine (Zittrich S. et al., 1994, Journal of Bacteriology, 176: 6892–6899 and Broer S. et al., 1991, European Journal of Biochemistry, 202: 131–153). A problem of those active transport systems is that the capacity of these “export carriers” is quickly exceeded, as soon as the contents of the metabolic product to be transported in the cell exceeds a threshold of the naturally present concentration. This means that, for example in the case of an increased biosynthesis of L-serine, the export thereof out of the cell may be limited.
Consequently, the availability of the genes from coryneform bacteria, which are crucially involved in the biosynthesis of L-serine, for expression in a homologous system is desirable, as is an improved secretion of the L-serine formed into the culture medium.
It is therefore an object of the present invention to provide a system which no longer has the aforementioned disadvantages and makes possible an improved production of L-serine or of metabolic products derivable therefrom and the isolation thereof.
SUMMARY OF THE INVENTION
The present invention relates to nucleotide sequences of coryneform bacteria, coding for proteins involved in the biosynthesis of L-serine and to methods for the isolation thereof. The invention further relates to an improved method for the production of L-serine. In addition, the present invention relates to the use of L-serine in the food, animal feed and/or pharmaceutical industries or in human medicine.
More specifically, the invention relates to providing an isolated nucleic acid which codes for a phosphoserine phosphatase and which comprises a gene serB selected from the sequences according to the SEQ ID No. 1 or 5 and 2 or 6 (FIG. 1) and an isolated nucleic acid which codes for a phosphoserine aminotransferase and which comprises a gene serC selected from the sequences according to the SEQ ID No. 3 or 7 and 4 or 8 (FIG. 1) or an allele, homolog or derivative of these nucleotide sequences or nucleotide sequences hybridizing to these nucleotide sequences.
The present invention likewise includes the nucleic acids coding for an L-threonine export carrier according to SEQ ID No. 9 or 11 and the polypeptide sequences according to SEQ ID No. 10 or 12 derived therefrom and also the use thereof in the inventive methods for the production of L-serine. The German patent application 199 41 478.5 discloses the isolation of said sequences from coryneform bacteria.
The nucleic acids used are distinguished by the fact that they are isolated from coryneform bacteria, preferably of the genus Corynebacterium or Brevibacterium, particularly preferably of the species Corynebacterium glutamicum or Brevibacterium flavum. Examples of wild-type coryneform bacteria deposited in stock cultures are Corynebacterium glutamicum ATCC 13032, Corynebacterium glutamicum ATCC 14752, Corynebacterium acetoglutamicum ATCC 15806, Corynebacterium acetoglutamicum ATCC 15806, Corynebacterium melassecola ATCC 17965, Corynebacterium thermoaminogenes FERM BP-1539, Brevibacterium flavum ATCC 14067, Brevibacterium lactofermentum ATCC 13869 and Brevibacterium divaricatum ATCC 14020. Examples of mutants or production strains suitable for the production of L-serine are Corynebacterium glutamicum ATCC 21586, Corynebacterium glutamicum KY 10150 and Brevibacterium ketoglutamicum ATCC 21222. The present invention is characterized in more detail by stating the aforementioned bacterial strains; this is not limiting, however.
According to the invention, an isolated nucleic acid or an isolated nucleic acid fragment means an RNA or DNA polymer which may be single- or double-stranded and which may contain natural, chemically synthesized, modified or artificial nucleotides. In this connection, the term DNA polymer also includes genomic DNA, cDNA or mixtures thereof.
In accordance with the invention, alleles mean functionally equivalent, i.e. essentially identically acting, nucleotide sequences. Functionally equivalent sequences are those sequences which, despite a deviating nucleotide sequence, still have the desired functions, for example due to the degeneracy of the genetic code. Functional equivalents thus comprise naturally occurring variants of the sequences described herein and also artificial nucleotide sequences which have been obtained, for example, by chemical synthesis and, where appropriate, have been adapted to the codon usage of the host organism. In addition, functionally equivalent sequences comprise those which have a modified nucleotide sequence which imparts to the enzyme, for example, an insensitivity or resistance to inhibitors.
A functional equivalent means in particular also natural or artificial mutations of an originally isolated sequence which continue to display the desired function. Mutations comprise substitutions, additions, deletions, exchanges or insertions of one or more nucleotide residues.
“Sense mutations” which can lead at the protein level, for example, to the exchange of conserved amino acids but which do not result in any fundamental change in the activity of the protein and are thus functionally neutral are also included here. This also includes modifications of the nucleotide sequence which, at the protein level, relate to the N- or C-terminus of a protein but which do not substantially impair the function of the protein. These modifications may even have a stabilizing influence on the structure of the protein.
Furthermore, the present invention also includes, for example, those nucleotide sequences which are obtained by modification of the nucleotide sequence, resulting in corresponding derivatives. The aim of such a modification may be, for example, a further narrowing-down of the coding sequence contained therein or else, for example, the introduction of further restriction enzyme cleavage sites. Functional equivalents are also those variants whose function is reduced or increased, compared with the starting gene or gene fragment.
Moreover, the present invention relates to artificial DNA sequences, as long as they provide for the desired properties, as described above. Such artificial DNA sequences may be determined, for example, by back-translating proteins which have been produced by means of computer programs (molecular modeling) or by in-vitro selection. Coding DNA sequences which have been obtained by back-translating a polypeptide sequence according to the host-specific codon usage are particularly suitable. The specific codon usage can be readily determined by a skilled worker familiar with molecular genetic methods by using computer analysis of other, already known genes of the organism to be transformed.
According to the invention, homologous sequences are to be considered those which are complementary to the nucleotide sequences of the invention and/or hybridized to these nucleotide sequences. The term hybridizing sequences includes according to the invention substantially similar nucleotide sequences of the group comprising DNA and RNA, which specifically interact with (bind to) the aforementioned nucleotide sequences under stringent conditions known per se. This also includes short nucleotide sequences of, for example, from 10 to 30, preferably 12 to 15, nucleotides in length. According to the invention, this also includes, inter alia, “primers” or “probes”.
The invention also includes the sequence regions 5′ upstream and/or the sequence regions 3′ downstream of the coding regions (structural genes). This includes in particular sequence regions having a regulatory function. They can influence transcription, RNA stability or RNA processing and translation. Examples of regulatory sequences are, inter alia, promoters, enhancers, operators, terminators and translation enhancers.
The present invention further relates to a gene structure comprising at least one of the above-described nucleotide sequences coding for a phosphoserine phosphatase, a phosphoserine aminotransferase and/or an L-threonine export carrier and also to regulatory sequences operatively linked thereto, which control expression of the coding sequences in the host cell.
An operative linkage means the sequential arrangement of, for example, promoter, coding sequence, terminator and, where appropriate, further regulatory elements such that each of the regulatory elements can carry out properly its function during expression of the coding sequence. These regulatory nucleotide sequences may be of natural origin or obtained by chemical synthesis. A suitable promoter is in principle any promoter which is capable of controlling gene expression in the appropriate host organism. According to the invention, this promoter may also be a chemically inducible promoter which makes it possible to control expression of the genes controlled by said promoter in the host cell at a particular time. An example which may be mentioned here is a promoter inducible by IPTG (isopropyl-β-thiogalactoside) (Eikmanns, B. J. et al., 1991, Gene, 102: 93–98).
A gene structure is prepared by fusing a suitable promoter to at least one nucleotide sequence of the invention according to recombination and cloning techniques as are described, for example, in T. Maniatis, E. F. Fritsch and J. Sambrook, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989).
The DNA fragments may be linked to one another by attaching adapters or linkers to the fragments.
In addition, the present invention relates to a vector comprising at least one nucleotide sequence of the above-described type, coding for a phosphoserine phosphatase, a phosphoserine aminotransferase and/or an L-threonine export carrier, to regulatory nucleotide sequences operatively linked thereto and to additional nucleotide sequences for the selection of transformed host cells, for replication within the host cell or for integration into the corresponding host-cell genome. The vector of the invention may further comprise a gene structure of the abovementioned type.
Suitable vectors are those which are replicated in coryneform bacteria (Process Biochem 33 (1998) 147–161). Numerous known plasmid vectors such as, for example, pZ1 (Menkel et al., Applied and Environmental Microbiology (1989) 64: 549–554), pEKEx1 (Eikmanns et al., Gene 102: 93–98 (1991)) or pHS2–1 (Sonnen et al., Gene 107: 69–74 (1991)) are based on the cryptic plasmids pHM1519, pBL1 or pGA1. Other plasmid vectors such as, for example, those based on pCG4 (U.S. Pat. No. 4,489,160), or pNG2 (Serwold-Davis et al., FEMS Microbiology Letters 66, 119–124 (1990)), or pAG1 (U.S. Pat. No. 5,158,891), may be used in the same way. However, the present invention is not limited by this list.
It is possible, by utilizing the nucleic acid sequences according to the SEQ ID No. 1, 3, 5, 7, 9 or 11 to synthesize appropriate probes or else primers and to use them, for example with the aid of the PCR technique, to amplify and isolate analogous genes from other microorganisms, preferably coryneform bacteria.
The present invention therefore also relates to a probe for identifying and/or isolating genes coding for proteins involved in the biosynthesis of L-serine or in the export of L-threonine and/or L-serine, said probe being prepared starting from the nucleic acid sequences of the above-described type and containing a label suitable for detection. The probe may be a part section of the sequence of the invention, for example from a conserved region, which is, for example, from 10 to 30 or preferably 12 to 15 nucleotides in length and which can hybridize specifically to homologous nucleotide sequences under stringent conditions. Numerous suitable labels are known from the literature.
Relevant instructions can be found by the skilled worker, inter alia, in the manual by Gait: Oligonucleotide synthesis: a practical approach (IRL Press, Oxford, UK, 1984) and in Newton and Graham: PCR (Spektrum Akademischer Verlag, Heidelberg, Germany, 1994), for example, or in the manual “The DIG System Users Guide for Filter Hybridization” from Roche Diagnostics (Mannheim, Germany) and in Liebl et al., (International Journal of Systematic Bacteriology (1991) 41: 255–260), for example.
The present invention further relates to a phosphoserine phosphatase or a part thereof encoded by a nucleic acid sequence selected from the sequences according to the SEQ ID No. 1 or 5 or variations thereof of the above-described type. The present invention likewise comprises a phosphoserine phosphatase having an amino acid sequence selected from the sequences according to the SEQ ID No. 2 or 6 or a modified form of these polypeptide sequences or isoforms thereof or mixtures thereof.
The invention likewise comprises a phosphoserine aminotransferase or a part thereof encoded by a nucleic acid sequence selected from the sequences according to the SEQ ID No. 3 or 7 or variations thereof of the above-described type. The present invention likewise relates to a phosphoserine phosphatase having an amino acid sequence selected from the sequences according to the SEQ ID No. 4 or 8 or a modified form of these polypeptide sequences or isoforms thereof or mixtures thereof.
The present invention also includes the use of the L-threonine export carrier having an amino acid sequence selected from the sequences according to SEQ ID No. 10 or 12 or a modified form of these polypeptide sequences or isoforms thereof or mixtures thereof, said carrier also mediating L-serine transport and being encoded by a nucleic acid sequence selected from the sequences according to SEQ ID No. 9 or 11 or variations thereof.
The polypeptides of the invention are further distinguished by the fact that they originate from coryneform bacteria, preferably of the genus Corynebacterium or Brevibacterium, particularly preferably of the species Corynebacterium glutamicum or Brevibacterium flavum. 
Isoforms mean enzymes which have identical or comparable substrate and action specificities but which have a different primary structure.
According to the invention, modified forms mean enzymes which contain changes in the sequence, for example at the N- and/or C-terminus of the polypeptide or in the region of conserved amino acids, but whose function is not impaired. These modifications may be carried out in the form of amino acid exchanges according to methods known per se.
A particular embodiment of the present invention comprises variants of the polypeptides of the invention, whose activity, compared to the particular starting protein, is reduced or increased, for example by amino acid exchanges. The same is true for the stability of the enzymes of the invention in the cells, which are, for example, susceptible to degradation by proteases in an increased or reduced manner.
The present invention further relates to polypeptides having the function of a phosphoserine phosphatase or phosphoserine aminotransferase, whose amino acid sequence has been modified such that they are insensitive to regulatory compounds, for example the final metabolic products regulating their activity (feedback insensitive).
The present invention further relates to the transfer of at least one of the nucleic acid sequences or a part thereof coding for a phosphoserine phosphatase or phosphoserine aminotransferase, an allele, homolog or derivative thereof according to SEQ ID No. 1, 3, 5 or 7 and of a nucleic acid sequence coding for an L-threonine export carrier, an allele, homolog or derivative thereof according to SEQ ID No. 9 or 11 into a homologous host system. This also includes the transfer of an above-described gene construct or vector into a homologous host system. This DNA transfer into a host cell is carried out using genetic engineering methods. A preferred method which may be mentioned here is transformation and, particularly preferably, the transfer of DNA by electroporation.
A homologous host system means microorganisms which all belong to a related family. According to the invention, this means coryneform bacteria into which the nucleic acids isolated from coryneform bacteria according to the invention are introduced. A transformed microorganism resulting from a successfully carried out nucleic acid transfer thus differs from the correspondingly untransformed microorganism by containing additional nucleic acids of the type of the invention and by being able to express them accordingly. A representative for a suitable homologous host system, which may be mentioned, is the bacterium Corynebacterium glutamicum, preferably the strain ATCC 13032, which can be cultured under standard conditions as follows:
Culturing is carried out in 500 ml shaker flasks at 120 rpm and 30° C., using 50 ml of culture medium per flask. The culture medium is inoculated by adding a bacterial (pre)culture of the strain Corynebacterium glutamicum ATCC 13032 which has been grown earlier under identical conditions over a period of 12–16 hours, the inoculated culture medium having an optical density in the range from 0.7 to 1.5.
Depending on the requirements, a suitable culture medium is a complex medium such as, for example, LB medium (T. Maniatis, E. F. Fritsch and J. Sambrook, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989)) or else a mineral salt medium such as, for example, CGXII medium (Keilhauer, C. et al., 1993, J. Bacteriol., 175: 5593–5603). After appropriate culturing, the bacterial suspension can be harvested and used for further studies, for example for transformation or isolation of nucleic acids according to common methods.
This procedure may also be applied in a similar way to other strains of coryneform bacteria. The preferred host systems are bacteria of the genus Corynebacterium or Brevibacterium. Within the genus Corynebacterium, particular preference is given to the species Corynebacterium glutamicum, and within the genus Brevibacterium, particular preference is given to the species Brevibacterium flavum. Representatives of these genera include on the one hand strains which have been characterized through their properties as wild type. Examples which may be mentioned here are Corynebacterium glutamicum ATCC 13032, Corynebacterium glutamicum ATCC 14752, Corynebacterium acetoglutamicum ATCC 15806, Corynebacterium acetoglutamicum ATCC 15806, Corynebacterium melassecola ATCC 17965, Corynebacterium thermoaminogenes FERM BP-1539, Brevibacterium flavum ATCC 14067, Brevibacterium lactofermentum ATCC 13869 and Brevibacterium divaricatum ATCC 14020.
In addition, the present invention also includes bacterial strains which are distinguished as L-serine-producing mutants or production strains. These may be prepared, for example starting from wild-type strains, by classical (chemical or physical) or genetic methods. Examples of strains suitable according to the invention are, inter alia, Corynebacterium glutamicum ATCC 21586, Corynebacterium glutamicum KY 10150 and Brevibacterium ketoglutamicum ATCC 21222. The selected examples of microorganisms characterize the present invention in more detail without limiting it.
The invention includes, besides the above-described bacterial strains which are distinguished as L-serine producers, also those production strains which have improved secretion of the desired metabolic products, preferably of L-amino acids, from the cells into the culture medium. This improved secretion may be achieved, for example, by overexpressing one or more genes coding for membrane transport proteins, for example export carrier proteins, inter alia specific L-amino-acid export carrier proteins.
In a particular embodiment of the present invention, the bacterial strain used for the production of L-serine is distinguished in that it is a genetically modified microorganism containing, in a replicable form, a nucleic acid coding for a phosphoserine phosphatase (serB) and/or a nucleic acid coding for a phosphoserine aminotransferase (serC) according to SEQ ID No. 1, 3, 5 or 7 and a nucleic acid coding for the L-threonine export carrier (thrE) according to SEQ ID No. 9 or 11, whose expression is enhanced and/or whose copy number is increased, compared to the correspondingly genetically unmodified microorganism.
The invention likewise comprises a genetically modified microorganism which contains polypeptides encoded by the genes serB and/or serC according to SEQ ID No. 2, 4, 6 or 8 and thrE according to SEQ ID No. 10 or 12, which have an increased activity and/or lifespan and/or a reduced final-product inhibition compared to the correspondingly genetically unmodified microorganism. Thus, the present invention likewise relates to a genetically modified microorganism which has at least an increased rate of production of L-serine and additionally an increased rate of secretion of L-serine and/or L-threonine.
The present invention likewise comprises a genetically modified microorganism containing, in a replicable form, a gene structure or a vector of the above-described type. A microorganism genetically modified according to the invention is further distinguished in that it is a coryneform bacterium, preferably of the genus Corynebacterium or Brevibacterium, particularly preferably of the species Corynebacterium glutamicum or Brevibacterium flavum. 
In principle, it is possible to amplify genes by methods known per se, such as, for example, the polymerase chain reaction (PCR) with the aid of short synthetic nucleotide sequences (primers), and then isolate them. The primers used are prepared in general on the basis of known gene sequences, due to existing homologies in conserved regions of the genes, and/or by taking into account the GC content of the DNA of the microorganism to be studied. However, this method has a number of disadvantages which are, for example, due to the defectiveness of the PCR method itself or to the fact that the gene sequences to be identified are less homologous to the already known sequences than assumed. This may cause the primers used to bind unspecifically or even fail to bind to the nucleic acid sequence to be studied.
Another procedure for isolating coding nucleotide sequences is complementation of “defective” mutants of the organism to be studied, which have at least phenotypically a functionally reduced activity of the gene to be studied or of the corresponding protein. Complementation means the removal of the genetic defect of the mutant and substantial restoration of the original phenotype prior to mutagenesis, which is achieved by introducing functional genes or gene fragments from the microorganism to be studied.
An example of a classical mutagenesis method for producing defective mutants is the treatment of bacterial cells with chemicals such as, for example, N-methyl-N-nitro-N-nitrosoguanidine or UV radiation. Such methods for causing mutations are generally known and can be found, inter alia, in Miller (A Short Course in Bacterial Genetics, A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria (Cold Spring Harbor Laboratory Press, 1992)) or in the “Manual of Methods for General Bacteriology” of the American Society for Bacteriology (Washington D.C., USA, 1981). Disadvantages here are a time-consuming and costly selection of mutants having the desired phenotype and the fact that the isolated mutants are genetically undefined, since the mutagenesis has been random. The latter frequently leads to unexpected problems, for example with respect to the stability of these mutants during a large-scale production process.
It is another object of the present invention to provide a method for isolating coding nucleic acid sequences from coryneform bacteria, which no longer has the disadvantages mentioned. The following description illustrates in more detail how the object is achieved according to the invention.
The invention relates to a method for isolating the nucleic acids of the invention, generating a coryneform bacterium whose genes serB and serC contain defects generated by transposon mutagenesis.
The method of transposon mutagenesis makes use of the property of a transposon which is capable of “jumping” into DNA sequences and thereby interfering with or eliminating the function of the gene in question.
Examples of transposons of coryneform bacteria are listed below. Thus the erythromycin-resistance transposon Tn5432 (Tauch et al., Plasmid (1995) 33: 168–179) and the chloroamphenicol-resistance transposon Tn5546 were isolated from the Corynebacterium xerosis strain M82B. Tauch et al. (Plasmid (1995) 34: 119–131 and Plasmid (1998) 40: 126–139) showed that it is possible to carry out a mutagenesis using these transposons. Furthermore, the insertion sequence IS31831 was isolated from Corynebacterium glutamicum ATCC 31831 (Vertes et al., Molecular Microbiology (1994) 11: 739–746). The artificial transposon Tn31831 was constructed by combining IS31831 with the kanamycin-resistance gene aphA (Vertes et al., Molecular and General Genetics (1994) 245: 397–405). Vertes et al. (Molecular and General Genetics (1994) 245: 397–405) and Jaeger et al. (FEMS Microbiology Letters (1995) 126: 1–6) demonstrated the application of these transposons in the strains Brevibacterium flavum MJ233C and Corynebacterium glutamicum ATCC 13058.
Another transposon is the transposon Tn5531 which is described in Ankri et al. (Journal of Bacteriology (1996) 178: 4412–4419) and used by way of example during the course of the present invention. To this end, in a particular embodiment of the present invention, the Corynebacterium glutamicum strain ATCC 14752 is subjected to an appropriate mutagenesis. Optionally it is also possible to use the Corynebacterium glutamicum strain ATCC 13032. The transposon Tn5531 contains the aph3 kanamycin-resistance gene and can be administered in the form of the plasmid vector pCGL0040 (FIG. 1). The nucleotide sequence of the transposon Tn5531 is freely available under accession number U53587 at the National Center for Biotechnology Information (NCBI, Bethesda, Md., USA). Listing the aforementioned transposons characterizes the present invention in more detail without limiting it.
Following transposon mutagenesis, a mutant defective in the desired gene(s) is selected. According to the invention, a mutant defective in the serB and/or serC genes is recognized by growing well on minimal medium containing L-serine but growing poorly on minimal medium without L-serine.
The appropriately selected defective mutants of strains of coryneform bacteria are then used for cloning and sequencing the serB and serC genes.
The genes may be cloned, for example, by complementing the defective mutants. To this end, a gene library of the DNA of the coryneform bacterium to be studied is generated. The generating of gene libraries is described in generally known textbooks and manuals. Examples which may be mentioned are the textbook by Winnacker: Gene und Klone, Eine Einfuhrung in die Gentechnologie (Verlag Chemie, Weinheim, Germany, 1990) and the manual by Sambrook et al.: Molecular Cloning, A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1989). Bathe et al. (Molecular and General Genetics, 252: 255–265, 1996) describe a Corynebacterium glutamicum ATCC 13032 gene library which was generated with the aid of the cosmid vector SuperCos I (Wahl et al., 1987, Proceedings of the National Academy of Sciences USA, 84: 2160–2164) in the E. coli K-12 strain NM554 (Raleigh et al., 1988, Nucleic Acids Research 16: 1563–1575). Vectors suitable according to the invention are those replicating in coryneform bacteria, preferably Corynebacterium glutamicum. Vectors of this kind are known in the art. An example which may be mentioned is the plasmid vector pZ1 described in Menkel et al. (Applied and Environmental Microbiology (1989) 64: 549–554).
The gene library is then transferred into the above-described bacterial strain having a defective serB or serC gene by means of transformation, according to the invention preferably by electroporation. Using methods known per se, those transformed bacteria are selected, which have the ability to grow on minimal medium in the absence of L-serine. The DNA fragments of the originally used gene library are re-isolated from said selected transformants and can then be subjected to a sequence analysis.
In another embodiment of the present invention, it is possible, due to the defective mutants of a coryneform bacterium generated by mutagenesis using the transposon Tn5531, such as, for example, the strains ATCC 14752serB::Tn5531 and ATCC 14752serC::Tn5531, to clone and isolate the serB::Tn5531 allele and the serC::Tn5531 allele, respectively, directly by utilizing the kanamycin-resistance gene aph3 contained in the transposon. To this end, known cloning vectors such as, for example, pUC18 (Norrander et al., Gene (1983) 26: 101–106 and Yanisch-Perron et al., Gene (1985) 33: 103–119) or pGEM-T (Zhou M-Y, Clark S E and Gomez-Sanchez C E (1995) BioTechniques 19: 34; Kobs G (1995) Promega Notes 55: 28; Promega Cooperation, Madison, USA), are used. Host systems suitable for cloning are in particular those Escherichia coli strains which are restriction and recombination defective. An example of these is the strain DH5αmcr which has been described by Grant et al. (Proceedings of the National Academy of Sciences USA, 87 (1990) 4645–4649). Transformants are selected in the presence of kanamycin.
The DNA isolated from the transformants obtained, which contains the genes of interest, is then sequenced. To this end, the dideoxy chain termination method described by Sanger et al. (Proceedings of the National Academy of Sciences of the United States of America USA (1977) 74: 5463–5467) can be employed. Thereafter, the genes present upstream and downstream of the Tn5531 insertion site are obtained. The nucleotide sequences obtained are then analyzed and assembled using commercially available sequence analysis programs such as, for example, the Laser gene program package (Biocomputing Software for Windows, DNASTAR, Madison, USA) or the HUSAR program package (Release 4.0, EMBL, Heidelberg, Germany). The inventive nucleic acids of the serB and serC genes of coryneform bacteria were isolated and their sequences were determined in the manner described above.
Surprisingly, homology comparisons with known sequences revealed that the serB-encoded polypeptide is moderately similar to Escherichia coli phosphoserine phosphatase, while the polypeptide derived from serC has only low, albeit significant, similarity to Escherichia coli phosophoserine aminotransferase. Likewise, the corynebacterial genes found have only low to moderate similarities to known phosphoserine phosphatases and phosphoserine aminotransferases from other organisms (e.g. yeast). Only the polypeptide sequences derived from the putative Mycobacterium tuberculosis serB and serC genes display high similarity to the corynebacterial proteins. Table 2 depicts the result of such a homology comparison. In addition, the nucleotide sequence of the coryneform genes reveals that the PCR primers used in EP 0 931 833, although suitable for amplifying the Escherichia coli genes, are unsuitable for isolating the coryneform serB and serC genes, due to said low sequence similarity.
This once more elucidates the advantage of the inventive method of transposon mutagenesis for cloning the genes serB and serC from coryneform bacteria.
The present invention additionally relates to a method for the microbial production of L-serine, in which at least one of the nucleic acids of the invention, isolated from a coryneform bacterium, is transferred into a homologous microorganism and expressed there, with gene expression and/or activity of the correspondingly encoded polypeptide being increased compared to the correspondingly genetically unmodified microorganism, this genetically modified microorganism is used for the fermentative production of L-serine and the L-serine formed accordingly is isolated from the culture medium.
Another variant of the present invention comprises a method for the improved microbial production of L-serine, in which

    
    
        a) at least one nucleic acid coding for a phosphoserine phosphatase (serB) and/or phosphoserine aminotransferase (serC) according to SEQ ID No. 1, 3, 5 and/or 7 and a nucleic acid according to SEQ ID No. 9 or 11 or alleles thereof or derivatives therefrom, isolated from a coryneform bacterium, are transferred into a homologous microorganism and expressed therein, and expression and/or lifespan of the nucleic acids and/or activity and/or lifespan of the correspondingly encoded polypeptides are increased compared to the correspondingly genetically unmodified microorganism,
        b) this genetically modified microorganism from step a) is used for the fermentative production of L-serine, L-serine being increasingly secreted into the culture medium, and
        c) the L-serine correspondingly formed is isolated from the culture medium.
    
    


Key to the sequence listing, figures and tables
Sequence listing:
Representation of the nucleic acid sequences containing the genes serB (SEQ ID No. 1), serC (SEQ ID No. 3) and thrE (SEQ ID No. 9) and of the amino acid sequences derived therefrom, SerB (SEQ ID No. 2), SerC (SEQ ID No. 4) and ThrE (SEQ ID No. 10) from Corynebacterium glutamicum ATCC 14752 and Corynebacterium glutamicum ATCC 13032 (corresponding to SEQ ID No. 5, 7, 6, 8, 11 and 12).



BRIEF DESCRIPTION OF THE DRAWINGS AND THE TABLES
FIG. 1: Schematic representation of the vector pCGLO04O
The meaning of the abbreviations used is as follows:

    Amp=β-lactamase gene which imparts resistance to ampicillin
    Kan=phosphotransferase gene which imparts resistance to kanamycin


Cleavage sites of restriction endonucleases are also indicated.
FIG. 2: Schematic representation of the vector pVWEx1serB
The meaning of the abbreviations used is as follows:

    Kan=phosphotransferase gene which imparts resistance to kanamycin
    lacIq=quantitatively expressed repressor of the E. coil lactose operon
    Ptac=IPTG-inducible artificial promoter composed of the trp promoter and the lac promoter of E. coil 


Cleavage sites of restriction endonucleases are also indicated
FIG. 3: Schematic representation of the vector pVWEx1serC-1
The meaning of the abbreviations used is as follows:

    Kan=phosphotransferase gene which imparts resistance to kanamycin
    Tet=tetα1 gene of plasmid pHY163PLK (Ishiwa & Shibahara, 1985, Jpn. J. Cenet., 60: 485–498), which imparts resistance to tetracycline
    lacIq=quantitatively expressed repressor of the E. coil lactose operon
    ptac=IPTO-inducible artificial promoter composed of the trp promoter and the lac promoter of E. coli 


Cleavage sites of restriction endonucleases are also indicated

    Table 1: Composition of the CGXII mineral-salt medium for culturing coryneform bacteria
    Table 2: Comparison of the similarities of phosphoserine aminotransferase (PSAT; serC) and phosphoserine phosphatase (PSP; serB) of Corynebacterium giutamicum to known phosphoserine aminotransferases and phosphoserme phosphatases of other organisms
    Table 3: Comparative overview of the accumulation of L-serine in the culture supernatant of Corynebacterium giutamicum wild type ATCC 13032 and of the Corynebacterium giutamicum strains ATCC 13032(pVWEX1), ATCC 13032(pVWEX1serB) and ATCC 13032(pVWEX2serC) transformed with the corresponding plasmids


In order to achieve an increased gene expression (overexpression) in a genetically engineered organism, the copy number of the appropriate genes may be increased. Furthermore, the promoter and/or regulatory regions and/or the ribosomal binding site which is located upstream of the structural gene can be modified accordingly so that the rate of expression is increased. Expression cassettes which are incorporated upstream of the structural gene act in a similar way. Additionally, inducible promoters make it possible to increase expression during the course of the fermentative production of L-serine. Expression is likewise improved by measures to extend the lifespan of the mRNA. The genes or gene constructs may be either present in plasmids with varying copy number or integrated and amplified in the chromosome. Furthermore, the enzyme activity itself may be increased or enhanced by preventing degradation of the enzyme protein. As an alternative, it is further possible to achieve overexpression of the relevant genes by modifying the medium composition and management of the culture.
Instructions for this can be found by the skilled worker, inter alia, in Martin et al., (Bio/Technology 5, 137–146 (1987)), in Guerrero et al. (Gene 138, 35–41 (1994)), Tsuchiya and Morinaga (Bio/Technology 6, 428–430 (1988)), in Eikmanns et al. (Gene 102, 93–98 (1991)), in the European patent EPS 0 472 869, in U.S. Pat. No. 4,601,893, in Schwarzer and Pühler (Bio/Technology 9, 84–87 (1991), in Reinscheid et al. (Applied and Environmental Microbiology 60, 126–132 (1994)), in LaBarre et al. (Journal of Bacteriology 175, 1001–1007 (1993)), in the patent application WO 96/15246, in Malumbres et al. (Gene 134, 15–24 (1993)), in the Japanese patent JP-A-10–229891, in Jensen and Hammer (Biotechnology and Bioengineering 58, 191–195 (1998)), in Makrides (Microbiological Reviews 60: 512–538 (1996)) and in well-known textbooks of genetics and molecular biology.
The genetically modified microorganisms prepared according to the invention may be cultured for the purpose of producing L-serine continuously or in a batch process or in a fed batch or repeated fed batch process. A review of known culturing methods can be found in the textbook by Chmiel (Bioprozesstechnik 1. Einfuhrung in die Bioverfahrenstechnik (Gustav Fischer Verlag, Stuttgart, 1991)) or in the textbook by Storhas (Bioreaktoren und periphere Einrichtungen (Vieweg Verlag, Brunswick/Wiesbaden, 1994)).
The culture medium to be used must satisfy the requirements of the particular strains in a suitable manner. The manual “Manual of Methods for General Bacteriology” of the American Society for Bacteriology (Washington D.C., USA, 1981) contains descriptions of culture media for various microorganisms. Carbon sources which may be used are sugars and carbohydrates such as, for example, glucose, sucrose, lactose, fructose, maltose, molasses, starch and cellulose, oils and fats such as, for example, soybean oil, sunflower oil, peanut oil and coconut fat, fatty acids such as, for example, palmitic acid, stearic acid and linoleic acid, alcohols such as, for example, glycerol and ethanol and organic acids such as, for example, acetic acid. These substances may be used individually or in a mixture. Nitrogen sources which may be used are compounds containing organic nitrogen, such as peptone, yeast extract, meat extract, malt extract, corn steep liquor, soybean meal and urea, or inorganic compounds such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate and ammonium nitrate. The nitrogen sources may be used individually or as a mixture. Phosphorus sources which may be used are phosphoric acid, potassium dihydrogen phosphate or dipotassium hydrogen phosphate or the corresponding sodium salts. The culture medium should furthermore contain metal salts such as, for example, magnesium sulfate or iron sulfate, which are required for growth. Finally, essential growth substances such as amino acids and vitamins may be used in addition to the abovementioned substances. Moreover, suitable precursors may be added to the culture medium. Said substances for use may be introduced into the culture in the form of a single addition or fed in a suitable manner during culturing.
The pH of the culture is controlled by using basic compounds such as sodium hydroxide, potassium hydroxide, ammonia or aqueous ammonia or acidic compounds such as phosphoric acid or sulfuric acid in a suitable manner. Foaming can be controlled by using antifoams such as, for example, fatty acid polyglycol esters. Plasmid stability can be maintained by adding to the medium suitable selectively acting substances such as, for example, antibiotics. Aerobic conditions are maintained by introducing into the culture oxygen or oxygen-containing gas mixtures such as, for example, air. The culture temperature is usually from 20° C. to 45° C. and preferably from 25° C. to 40° C. Culturing is continued until a maximum amount of L-serine has been produced. This target is usually reached within 10 to 160 hours.
L-serine formation can be analyzed via anion exchange chromatography with subsequent ninhydrin derivatization, as described in Spackman et al. (Analytical Chemistry, 30, (1958), 1190), or via reversed phase HPLC, as described in Lindroth et al. (Analytical Chemistry (1979) 51: 1167–1174).
The microorganisms which are the subject of the present invention are capable of producing L-serine from glucose, sucrose, lactose, mannose, fructose, maltose, molasses, starch, cellulose or from glycerol and ethanol. They may be the representatives of coryneform bacteria already described in detail hereinbefore.
Table 3 depicts a selection of results of the fermentation. Here, the microorganisms genetically modified in accordance with the invention are distinguished by a substantially improved production of L-serine compared to the correspondingly untransformed microorganisms (wild types) or to those microorganisms merely containing the vector without gene insert.
A particular embodiment of the present invention shows that overexpression of the homologous serB gene in C. glulamicum ATCC 13032 (13032(pVWEx1serB)) results in an at least 4-fold increase in the accumulation of L-serine in the medium in comparison with the control strains. Overexpression of the homologous serC gene (13032(pVWEx2serC)) can achieve an at least 20-fold increase in the accumulation of L-serine. A further increase in the production of L-serine can be expected from joint overexpression of both genes, serB and serC, in a homologous system.
In this connection, the fact that the increase in the accumulation of L-serine is achieved even by using the Corynebacterium glutamicum ATCC 13032 wild type is especially remarkable. The use according to the invention of a homologous amino-acid production strain may thus attain a still further increased production of L-serine.
Amino-acid production strains mean in accordance with the present invention Corynebacterium glutamicum strains or homologous microorganisms which have been modified by classical and/or molecular genetic methods such that their metabolic flow flows increasingly in the direction of biosynthesis of amino acids or derivatives thereof (metabolic engineering). These amino-acid production strains contain, for example, one or more genes and/or the corresponding enzymes which are in key positions of the metabolic pathway, which are crucial and, accordingly, regulated in a complex manner (bottle neck), and whose regulation has been modified or which are even deregulated. In this connection, the present invention comprises all already known amino-acid production strains, preferably of the genus Corynebacterium or of homologous organisms. Furthermore, the invention also comprises those production strains which can be prepared by the skilled worker using common methods and according to findings in other microorganisms, for example enterobacteria, bacillaceae or yeast species.
Furthermore, the invention also comprises those amino-acid production strains in which L-serine degradation has been modified, preferably reduced. This may be carried out, for example, by specific genetic modifications of L-serine-degrading enzymes or of the corresponding genes.
According to the invention, the yield of L-serine in the final product is further improved by considerably improving L-serine export out of the cells into the surrounding medium. According to the invention, this is achieved by increased expression of the L-threonine export carrier which, surprisingly, also transports, inter alia, the L-serine formed actively via the cell membrane. This increases the L-serine content in the culture medium still further and results in a final product of considerably improved quality compared to hitherto known products.
The present invention also comprises bacterial strains which, in addition to the advantageous properties regarding the production of L-serine, have an improved ability to export L-serine out of the cells into the culture medium. In this connection, preference is given to bacteria having an increased content of membrane transport proteins such as, for example, an L-amino acid-specific export carrier, in particular the L-threonine export carrier.
The present invention further relates to the use of a genetically modified microorganism of the above-described type for the production of L-serine and/or secondary products thereof according to a method of the type described at the beginning.
The present invention further relates to the use of the L-amino acids prepared in the above-described manner for use in the food, animal feed and/or pharmaceutical industries or in human medicine. In addition, the amino acid L-serine prepared according to the invention can be used as a precursor for the synthesis of L-glycine, L-cysteine and/or L-tryptophan and/or of metabolic products derivable therefrom.



EXAMPLES
The examples below illustrate the present invention in more detail but are not limiting:
General Techniques:
Isolation of plasmid DNA from Escherichia coli and all techniques regarding restriction, Klenow treatment and alkaline phosphatase treatment were carried out according to Sambrook et al. (Molecular cloning. A laboratory manual (1989) Cold Spring Harbor Laboratory Press). Escherichia coli were transformed according to Chung et al. (Proceedings of the National Academy of Sciences of the United States of America USA (1989) 86: 2172–2175), unless described otherwise.
Cloning and Sequencing of the Corynebacterium glutamicum ATCC 14752 serB and serC Genes
1. Transposon Mutagenesis
The Corynebacterium glutamicum strain ATCC 14752 was subjected to a mutagenesis using the transposon Tn5531 whose sequence has been deposited under accession number U53587 in the nucleotide database of the National Center for Biotechnology Information (Bethesda, USA). The plasmid pCGL0040 which contains the assembled transposon Tn5531 (Ankri et al., Journal of Bacteriology (1996) 178: 4412–4419) was isolated from the methylase-defective Escherichia coli strain GM2929pCGL0040 (Escherichia coli GM2929: Palmer et al., Gene (1994) 143: 1–12). The Corynebacterium glutamicum strain ATCC 14752 was transformed with the plasmid pCGL0040 by means of electroporation (Haynes et al., FEMS Microbiology Letters (1989) 61: 329–334). Clones which had the transposon Tn5531 integrated into their genome were identified on the basis of their resistance to kanamycin on LBHIS agar plates containing 15 μg/ml kanamycin (Liebl et al., FEMS Microbiology Letters (1989) 65: 299–304). In this manner, 1800 clones were obtained which were tested for delayed growth in the presence of seryl-alanine. For this purpose, all clones were transferred individually to CGXII minimal medium agar plates with and without 2 mM seryl-alanine. The medium was identical to the CGXII medium described in Keilhauer et al. (Journal of Bacteriology (1993) 175: 5593–5603) but contained additionally 25 μg/ml kanamycin and 15 g/l agar. Table 1 depicts the composition of the medium described by Keilhauer et al.
The agar plates were incubated at 30° C. and growth was examined after 12, 18 and 24 hours. Two transposon mutants were obtained which grew in the presence of seryl-alanine in a manner comparable to the starting strain Corynebacterium glutamicum ATCC 14752 but which showed no growth in the absence of seryl-alanine. The mutants also grew in the presence of serine alone, proving that they are serine-auxotrophic mutants which must have a defect in serine metabolism. These mutants were referred to as ATCC 14752ser1::Tn5531 and ATCC 14752ser2::Tn5531.
2. Cloning and Sequencing of the Tn5531 Insertion Sites in ATCC 14752ser1::Tn5531 and ATCC 14752ser2::Tn5531
In order to clone the insertion sites in the mutants described, which are located upstream of the transposon Tn5531, first the chromosomal DNA of these mutant strains was isolated as described in Schwarzer et al. (Bio/Technology (1990) 9: 84–87) and 400 ng thereof were cleaved using the restriction endonuclease XbaI. The entire restriction mixture was ligated into the pUC18 vector (Norander et al., Gene (1983) 26: 101–106) from Roche Diagnostics (Mannheim, Germany), which had likewise been linearized using XbaI. The entire ligation mixture was used to transform the Escherichia coli strain DH5αmcr (Grant et al., Proceedings of the National Academy of Sciences of the United States of America USA (1990) 87: 4645–4649) by means of electroporation (Dower et al., Nucleic Acid Research (1988) 16: 6127–6145). Transformants which contained the cloned transposon Tn5531 insertion sites on the pUC18 vector were identified on the basis of their resistance to carbenicillin and kanamycin on LB agar plates containing 50 μg/ml carbenicillin and 25 μg/ml kanamycin. Plasmids were prepared in each case from three transformants and the sizes of the cloned inserts were determined by restriction analysis. The nucleotide sequences of the insertion sites on the plasmids, which contained an approx. 10 kb insert in the case of ser1::Tn5531 and a 4.5 kb insert in the case of ser2::Tn5531, were determined according to the dideoxy chain termination method of Sanger et al. (Proceedings of the National Academy of Sciences of the United States of America USA (1977) 74: 5463–5467). To this end, first in each case approx. 600 bp of the two inserts were sequenced, starting from the following oligonucleotide primer: SEQ ID NO. 13: 5′-CGG GTC TAC ACC GCT AGC CCA GG-3′. Sequence extensions were then carried out in each case by means of primer walking so that it was possible to sequence in total approx. 1.4 kb of the ser1::Tn5531 insert and 1.2 kb of the ser2::Tn5531 insert, respectively. The Laser gene program package (Biocomputing Software for Windows, DNASTAR, Madison, USA) analysis revealed that in both cases the transposon had been inserted into the start of an open reading frame.
The insertion sites located downstream of the transposon were identified by cleaving the chromosomal DNA of the mutants with the restriction endonuclease EcoRI followed by ligation into the EcoRI-linearized pUC18 vector. Further cloning was carried out as described above. The nucleotide sequences of the insertion sites on one of the plasmids having an approx. 6.5 kb insert starting from ser1::Tn5531 and, respectively, on one of the plasmids having an approx. 5.0 kb insert starting from ser2::Tn5531 were determined according to the dideoxy chain termination method of Sanger et al. (Proceedings of the National Academy of Sciences of the United States of America USA (1977) 74: 5463–5467). To this end, approx. 400 bp of the ser1::TN5531 insert and approx. 220 bp of the ser2::Tn5531 insert, respectively, were sequenced starting from the following oligonucleotide primer: SEQ ID NO. 14: 5′-CGG TGC CTT ATC CAT TCA GG-3′.
The nucleotide sequences obtained were analyzed and assembled using the Laser gene program package (Biocomputing Software for Windows, DNASTAR, Madison, USA). The nucleotide sequences are depicted as SEQ ID No. 1 and SEQ ID No. 3. The analysis identified in each case an open reading frame of 1209 bp for ser1::Tn5531, the corresponding gene being referred to as serB, and of 1128 bp for ser2::Tn5531, the corresponding gene being referred to as serC. The corresponding gene products comprise 403 and 376 amino acids, respectively, and are depicted as SEQ ID No. 2 and SEQ ID No. 4, respectively.
Cloning and Sequencing of the serB and serC Genes from Corynebacterium glutamicum ATCC 13032
The genes serB and serC were cloned into the Escherichia coli cloning vector pGEM-T (Zhou M-Y, Clark S E and Gomez-Sanchez C E (1995) BioTechniques 19: 34; Kobs G (1995) Promega Notes 55: 28; Promega Cooperation, Madison, USA). Cloning was carried out in two steps. First, the genes from Corynebacterium glutamicum ATCC 13032 were in each case amplified using a polymerase chain reaction (PCR) by means of the following oligonucleotide primers derived from SEQ ID No. 1 and SEQ ID No. 3, respectively.







serB-forward:


SEQ ID NO. 15: 5′-GCAGAGGCACACACTGGAC-3′


 


serB-reverse:


SEQ ID NO. 16: 5′-CTTGAGGAGGAGGTGGGC-3′


 


serC-forward:


SEQ ID NO. 17: 5′-CATCGTTTGGGAGACTGCG-3′


 


serC-reverse:


SEQ ID NO. 18: 5′-CGTACTGGTGTAACTGTACGGG-3′.






The PCR reaction was carried out in 30 cycles in the presence of 200 μM deoxynucleotide triphosphates (dATP, dCTP, dGTP, dTTP), in each case 1 μM of the appropriate oligonucleotide, 100 ng of chromosomal DNA from Corynebacterium glutamicum ATCC 13032, 1/10 volume of 10 times reaction buffer and 2.6 units of a heat-stable Taq/Pwo DNA polymerase mixture (Expand High Fidelity PCR System from Roche Diagnostics, Mannheim, Germany) in a thermocycler (PTC-100, MJ Research, Inc., Watertown, USA) under the following conditions: 94° C. for 60 seconds, 56° C. for 90 seconds and 72° C. for 2 minutes.
The amplified, about 1.7 kb sized serB fragment and the amplified, about 1.3 kb sized serC fragment were then ligated with the pGEM-T vector with the aid of the Promega PCR Cloning Kit according to the manufacturer's instructions. The Escherichia coli strain DH5αmcr (Grant et al., Proceedings of the National Academy of Sciences of the United States of America USA (1990) 87: 4645–4569) was transformed with both ligation mixtures. Transformants were identified on the basis of their resistance to ampicillin on LB agar plates containing 50 μg/ml ampicillin. Plasmids were prepared from in each case 10 transformants and tested for the presence of the 1.7 kb and, respectively, 1.3 kb PCR fragments as inserts by restriction analysis. The recombinant plasmids produced in this way are referred to as pGEM-TserB and pGEM-TserC below.
The nucleotide sequences of the 1.7 kb and 1.3 kb PCR fragments in plasmid pGEM-TserBexp and plasmid pGEM-TserCexp, respectively, were determined according to the dideoxy chain termination method of Sanger et al. (Proceedings of the National Academy of Sciences of the United States of America USA (1977) 74: 5463–5467). To this end, the complete inserts of pGEM-TserB and pGEM-TserC were sequenced with the aid of the following primers from Roche Diagnostics (Mannheim, Germany).







Universal primer:


SEQ ID NO. 19: 5′-GTA AAA CGA CCC CCA GT-3′


 


Reverse primer:


SEQ ID NO. 20: 5′-GGA AAC AGC TAT GAC CAT G-3′






SEQ ID No. 5 depicts the nucleotide sequence of the insert in plasmid pGEM-TserB, and SEQ ID No. 7 depicts the nucleotide sequence of the insert in plasmid pGEM-TserC. The nucleotide sequence obtained was analyzed using the Laser gene program package (Biocomputing Software for Windows, DNASTAR, Madison, USA). The analysis identified in each case an open reading frame of 1209 bp and 1128 bp in length, respectively. The corresponding genes were referred to as serB and serC. The corresponding gene products code for polypeptides of 403 and, respectively, 376 amino acids in length, which are depicted in SEQ ID No. 6 and SEQ ID No. 8, respectively.
Overexpression of the Genes for Phosphoserine Phosphatase, serB, and Phosphoserine Aminotransferase, serC
The effect of overexpressing the genes for phosphoserine phosphatase, serB, and phosphoserine aminotransferase, serC on the production of serine was studied by using the expression vectors pVWEX1 (Wendisch, V., Dissertation Heinrich-Heine Universitat, Düsseldorf, 1997; imparts a resistance to kanamycin) and pVWEX2 (Wendisch, V., PhD thesis, Heinrich-Heine Universitat, Dusseldorf, 1997; imparts a resistance to tetracycline) which allow IPTG-inducible expression (Molecular Cloning, A laboratory manual (1989) Cold Spring Harbor Laboratory Press). The serB gene was cloned into the pVWEX1 vector and the serC gene was cloned into the pVWEX2 vector, both without their respective promoters. For this purpose, the following primers were synthesized first:







serB-exp-for:


SEQ ID NO. 21: 5′-ATCTAGAATGATCACAGTGAGCCGTAAAG-3′


 


serB-exp-rev:


SEQ ID NO. 22: 5′-AGGATCCTTAGGCATTTGTCAATGGAACGC-3′


 


serC-exp-for:


SEQ ID NO. 23: 5′-AGCATGCATGCCCGAAGACATGACCG-3′


 


serC-exp-rev:


SEQ ID NO. 24: 5′-ATCTAGATTACTTCCTTGCAAAACCGC-3′






The promoterless serB gene was amplified as a 1226 bp fragment (SEQ ID No. 5, bases 382 to 1594) and the promoterless serC gene as a 1157 bp fragment (SEQ ID No. 7, bases 132 to 1261) from chromosomal DNA of Corynebacterium glutamicum ATCC 13032 by means of PCR. The primers were chosen for the primer serB-exp-for to mediate an XbaI cleavage site, for the primer serB-exp-rev to mediate a BamHI cleavage site, for the primer serC-exp-for to mediate an SphI cleavage site and for the primer serC-exp-rev to mediate an XbaI cleavage site. The isolated PCR products were, as described above, first cloned into the pGEM-T vector, resulting in the plasmids pGEM-TserB-exp and PGEM-TserC-exp. Subsequently, the promoterless serB gene was excised from the vector pGEM-TserBexp by means of XbaI-BamHI restriction digest and ligated into the pVWEX1 vector linearized correspondingly with XbaI-BamHI. After an SpeI-XbaI restriction digest, the promoterless serC gene was excised from the vector pGEM-TserBexp and ligated into the XbaI-linearized vector pVWEX2. The constructs obtained, pVWEX1serB (FIG. 2) and pVWEX2serC (FIG. 3) were tested by restriction digest.
Increased Accumulation of L-Serine by Overexpression of the Genes for Phosphoserine Phosphatase, serB and Phosphoserine Aminotransferase, serC
The plasmids pVWEX1-serB and pVWEX2-serC were introduced, in each case individually, into the wild-type strain Corynebacterium glutamicum ATCC 13032 by electroporation, resulting in the strains C. glutamicum 13032(pVWEX1serB) and C. glutamicum 13032 (pVWEX2serC). The wild-type, Corynebacterium glutamicum ATCC 13032, and the C. glutamicum strain ATCC containing the pVWEX1 vector without insert were cultured as negative controls. L-serine elimination from all of the above-mentioned strains was then determined and the results are comparatively summarized in Table 3.
For this purpose, the strains were cultivated in complex medium (2×TY; Molecular Cloning, A laboratory manual (1989) Cold Spring Harbor Laboratory Press; with 50 μg/l kanamycin, 25 μg/l tetracycline and, respectively, 50 μg/l kanamycin and 25 μg/l tetracycline), and the CGXII fermentation medium (J Bacteriol (1993) 175: 5595–5603) was inoculated, in each case separately, with the precultures. The medium additionally contained the appropriate antibiotic(s) and 200 μg/ml IPTG. After culturing on a rotary shaker at 120 revolutions per minute and at 30° C. for 24 hours, the amount of L-serine accumulated in the medium was determined. The amino-acid concentration was determined by means of high pressure liquid chromatography (J Chromat (1983) 266: 471–482).
Tables










TABLE 1







Component
Concentration




















(NH4)2SO4
20
g/l



Urea
5
g/l



KH2PO4
1
g/l



K2HPO4
1
g/l



MgSO4 × 7H2O
0.25
g/l



3-morpholinopropanesulfonic
42
g/1



acid



CaCl2
10
mg/l



FeSO4 × 7H2O
10
mg/l



MnSO4 × H2O
10
mg/l



ZnSO4 × 7H2O
1
mg/l



CuSO4
0.2
mg/l



NiCl2 × 6H2O
0.02
mg/l



Biotin
0.2
mg/l



Glucose
40
g/l



Protocatechuic acid
30
mg/l




















TABLE 2









PSAT
PSP












%
%
%
%



Identity
Similarity
Identity
Similarity

















Escherichia
23
33
49
40



coli



Saccharo-
27
36
36
49



myces



cerevisiae



Mycobac-
61
69
55
64



terium



tuberculosis




















TABLE 3







C. glutamicum strain
L-serine [μM]









13032
≦10



13032 (pVWEx1)
≦10



13032 (pVWEx2)
≦10



13032 (pVWEx1serB)
≧40



13032 (pVWEx2serC)
≧200

## Claims

1. A method for the microbial production of L-serine comprising the steps of:
a) isolating at least one nucleic acid from a coryneform bacterium, coding for a phosphoserine phosphatase (serB) or a phosphoserine aminotransferase (serC) according to one of SEQ no. 1, 3, 5, or 7 and a nucleic acid coding for an L-threonine export carrier according to one of SEQ ID NO. 9 or 11, transferring the isolated nucleic acid to a coryneform bacterium and expressing it therein, increasing the gene expression as compared to the corresponding genetically unmodified microorganism,
b) using the genetically modified microorganism from step a) for the fermentative production of L-serine in a culture medium, and
c) isolating the L-serine formed from the culture medium.

2. A method for the microbial production of L-serine, comprising the steps of
a) transferring at least one nucleic acid coding for a phosphoserine phosphatase (serB) or phosphoserine aminotransferase (serC) according to SEQ ID No. 1, 3, 5, or 7 and a nucleic acid coding for an L-threonine export carrier according to SEQ ID NO. 9 or 11, isolated from a coryneform bacterium, into a coryneform bacterium and expressing them therein, increasing the gene expression as compared to the corresponding genetically unmodified microorganism,
b) using this genetically modified microorganism from step a) for the fermentative production of L-serine, whereby L-serine is increasingly secreted into the culture medium, and
c) isolating the L-serine formed from the culture medium.