# Patent

## Title
Method for the production of sulpher-containing fine chemicals by fermentation

## Abstract

The invention relates to methods for the production of sulfur-containing fine chemicals, in particular L-methionine, by fermentation using bacteria in which a nucleotide sequence encoding an S-adenosylmethionine synthase (metK) gene is expressed.

## Background
The invention relates to a novel method for the production by fermentation of sulfur-containing fine chemicals, in particular L-methionine and L-cysteine, which makes use of bacteria in which nucleotide sequences encoding mutants of S-adenosylmethionine synthase (metK) (E.C.2.5.1.6) are expressed; to nucleotide sequences which encode these mutants, to the recombinant microorganisms transformed therewith, and to novel metK mutants with modified enzyme activity.
PRIOR ART
Sulfur-containing fine chemicals such as, for example, methionine, homocysteine, S-adenosylmethionine, glutathione, cysteine, biotin, thiamine and liponic acid, are produced in cells via natural metabolic processes and used in a large number of industries including the food, feed, cosmetics and pharmaceutical industries. These substances, which are referred to generically as “sulfur-containing fine chemicals”, encompass organic acids, proteinogenic and nonproteinogenic amino acids, vitamins and cofactors. Most expediently they are produced on an industrial scale by growing bacteria which have been developed for producing and secreting large amounts of the desired substance in question. Organisms which are particularly suitable for this purpose are the Gram-positive, nonpathogenic coryneform bacteria.
It is known that amino acids are produced by fermenting strains of coryneform bacteria, in particular Corynebacterium glutamicum. Owing to their high importance, the production methods are constantly being improved. Improvements with regard to the production methods may relate to aspects of fermentation technology, such as, for example, stirring and nitrogen supply, or the composition of the nutrient media, such as, for example, the sugar concentration during fermentation, or downstream processing, for example by ion-exchange chromatography, or the intrinsic performance parameters of the microorganism itself.
Strain selection has given rise to a series of mutant strains which produce a group of desirable compounds from the series of the sulfur-containing fine chemicals. Methods applied for improving the performance parameters of these microorganisms with regard to the production of a particular molecule are mutagenesis, selection and choice of mutants. However, this is a time-consuming and difficult procedure. In this manner, strains are obtained which are, for example, resistant to antimetabolites, such as, for example, to the methionine analogs a-methylmethionine, ethionine, norleucin, N-acetylnorleucine, S-trifluoromethylhomocysteine, 2-amino-5-heptenoic acid, selenomethionine, methionine sulfoximine, methoxine or 1-aminocyclopentanecarboxylic acid, or which are auxotrophic with regard to metabolites of regulatory importance and which produce sulfur-containing fine chemicals, such as, for example, L-methionine.
Methods of recombinant DNA technology have also been employed for some years for the strain improvement of L-amino-acid-producing Corynebacterium strains, in which individual amino acid biosynthesis genes are amplified and the effect on the amino acid production is studied.
JP-A-06-020809 discloses a nucleotide sequence for a gene from Brevibacterium flavum MJ-233, a coryneform bacterial, which encodes S-adenosylmethionine. The corresponding amino acid sequence encompasses 412 amino acids. In each of positions 24 and 94, inter alia, which are conserved in the corresponding enzymes of a large number of other coryneform bacteria, the protein has a cysteine residue. The amino acid sequence disclosed has a characteristic sequence segment between residues 137 and 154. The generation of mutants and their use in the production by fermentation of sulfur-containing fine chemicals is not described therein.
WO-A-01/00843 discloses a metK gene from C. glutamicum, which encodes a protein with 407 amino acids and has a sequence as shown in SEQ ID NO:16.
As a rule, improvements in the production by fermentation of fine chemicals correlate with improved substance fluxes and yields. It is important to prevent, or to reduce, intermediate inhibition or end-product inhibition of enzymes which are important for the synthesis. The prevention or reduction of diversions of the carbon flux toward undesired products or byproducts is likewise advantageous.
The effect of metabolites on the enzymatic activities of metabolic enzymes can be studied. Examples of such enzymes can be meta, metB, metC, MetY, metH, metE, metF and other enzymes in the metabolism of microorganisms. An important metabolite of methionine, and thus an important diversion, is S-adenosylmethionine.
However, S-adenosylmethionine is simultaneously also a crucial regulator of methoinine biosynthesis. For example, it is known that the biosynthesis of L-methione in E. coli is inhibited by S-adenosylmethionine. In this system, S-adenosylmethionine acts as a corepressor of the repressor metJ (Weissbach, H. Brot, N. (1991) Mol Microbiol. 5 (7), 1593-1597).
At the same time, the synthesis of S-adenosylmethionine is an important diversion from the desired product of interest, L-methionine. Reducing the amount of S-adenosylmethionine formed is therefore desirable for several reasons, namely:

    
    
        a) the amount of L-methionine formed would be increased,
        b) the repression of genes of methionine biosynthesis would be reduced, and
        c) the feedback inhibition of enzymes of methionine biosynthesis would be reduced.
    
    


Deletion of the metK gene would be the simplest way of preventing the formation of S-adenosylmethionine. In Wei, Y. and Newman, E. B. (2002) Mol. Microbiol. 43 (6), 1651-1656, however, metK is described as an essential gene and thus appears to the skilled worker as a starting point for the improved production by fermentation of sulfur-containing fine chemicals, in particular L-methionine.
SUMMARY OF THE INVENTION
It is an object of the present invention to provide a novel method for the improved production by fermentation of sulfur-containing fine chemicals, in particular L-methionine, and the means required therefore.
Surprisingly, it has been found that this object is achieved by providing a method for the production by fermentation of a sulfur-containing fine chemical which comprises the expression of a metK nucleotide sequence in a coryneform bacterium, the nucleotide sequence encoding an S-adenosylmethionine synthase mutant whose activity is modified, preferably reduced, over the wild-type enzyme. For example, the S-adenosylmethionine synthase mutant is derived from Corynebacterium glutamicum and, measured in Corynebacterium glutamicum, shows less activity than the wild-type enzyme.
A first subject matter of the invention relates to a method for the production by fermentation of at least one sulfur-containing fine chemical, which comprises the following steps:

    
    
        a) fermentation of a coryneform bacterial culture which produces the desired sulfur-containing fine chemical, the coryneform bacteria expressing at least one nucleotide sequence which encodes a protein with modified S-adenosylmethionine synthase (metK) activity;
        b) enrichment of the sulfur-containing fine chemical in the medium and/or in the bacterial cells, and
        c) isolation of the sulfur-containing fine chemical, which preferably comprises L-methionine.
    
    


In accordance with a preferred embodiment, the mutated coryneform bacterium additionally has an improved metY activity and/or an increased L-methionine amount in comparison with the unmutated wild type (for example expressed in g/l fermentation liquor).
The metK-encoding sequence which is used in particular in the method according to the invention is a coding nucleotide sequence which encodes a protein with reduced metK activity in which at least one cysteine residue of the wild-type protein is substituted.
Preferably, the metK-encoding sequence is a coding nucleotide sequence which encodes a protein with metK activity which has the following amino acid part-sequence as shown in SEQ ID NO:23:










G(F/Y)(D/S)X1X2(S/T)X3(G/A)V







    
    
        where
        X1 and X2 independently of one another represent any amino acid;
        and
        X3 represents an amino acid other than Cys.
    
    


Especially preferred is a method in accordance with the above definition in which the metK-encoding sequence encodes a protein with metK activity, the protein encompassing an amino acid sequence from Val1 to Ala407 as shown in SEQ ID NO: 22 or an amino acid sequence which is homologous thereto and which represents a protein with functional equivalence.
The metK-encoding sequence employed in accordance with the invention preferably comprises a coding sequence as shown in SEQ ID NO: 21 or a nucleotide sequence which is homologous thereto and which encodes a protein with metK activity.
The coding metK sequence is preferably a DNA which is capable of replication in coryneform bacteria or stably integrated into the chromosome, or an RNA.
In accordance with a preferred embodiment, the method according to the invention is carried out by

    
    
        a) using a bacterial strain which has been transformed with a plasmid vector and which carries at least one copy of the coding metK sequence under the control of regulatory sequences, or
        b) using a strain in which the coding metK sequence has been integrated into the bacterial chromosome.
    
    


Especially preferred are strains as defined above in which, additionally, all or some of the activity of the metK wild type enzyme has been removed, such as, for example, by deletion of the coding sequence of the wild-type enzyme.
Moreover, it may be desirable to ferment bacteria in which additionally at least one further gene of the biosynthetic pathway of the desired sulfur-containing fine chemical is enhanced and/or in which at least one metabolic pathway which reduces the formation of the desired sulfur-containing fine chemical is at least partly eliminated.
This is why, in accordance with a further embodiment of the method according to the invention, coryneform bacteria in which at least one of the genes selected from among

    
    
        1) the gene lysC, which encodes an aspartate kinase,
        2) the gene asd, which encodes an aspartate-semialdehyde dehydrogenase,
        3) the gene gap, which encodes glycerinaldehyde-3-phosphate dehydrogenase,
        4) the gene pgk, which encodes 3-phosphoglycerate kinase,
        5) the gene pyc, which encodes pyruvate carboxylase,
        6) the gene tpi, which encodes triose-phosphate isomerase,
        7) the gene meta, which encodes homoserine O-acetyltransferase,
        8) the gene metB, which encodes cystathionine-gamma synthase,
        9) the gene metC, which encodes cystathionine-gamma lyase,
        10) the gene metH, which encodes methionine synthase,
        11) the gene glyA, which encodes serine hydroxymethyltransferase,
        12) the gene metY, which encodes O-acetylhomoserine sulfhydrylase,
        13) the gene metF, which encodes methylenetetrahydrofolate reductase,
        14) the gene serC, which encodes phosphoserine aminotransferase,
        15) the gene serB, which encodes phosphoserine phosphatase,
        16) the gene cysE, which encodes serine acetyltransferase,
        17) the gene cysk, which encodes cysteine synthase,
        18) the gene hom, which encodes homoserine dehydrogenase, is simultaneously overexpressed, are fermented.
    
    


In accordance with another embodiment of the method according to the invention, coryneform bacteria are fermented in which at least one of the genes selected among genes of the abovementioned groups 1) to 18) is simultaneously mutated in such a way that the activity of the corresponding proteins influenced to a lesser degree in comparison with unmutated proteins, or unaffected by metabolites and that in particular the production according to the invention of the fine chemical is not adversely affected, or in such a way that their specific enzyme activity is increased.
In accordance with another embodiment of the method according to the invention coryneform bacteria are fermented in which simultaneously at least one of the genes selected from among

    
    
        19) the gene thrB, which encodes homoserine kinase,
        20) the gene ilvA, which encodes threonine dehydratase,
        21) the gene thrC, which encodes threonine synthase,
        22) the gene ddh, which encodes meso-diaminopimelate D dehydrogenase,
        23) the gene pck, which encodes phosphoenol-pyruvate carboxykinase,
        24) the gene pgi, which encodes glucose-6-phosphate-6 isomerase,
        25) the gene poxB, which encodes pyruvate oxidase,
        26) the gene dapA, which encodes dihydrodipicolinate synthase,
        27) the gene dapB, which encodes dihydrodipicolinate reductase, or
        28) the gene lysA, which encodes diaminopicolinate decarboxylase, is attenuated, in particular by reducing the expression rate of the corresponding gene.
    
    


In accordance with another embodiment of the method according to the invention, coryneform bacteria are fermented in which at least one of the genes of the above groups 19) to 28) is simultaneously mutated in such a way that the enzyme activity of the corresponding protein is reduced in part or fully.
Microorganisms which are preferably used in the method according to the invention are those of the species Corynebacterium glutamicum. 
The invention furthermore relates to a method for producing an L-methionine-containing animal feed additive from fermentation broths, which comprises the following steps:

    
    
        a) culturing and fermention of an L-methionine-producing microorganism, preferably with a reduced metK activity in accordance with the above definition, in a fermentation medium,
        b) removal of water from the L-methionine-containing fermentation broth;
        c) removal of from 0 to 100% by weight of the biomass formed during fermentation; and
        d) drying of the fermentation broth obtained according to b) and/or c), in order to obtain the animal feed additive in the desired powder or granule form.
    
    


The invention furthermore relates to isolated polynucleotides which encode a polypeptide with reduced metK activity in accordance with the above definition, and to metK mutants with reduced activity which are encoded by these polynucleotides.
Furthermore, the invention relates to recombinant coryneform bacteria which express a mutated metK gene in accordance with the above definition, in particular those recombinant coryneform bacteria which no longer express the metK wild-type enzyme.
In comparison with the corresponding wild-type strain, preferred recombinant coryneform bacteria show at least one of the following traits:

    
    
        a) lower intracellular S-adenosylmethionine titer
        b) lower intracellular S-adenosylmethionine synthase concentration, or
        c) lower S-adenosylmethionine synthase activity, determined with reference to the rate of S-adenosylmethionine formation,

and additionally if appropriate at least one of the following traits:

        d) improved metY activity or
        e) increased amount of L-methionine.
    
    




DETAILED DESCRIPTION OF THE INVENTION 


    
    
        a) General Terms
    
    


The term proteins with the biological activity of “S-adenosylmethionine synthase”, also abbreviated to metK (E.C.2.5.1.6) refers to those proteins which are capable of converting L-methionine and ATP into S-adenosylmethionine. The skilled worker is familiar with other details of the metK protein. The enzyme activity of metK can be detected by enzyme assays, protocols for which are found in: Markham, G. D. et al. (1983) Methods in Enzymology 94:219-222.
Within the scope of the present invention, the term “sulfur-containing fine chemical” encompasses any chemical compound which contains at least one sulfur atom bonded covalently and which can be obtained by a fermentation method according to the invention. Nonlimiting examples are methionine, homocysteine, S-adenosylmethionine, cysteine and in particular methionine and S-adenosylmethionine.
Within the scope of the present invention, the terms “L-methionine”, “methionine”, “homocysteine” and “S-adenosylmethionine” also encompass the corresponding salts such as, for example, methionine-hydrochloride or methionine sulfate.
“Polynucleotides” generally refers to polyribonucleotides (RNA) and polydeoxyribonucleo-tides (DNA), which may take the form of unmodified RNA or DNA or modified RNA or DNA.
“Polypeptides” are understood as meaning, in accordance with the invention, peptides or proteins comprising two or more amino acids which are bonded via peptide bonds.
The term “metabolite” refers to chemical compounds which occur in the metabolism of organisms as intermediates or else end products and which, besides their property as chemical units, may also exert a modulatory effect on enzymes and their catalytic activity. It is known from the literature that such metabolites can have both an inhibitory and stimulatory effect on the activity of enzymes (Biochemistry, Stryer, Lubert, 1995 W. H. Freeman & Company, New York, N.Y.). The literature also describes that it is possible to produce, by measures such as mutating the genomic DNA by UV radiation, ionizing radiation or mutagenic substances and subsequently selecting for specific phenotypes, in organisms, those enzymes in which the influence by metabolites has been modified (Sahm H., Eggeling L., de Graaf A. A. Biological Chemistry 381(9-10):899-910, 2000; Eikmanns B J., Eggeling L., Sahm H. Antonie van Leeuwenhoek. 64:145-63, 1993-94). These modified properties can also be obtained by targeted measures. In this context, the skilled worker also knows to specifically modify, in genes for enzymes, specific nucleotides of the DNA which encodes the protein in such a manner that the protein resulting from the expressed DNA sequence has specific novel characteristics. For example, this may result in the modulating effect of metabolites being modified over the unmodified protein. Also, the activity of enzymes can be affected in such a way that a diminished reaction rate or a change in affinity to the substrate results.
In the context of the invention, the terms “express” or “enhancement” or “overexpression” in the context of the invention describe the production or increase of the intracellular activity of one or more enzymes in a microorganism which are encoded by the DNA in question. To this end, it is possible, for example, to introduce a gene into an organism, to replace an existing gene by another gene, to increase the copy number of the gene or genes, to use a strong promoter or to use a gene which encodes an enzyme in question with high activity; if appropriate, these measures can be combined.
Within the context of the invention, the terms “to attenuate” and “to reduce” describe the attenuation or reduction of the intracellular activity of one or more enzymes in a micro-organism which are encoded by the DNA in question. To this end, it is possible, for example, to delete a gene in an organism, to replace an existing gene by another gene, to reduce the copy number of a transcript of the gene or genes, to use a weak promoter or to use a gene which encodes a corresponding enzyme with low activity; if appropriate, these measures can be combined.
The “reduced activity” of an S-adenosylmethionine synthase mutant according to the invention or of a functional equivalent can be determined by comparison with the activity of the native S-adenosylmethionine synthase, such as, for example, from Corynebacterium glutamicum wild type, ATCC 13032. To this end, plasmids which replicate in Corynebacterium glutamicum and which carry the genes for S-adenosylmethionine synthase mutants are suitably introduced by transformation into, for example, Corynebacterium glutamicum wild type, ATCC 13032. Moreover, suitable plasmids which express the wild-type enzyme S-adenosylmethionine synthase are introduced into Corynebacterium glutamicum wild type, ATCC 13032. Corynebacterium glutamicum transformants thus obtained are grown in suitable media and harvested during the logarithmic growth phase at the same OD600. Thereafter, protein extracts are prepared from the harvested cells of the two transformants following known protocols. Identical amounts of these protein extracts (following protein identification) are then employed in an S-adenosylmethionine synthase assay by the method of Markham, G. D. et al. (1983) Methods in Enzymology 94: 219-222. The radioactivity of the S-adenosylmethionine formed is determined in a scintillation counter. Taking into consideration the specific activity of the radioactive L-methionine and the amount of protein employed, the rate of S-adenosylmethionine formation can be determined from the increase in incorporated radioactivity per unit time. It has the unit μmol S-adenosylmethionine/min*mg protein. This rate can be compared between wild-type enzyme and mutant enzyme. Starting from other wild-type enzymes with S-adenosylmethionine synthase activity, mutants which are useful in accordance with the invention can be generated by the same principle.
A “reduced activity” is present in accordance with the invention in particular when the specific activity of the mutant is reduced to a residual activity of approximately 1 to 90%, preferably 3 to 70%, such as, for example, 5 to 10% of the wild-type activity.

    
    
        b) metK proteins according to the invention
    
    


The polynucleotide sequences according to the invention encode proteins with modified, in particular reduced, S-adenosylmethionine synthase activity as defined above.
The mutants which are useful according to the invention are preferably obtained by substituting one or more conserved cysteine residues within the metK amino acid sequence of Gram-positive and/or Gram-negative, or in particular coryneform, bacteria. Conserved cysteine residues can be identified readily with the aid of sequence alignments. Nonlimiting examples of conserved Cys residues in bacterial S-adenosylmethionine synthases are Cys24 and Cys94 of the enzyme from C. glutamicum, which are found in a multiplicity of bacteria.
In a preferred group of mutants according to the invention, Cys24 and/or Cys94 (according to C. glutamicum ATCC 13032 metK) are substituted by an amino acid other than Cys, preferably alanine, whereby the enzyme activity is reduced in the above manner.
“Functional equivalents” or analogs of the specifically disclosed polypeptides are, within the scope of the present invention, polypeptides which differ from them but which still retain the desired biological activity such as, for example, substrate specificity.
In accordance with the invention, “functional equivalents” are understood as meaning, in particular, mutants which have another amino acid than the amino acid which has been mentioned specifically in at least one of the abovementioned sequence positions, but which still retain one of the abovementioned biological activities. Thus, “functional equivalents” encompass the mutants obtainable by one or more amino acid additions, substitutions, deletions and/or inversions, it being possible for the abovementioned modifications to be located at any sequence position as long as they give rise to a mutant with the profile of characteristics according to the invention. In particular, functional equivalence also exists when the reactivity pattern between mutant and unmodified polypeptide agree in quality, i.e. for example when identical substrates are converted at different rates.
Naturally, “functional equivalents” also encompass polypeptides which can be obtained from other organisms, and naturally occurring variants. For example, ranges of homologous sequence regions can be identified by sequence, and equivalent enzymes can be determined with a view to the specific aims of the invention.
Likewise, “functional equivalents” encompass fragments, preferably individual domains or sequence motifs, or the polypeptides according to the invention which have for example the desired biological function.
Moreover, “functional equivalents” are fusion proteins with one of the abovementioned poly-peptide sequences or functional equivalents derived therefrom and at least one further, functionally different, heterologous sequence in functional N- or C-terminal linkage (i.e. without the fusion protein moieties being substantially adversely affected functionally by each other). Nonlimiting examples of such heterologous sequences are, for example, signal peptides, enzymes, immunoglobulins, surface antigens, receptors or receptor ligands.
“Functional equivalents” which are also encompassed in accordance with the invention are homologs to the specifically disclosed proteins. These homologs have at least 20%, 30%, or for example 40%, 50%, preferably at least approximately 60%, 65%, 70%, or 75%, in particular at least 85%, such as, for example, 90%, 95% or 99%, homology with one of the specifically disclosed sequences, calculated using Pearson and Lipman's algorithm, Proc. Natl. Acad, Sci. (USA) 85(8), 1988, 2444-2448.
Mutants and functional analogs which are especially preferred are those which contain the characteristic part-sequence










G(F/Y)(D/S)X1X2(S/T)X3(G/A)V







as defined above, where X3 is an amino acid introduced by mutation other than Cys, in particular alanine. X3 corresponds to Cys94 of the metK wild-type sequence of C. glutamicum (SEQ ID NO: 16). X2 preferably represents Ala, Glu, Asp, Asn or Arg, and X1 preferably represents Gly, Cys, Ser or Ala.

Homologs of the proteins or polypeptides according to the invention can be generated by mutagenesis, for example by point mutation or truncation of the protein. The term “homolog” as used in the present context relates to a variant form of the protein which acts as agonist or antagonist of the protein activity.
Homologs of the proteins according to the invention can be identified by screening combinatory libraries of mutants, such as, for example, truncated mutants. A variegated library of protein variants can be generated for example by combinatory mutagenesis at the nucleic acid level, such as, for example, by enzymatically ligating a mixture of synthetic oligonucleotides. A multiplicity of methods are available which can be used for generating libraries of potential homologs from a degenerate oligonucleotide sequence. The degenerate gene sequence can be synthesized chemically in a DNA synthesizer, and the synthetic gene can then be ligated into a suitable expression vector. The use of a set of degenerate genes makes it possible to provide, in a mixture, all sequences which encode the desired set of potential protein sequences. Methods for the synthesis of degenerate oligonucleotides are known to the skilled worker (for example 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 Acids Res. 11:477).
Libraries of fragments of the protein codon may additionally be used for generating a variegated population of protein fragments for screening and subsequently selecting homologs of a protein according to the invention. In one embodiment, a library of coding sequence fragments can be generated by treating a double-stranded PCR fragment of a coding sequence with a nuclease under conditions under which nicking only takes place approximately once per molecule, denaturing the double-stranded DNA, renaturing the DNA with the formation of double-stranded DNA which may encompass sense/antisense pairs of various nicked products, removing single-stranded segments from newly-formed duplices by treatment with S1 nuclease, and ligating the resulting fragment library into an expression vector. This method allows an expression library which encodes N-terminal, C-terminal and internal fragments with various sizes of the protein according to the invention to be generated.
A plurality of techniques for the mutagenesis of genes are known in the prior art: Coco, W M et al. 2001. DNA shuffling method for generating highly recombined genes and evolved enzymes. Nature Biotechnol. 19:354-359; DE 19953854; Leung D W et al. 1989. A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Technique 1:11-15; Stemmer WPC 1994. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl. Acad. Sci USA 91:10747-10751; and U.S. Pat. No. 5,811,238. These methods can be employed for generating mutants which are useful in accordance with the invention.
A plurality of techniques for screening gene products of combinatory libraries which have been generated by point mutations or truncation and for screening cDNA libraries for gene products with a selected characteristic are known in the prior art. These techniques can be adapted to rapid screening of the gene libraries which have been generated by combinatory mutagenesis of homologs according to the invention. Techniques which are most frequently used for screening large gene libraries which are subjected to high-throughput analysis include cloning the gene library into replicable expression vectors, transforming the suitable cells with the resulting vector library and expressing the combinatory genes under conditions under which the detection of the desired activity simplifies the isolation of the vector encoding the gene whose product has been detected. Recursive ensemble mutagenesis (REM), a technique which increases the frequency of functional mutants in the libraries, can be used in combination with the screening assays for identifying homologs (Arkin and Yourvan (1992) PNAS 89:7811-7815; Delgrave et al. (1993) Protein Engineering 6(3):327-331.

    
    
        c) Polynucleotides According to the Invention
    
    


Likewise, the invention relates to nucleic acid sequences (single- and double-stranded DNA and RNA sequences such as, for example, cDNA and mRNA) encoding a metK enzyme according to the invention and its functional equivalents which can be obtained for example using synthetic nucleotide analogs, inter alia.
The invention relates both to isolated nucleic acid molecules which encode polypeptides or proteins according to the invention, or biologically active segments of these, and to nucleic acid fragments which can be used for example as hybridization probes or primers for identifying or amplifying coding nucleic acids according to the invention.
Moreover, the nucleic acid molecules according to the invention may contain 3′- and/or 5′-end untranslated sequences of the coding region of genes.
An “isolated” nucleic acid molecule is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid, and, if it is prepared by recombinant techniques, may be additionally free from other cellular material or culture medium, or, if it is synthesized chemically, free from chemical precursors or other chemicals.
The invention furthermore encompasses the nucleic acid molecules which are complementary to the nucleotide sequences described specifically, or a segment of the former.
The nucleotide sequences according to the invention make possible the generation of probes and primers which can be used for identifying and/or cloning homologous sequences in other cell types and organisms. Such probes or primers usually encompass a nucleotide sequence region which hybridizes under stringent conditions to at least approximately 12, preferably at least approximately 25, such as, for example, approximately 40, 50 or 75, consecutive nucleotides of a sense strand of a nucleic acid sequence according to the invention or of a corresponding antisense strand.
Further nucleic acid sequences according to the invention are derived from SEQ ID NO: 21 and differ therefrom by the addition, substitution, insertion or deletion of individual or several nucleotides, but continue to encode polypeptides with the desired profile of characteristics. They may take the form of polynucleotides which are identical with the above sequences in at least approximately 50%, 55%, 60%, 65%, 70%, 80% or 90%, preferably in at least approximately 95%, 96%, 97%, 98% or 99% of the sequence positions.
Also encompassed in accordance with the invention are those nucleic acid sequences which encompass what are known as silent mutations or which are modified in comparison with a specifically mentioned sequence in accordance with the codon usage of a specific organism of origin, or host organism, as are naturally occurring variants, such as, for example, allelic variants, thereof. Another subject are sequences which can be obtained by conservative nucleotide substitutions (i.e. the amino acid in question is replaced by an amino acid of the same charge, size, polarity and/or solubility).
Another subject of the invention are the molecules derived from the specifically disclosed nucleic acids by means of sequence polymorphisms. These genetic polymorphisms may exist between individuals within a population owing to natural variation. These natural variations usually bring about a variance of from 1 to 5% in the nucleotide sequence of a gene.
The invention furthermore also encompasses nucleic acid sequences which hybridize with abovementioned coding sequences or are complementary thereto. These polynucleotides can be found when screening genomic or cDNA libraries and, if appropriate, amplified therefrom with suitable primers by means of PCR and subsequently isolated, for example using suitable probes. Another possibility is the transformation of suitable microorganisms with polynucleotides according to the invention or vectors, the multiplication of the microorganisms, and thus amplification of the polynucleotides, and their subsequent isolation. Moreover, polynucleotides according to the invention can also be synthesized chemically.
The characteristic of being capable to “hybridize” with polynucleotides is understood as meaning the ability of a polynucleotide or oligonucleotide to bind to a virtually complementary sequence under stringent conditions, while unspecific binding between non-complementary partners does not take place under these conditions. To this end, the sequences should show 70-100%, preferably 90-100% complementarity. The characteristic of complementary sequences of being capable of binding specifically with one another is exploited for example in the Northern or Southern blot technique, or in the primer hybridization in PCR or RT-PCR. Usually oligonucleotides from a length of 30 base pairs are used. Stringent conditions are understood as meaning, for example, in the Northern blot technique, the use of a wash solution, preferably 0.1×SSC buffer with 0.1% SDS (20×SSC: 3M NaCl, 0.3M Na citrate, pH 7.0) at a temperature of 50-70° C., preferably 60-65° C., for the elution of unspecifically hybridized cDNA probes or oligonucleotides. As mentioned above, only those nucleic acids remain bound to each other which show a high degree of complementarity. The setting of stringent conditions is known to the skilled worker and described, for example, in Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.

    
    
        d) Isolation of the Coding metK Genes and of Other Genes
    
    


The metK genes which encode the enzyme S-adenosylmethionine synthase (EC 2.5.1.6) can be isolated in a manner known per se.
To isolate the metK genes, or else other genes of other organisms, a gene library of this organism in Escherichia coli (E. coli) is established as the first step. Establishing gene libraries is described in detail in generally known textbooks and reference books. Examples which may be mentioned are the textbook by Winnacker: Gene and Klone, Eine Einführung in die Gentechnologie [Genes and clones, An introduction to genetic engineering] (Verlag Chemie, Weinheim, Germany, 1990), or the reference book by Sambrook et al.: Molecular Cloning, A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1989). A very well known gene library is that of E. coli K-12 strain W3110, which has been established by Kohara et al. (Cell 50, 495-508 (198)) in λ vectors.
Cosmids, such as the cosmid vector SuperCos I (Wahl et al. (1987), Proceedings of the National Academy of Sciences USA 84: 2160-2164), but also plasmids such as pBR322 (Bolivar; Life Sciences, 25, 807-818 (1979)) or pUC9 (Vieira et al., 1982, Gene, 19: 259-268), may be used for establishing a gene library in E. coli. E. coli strains which are particularly suitable as hosts are those which are restriction deficient and recombination deficient. An example is the strain DH5αmcr, which has been described by Grant et al. (Proceedings of the National Academy of Sciences USA, 87 (1990) 4645-4649). The long DNA fragments which are cloned with the aid of cosmids can, in turn, subsequently be subcloned into customary vectors which are suitable for sequencing and subsequently sequenced, as is described for example by Sanger et al. (Proceedings of the National Academy of Sciences of the United States of America, 74: 5463-5467, 1977).
The resulting DNA sequences can then be studied with known algorithsms or sequence analysis programs, such as, for example, the program by Staden (Nucleic Acids Research (1986) 14,217-232), the program by Marck (Nucleic Acids Research (1988) 16, 1829-1836) or Butler's GCG program (Methods of Biochemical Analysis (1998) 39, 74-97).
The skilled worker will find protocols for identifying DNA sequences by means of hybridizing in, inter alia, the reference book “The DIG System Users Guide for Filter Hybridization” by Boehringer Mannheim GmbH (Mannheim, Germany, 1993) and in Liebl et al. (International Journal of Systematic Bacteriology (1991) 41: 255-260). The skilled worker will find protocols for amplifying DNA sequences with the aid of the polymerase chain reaction (PCR) in, inter alia, the reference book by Gait: Oligonucleotide synthesis: A Practical Approach (IRL Press, Oxford, UK, 1984) and in Newton and Graham: PCR (Spektrum Akademischer Verlag, Heidelberg, Germany, 1994).
It is furthermore known that modifications of the N and/or C terminus of a protein do not substantially affect the function of the latter; indeed, they are even capable of stabilizing it. The skilled worker will find information on this subject in, inter alia, Ben-Bassat et al. (1987) Journal of Bacteriology 169: 751-757, in O'Regan et al. (1989) Gene 77: 237-251, in Sahin-Toth et al. (1994) Protein Sciences 3: 240-247, in Hochuli et al. (1988) Biotechnology 6: 1321-1325 and in known textbooks of genetic and molecular biology.

    
    
        e) Host Cells Used in Accordance with the Invention
    
    


Host cells which are used for the method according to the invention are, preferably, coryneform bacteria whose reduced metK activity can be detected via at least one of the following characteristics:

    
    
        a) an intracellular S-adenosylmethionine titer which is reduced in comparison with the wild-type strain,
        b) a reduced intracellular S-adenosylmethionine synthase concentration (less S-adenosylmethionine synthase based on the total protein), or
        c) a reduced intracellular S-adenosylmethionine synthase activity (less S-adenosyl-methionine synthase enzyme activity based on the S-adenosylmethionine synthase protein content.
    
    


All of these characteristics can be determined by the skilled worker in a simple manner, if appropriate taking into consideration the above description.
The invention furthermore relates in particular to microorganisms which act as host cells, in particular coryneform bacteria which contain a vector, in particular shuttle vector or plasmid vector which bears at least one metK gene as defined in accordance with the invention, or coryneform bacteria in which a metK gene according to the invention with reduced activity is expressed.
These microorganisms are capable of producing sulfur-containing fine chemicals, in particular L-methionine, from glucose, sucrose, lactose, fructose, maltose, molasses, starch, cellulose or from glycerol and ethanol. They are preferably coryneform bacteria, in particular of the genus Corynebacterium. Among the genus Corynebacterium, the species Corynebacterium glutamicum, which is known in expert circles for its ability to produce L-amino acids, must be mentioned in particular.
Examples which must be mentioned of suitable strains of coryneform bacteria are those of the genus Corynebacterium, in particular of the species Corynebacterium glutamicum (C. glutamicum), such as
Corynebacterium glutamicum ATCC 13032,
Corynebacterium acetoglutamicum ATCC 15806,
Corynebacterium acetoacidophilum ATCC 13870,
Corynebacterium thermoaminogenes FERM BP-1539,
Corynebacterium melassecola ATCC 17965
or of the genus Brevibacterium, such as
Brevibacterium flavum ATCC 14067
Brevibacterium lactofermentum ATCC 13869 and
Brevibacterium divaricatum ATCC 14020,
or strains derived from them, such as
Corynebacterium glutamicum KFCC10065
Corynebacterium glutamicum ATCC21608
which likewise produce the desired fine chemical or its precursor(s) (KFCC=Korean Federation of Culture Collection; ATCC=American Type Culture Collection)

    
    
        f) Carrying Out the Fermentation According to the Invention
    
    


It has been found in accordance with the invention that coryneform bacteria, after expressing a metK gene according to the invention, produce sulfur-containing fine chemicals, in particular L-methionine, in an advantageous manner.
Various measures may be taken by the skilled worker, either individually or in combination, in order to reduce the activity or amount of an enzyme, for example S-adenosylmethionine synthase, metK. The concentration of the protein in question can be reduced by reducing the transcription frequency of the gene which encodes the protein according to the invention. This can be achieved by the skilled worker by modifying or substituting the promoter region, the regulatory region or else the ribosome binding site of the coding gene. Downstream of the coding region, the skilled worker can modify terminators or insert sequences which lead to reduced stability of the transcript. These measures, which reduce the lifespan of the mRNA, make it possible to diminish the expression of the corresponding protein and thus its concentration.
At the level of the expressed enzyme, fused sequences may lead to an increased breakdown rate and thus likewise to a reduced concentration of the protein. Moreover, the skilled worker can modify the activity, substrate affinity and substrate specificity by subjecting the coding gene to directed or undirected mutagenesis. The activity of enzymes can be influenced by mutations in the corresponding genes in such a way that the result is a degree of, or complete, reduction of the reaction rate of the enzyme reaction. Examples of such mutations are known to the skilled worker (Motoyama H. Yano H. Terasaki Y. Anazawa H. Applied & Environmental Microbiology. 67:3064-70, 2001, Eikmanns B J. Eggeling L. Sahm H. Antonie van Leeuwenhoek. 64:145-63, 1993-94). Mutants of the protein may also lead to reduced or hindered homo- or heteromultimerization of enzyme complexes and thus again to a deterioration of the enzymatic properties.
Genes which have been modified in such a way may be present either in plasmids or, preferably, integrated into the chromosome. The original gene, which has not been modified in this manner, may additionally still be present, but is preferably substituted for the modified gene.
In order to reduce the activity of an enzyme, for example S-adenosylmethionine synthase (metK), as measured in a coryneform bacterium, it may suffice to express genes which encode functional equivalents, such as artificially generated mutants or natural homologs from other organisms. The original gene may additionally be present, but is preferably substituted by the modified or homologous gene.
When producing sulfur-containing fine chemicals, in particular L-methionine, in coryneform bacteria by means of fermentation it may additionally be advantageous not only to express a metK gene according to the invention, but also to enhance one or more enzymes of the biosynthetic pathway in question, of the cysteine metabolic pathway, of the aspartate semialdehyde synthesis, of glycolysis, of anaplerotics, of the pentose-phosphate metabolism, of the citrate cycle or of the amino acid export.
Thus, one or more of the following genes may be enhanced for the production of sulfur-containing fine chemicals, in particular L-methionine:
the gene lysC, which encodes an aspartate kinase (EP 1 108 790 A2; DNA-SEQ NO. 281),
the gene asd, which encodes an aspartate semialdehyde (EP 1 108 790 A2; DNA-SEQ NO. 282),
the gene gap, which encodes glycerinaldehyde-3-phosphate dehydrogenase (Eikmanns (1992), Journal of Bacteriology 174: 6076-6086),
the gene pgk, which encodes 3-phosphoglycerate kinase (Eikmanns (1992), Journal of Bacteriology 174: 6076-6086),
the gene pyc, which encodes pyruvate carboxylase (Eikmanns (1992), Journal of Bacteriology 174: 6076-6086),
the gene tpi, which encodes triose-phosphate isomeraze (Eikmanns (1992), Journal of Bacteriology 174: 6076-6086),
the gene metA, which encodes homoserine O-acetyltransferase (EP 1 108 790 A2; DNA-SEQ NO. 725),
the gene metB, which encodes cystathionine-gamma synthase (EP 1 108 790 A2; DNA-SEQ NO. 3491),
the gene metC, which encodes cystathionine-gamma lyase (EP 1 108 790 A2; DNA-SEQ NO. 3061),
the gene mett, which encodes methionine-synthase (EP 1 108 790 A2; DNA-SEQ NO. 1663),
the gene glyA, which encodes serine hydroxymethyltransferase (EP 1 108 790 A2; DNA-SEQ NO. 1110),
the gene mety, which encodes O-acetylhomoserine sulfhydrylase (EP 1 108 790 A2; DNA-SEQ NO. 726),
the gene metF, which encodes methylenetetrahydrofolate reducase (EP 1 108 790 A2; DNA-SEQ NO. 2379),
the gene serC, which encodes phosphoserine aminotransferase (EP 1 108 790 A2; DNA-SEQ NO. 928)
a gene serB encoding phosphoserine-phosphatase (EP 1 108 790 A2; DNA-SEQ NO. 334, DNA-SEQ NO. 467, DNA-SEQ NO. 2767)
the gene cysE, which encodes serine acetyl transferase (EP 1 108 790 A2; DNA-SEQ NO. 2818)
the gene cysK, which encodes cysteine synthase (EP 1 108 790 A2; DNA-SEQ NO. 2817),
the gene hom, which encodes a homoserine dehydrogenase (EP 1 108 790 A2; DNA-SEQ NO. 1306)
Thus, it may be advantageous for the production of sulfur-containing fine chemicals, in particular L-methionine in coryneform bacteria simultaneously to mutate at least one of the following genes such that the corresponding proteins are affected less or not at all by a metabolite with regard to their activity with comparison with unmutated proteins, or so that their specific activity is enhanced:
the gene lysC, which encodes an aspartate kinase (EP 1 108 790 A2; DNA-SEQ NO. 281),
the gene pyc, which encodes pyruvate carboxylase (Eikmanns (1992), Journal of Bacteriology 174: 6076-6086),
the gene metA, which encodes homoserine O-acetyltransferase (EP 1 108 790 A2; DNA-SEQ NO. 725),
the gene metB, which encodes cystathionine-gamma synthase (EP 1 108 790 A2; DNA-SEQ NO. 3491),
the gene metC, which encodes cystathionine-gamma lyase (EP 1 108 790 A2; DNA-SEQ NO. 3061),
the gene metH, which encodes methionine synthase (EP 1 108 790 A2; DNA-SEQ NO. 1663),
the gene glyA, which encodes serine hydroxymethyltransferase (EP 1 108 790 A2; DNA-SEQ NO. 1110),
the gene metY, which encodes O-acetylhomoserine sulfhydrylase (EP 1 108 790 A2; DNA-SEQ NO. 726),
the gene metF, which encodes methylene tetrahydrofolate reductase (EP 1 108 790 A2; DNA-SEQ NO. 2379),
the gene serC, which encodes phosphoserine aminotransferase (EP 1 108 790 A2; DNA-SEQ NO. 928)
a gene serB which encodes phosphoserine-phosphatase (EP 1 108 790 A2; DNA-SEQ NO. 334, DNA-SEQ NO. 467, DNA-SEQ NO. 2767)
the gene cysE, which encodes serine acetyltransferase (EP 1 108 790 A2; DNA-SEQ NO. 2818)
the gene cysK, which encodes cysteine synthase (EP 1 108 790 A2; DNA-SEQ NO. 2817),
the gene hom, which encodes homoserine dehydrogenase (EP 1 108 790 A2; DNA-SEQ NO. 1306)
Moreover, it may be advantageous for the production of sulfur-containing fine chemicals, in particular L-methionine, additionally to the expression of one of the metK genes according to the invention to attenuate one or more of the following genes, in particular to reduce or switch off their expression:
the gene thrB, which encodes homoserine kinase (EP 1 108 790 A2; DNA-SEQ NO. 3453)
the gene ilvA, which encodes threonine dehydratase (EP 1 108 790 A2; DNA-SEQ NO. 2328)
the gene thrC, which encodes threonine synthase (EP 1 108 790 A2; DNA-SEQ NO. 3486)
the gene ddh, which encodes meso-diaminopimelate D-dehydrogenase (EP 1 108 790 A2; DNA-SEQ NO. 3494)
the gene pck, which encodes phosphoenolpyruvate carboxykinase (EP 1 108 790 A2; DNA-SEQ NO. 3157)
the gene pgi, which encodes glucose-6-phosphate 6-isomerase (EP 1 108 790 A2; DNA-SEQ NO. 950)
the gene poxB, which encodes pyruvate oxidase (EP 1 108 790 A2; DNA-SEQ NO. 2873)
the gene dapA, which encodes dihydrodipicolinate synthase (EP 1 108 790 A2; DNA-SEQ NO. 3476)
the gene dapB, which encodes dihydrodipicolinate reductase (EP 1 108 790 A2; DNA-SEQ NO. 3477)
the gene lysA, which encodes diaminopicolinate decarboxylase (EP 1 108 790 A2; DNA-SEQ NO. 3451)
Furthermore, it may be advantageous for the production of sulfur-containing fine chemicals, in particular L-methionine, additionally to the expressionof one of the metK genes according to the invention in coryneform bacteria simultaneously to mutate at least one the following genes in such a way that the enzyme activity of the corresponding protein is reduced to a degree or completely:
the gene thrB, which encodes homoserine kinase (EP 1 108 790 A2; DNA-SEQ NO. 3453)
the gene ilvA, which encodes threonine dehydratase (EP 1 108 790 A2; DNA-SEQ NO. 2328)
the gene thrC, which encodes threonine synthase (EP 1 108 790 A2; DNA-SEQ NO. 3486)
the gene ddh, which encodes meso-diaminopimelate D-dehydrogenase (EP 1 108 790 A2; DNA-SEQ NO. 3494)
the gene pck, which encodes phosphoenolpyruvate carboxykinase (EP 1 108 790 A2; DNA-SEQ NO. 3157)
the gene pgi, which encodes glucose-6-phosphate 6-isomerase (EP 1 108 790 A2; DNA-SEQ NO. 950)
the gene poxB, which encodes pyruvate oxidase (EP 1 108 790 A2; DNA-SEQ NO. 2873)
the gene dapA, which encodes dihydrodipicolinate synthase (EP 1 108 790 A2; DNA-SEQ NO. 3476)
the gene dapB, which encodes dihydrodipicolinate reductase (EP 1 108 790 A2; DNA-SEQ NO. 3477)
the gene lysA, which encodes diaminopicolinate decarboxylase (EP 1 108 790 A2; DNA-SEQ NO. 3451)
Furthermore, it may be advantageous for the production of sulfur-containing fine chemicals, in particular L-methionine, in addition to the expression of a metK gene according to the invention to eliminate undesired secondary reactions (Nakayama: “Breeding of Amino Acid Producing Microorganisms”, in: Overproduction of Microbial Products, Krumphanzl, Sikyta, Vanek (eds.), Academic Press, London, UK, 1982).
The skilled worker can take various measures, individually or in combination, in order to achieve overexpression. Thus, the copy number of the genes in question can be increased, or the promoter region and regulatory region or the ribosome binding site which is located upstream of the structural gene can be mutated. Expression cassettes which are introduced upstream of the structural gene act in the same fashion. In addition, inducible promoters make it possible to increase expression during the production of L-methionine by fermentation. Expression is also improved by measures which extend the life of mRNA.
Moreover, the enzyme activity is also increased by preventing the degradation of the enzyme protein. The genes or gene constructs can either be present in plasmids with different copy numbers or else be integrated and amplified in the chromosome. As an alternative, overexpression of the genes in question can furthermore be achieved by modifying the media composition and fermentation process.
The skilled worker will find information on the subject in, inter alia, Martin et al. (Biotechnology 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 EP 0472869, in U.S. Pat. No. 4,601,893, in Schwarzer and Pühler (Biotechnology 9, 84-87 (1991), in Remscheid et al. (Applied and Environmental Microbiology 60,126-132 (1994), in LaBarre et al. (Journal of Bacteriology 175, 1001-1007 (1993)), in WO 96/15246, in Malumbres et al. (Gene 134, 15-24 (1993)), in 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 known textbooks of genetics and molecular biology.
The invention therefore also relates to expression constructs comprising a nucleic acid sequence encoding a polypeptide according to the invention under the genetic control of regulatory nucleic acid sequences, and to vectors encompassing at least one of these expression constructs. Preferably, such constructs according to the invention comprise a promoter 5′-upstream of the coding sequence in question and, 3′-downstream, a termination sequence and, if appropriate, further customary regulatory elements, in each case in operative linkage with the coding sequence. “Operative linkage” is understood as meaning the sequential arrangement of promoter, coding sequence, terminator and, if appropriate, further regulatory elements in such a way that each of the regulatory elements can fulfill its intended function upon expression of the coding sequence. Examples of sequences capable of operative linkage are activation sequences and enhancers and the like. Further regulatory elements encompass selectable markers, amplification signals, replication origins and the like. Suitable regulatory sequences are described, for example, in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990).
The natural regulatory sequence may still be present upstream of the actual structural gene, in addition to the artificial regulatory sequences. If appropriate, this natural regulation can be eliminated by genetic modification, and gene expression can be increased or reduced. However, the gene construct may also be simpler in construction, that is to say no additional regulatory signals are inserted before the structural gene, and the natural promoter with its regulation is not removed. Instead, the natural regulatory sequence is mutated in such a way that regulation no longer takes place, and gene expression is increased or reduced. One or more copies of the nucleic acid sequences may be present in the gene construct.
Examples of useful promoters are: the promoters ddh, amy, lysC, dapA, lysA from Corynebacterium glutamicum, but also Gram-positive promoters SPO2 as are described in Bacillus Subtilis and Its Closest Relatives, Sonenshein, Abraham L., Hoch, James A., Losick, Richard; ASM Press, District of Columbia, Wash. and Patek M. Eikmanns B J. Patek J. Sahm H. Microbiology. 142 1297-309, 1996, or else cos, tac, trp, tet, trp-tet, lpp, lac, Ipp-lac, laclq, T7, T5, T3, gal, trc, ara, SP6, I-PR or l-PL promoters, which are advantageously used in Gram-negative bacteria. Also preferred is the use of inducible promoters, such as, for example, light-inducible and, in particular, temperature-inducible promoters, such as the PrPl promoter. In principle, all natural promoters together with their regulatory sequences may be used. In addition, synthetic promoters may also be used advantageously.
The abovementioned regulatory sequences are intended to make possible the targeted expression of the nucleic acid sequences and of protein expression. Depending on the host organism, this may mean, for example, that the gene is expressed or overexpressed only after induction, or that it is expressed and/or overexpressed immediately.
In this context, the regulatory sequences or factors can preferably have an adverse effect on expression, thus reducing it. Thus, diminution may take place at the transcriptional level by using weak transcription signals such as promoters and/or enhancers. However, diminution of translation is also possible, for example by reducing mRNA stability.
In this context, the regulatory sequences or factors may preferably have a positive effect on expression, thus increasing or reducing it. Thus, an enhancement of the regulatory elements may advantageously take place at the transcriptional level by using strong transcription signals such as promoters and/or enhancers. However, enhancement of translation is also possible, for example by increasing mRNA stability.
An expression cassette is generated by fusing a suitable promoter, a suitable Shine-Dalgarno sequence with a metK nucleotide sequence and a suitable termination signal. Customary recombination and cloning techniques as are described, for example, in Current Protocols in Molecular Biology, 1993, John Wiley & Sons, Incorporated, New York N.Y., PCR Methods, Gelfand, David H., Innis, Michael A., Sinsky, John J. 1999, Academic Press, Incorporated, Calif., San Diego, PCR Cloning Protocols, Methods in Molecular Biology Ser., Vol. 192, 2nd ed., Humana Press, New Jersey, Totowa. T. Maniatis, E. F. Fritsch and J. Sambrook, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989) and in T. J. Silhavy, M. L. Berman and L. W. Enquist, Experiments with Gene Fusions, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1984) and in Ausubel, F. M. et al., Current Protocols in Molecular Biology, Greene Publishing Assoc. and Wiley Interscience (1987) are used for this purpose.
For expression in a suitable host organism, the recombinant nucleic acid construct or gene construct is advantageously inserted into a host-specific vector which makes possible optimal expression of the genes in the host. Vectors are well known to the skilled worker and can be found, for example, in “Cloning Vectors” (Pouwels P. H. et al., Ed., Elsevier, Amsterdam-New York-Oxford, 1985). Apart from plasmids, vectors are also understood as meaning all the other vectors with which the skilled worker is familiar, such as, for example, phages, transposons, IS elements, phagemids, cosmids, and linear or circular DNA. These vectors can be replicated autonomously in the host organism or else replicated chromosomally.
metK genes according to the invention are expressed for example with the aid of episomal plasmids. Suitable plasmids are those which are replicated in coryneform bacteria. A large number of know 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, pCLiK5MCS, SEQ ID NO: 9, or those which are 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 likewise be used.
Other suitable plasmid vectors are those with the aid of which the method of gene amplification by integration into the chromosome can be applied, as has been described, for example, by Remscheid et al. (Applied and Environmental Microbiology 60,126-132 (1994)) for duplicating or amplifying the hom-thrB operon. In this method, the complete gene is cloned into a plasmid vector which is capable of replication in a host (typically E. coli), but not in C. glutamicum. Suitable vectors are, for example, pSUP301 (Simon et al., Bio/Technology 1,784-791 (1983)), pK18mob or pK19mob (Schafer et al., Gene 145,69-73 (1994)), Bernard et al., Journal of Molecular Biology, 234: 534-541 (1993)), pEM1 (Schrumpf et al. 1991, Journal of Bacteriology 173: 4510-4516) or pBGS8 (Spratt et al., 1986, Gene 41: 337-342). Other plasmid vectors, such as, for example, pCLiK5MCS integrative sacB, SEQ ID NO:12, may likewise be used.
The plasmid vector containing the gene to be amplified is subsequently transferred into the desired C. glutamicum strain by transformation. Transformation methods are described, for example, by Thierbach et al. (Applied Microbiology and Biotechnology 29, 356-362 (1988)), Dunican and Shivnan (Biotechnology 7, 1067-1070 (1989)) and Tauch et al. (FEMS Microbiological Letters 123,343-347 (1994)).
The microorganisms which have been produced in accordance with the invention can be grown continuously or discontinuously by the batch method, the fed-batch method or the repeated fed-batch method for producing sulfur-containing fine chemicals, in particular L-methionine. An overview over known culture methods can be found in the textbook by Chmiel (Bioprozeβtechnik 1. Einführung in die Bioverfahrenstechnik [Bioprocess Engineering 1. Introduction to Bioprocess Technology] (Gustav Fischer Verlag, Stuttgart, 1991)) or in the textbook by Storhas (Bioreaktoren and periphere Einrichtungen [Bioreactors and Peripheral Units] (Vieweg Verlag, Brunswick/Wiesbaden, 1994)).
The culture medium to be used must suitably meet the needs of the strains in question. Descriptions of culture media for a variety of microorganisms are found in the manual “Manual of Methods fur General Bacteriology” of the American Society for Bacteriology (Washington D.C., USA, 1981).
These media which can be employed in accordance with the invention usually encompass one or more carbon sources, nitrogen sources, inorganic salts, vitamins and/or trace elements.
Preferred carbon sources are sugars such as mono-, di- or polysaccharides. Examples of very good carbon sources are glucose, fructose, mannose, galactose, ribose, sorbose, ribulose, lactose, maltose, sucrose, raffinose, starch or cellulose. Sugars may also be added to the media via complex compounds, such as molasses, or other by-products of sugar refining. It may also be advantageous to add mixtures of various carbon sources. Other possible carbon sources are oils and fats such as, for example, soya oil, sunflower oil, peanut oil and coconut fat, fatty acids such as, for example, palmitic acid, stearic acid or linoleic acid, alcohols such as, for example, glycerol, methanol or ethanol, and organic acids such as, for example, acetic acid or lactic acid.
Nitrogen sources are usually organic or inorganic nitrogen compounds or materials comprising these compounds. Examples of nitrogen sources encompass ammonia gas or ammonium salts such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate or ammonium nitrate, nitrates, urea, amino acids or complex nitrogen sources such as corn steep liquor, soya meal, soya protein, yeast extract, meat extract and others. The nitrogen sources can be used individually or as a mixture.
Inorganic salt compounds which may be present in the media encompass the chloride, phosphorus or sulfate salts of calcium, magnesium, sodium, cobalt, molybdenum, potassium, manganese, zinc, copper and iron.
Inorganic sulfur-containing compouds such as, for example, sulfates, sulfites, dithionites, tetrathionates, thiosulfates, sulfides, but also organic sulfur compounds, such as mercaptans and thiols, may be used as sulfur source for the production of sulfur-containing fine chemicals, in particular of methionine.
Phosphoric acid, potassium dihydrogenphosphate or dipotassium hydrogenphosphate or the corresponding sodium-containing salts may be used as phosphorus source.
Sequestrants may be added to the medium in order to maintain the metal ions in solution. Particularly suitable sequestrants encompass dihydroxyphenols, such as catechol or protocatechuate, or organic acids such as citric acid.
Usually, the fermantation media employed in accordance with the invention also comprise other growth factors such as vitamins or growth promoters, which include, for example, biotin, riboflavin, thiamine, folic acid, nicotinic acid, panthothenate and pyridoxine. Growth factors and salts are frequently obtained from complex media components such as yeast extract, molasses, corn steep liquor and the like. Moreover, suitable precursors may be added to the culture medium. The exact composition of the compounds in the media depends greatly on the experiment in question and will be decided individually for each individual case. Information on the optimization of media can be found in the textbook “Applied Microbiol. Physiology, A Practical Approach” (Ed. P. M. Rhodes, P. F. Stanbury, IRL Press (1997) pp. 53-73, ISBN 0 19 963577 3). Growth media can also be obtained from commercial sources, such as Standard 1 (Merck) or BHI (brain heart infusion, DIFCO) and the like.
All components of media are sterilized, either by means of heat (20 minutes at 1.5 bar and 121° C.) or by filter sterilization. The components may be sterilized either together or, if appropriate, separately. All of the components of the media may be present at the beginning of the fermentation or else be added continuously or batchwise, as desired.
The culture temperature is normally between 15° C. and 45° C., preferably 25° C. to 40° C., and can be kept constant during the experiment or else be varied. The pH of the medium should be in the range of from 5 to 8.5, preferably around 7.0. The pH for the fermentation can be controlled during the fermentation by addition of basic compounds such as sodium hydroxide, potassium hydroxide, ammonia or ammonia water, or acidic compounds such as phosphoric acid or sulfuric acid. Antifoam agents such as, for example, fatty acid polyglycol esters may be employed to control foam development. To maintain plasmid stability, suitable selectively acting substances such as, for example, antibiotics may be added to the medium. To maintain aerobic conditions, oxygen or oxygen-containing gas mixtures, for example ambient air, are passed into the culture. The culture temperature is normally 20° C. to 45° C., preferably 25° C. to 40° C. Fermentation is continued until a maximum of the desired product has formed. This aim is normally achieved within 10 hours to 160 hours.
The fermentation broths obtained in this way, in particular fermentation broths comprising L-methionine, usually contain a dry biomass of 7.5 to 25% by weight.
An additional advantage is to carry out the fermentation under sugar limitation conditions, at least at the end, but in particular over at least 30% of the fermentation period. This means that during this time the concentration of utilizable sugar in the fermentation medium is maintained at or reduced to >0 to 3 g/l.
The fermentation broth is then processed further. According to requirement, all or some of the biomass may be removed from the fermentation broth by separation methods such as, for example, centrifugation, filtration, decanting or a combination of these methods, or else be left completely in said broth.
Subsequently, the fermentation broth may be thickened or concentrated with the aid of known methods, such as, for example, with the aid of a rotary evaporator, a thin-film evaporator, a falling-film evaporator, by reverse osmosis, or by nanofiltration. This concentrated fermentation broth can then be worked up by freeze drying, spray drying, spray granulation or by other methods.
However, it is also possible to further purify the sulfur-containing fine chemicals, in particular L-methionine. To this end, the product-containing broth, after removing the biomass, is subjected to a chromatography using a suitable resin, with all or some of the desired product or contaminants being retained on the chromatography resin. These chromatography steps can be repeated, if necessary, using the same or other chromatography resins. The skilled worker is familiar with the selection of suitable chromatography resins and their most effective use. The purified product can be concentrated by filtration or ultrafiltration and stored at a temperature at which the stability of the product is greatest.
The identity and purity of the isolated compound(s) can be determined by techniques of the art. These include high performance liquid chromatography (HPLC), spectroscopic methods, staining methods, thin-layer chromatography, NIRS, enzyme assay or microbiological assays. These analytic methods are summarized 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, pp. 89-90, pp. 521-540, pp. 540-547, pp. 559-566, 575-581 and pp. 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, Volume 17.
The following nonlimiting examples describe the invention in more detail:
FIG. 1 shows the results of a radioactive metK assay using wild-type enzyme and C94A mutants, respectively.
EXAMPLE 1
Construction of the Vector pCLiK5MCS
First ampicillin resistance and origin of replication of the vector pBR322 were amplified using the oligonucleotide primers SEQ ID NO: 1 and SEQ ID NO: 2 with the aid of the polymerase chain reaction (PCR).








SEQ ID NO:1









5′-CCCGGGATCCGCTAGCGGCGCGCCGGCCGGCCCGGTGTGAAATACCG



CACAG-3′


 








SEQ ID NO:2









5′-TCTAGACTCGAGCGGCCGCGGCCGGCCTTTAAATTGAAGACGAAAGG



GCCTCG-3′






In addition to the sequences complementary to pBR322, the oligonucleotide primer SEQ ID NO: 1 contains in 5′-3′ direction the cleavage sites for the restriction nucleases SmaI, BamHI, NheI and AscI and the oligonucleotide primer SEQ ID NO: 2 contains in 5′-3′ direction the cleavage sites for the restriction endonucleases XbaI, XhoI, NotI and DraI. The PCR reaction was carried out according to a standard method such as that by Innis et al. (PCR Protocols. A Guide to Methods and Applications, Academic Press (1990)) using PfuTurbo polymerase (Stratagene, La Jolla, USA). The DNA fragment obtained of approximately 2.1 kb in size was purified using the GFXTMPCR, DNA and gel band purification kit (Amersham Pharmacia, Freiburg) according to the manufacturer's instructions. The blunt ends of the DNA fragment were ligated to one another using the rapid DNA ligation kit (Roche Diagnostics, Mannheim) according to the manufacturer's instructions and the ligation mixture was transformed into competent E. coli XL-1 Blue (Stratagene, La Jolla, USA) according to standard methods, as described in Sambrook et al. (Molecular Cloning. A Laboratory Manual, Cold Spring Harbor, (1989)). Plasmid-carrying cells were selected by plating out onto ampicillin (50 μg/ml)-containing LB agar (Lennox, 1955, Virology, 1:190).
The plasmid DNA of an individual clone was isolated using the Qiaprep spin miniprep kit (Qiagen, Hilden) according to the manufacturer's instructions and checked by restriction digests. The plasmid obtained in this way is denoted pCLiK1.
Starting from plasmid pWLT1 (Liebl et al., 1992) as template for a PCR reaction, a kanamycin resistance cassette was amplified using the oligonucleotide primers SEQ ID NO: 3 and SEQ ID NO: 4.








SEQ ID NO:3:



5′-GAGATCTAGACCCGGGGATCCGCTAGCGGGCTGCTAAAGGAAGCGG


A-3′


 


SEQ ID NO:4:


5′-GAGAGGCGCGCCGCTAGCGTGGGCGAAGAACTCCAGCA-3′






Apart from the sequences complementary to pWLT1, the oligonucleotide primer SEQ ID NO:3 contains in 5′-3′ direction the cleavage sites for the restriction endonucleases XbaI, SmaI, BamHI, NheI and the oligonucleotide primer SEQ ID NO: 4 contains in the 5′-3′ direction the cleavage sites for the restriction endonucleases AscI and NheI. The PCR reaction was carried out using PfuTurbo polymerase (Stratagene, La Jolla, USA) according to a standard method such as that of Innis et al. (PCR Protocols. A Guide to Methods and Applications, Academic Press (1990)). The DNA fragment obtained approximately 1.3 kb in size was purified using the GFXTMPCR, DNA and gel band purification kit (Amersham Pharmacia, Freiburg) according to the manufacturer's instructions. The DNA fragment was cleaved with restriction endonucleases XbaI and AscI (New England Biolabs, Beverly, USA) and, following that, again purified using the GFXTMMPCR, DNA and gel band purification kit (Amersham Pharmacia, Freiburg) according to the manufacturer's instructions. The vector pCLiK1 was likewise cleaved with the restriction endonucleases XbaI and AscI and dephosphorylated using alkaline phosphatase I (Roche Diagnostics, Mannheim) according to the manufacturer's instructions. After electrophoresis in a 0.8% strength agarose gel, the linearized vector (approx. 2.1 kb) was isolated using the GFXTMPCR, DNA and gel band purification kit (Amersham Pharmacia, Freiburg) according to the manufacturer's instructions. This vector fragment was ligated with the cleaved PCR fragment with the aid of the rapid DNA ligation kit (Roche Diagnostics, Mannheim) according to the manufacturer's instructions and the ligation mixture was transformed into competent E. coli XL-1Blue (Stratagene, La Jolla, USA) according to standard methods, as described in Sambrook et al. (Molecular Cloning. A Laboratory Manual, Cold Spring Harbor, (1989)). Plasmid-carrying cells were selected by plating out onto ampicillin (50 μg/ml) and kanamycin (20 μg/ml)-containing LB agar (Lennox, 1955, Virology, 1:190).
The plasmid DNA of an individual clone was isolated using the Qiaprep spin miniprep kit (Qiagen, Hilden) according to the manufacturer's instructions and checked by restriction digests. The plasmid obtained in this way is denoted pCLiK2.
The vector pCLiK2 was cleaved with the restriction endonuclease Dral (New England Biolabs, Beverly, USA). After electrophoresis in 0.8% strength agarose gel, an approx. 2.3 kb vector fragment was isolated using the GFXTMPCR, DNA and gel band purification kit (Amersham Pharmacia, Freiburg) according to the manufacturer's instructions. This vector fragment was religated with the aid of the rapid DNA ligation kit (Roche Diagnostics, Mannheim) according to the manufacturer's instructions and the ligation mixture was transformed into competent E. coli XL-1 Blue (Stratagene, La Jolla, USA) according to standard methods, as described in Sambrook et al. (Molecular Cloning. A Laboratory Manual, Cold Spring Harbor, (1989)). Plasmid-carrying cells were selected by plating out onto kanamycin (20 μg/ml)-containing LB agar (Lennox, 1955, Virology, 1:190).
The plasmid DNA of an individual clone was isolated using the Qiaprep spin miniprep kit (Qiagen, Hilden) according to the manufacturer's instructions and checked by restriction digests. The plasmid obtained in this way is denoted pCLiK3.
Starting from plasmid pWLQ2 (Liebl et al., 1992) as template for a PCR reaction, the origin of replication pHM1519 was amplified using the oligonucleotide primers SEQ ID NO: 5 and SEQ ID NO:6.










SEQ ID NO:5:




5′-GAGAGGGCGGCCGCGCAAAGTCCCGCTTCGTGAA-3′



 



SEQ ID NO:6:



5′-GAGAGGGCGGCCGCTCAAGTCGGTCAAGCCACGC-3′






Apart from the sequences complementary to pWLQ2, the oligonucleotide primers SEQ ID NO:5 and SEQ ID NO:6 contain cleavage sites for the restriction endonuclease NotI. The PCR reaction was carried out using PfuTurbo polymerase (Stratagene, La Jolla, USA) according to a standard method such as that of Innis et al. (PCR Protocols. A Guide to Methods and Applications, Academic Press (1990)). The DNA fragment obtained approximately 2.7 kb in size was purified using the GFXTMPCR, DNA and gel band purification kit (Amersham Pharmacia, Freiburg) according to the manufacturer's instructions. The DNA fragment was cleaved with restriction endonuclease Notl (New England Biolabs, Beverly, USA) and, following that, again purified using the GFXTMPCR, DNA and gel band purification kit (Amersham Pharmacia, Freiburg) according to the manufacturer's instructions. The vector pCLiK3 was likewise cleaved with the restriction endonuclease NotI and dephosphorylated using alkaline phosphatase I (Roche Diagnostics, Mannheim) according to the manufacturer's instructions. After electrophoresis in a 0.8% strength agarose gel, the linearized vector (approx. 2.3 kb) was isolated using the GFXTMPCR, DNA and gel band purification kit (Amersham Pharmacia, Freiburg) according to the manufacturer's instructions. This vector fragment was ligated with the cleaved PCR fragment with the aid of the rapid DNA ligation kit (Roche Diagnostics, Mannheim) according to the manufacturer's instructions and the ligation mixture was transformed into competent E. coli XL-1 Blue (Stratagene, La Jolla, USA) according to standard methods, as described in Sambrook et al. (Molecular Cloning. A Laboratory Manual, Cold Spring Harbor, (1989)). Plasmid-carrying cells were selected by plating out onto kanamycin (20 μg/ml)-containing LB agar (Lennox, 1955, Virology, 1:190).
The plasmid DNA of an individual clone was isolated using the Qiaprep spin miniprep kit (Qiagen, Hilden) according to the manufacturer's instructions and checked by restriction digests. The plasmid obtained in this way is denoted pCLiK5.
pCLiK5 was extended by a multiple cloning site (MCS) by combining the two synthetic essentially complementary oligonucleotides SEQ ID NO:7 and SEQ ID NO:8, which contain cleavage sites for the restriction endonucleases SwaI, XhoI, AatI, ApaI, Asp718, MluI, NdeI, SpeI, EcoRV, SaII, CIaI, BamHI, XbaI and SmaI to give a double-stranded DNA fragment by heating them together to 95° C. followed by slow cooling.








SEQ ID NO:7:



5′-TCGAATTTAAATCTCGAGAGGCCTGACGTCGGGCCCGGTACCACGCG


 


TCATATGACTAGTTCGGACCTAGGGATATCGTCGACATCGATGCTCTTCT


 


GCGTTAATTAACAATTGGGATCCTCTAGACCCGGGATTTAAAT-3′


 


SEQ ID NO:8:


5′-GATCATTTAAATCCCGGGTCTAGAGGATCCCAATTGTTAATTAACGC


 


AGAAGAGCATCGATGTCGACGATATCCCTAGGTCCGAACTAGTCATATGA


 


CGCGTGGTACCGGGCCCGACGTCAGGCCTCTCGAGATTTAAAT-3′






The vector pCLiK5 was cleaved with the restriction endonucleases XhoI and BamHI (New England Biolabs, Beverly, USA) and dephosphorylatted using alkaline phosphatase I (Roche Diagnostics, Mannheim) according to the manufacturer's instructions. After electrophoresis in a 0.8% strength agarose gel, the linearized vector (approx. 5.0 kb) was isolated using the GFXTMPCR, DNA and gel band purification kit (Amersham Pharmacia, Freiburg) according to the manufacturer's instructions. This vector fragment was ligated with the synthetic double-stranded DNA fragment with the aid of the rapid DNA ligation kit (Roche Diagnostics, Mannheim) according to the manufacturer's instructions and the ligation mixture was transformed into competent E. coli XL-1 Blue (Stratagene, La Jolla, USA) according to standard methods as described in Sambrook et al. (Molecular Cloning. A Laboratory Manual, Cold Spring Harbor, (1989)). Plasmid-carrying cells were selected by plating out onto kanamycin (20 μg/ml)-containing LB agar (Lennox, 1955, Virology, 1:190).
The plasmid DNA of an individual clone was isolated using the Qiaprep spin miniprep kit (Qiagen, Hilden) according to the manufacturer's instructions and checked by restriction digests. The plasmid obtained in this way is denoted pCLiK5MCS.
Sequencing reactions were carried out according to Sanger et al. (1977) Proceedings of the National Academy of Sciences USA 74:5463-5467. The sequencing reactions were fractionated and analyzed by means of ABI Prism 377 (PE Applied Biosystems, Weiterstadt).
The resultant plasmid pCLiK5MCS is listed as SEQ ID NO:9.
EXAMPLE 2
Construction of the vector pCLiK5MCS integrativ sacB
Starting from the plasmid pK19mob (Schafer et al., Gene 145,69-73(1994)) as template for a PCR reaction, the Bacillus subtilis sacB gene was amplified using the oligonucleotide primers SEQ ID NO:10 and SEQ ID NO:11.










SEQ ID NO:10:




5′-GAGAGCGGCCGCCGATCCTTTTTAACCCATCAC-3′



 



SEQ ID NO:11:



5′-AGGAGCGGCCGCCATCGGCATTTTCTTTTGCG-3′






Apart from the sequences complementary to pK19mobsac, the oligonucleotide primers SEQ ID NO:10 and SEQ ID NO:11 contain cleavage sites for the restriction endonuclease NotI. The PCR reaction was carried out using PfuTurbo polymerase (Stratagene, La Jolla, USA) according to a standard method such as that of Innis et al. (PCR Protocols. A Guide to Methods and Applications, Academic Press (1990)). The DNA fragment obtained of approximately 1.9 kb in size was purified using the GFXTMPCR, DNA and gel band purification kit (Amersham Pharmacia, Freiburg) according to the manufacturer's instructions. The DNA fragment was cleaved with the restriction endonuclease NotI (New England Biolabs, Beverly, USA) and, following that, again purified using the GFXTMPCR, DNA and gel band purification kit (Amersham Pharmacia, Freiburg) according to the manufacturer's instructions. The vector pCLiK5MCS was likewise cleaved with the restriction endonuclease NotI and dephosphorylated using alkali phosphatase I (Roche Diagnostics, Mannheim) according to the manufacturer's instructions. After electrophoresis in a 0.8% strength agarose gel, an approximately 2.4 kb in size vector fragment was isolated using the GFXTMPCR, DNA and gel band purification kit (Amersham Pharmacia, Freiburg) according to the manufacturer's instructions. This vector fragment was ligated with the cleaved PCR fragment with the aid of the rapid DNA ligation kit (Roche Diagnostics, Mannheim) according to the manufacturer's instructions and the ligation mixture was transformed into competent E. coli XL-1 Blue (Stratagene, La Jolla, USA) according to standard methods, as described in Sambrook et al. (Molecular Cloning. A Laboratory Manual, Cold Spring Harbor, (1989)). Plasmid-carrying cells were selected by plating out onto kanamycin (20 μg/ml)-containing LB agar (Lennox, 1955, Virology, 1:190).
The plasmid DNA of an individual clone was isolated using the Qiaprep spin miniprep kit (Qiagen, Hilden) according to the manufacturer's instructions and checked by restriction digests. The plasmid obtained in this way is noted pCLiK5MCS integrativ sacB.
Sequencing reactions were carried out according to Sanger et al. (1977) Proceedings of the National Academy of Sciences USA 74:5463-5467. The sequencing reactions were fractionated and analyzed by means of ABI Prism 377 (PE Applied Biosystems, Weiterstadt).
The resultant plasmid pCLiK5MCS integrativ sacB is listed as SEQ ID NO:12.
EXAMPLE 3
Isolation and cloning of the metK gene from C. glutamicum 
Chromosomal C. glutamicum ATCC 13032 DNA was prepared using the method of Tauch et al. (1995) Plasmid 33:168-179 or Eikmanns et al. (1994) Microbiology 140:1817-1828. The following oligonucleotide primers were synthesized starting from the metK sequence of Groβmann et al. (2000) FEMS Microbiology Letters 193:99-103:








SEQ ID NO:13











5′-GAGAGCCCGGGAAGAAGGGCTGCGACCTCCTCAT-3′




and



 








SEQ ID NO:14











5′-CTCTCACGCGTCATATGCAGGTGAGGTAACCCCA-3′







A 1640 base pair DNA fragment was amplified from the genomic C. glutamicum DNA using standard methods as described by Innis et al. (1990) PCR Protocols. A Guide to Methods and Applications, Academic Press using the abovementioned oligonucleotide primers and Pfu Turbo Polymerase (Stratagene).
The fragment was cleaved with the restirction enzymes Mlu I and Sma I (Roche Diagnostics, Mannheim) which had been introduced via the PCR oligonucleotide primers and separated by gel electrophoresis. The DNA fragment was subsequently isolated from the agarose using GFXTMPCR, DNA and Gel Band Purification Kit (Amersham Pharmacia, Freiburg).
The vector pCLiK5MCS, SEQ ID NO:9 was likewise cleaved with the restriction enzymes Sma I and Mlu I and dephosphorylated with alkaline phosphatase I (Roche Diagnostics, Mannheim) following the manufacturer's instructions. The vector and the DNA fragment were ligated with T4 DNA ligase (Amersham Pharmacia, Freiburg) and transformed into E. coli XL-1Blue (Stratagene) using standard methods as described by Sambrook et al. (1989), Molecular Cloning. A Laboratory Manual, Cold Spring Harbor.
Plasmid DNA was prepared by methods and materials from Quiagen. Sequencing reactions were carried out as described by Sanger et al. (1977) Proceedings of the National Academy of Sciences USA 74:5463-5467. The sequencing reactions were separated and evaluated by means of ABI Prism 377 (PE Applied Biosystems, Weiterstadt).
The resultant plasmid pCLiK5MCS/metKwt is listed as SEQ ID NO:15.
EXAMPLE 4
Mutagenesis of the C. glutamicum metK Gene
Directed mutagenesis of the C. glutamicum metK gene was carried out using the QuickChange Kit (Stratagene), following the manufacturer's instructions. The mutagenesis was carried out in plasmid pCLiK5MCS/metKwt, SEQ ID NO:15. The following oligonucleotide primers were synthesized for substituting cysteine 94 of SEQ ID NO: 16 for alanine 94:








SEQ ID NO:17











5′-GATTCGACGGACGCACCGCTGGCGTCTCAGTATCCATC-3′




and



 








SEQ ID NO:18











5′-GATGGATACTGAGACGCCAGCGGTGCGTCCGTCGAATC-3′







The use of these oligonucleotide primers resulted in SEQ ID NO:15 in a substitution of the nucleotides in position 1056 (C was substituted by G) and 1057 (A was substituted by C). The resulting amino acid substitution Cys94Ala in the metK gene was confirmed by sequencing reactions following transformation and plasmid preparation. The plasmid was denoted pCLiK5MCS/metKC94A and is listed as SEQ ID NO:19.
SAM Synthetase (metK) Assay
C. glutamicum strains which had been transformed either with the plasmid pCLiK5MCS/metKwt, SEQ ID NO: 15 or with the plasmid pCLiK5MCS/metKC94A, SEQ ID NO: 19 were grown in BHI/glucose medium (37 g/l prepared brain heart infusion medium, Difco, 10 mM (NH4)2SO4, 4% glucose) at 30° C. to an OD600 of 20. The cells were spun down at 4° C. and the pellet was washed with cold physiological saline. After recentrifugation, 0.25 g of moist cell pellet was resuspended in 1 ml of disruption buffer (50 mM Tris pH 7.5, 10 mM MgCl2, 50 mM KCI, 1 mM DTT) at 4° C. The bacterial suspension was lysed three times for in each case 30 seconds in a Ribolyser from Hybaid and in blue Ribolyser tubes from Hybaid and at rotation setting 6.0. The lysate was clarified by centrifugation for 45 minutes in an Eppendorf centrifuge at 13 000 rpm, and the supernatant was diluted with water 1:10. The protein content was determined by the method of Bradford, M. M. (1976) Anal. Biochem. 72:248-254.
The enzyme activity of SAM synthase was determined by the method of Markham, G. D. et al. (1983) Methods in Enzymology 94: 219-222, with the following modifications:
Reaction mixtures of 100 μl, containing 100 mM Tris pH 8.0, 100 mM KCI, 20 mM MgCl2, 1.2 mM L-methionine, 10 mM ATP, 1 μl 35S-L-methionine, corresponding to 15.15 μCi (Amersham SJ204, specific activity 1 Ci/μmol) and H2O to 100 μl were started with 100 μg of the protein lysates in question and incubated at 37° C. After 0, 5, 10, 20, 30 and 60 minutes, 10 μl aliquots of the reaction mixture were removed and stopped on ice using 20 μl of 50 mM EDTA.
30 μl of the stopped reaction were placed on phosphocellulose filter units (Pierce, No. 29520) and spun down for 1 minute in an Eppendorf centrifuge at 6000 rpm. The filter was washed twice with 500 μl of 75 mM phosphoric acid and then placed into a counting tube containing scintillation liquid. The radioactivity of the S-adenosylmethionine formed is determined in a scintillation counter (Beckman).
The data are shown in the appended FIG. 1.
Taking into consideration the specific activity of the radioactive L-methionine, and the protein quantity employed, the rate of S-adenosylmethionine formation can be determined from the increase in radioactivity incorporated per unit time. Its unit is μmol S-adenosylmethionine/min*mg protein. This rate can be compared between wild-type enzyme and mutant enzyme.
EXAMPLE 6
Determination of the Cellular S-adenosylmethionine titer in C. glutamicum 
To determine the cellular S-adenosylmethionine titers in C. glutamicum strains which have been transformed either with pCLiK5MCS/metKwt (SEQ ID NO:15) or pCLiK5MCS/metKC94A (SEQ ID NO:19), the following procedure was used. A cell pellet obtained as described in Example 5 which had been washed with ice-cold physiological saline was resuspended in trichloroacetic acid (200 μl of TCA per 0.1 g moist pellet). After 5 minutes on ice, the suspension was clarified for 5 minutes in an Eppendorf centrifuge at 4° C. and 13 000 rpm. The S-adenosylmethionine content in the supernatant was determined by means of HPLC (lonospher 5C cation exchange column, injection volume 10 μl, mobile phase: 70% vol/vol 0.2 M Ammonium formate pH 4.0 30% vol/vol methanol; UV detection 260 nm; 40° C.; retention time 8.5 minutes).







TABLE 1







S-Adenosylmethionine titers









mg/l














ATCC 13032 + metK
73.94



ATCC 13032 + metK C94A
47.36










EXAMPLE 7
Substitution of the metK wt Gene in C. glutamicum for metK C94A
For the allelic substitution of the metK wild-type gene in C. glutamicum KFCC10065 by the mutant metK C94A, the metK C94A sequence from SEQ ID NO:19 was first cloned into pCLiK5MCS integrativ sacB (SEQ ID NO:12). To this end, the plasmid pCLiK5MCS/metKC94A (SEQ ID NO:19) was cleaved with the restriction endonucleases Bgl II and Xho I (NEB, Schwalbach). The resulting 1962 base pair fragment was purified as described in Example 3. The vector pCLiK5MCS integrativ sacB was likewise cleaved with Bgl II and XhoI and purified as described in Example 3. Vector and fragment were ligated and transformed into E. coli XL-1 Blue as described in Example 3. The plasmid was purified and, after sequencing, confirmed. The resulting plasmid pCLiK5MCS integrativ sacB/metKC94A is listed as SEQ ID NO:20.
The plasmid pCLiK5MCS integrativ sacB/metKC94A was transformed into C. glutamicum KFCC10065 by electroporation as described by Liebl, et al. (1989) FEMS Microbiology Letters 53:299-303. Modifications of the protocol are described in DE 10046870. The chromosomal arrangement of the metK locus of individual transformants was verified by standard methods by Southern blots and hybridization as described by Sambrook et al. (1989), Molecular Cloning. A Laboratory Manual, Cold Spring Harbor. It was thereby ensured that the transformants were those which have the transformed plasmid integrated at the metK locus by homologous recombination. After such colonies were grown overnight in media without antibiotic, these transformants were then plated onto a sucrose CM agar medium (10% sucrose) and incubated for 24 hours at 30° C.
Since the sacB gene, which is present in the vector pCLiK5MCS integrativ sacB/metKC94A, converts sucrose into a toxic product, only those colonies which have the sacB gene deleted by a second homologous recombination step between the wild-type metK gene and the mutated metKC94A gene are capable of growth. Either the wild-type gene or the mutated gene together with the sacB gene can be deleted while homologous recombination takes place. If the sacB gene together with the wild-type gene is removed, a mutant transformant results.
Growing colonies were picked out, their genomic DNA was prepared, and the metK gene was analyzed by two methods. Firstly, the substitution of two nucleotides as described in Example 4 was exploited. Diagnostic PCR fragments were generated with the aid of a specific PCR oligonucleotide primer which is capable of differentiating between the two alleles at its 3′ end and a second, metK-specific oligonucleotide primer. Secondly, the metK locus of approximately 100 transformants was sequenced, after PCR amplification, with PCR oligonucleotide primers which bind upstream or downstream of the mutation. Several mutated metK clones were obtained. One such a clone was termed KFCC10065metKC94A. The amino acid sequence of mutant C94A corresponds to SEQ ID NO:22.
EXAMPLE 8
Production of Methionine using Strain KFCC10065metKC94A
The strain KFCC10065metKC94A, which had been generated in Example 6, was grown on an agar plate containing BHI medium (Difco) for 2 days at 30° C. The cells which had grown were suspended in saline from the agar plate and transferred into medium II at an OD 600 nm of 1.5. Medium II was composed as follows.










Medium IIA

















0.6
g/l
KH2PO4


0.4
g/l
MgSO4*7H2O


25
g/l
(NH4)2SO4


40
g/l
raw sugar


60
g/l
molasses









The medium prepared thus was brought to pH 7.8 with NH4OH and sterilized for 30 minutes at 120° C.










Medium IIB:

















0.3
mg/l
thiamine*HCl


1
mg/l
biotin


2
mg/l
FeSO4


2
mg/l
MnSO4


0.1
mg/l
vitamin B12









Medium IIB was prepared separately, filter-sterilized and added to medium IIA. The two components IIa and IIB together form medium II.
10 ml of medium II (=IIA+B) were treated, in a 100 ml Erlenmyer flask containing 0.5 g sterilized CaCO3, with cells of the abovementioned strain and incubated for 72 hours on an orbital shaker at 30° C. at 200 rpm.
Formed methionine in the culture broth was determined with the aid of the amino acid determination method from Agilent on an Agilent 1100 Series LC System HPLC. Pre-column derivatization with ortho-phthalaldehyde permits the quantification of the amino acid formed, while the amino acid mixture is separated on a Hypersil AA column (Agilent).

## Claims

1. A method for producing L-methionine by fermentation, which comprises:
a) fermenting a coryneform bacteria which produces L-methionine, the coryneform bacteria expressing at least one nucleotide sequence which encodes a protein with modified S-adenosyl-methionine synthase (metK) activity comprising the amino acid sequence of SEQ ID NO:22;
b) enriching the L-methionine in the medium and/or in the bacterial cells, and
c) isolating the L-methionine.

2. The method of claim 1, wherein said nucleotide sequence comprises SEQ ID NO:21.

3. The method of claim 1, wherein in said coryneform bacteria the metK activity is reduced in comparison with the wild type.

4. The method of claim 1, wherein the encoding metK sequence is a DNA which is capable of replication in coryneform bacteria or stably integrated into the chromosome, or an RNA.

5. The method of claim 1, wherein
a) a bacterium which has been transformed with a plasmid vector which encodes amino acid sequence of SEQ ID NO:22 under the control of regulatory sequences is used, or
b) a bacterium in which a nucleotide sequence, which encodes the amino acid sequence of SEQ ID NO:22 has been integrated into the bacterial chromosome is used.

6. The method of claim 1, wherein the nucleotide sequence of at least one of the genes selected from:
a) gene lysC, which encodes an aspartate kinase,
b) gene asd, which encodes an aspartate-semialdehyde dehydrogenase,
c) gene gap, which encodes glycerinaldehyde-3-phosphate dehydrogenase,
d) gene pgk, which encodes 3-phosphoglycerate kinase,
e) gene pyc, which encodes pyruvate carboxylase,
f) gene tpi, which encodes triose-phosphate isomerase,
g) gene meta, which encodes homoserine O-acetyltransferase,
h) gene metB, which encodes cystathionine-gamma synthase,
i) gene metC, which encodes cystathionine-gamma lyase,
j) gene metH, which encodes methionine synthase,
k) gene glyA, which encodes serine hydroxymethyltransferase,
i) gene metY, which encodes O-acetylhomoserine sulfhydrylase,
m) gene metF, which encodes methylenetetrahydrofolate reductase,
n) gene serC, which encodes phosphoserine aminotransferase,
o) gene serB, which encodes phosphoserine phosphatase,
p) gene cysE, which encodes serine acetyltransferase,
q) gene cysK, which encodes cysteine synthase,
r) gene hom, which encodes homoserine dehydrogenase, is simultaneously overexpressed, by increasing the copy number or using a strong promoter, in the coryneform bacteria.

7. The method of claim 1, wherein the nucleotide sequence of at least one of the genes selected from:
a) gene thrB, which encodes homoserine kinase,
b) gene ilvA, which encodes threonine dehydratase,
c) gene thrC, which encodes threonine synthase,
d) gene ddh, which encodes meso-diaminopimelate D dehydrogenase,
e) gene pck, which encodes phosphoenol-pyruvate carboxykinase,
f) gene pgi, which encodes glucose-6-phosphate-6 isomerase,
g) gene poxB, which encodes pyruvate oxidase,
h) gene dapA, which encodes dihydrodipicolinate synthase,
i) gene dapB, which encodes dihydrodipicolinate reductase, or
j) gene lysA, which encodes diaminopicolinate decarboxylase, is simultaneously attenuated, by deletion of the gene or substituting the native promoter with a weak promoter, in the coryneform bacteria.

8. The method of claim 1, wherein microorganisms of the species Corynebacterium glutamicum are used.