CITB GENE FROM CORYNEBACTERIA AND USE THEREOF IN SYNTHESIS OF L-AMINO ACIDS

Abstract: The invention provides nucleotide sequences from coryneform bacteria which code for the citB gene and a process for the fermentative preparation of amino acids, in particular L-lysine, by attenuation of the citB gene. The citB gene codes for the citB protein, which is a transciption regulator of a two-component system.

Description: CITB GENE FROM CORYNEBACTERIA AND USE THEREOF IN SYNTHESIS OF L-AMINO ACIDS Field of the Invention The invention provides nucleotide sequences from coryneform bacteria which code for the citB gene and a process for the 5 fermentative preparation of amino acids, in particular L- lysine, by attenuation of the citB gene. The citB gene codes for the CitB protein, which is a transcription regulator of a two-component system. Prior Art 10 L-Amino acids, in particular L-lysine, are used in human medicine and in the pharmaceuticals industry, in the foodstuffs industry and very particularly in animal nutrition. It is known that amino acids are prepared by fermentation 15 from strains of coryneform bacteria, in particular Corynebacterium glutamicum. Because of their great importance, work is constantly being undertaken to improve the preparation processes. Improvements to the process can relate to fermentation measures, such as, for example, 20 stirring and supply of oxygen, or the composition of the nutrient media, such as, for example, the sugar concentration during the fermentation, or the working up to the product form by, for example, ion exchange chromatography, or the intrinsic output properties of the 25 microorganism itself. Methods of mutagenesis, selection and mutant selection are used to improve the output properties of these microorganisms. Strains which are resistant to antimetabolites or are auxotrophic for metabolites of 30 regulatory importance and which produce amino acids are obtained in this manner. Methods of the recombinant DNA technique have also been employed for some years for improving the strain of Corynebacterium strains which produce L-amino acids. Object of the Invention The inventors had the object of providing new measures for improved fermentative preparation of amino acids, in particular L-lysine. Summary of the Invention If L-lysine or lysine are mentioned in the following, this also means the salts, such as e. g. lysine monohydrochloride or lysine sulfate. The invention provides an isolated polynucleotide from coryneform bacteria, comprising a polynucleotide sequence which codes for the citB gene chosen from the group consisting of a) polynucleotide which is identical -to the extent of at least 70 % to a polynucleotide which codes for a polypeptide which comprises the amino acid sequence of SEQ ID No. 2, b) polynucleotide which codes for a polypeptide which comprises an amino acid sequence which is identical to the extent of at least 70 % to the amino acid sequence of SEQ ID No. 2, c) polynucleotide which is complementary to the polynucleotides of a) or b) , and d) polynucleotide comprising at least 15 successive nucleotides of the polynucleotide sequence of a) , b) or c), the polypeptide preferably having the activity of the citB protein. The invention also provides the above entioned polynucleotide, this preferably being a DNA which is capable of replication, comprising: (i) the nucleotide sequence shown in SEQ ID No.l or (ii) at least one sequence which corresponds to sequence (i) within the range of the degeneration of the genetic code, or (iii) at least one sequence which hybridizes with the sequences complementary to sequences (i) or (ii) , and optionally (iv) sense mutations of neutral function in (i) . The invention also provides: a polynucleotide, in particular DNA, which is capable of replication and comprises the nucleotide sequence as shown in SEQ ID No.l; a polynucleotide which codes for a polypeptide which comprises the amino acid sequence as shown in SEQ ID No. 2; a vector containing parts of the polynucleotide according to the invention, at least 15 successive nucleotides of the sequence claimed and coryneform bacteria in which the citB gene is attenuated, in particular by an insertion or deletion. The invention also provides polynucleotides which substantially comprise a polynucleotide sequence, which are obtainable by screening by means of hybridization of a corresponding gene library of a coryneform bacterium, which comprises the complete gene or parts thereof, with a probe which comprises the sequence of the polynucleotide according to the invention or a fragment thereof, and isolation of the polynucleotide sequence mentioned. Detailed Description of the Invention Polynucleotides comprising the sequences according to the invention are suitable as hybridization probes for RNA, cDNA and DNA, in order to isolate, in the . full length, nucleic acids or polynucleotides or genes which code for the CitB protein or to isolate those -nucleic acids or polynucleotides or genes which have a high similarity with the sequence of the citB gene. They are also suitable for incorporation into so-called "arrays", "micro arrays" or "DNA chips" in order to detect and determine the corresponding polynucleotides. Polynucleotides comprising the sequences according to the invention are furthermore suitable as primers with the aid of which DNA of genes which code for the CitB protein can be prepared by the polymerase chain reaction (PCR) . Such oligonucleotides which serve as probes or primers comprise at least 30, preferably at least 20, very particularly preferably at least 15 successive nucleotides. Oligonucleotides which have a length of at least 40 or 50 nucleotides are also suitable. "Isolated" means separated out of its natural environment. "Polynucleotide" in general relates to polyribonucleotides and polydeoxyribonucleotides, it being possible for these to be non-modified RNA or DNA or modified RNA or DNA. The polynucleotides according to the invention include a polynucleotide according to SEQ ID No. 1 or a fragment prepared therefrom and also those which are at least 70 %, preferably at least 80 % and in particular at least 90 % to 95 % identical to the polynucleotide according to SEQ ID No. 1 or a fragment prepared therefrom. "Polypeptides" are understood as meaning peptides or proteins which comprise two or more amino acids bonded via peptide bonds . The polypeptides according to the invention include a polypeptide according to SEQ ID No. 2, in particular those with the biological activity of the CitB protein, and also those which are at least 70 %, preferably at least 80 % and in particular at least 90 % to 95 % identical to the polypeptide according to SEQ ID No. 2 and have the activity mentioned. The invention moreover provides a process for the fermentative preparation of amino acids, in particular L- lysine, using coryneform bacteria which in particular already produce amino acids, and in which the nucleotide sequences which code for the citB gene are attenuated, in particular eliminated or expressed at a low level. The term "attenuation" in this connection describes the reduction or elimination of the intracellular activity of one or more enzymes (proteins) in a microorganism which are coded by the corresponding DNA, for example by using a weak promoter or using a gene or allele which codes for a corresponding enzyme with a low activity or inactivates the corresponding gene or enzyme (protein) , and optionally combining these measures. The microorganisms which the present invention provides can prepare amino acids, in particular L-lysine, from glucose, sucrose, lactose, fructose, maltose, molasses, starch, cellulose or from glycerol and ethanol. They can be representatives of coryneform bacteria, in particular of the genus Corynebacterium. Of the genus Corynebacterium, there may be mentioned in particular the species Corynebacterium glutamicum, which is known among experts for its ability to produce L-amino acids. Suitable strains of the genus Corynebacterium, in particular of the species Corynebacterium glutamicum (C. glutamicum) , are in particular the known wild-type strains Corynebacterium glutamicum ATCC13032 Corynebacterium acetoglutamicum ATCC15806 Corynebacterium acetoacidophilum ATCC13870 Corynebacterium melassecola ATCC17965 Corynebacterium thermoaminogenes FERM BP-1539 Brevibacterium flavum ATCC14067 Brevibacterium lactofermentum ATCC13869 and Brevibacterium divaricatum ATCC14020 or L-amino acid-producing mutants or strains prepared therefrom, such as, for example, the L-lysine-producing strains Corynebacterium glutamicum FERM-P 1709 Brevibacterium flavum FERM-P 1708 Brevibacterium lactofermentum FERM-P 1712 Corynebacterium glutamicum FERM-P 6463 Corynebacterium glutamicum FERM-P 6464 Corynebacterium glutamicum DM58-1 Corynebacterium glutamicum DG52-5 Corynebacterium glutamicum DSM 5715 and . Corynebacterium glutamicum DSM 12866 The inventors have succeeded in isolating the new citB gene of C. glutamicum which codes for the CitB protein, which is a transcription regulator of a two-component system. To isolate the citB gene or also other genes of C. glutamicum, a gene library of this microorganism is first set up in Escherichia coli (E. coli) . The setting up of gene libraries is described in generally known textbooks and handbooks. The textbook by innacker: Gene und Klone, Eine Einfϋhrung in die Gentechnologie (Verlag Chemie, einhei , Germany, 1990) , or the handbook by Sambrook et al.: Molecular Cloning, A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1989) may be mentioned as an example. A well-known gene library is that of the E. coli K-12 strain 3110 set up in λ vectors by Kohara et al. (Cell 50, 495 -508 (1987)). Bathe et al. (Molecular and General Genetics, 252:255-265, 1996) describe a gene library of C. glutamicum ATCC13032, which was set up with the aid of the cosmid vector SuperCos I ( ahl et al., 1987, Proceedings of the National Academy of Sciences USA, 84:2160-2164) in the E. coli K-12 strain NM554 (Raleigh et al., 1988, Nucleic Acids Research 16:1563-1575). Bδrmann et al. (Molecular Microbiology 6 (3) , • 317-326) ) (.1992)) in turn describe a gene library of C. glutamicum ATCC13032 using the cosmid pHC79 (Hohn and Collins, 1980, Gene 11, 291- 298). To prepare a gene library of C. glutamicum in E. coli it is also possible to use plasmids such as pBR322 (Bolivar, 1979, Life Sciences, 25, 807-818) or pϋC9 (Vieira et al., 1982, Gene, 19:259-268) . Suitable hosts are, in particular, those E. coli strains which are restriction- and recombination-defective, such as, for example, the strain DH5α (Jeffrey H. Miller: "A Short Course in Bacterial Genetics, A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria", Cold Spring Harbour Laboratory Press, 1992) . The long DNA fragments cloned with the aid of cosmids or other λ-vectors can then be subcloned in turn into the usual vectors suitable for DNA sequencing. Methods of DNA sequencing are described, inter alia, by Sanger et al. (Proceedings of the National Academy of Sciences of the United States of America USA, 74:5463-5467, 1977) . The resulting DNA sequences can then be investigated with known algorithms or sequence analysis programs, such as e.g. that of Staden (Nucleic Acids Research 14, 217- 232(1986)), that of Marck (Nucleic Acids Research 16, 1829- 1836 (1988)) or the GCG program of Butler (Methods of Biochemical Analysis 39, 74-97 (1998)). The new DNA sequence of C. glutamicum which codes for the citB gene and which, as SEQ ID No. 1, is a constituent of the present invention has been obtained in this manner. The amino acid sequence of the corresponding protein has furthermore been derived from the present DNA sequence by the methods described above. The resulting amino acid sequence of the citB gene product is shown in SEQ ID No. 2. Coding DNA sequences which result from SEQ ID No. 1 by the degeneracy of the genetic code are also a constituent of the invention. In the same way, DNA sequences which hybridize with SEQ ID No. 1 or parts of SEQ ID No. 1 are a constituent of the invention. Conservative amino acid exchanges, such as e.g. exchange of glycine for alanine or of aspartic acid for glutamic acid in proteins, are furthermore known among experts as "sense mutations" which do not lead to a fundamental change in the activity of the protein, i.e. are of neutral function. It is furthermore known that changes on the N and/or C terminus of a protein cannot substantially impair or can even stabilize the function thereof. Information in this context can be found by the expert, inter alia, in Ben-Bassat et al. (Journal of Bacteriology 169:751-757 (1987)), in O'Regan et al . (Gene 77:237-251 (1989)), in Sahin-Toth et al. (Protein Sciences 3:240-247 (1994)), in Hochuli et al. (Bio/Technology 6:1321-1325 (1988)) and in known textbooks of genetics and molecular biology. Amino acid sequences which result in a corresponding manner from SEQ ID No. 2 are also a constituent of the invention. Finally, DNA sequences which are prepared by the polymerase chain reaction (PCR) using primers which result from SEQ ID No. 1 are a constituent of the invention. Such oligonucleotides typically have a length of at least 15 nucleotides. Instructions for identifying DNA sequences by means of hybridization can be found by the expert, inter alia, in the handbook "The DIG System Users Guide for Filter Hybridization" from Boehringer Mannheim GmbH (Mannheim, Germany, 1993) and in Liebl et al. (International Journal of Systematic Bacteriology 41: 255-260 (1991)). The hybridization takes place under stringent conditions, that is to say only hybrids in which the probe and target sequence, i. e. the polynucleotides treated with the probe, are at least 70 % identical are formed. It is known that the stringency of the hybridization, including the washing steps, is influenced or determined by varying the buffer composition, the temperature and the salt concentration. The hybridization reaction is preferably carried out under a relatively low stringency compared with the washing steps (Hybaid Hybridisation Guide, Hybaid Limited, Teddington, UK, 1996) .A 5x SSC buffer at a temperature of approx. 50 - 68°C, for example, can be employed for the hybridization reaction. Probes can also hybridize here with polynucleotides which are less than 70 % identical to the sequence of the probe. Such hybrids are less stable and are removed by washing under stringent conditions . This can be achieved, for example, by lowering the salt concentration to 2x SSC and optionally subsequently 0.5x SSC (The DIG System User's Guide for Filter Hybridisation, Boehringer Mannheim, Mannheim, Germany, 1995) a temperature of approx. 50 - 68 °C being established. Polynucleotide fragments which are, for example, at least 70 % or at least 80 % or at least 90 % to 95 % identical to the sequence of the probe employed can be isolated by increasing the hybridization temperature stepwise from 50 to 68°C in steps of approx. 1 - 2°C. Further instructions on hybridization are obtainable on the market in the form of so-called kits CO to ιV> I- 1 μ 1 o Cn o Cπ o cn Mutations which lead to a change or reduction in the catalytic properties of enzyme proteins are known from the prior art; examples which may be mentioned are the works by Qiu and Goodman (Journal of Biological Chemistry 272: 8611- 8617 (1997)), Sugimoto et al. (Bioscience Biotechnology and Biochemistry 61: 1760-1762 (1997)) and Mδckel ("Die Threonindehydratase aus Corynebacterium glutamicum: Aufhebung der allosterischen Regulation und Struktur des Enzyms", Reports from the Jϋlich Research Centre, Jϋl-2906, ISSN09442952, Jϋlich, Germany, 1994) . Summarizing descriptions can be found in known textbooks of genetics and molecular biology, such as e.g. that by Hage ann ("Allgemeine Genetik", Gustav Fischer Verlag, Stuttgart, 1986) . Possible mutations are transitions, transversions, insertions and deletions. Depending on the effect of the amino acid exchange on the enzyme activity, missense mutations or nonsense mutations are referred to. Insertions or deletions of at least one base pair (bp) in a gene lead to frame shift mutations, as a consequence of which incorrect amino acids are incorporated or translation is interrupted prematurely. Deletions of several codons typically lead to a complete loss of the enzyme activity. Instructions on generation of such mutations are prior art and can be found in known textbooks of genetics and molecular biology, such as e.g. the textbook by Knippers ("Molekulare Genetik", 6th edition, Georg Thieme Verlag, Stuttgart, Germany, 1995), that by Winnacker ("Gene und Klone", VCH Verlagsgesellschaft, Weinheim, Germany, 1990) or that by Hagemann ("Allgemeine Genetik", Gustav Fischer Verlag, Stuttgart, 1986) . A common method of mutating genes of C. glutamicum is the method of gene disruption and gene replacement described by Schwarzer and Pϋhler (Bio/Technology 9, 84-87 (1991)). CO CO ro rv> cπ o cπ o Cπ O cπ £>. fi ¬ <! DJ H φ Φ O rt (i- 3 J S 03 Φ O O o <! l- 1 03 Q CO _ C-i -j _ Φ Ω J O H 1— ' eμ- 3 I- 1 rt 3 tr if if O μ- 03 μ- 1 > Hi • Hi Φ VO μ- li ιl ω TJ O CO μ> X o o 3 0 ri rt a vo a rt Φ φ 3 Ω μ- o DJ VD TJ Ω VD o o ^ . 3 * ϋ 0 VD DJ OJ a rr 3 H Φ rt VD DJ D o H o ti3 VD TJ Ω sQ rt rt h- 1 3 3 o H . — ^ CO 3 μ- CO μ- rt DJ O r-> if J-. I- 1 μ- < Ω O \ ro TJ J-. 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DJ rt <l Hi ro co o Φ I if a O 3- S 1 o rt 3 μ> H ^ Φ ø O IV ) ^ H Φ φ ti ¬ rt if υa a ^j 0 ) : H a Φ Φ O r H M Φ CO TJ μ- O a Hi a μ- 0 0 • ^ μ- rt φ H H ro μ- • *» cn Hi if O μ- . rt H n O S 0 ) μ- 3 Hi Φ O O if 3 rt 3- li 3 li DJ <1 VD Φ Φ rt 3 TJ Φ VD rø 1 - ι OJ Ω CO H μ- if • cπ N φ 0 1 3 DJ Hi H H \Q h- 1 0 ) Ω O m • * * CO li OJ DJ rt μ- Cfl Φ DJ -J TJ TJ Φ • DJ 3 O 3 DJ OJ l— 1 d CO cπ Φ if ϋ O a CO Cn DJ Cπ rt <! 3 a li Φ Φ μ- H Cfl ^ 1 to ^ 1 * * Φ φ • μ- 1 rt - Φ Φ ^ -~. rt rf 3 Φ 3 DJ cn - "< a 3 μ- φ cn H a 3 Tl if iQ μ- H -4 cn vo Hi 3 CO μ- H- DJ o O μ- a CO VD > O W iQ O Ω tr 1 1 H pr a Hi O ω 3 host of C. glutamicum by transformation or conjugation. After homologous recombination by means of a first "crossover" event which effects integration and a suitable second "cross-over" event which effects excision in the target gene or in the target sequence, the incorporation of the mutation or of the allele is achieved. This method was used, for example, by Peters- endisch et al. (Microbiology 144, 915 - 927 (1998)) to eliminate the pyc gene of C. glutamicum by a deletion. A deletion, insertion or a base exchange can be incorporated into the citB gene in this manner. In addition, it may be advantageous for the production of L-amino acids, in particular L-lysine, to enhance, in particular to over-express, one or more enzymes of the particular biosynthesis pathway, of glycolysis, of anaplerosis, of the citric acid cycle, of the pentose phosphate cycle, of amino acid export and optionally regulatory proteins, in addition to attenuation of the citB gene. The term "enhancement" in this connection describes the increase in the intracellular activity of one or more enzymes (proteins) in a microorganism which are coded by the corresponding DNA, for example by increasing the number of copies of the gene or genes, using a potent promoter or using a gene or allele which codes for a corresponding enzyme (protein) having a high activity, and optionally combining these measures. Thus, for example, for the preparation of L-lysine, at the same time one or more of the genes chosen from the group consisting of • the dapA gene which codes for dihydrodipicolinate synthase (EP-B 0 197 335), • the gap gene which codes for glyceraldehyde 3-phosphate dehydrogenase (Eikmanns (1992), Journal of Bacteriology 174:6076-6086), • the zwf gene which codes for glucose 6-phosphate dehydrogenase (JP-A-09224661) , • the pyc gene which codes for pyruvate carboxylase (DE-A- 198 31 609) , • the lysE gene which codes for lysine export (DE-A-195 48 222) • the lysC gene which codes for a feed back resistant aspartate kinase (EP-B-0387527; EP-A-0699759; WO 00/63388), or • the zwal gene which codes for the Zwal protein (DE: 199 59 328.0, DSM 13115) can be enhanced, in particular over-expressed. It may furthermore be advantageous for the production of amino acids, in particular L-lysine, in addition to the attenuation of the citB gene, for one or more of the genes chosen from the group consisting of • the pck gene which codes for phosphoenol pyruvate carboxykinase (DE 199 50 409.1, DSM 13047), • the pgi gene which codes for glucose 6-phosphate isomerase(US 09/396,478, DSM 12969), • the poxB gene which codes for pyruvate oxidase (DE-.1995 1975.7, DSM 13114) • the zwa2 gene which codes for the Zwa2 protein (DE: 19959327.2, DSM 13113) to be attenuated at the same time. CO to ro μ> o cπ o cπ O cπ 3 Ω Hi Φ CO Hi Φ 3 CO rjd μ- o rt m 03 TJ μ» 03 rr CO TJ tr Ω Ω 0 ) ι-3 tr 1 TJ TJ Cfl DJ Hi H μ- DJ o X rt DJ X o 0 2! 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TJ H O 3" hi P- hi o a 3 0 O iQ DJ Φ Ω Φ Ω Hi li Φ if a a φ 3 CO hi Ω hi O Ω d μ- 0 • rt Ω DJ μ- rt < μ- • * a a ^ d μ- Φ H to Φ 3 a H μ- rt Cfl 3 3 μ- Φ a rt Ω 0 ) Ω rt μ- H cn Φ TJ CD φ CO ( -3 3 rt if rt φ o μ- 1 3" DJ Ω TJ o DJ 0 CD <! 3 Hi φ O CO if 3 ^ • 3" 0 O Φ 3 øJ a 3 o TJ Φ 3 μ- o li 3 d μ- 0 ) 0J Hi TJ DJ O P- μ- Φ μ- μ- μ- TJ o a rr rt σ rt μ j rt Cfl O <τ Hi rt DJ Cfl a Ω X 3 0 3 H" Ω tr DJ Ω tr 3- CO DJ - 1 φ OJ TJ 3 Φ H 3 Cπ 0 rt 3 CO ro ^ 0 φ Ω CO DJ Φ Φ rt 3 • μ- if a 3 DJ rt ø o μ- 0 DJ ø 3 i o CO 3 OJ μ- ^ O ri- O μ- O μ- ti ¬ o DJ 3 Ω rt li Φ (1- Ω rt rt φ 3 μ- OJ Ω 3 3 li Cfl CO 3 hi rt ro 3 H rr 0 Φ hj 0 if >< 0 TJ 0 tr a d Ω Cfl φ TJ iQ H "* μ- sQ μ- H CO O o Ω ii TJ o 3 φ a Φ ^ n μ- o if O d Φ DJ Φ tr DJ Hi O Φ μ j 0 Φ rt CD cn h Hi rr o CO vQ Ω 3 μ- CO • 3 o 3 Hi a d • Ω φ O hi O Φ DJ 0 ) a O Ω Hi •<: a Φ li DJ 3 3 d a 3 3 μ- m 0 O Φ CO Hi a (1- Φ 3 rt Cfl μ- CO if Ω DJ a » O μ- 0 Ω tr Φ 3 * O 3 μ- tr DJ ro li 3 DJ 3 Φ μ j 1 3 Methods for the determination of L-amino acids are known from the prior art. The analysis can thus be carried out, for example, as described by Spackman et al. (Analytical Chemistry, 30, (1958) , 1190) by anion exchange chromatography with subsequent ninhydrin derivatization, or it can be carried out by reversed phase HPLC, for example as described by Lindroth et al. (Analytical Chemistry (1979) 51: 1167-1174). The invention furthermore relates to a process for the fermentative preparation of an amino acid chosen from the group consisting of L-asparagine, L-threonine, L-serine, L- glutamate, L-glycine, L-alanine, L-cysteine, L-valine, L- methionine, L-isoleucine, L-leucine, L-tyrosine, L- phenylalanine, L-histidine, L-lysine, L-tryptophan and L- arginine, in particular L-lysine, using coryneform bacteria which in particular already produce one or more of the amino acids mentioned. The following microorganism was deposited on 23.08.2000 as a pure culture at the Deutsche Sammlung fur Mikroorganismen und Zellkulturen (DSMZ = German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany) in accordance with the Budapest Treaty: • Escherichia coli strain ToplO/pCR2. IcitBint as DSM 13672. The present invention is explained in more detail in the following with the aid of embodiment examples . The isolation of plasmid DNA from Escherichia coli and all techniques of restriction, Klenow and alkaline phosphatase treatment were carried out by the method of Sambrook et al. (Molecular Cloning. A Laboratory Manual, 1989, Cold Spring Harbour Laboratory Press, Cold Spring Harbor, NY, USA) . Methods for ■ transformation of Escherichia coli are also described in this handbook. The composition of the usual nutrient media, such as LB or TY medium, can also be found in the handbook by Sambrook et al. * Example 1 Preparation of a genomic cosmid gene library from C. glutamicum ATCC 13032 Chromosomal DNA from C. glutamicum ATCC 13032 was isolated as described by Tauch et al. (1995, Plasmid 33:168-179) and partly cleaved with the restriction enzyme Sau3AI (Amersham Pharmacia, Freiburg, Germany, Product Description Sau3AI, Code no. 27-0913-02). The DNA fragments were dephosphorylated with shrimp alkaline phosphatase (Roche Molecular Biochemicals, Mannheim, Germany, Product Description SAP, Code no. 1758250) . The DNA of the cosmid vector SuperCosl (Wahl et al. (1987), Proceedings of the National Academy of Sciences, USA 84:2160-2164), obtained from Stratagene (La Jolla, USA, Product Description SuperCosl Cosmid Vector Kit, Code no. 251301) was cleaved with the restriction enzyme Xbal (Amersham Pharmacia, Freiburg, Germany, Product Description Xbal, Code no. 27- 0948-02) and likewise dephosphorylated with shrimp alkaline phosphatase. The cosmid DNA was then cleaved with the restriction enzyme BamHI (Amersham Pharmacia, Freiburg, Germany, Product Description BamHI, Code no. 27-0868-04) . The cosmid DNA treated in this manner was mixed with the treated ATCC13032 DNA and the batch was treated with T4 DNA ligase (Amersham Pharmacia, Freiburg, Germany, Product Description T4-DNA- Ligase, Code no.27-0870-04) . The ligation mixture was then packed in phages with the aid of Gigapack II XL Packing Extract (Stratagene, La Jolla, USA, Product Description Gigapack II XL Packing Extract, Code no. 200217) . For infection of the E. coli strain NM554 (Raleigh et al . 1988, Nucleic Acid Res. 16:1563-1575) the cells were taken up in 10 mM MgS0 and mixed with an aliquot of the phage suspension. The infection and titering of the cosmid library were carried out as described by Sambrook et al. (1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor) , the cells being plated out on LB agar (Lennox, 1955, Virology, 1:190) + 100 μg/ml ampicillin. After incubation overnight at 37°C, recombinant individual clones were selected. Example 2 Isolation and sequencing of the citB gene The cosmid DNA of an individual colony was isolated with the Qiaprep Spin Miniprep Kit (Product No. 27106, Qiagen, Hilden, Germany) in accordance with the manufacturer's instructions and partly cleaved with the restriction enzyme Sau3AI (Amersham Pharmacia, Freiburg, Germany, Product Description Sau3AI, Product No. 27-0913-02). The DNA fragments were dephosphorylated with shrimp alkaline phosphatase (Roche Molecular Biochemicals, Mannheim, Germany, Product Description SAP, Product No. 1758250) . After separation by gel electrophoresis, the cosmid fragments in the size range of 1500 to 2000 bp were isolated with the QiaExII Gel Extraction Kit (Product No. 20021, Qiagen, Hilden, Germany) . The DNA of the sequencing vector pZero-1, obtained from Invitrogen (Groningen, The Netherlands, Product Description Zero Background Cloning Kit, Product No. K2500-01) was cleaved with the restriction enzyme BamHI (Amersham Pharmacia, Freiburg, Germany, Product Description BamHI, Product No. 27-0868-04). The ligation of the cosmid fragments in the sequencing vector pZero-1 was carried out as described by Sambrook et al. (1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor) , the DNA mixture being incubated overnight with T4 ligase (Pharmacia Biotech, Freiburg, Germany) . This ligation mixture was then electroporated (Tauch et al. 1994, FEMS Microbiol Letters, 123:343-7) into the E. coli strain DH5αMCR (Grant, 1990, Proceedings of the National Academy of Sciences, U.S.A., 87:4645-4649) and plated out on LB agar (Lennox, 1955, Virology, 1:190) with 50 μg/ml zeocin. The plasmid preparation of the recombinant clones was carried out with the Biorobot 9600 (Product No. 900200, Qiagen, Hilden, Germany) . The sequencing was carried out by the dideoxy chain termination method of Sanger et al. (1977, Proceedings of the National Academies of Sciences, U.S.A., 74:5463-5467) with modifications according to Zimmermann et al. (1990, Nucleic Acids Research, 18:1067). The "RR dRhodamin Terminator Cycle Sequencing Kit" from PE Applied Biosystems (Product No. 403044, Weiterstadt, Germany) was used. The separation by gel electrophoresis and analysis of the sequencing reaction were carried out in a "Rotiphoresis NF Acrylamide/Bisacrylamide" Gel (29:1) (Product No. A124.1, Roth, Karlsruhe, Germany) with the "ABI Prism 377" sequencer from PE Applied Biosystems (Weiterstadt, Germany) . The raw sequence data obtained were then processed using the Staden program package (1986, Nucleic Acids Research, 14:217-231) version 97-0. The individual sequences of the pZerol derivatives were assembled to a continuous contig. The computer-assisted coding region analyses were prepared with the XNIP program (Staden, 1986, Nucleic Acids Research, 14:217-231). Further analyses were carried out with the "BLAST search program" (Altschul et al., 1997, Nucleic Acids Research, 25:3389-3402) against the non- redundant databank of the "National Center for Biotechnology Information" (NCBI, Bethesda, MD, USA) . The resulting nucleotide sequence is shown in SEQ ID No. 1. Analysis of the nucleotide sequence showed an open reading frame of 657 base pairs, which was called the citB gene. The citB gene codes for a polypeptide of 219 amino acids. Example 3 Preparation of an integration vector for integration mutagenesis of the citB gene From the strain ATCC 13032, chromosomal DNA was isolated by the method of Eik anns et al. (Microbiology 140: 1817 - 1828 (1994)). On the basis of the sequence of the citB gene known for C. glutamicum from example 2, the following oligonucleotides were chosen for the polymerase chain reaction (see SEQ ID No. 4 and SEQ ID No. 5) : citB-intl: 5 CCC GGA TCT CCT ACT TGT TG 3 citB-int2: 5" TCT GTG GCG GAT CTA GAG AC 3 The primers shown were synthesized by MWG Biotech (Ebersberg, Germany) and the PCR reaction was carried out by the standard PCR method of Innis et al. (PCR protocols. A guide to methods and applications, 1990, Academic Press) with the Taq-polymerase from Boehringer Mannheim (Germany, Product Description Taq DNA polymerase, Product No. 1 146 165) . With the aid of the polymerase chain reaction, the primers allow amplification of an internal fragment of the citB gene 318 bp in size. The product amplified in this way was tested electrophoretically in a 0.8% agarose gel. The amplified DNA fragment (see SEQ ID No. 3) was ligated with the TOPO TA Cloning Kit from Invitrogen Corporation (Carlsbad, CA, USA; Catalogue Number K4500-01) in the vector pCR2.1-TOPO (Mead at al. (1991) Bio/Technology 9:657-663). The E. coli strain TOP10 was then electroporated with the ligation batch (Hanahan, In: DNA cloning. A practical approach. Vol. I. IRL-Press, Oxford, Washington DC, USA, 1985) . Selection of plasmid-carrying cells was carried out by plating out the transformation batch on LB Agar (Sambrook et al., Molecular cloning: a laboratory manual. 2 nd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989), which had been supplemented with 50 mg/l kanamycin. Plasmid DNA was isolated from a transformant with the aid of the QIAprep Spin Miniprep Kit from Qiagen and checked by restriction with the restriction enzyme EcoRI and subsequent agarose gel electrophoresis (0.8%). The plasmid was called pCR2. IcitBint and is shown in figure 1. Example 4 Integration mutagenesis of the citB gene in the strains DSM 5715 and FERM-BP 1763 The vector pCR2. IcitBint mentioned in example 3 was electroporated by the electroporation method of Tauch et al. (FEMS Microbiological Letters, 123:343-347 (1994)) into the strains Corynebacterium glutamicum DSM 5715 and Brevibacterium lactofermentum FERM-BP 1763. The strain DSM 5715 is an AEC-resistant lysine producer (EP-B-0435132) , and the strain FERM-BP 1763 is a mycophenolic acid- resistant valine producer (US-A-5, 188, 948) . The vector pCR2. IcitBint cannot replicate independently in DSM5715 and FERM-BP 1763 and is retained in the cell only if it has integrated into the chromosome of DSM 5715 or FERM-BP 1763. Selection of clones with pCR2. IcitBint integrated into the chromosome was carried out by plating out the electroporation batch on LB agar (Sambrook et al., Molecular cloning: a laboratory manual. 2 nd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.), which had been supplemented with 15 mg/l kanamycin. For detection of the integration, the citBint fragment was labelled with the Dig hybridization kit from Boehringer by the method of "The DIG System Users Guide for Filter Hybridization" of Boehringer Mannheim GmbH (Mannheim, Germany, 1993) . Chromosomal DNA of in each case a potential integrant was isolated by the method of Eikmanns et al. (Microbiology 140: 1817 - 1828 (1994)) and in each case cleaved with the restriction enzymes -EcoRI, BamHI and Hindlll. The fragments formed were separated by means of agarose gel electrophoresis and hybridized at 68°C with the Dig hybridization kit from Boehringer. The plasmid pCR2. IcitBint mentioned in example 3 had been inserted into the chromosome of DSM5715 and into the chromosome of FERM- BP 1763 within the chromosomal citB gene. The strains were called DSM5715 : :pCR2. IcitBint and FERM-BP 1763::pCR2. IcitBint . Example 5 Preparation of lysine The C. glutamicum strain DSM5715: :pCR2. IcitBint obtained in example 4 was cultured in a nutrient medium suitable for the production of lysine and the lysine content in the culture supernatant was determined. For this, the strain was first incubated on an agar plate with the corresponding antibiotic (brain-heart agar with kanamycin (25 mg/l) for 24 hours at 33°C. Starting from this agar plate culture, a preculture was seeded (10 ml medium in a 100 ml conical flask) . The complete medium Cglll was used as the medium for the preculture. Medium Cg III NaCl 2.5 g/1 Bacto-Peptone 10 g/1 Bacto-Yeast extract 10 g/1 Glucose (autoclaved separately) 2% (w/v) The pH is brought to pH 7.4 Kanamycin (25 mg/l) was added to this. The preculture was incubated for 16 hours at 33°C at 240 rpm on a shaking machine. A main culture was seeded from this preculture such that the initial OD (660 nm) of the main culture is 0.1 OD. The medium MM-L was used for the main culture. Medium MM-L CSL (corn steep liquor) 5 g/1 MOPS (morpholinopropanesulfonic acid) 20 g/1 Glucose (autoclaved separately) 50g/l Salts; (NH 4 ) 2 S0 4 25 g/1 KH 2 P0 0.1 g/1 MgS0 4 * 7 H 2 0 1.0 g/1 CaCl 2 * 2 H 2 0 10 mg/l FeS0 4 * 7 H 2 0 10 mg/l MnS0 4 * H 2 0 5.0mg/l Biotin (sterile-filtered) 0.3 mg/l Thiamine * HCl (sterile-filtered) 0.2 mg/l Leucine (sterile-filtered) 0.1 g/1 CaC0 3 25 g/1 The CSL, MOPS and the salt solution were brought to pH 7 with aqueous ammonia and autoclaved. The sterile substrate, amino acid and vitamin solutions, as well as the CaC0 3 autoclaved in the dry state were then added. Culturing was carried out in a 10 ml volume in a 100 ml conical flask with baffles. Kanamycin (25 mg/l) was added. Culturing was carried out at 33°C and 80% atmospheric humidity. After 72 hours, the OD was determined at a measurement wavelength of 660 nm with a Biomek 1000 (Beckmann Instruments GmbH, Munich) . The amount of lysine formed was determined with an amino acid analyzer from Eppendorf- BioTronik (Hamburg, Germany) by ion exchange chromatography and post-column derivatization with ninhydrin detection. The result of the experiment is shown in table 1. Table 1 Example 6 Preparation of valine The B. lactofermentum strain FERM-BP 1763: :pCR2. IcitBint obtained in example 4 was cultured in a nutrient medium suitable for the production of valine and the valine content in the culture supernatant was determined. For this, the strain was first incubated on an agar plate with the corresponding antibiotic (brain-heart agar with kanamycin (25 mg/l) for 24 hours at 33°C. Starting from this agar plate culture, a preculture was seeded (10 ml medium in a 100 ml conical flask) . The complete medium Cglll was used as the medium for the preculture. Kanamycin (25 mg/l) was added to this. The preculture was incubated for 16 hours at 33°C at 240 rpm on a shaking machine. A main culture was seeded from this preculture such that the initial OD (660nm) of the main culture was 0.1 OD. The medium MM-V was used for the main culture. Medium MM-V CSL (corn steep liquor) 5 g/1 MOPS (morpholinopropanesulfonic acid) 20 g/1 Glucose (autoclaved separately) 50g/l Salts: (NH 4 ) 2 S0 4 ) 25 g/1 KH 2 P0 4 0.1 g/1 MgS0 4 * 7 H 2 0 1.0 g/1 CaCl 2 * 2 H 2 0 10 mg/l FeS0 4 * 7 H 2 0 10 mg/l MnS0 * H 2 0 5.0mg/l Isoeucine (sterile-filtered) 0.1 g/1 Methionine (sterile-filtered) 0.1 g/1 Thiamine * HCl (sterile-filtered) 0.2 mg/l Leucine (sterile-filtered) 0.1 g/1 CaC0 3 25 g/1 The CSL (corn steep liquor) , MOPS (morpholinopropanesulfonic acid) and the salt solution were brought to pH 7 with aqueous ammonia and autoclaved. The sterile substrate, amino acid and vitamin solutions, as well as the CaC0 3 autoclaved in the dry state were then added. Culturing was carried out in a 10 ml volume in a 100 ml conical flask with baffles. Kanamycin (25 mg/l) was added. Culturing was carried out at 33°C and 80% atmospheric humidity. After 48 hours, the OD was determined at a measurement wavelength of 660 nm with a Biomek 1000 (Beckmann Instruments GmbH, Munich) . The amount of valine formed was determined with an amino acid analyzer from Eppendorf- BioTronik (Hamburg, Germany) by ion exchange chromatography and post-column derivatization with ninhydrin detection. The result of the experiment is shown in table 2. Table 2 Brief Description of the Figure: Figure 1: Map of the plasmid pCR2. IcitBint . The abbreviations and designations used have the following meaning. KmR: Kanamycin resistance gene EcoRI Cleavage site of the restriction enzyme EcoRI Hindlll Cleavage site of the restriction enzyme HindiII BamHI: Cleavage site of the restriction enzyme BamHI citBint: Internal fragment of the citB gene ColEl: Replication origin of the plasmid ColEl

Claims: What is claimed is: 1. Isolated polynucleotide from coryneform bacteria, comprising a polynucleotide sequence which codes for the citB gene, chosen from the group consisting of a) polynucleotide which is identical to the extent of at least 70 % to a polynucleotide which codes for a polypeptide which comprises the amino acid sequence of SEQ ID No. 2, b) polynucleotide which codes for a polypeptide which comprises an amino acid sequence which is identical to the extent of at least 70% to the amino acid sequence of SEQ ID No. 2, c) polynucleotide which is complementary to the polynucleotides of a) or b) , and d) polynucleotide comprising at least 15 successive nucleotides of the polynucleotide sequence of a) , b) , or c) , the polypeptide preferably having the activity of the transcription regulator CitB. 2. Polynucleotides according to claim 1, wherein the polynucleotide is a preferably recombinant DNA which is capable of replication in coryneform bacteria. 3. Polynucleotides according to claim 1, wherein the polynucleotide is an RNA. 4. Polynucleotide according to claim 2, comprising the nucleic acid sequence as shown in SEQ ID No. 1. 5. DNA according to claim 2 which is capable of replication, comprising (i) the nucleotide sequence shown in SEQ ID No. 1, or (ii) at least one sequence which corresponds to sequence (i) within the range of the degeneration of the genetic code, or (iii) at least one sequence which hybridizes with the sequences complementary to sequences (i) or (ii) , and optionally (iv) sense mutations of neutral function in ' (i) . 6. DNA according to claim 5, wherein the hybridization is carried out under a stringency corresponding to at most 2x SSC. 7. Polynucleotide sequence according to claim 2, which codes for a polypeptide which comprises the amino acid sequence shown in SEQ ID No. 2. 8. The vector pCR2. IcitBint, which 8.1. carries an internal fragment of the citB gene 318 bp in size, shown in SEQ ID. No. 3, 8.2 the restriction map of which is reproduced in figure 1, and 8.3 which is deposited in the E. coli strain ToplO/pCR2. IcitBint under no. DSM 13672 at the Deutsche Sammlung fur Mikroorganismen und Zellenkulturen [German Collection of Microorganisms and Cell Cultures] . 9. Internal fragment of the citB gene with a length of 318 bp, shown in SEQ ID No. 3. 10. Coryneform bacteria, in which the citB gene is attenuated, preferably eliminated. 1. Process for the preparation of L-amino acids, in particular L-lysine, wherein the following steps are carried out a) fermentation of the coryneform bacteria which produce the desired L-amino acid and in which at least the citB gene is attenuated, b) concentration of the desired product in the medium or in the cells of the bacteria and c) isolation of the L-amino acid. 12. Process according to claim 11, wherein bacteria in which further genes of the biosynthesis pathway of the desired L-amino acid are additionally enhanced are employed. 13. Process according to claim 11, wherein bacteria in which the metabolic pathways which reduce the formation of the desired L-amino acid are at least partly eliminated are employed. 14. Process according to claim 11, wherein the expression of the polynucleotide (s) which codes (code) for the citB gene is decreased, in particular eliminated. 15. Process according to claim 11, wherein the regulatory or catalytic properties of the polypeptide for which the polynucleotide citB codes are decreased. 16. Process according to claim 11, wherein for the preparation of L-amino acids, in particular L-lysine, bacteria in which at the same time one or more of the genes chosen from the group consisting of 16.1 the dapA gene which codes for " dihydrodipicoliήate synthase, 16.2 the gap gene which codes for glyceraldehyde 3- phosphate dehydrogenase 16.3 the zwf gene which codes for glucose 6-phosphate dehydrogenase, 16.4the pyc gene which codes for pyruvate carboxylase, 16.5 the lysE gene which codes for lysine export, 16.6 the lysC gene which codes for a feed back resistant aspartate kinase, 16.7 the zwal gene which codes for the Zwal protein is or are enhanced, preferably over-expressed, are fermented. 17. Process according to claim 11, wherein at the same time one or more of the genes chosen from the group consisting of: 17.1 the pck gene which codes for phosphoenol pyruvate carboxykinase, 17.2 the pgi gene which codes for glucose 6-phosphate isomerase, 17.3 the poxB gene which codes for pyruvate oxidase, 17.4 the zwa2 gene which codes for the Zwa2 protein is or are attenuated. 18. Coryneform bacteria which contain a vector which carries parts of the polynucleotide, but at least 15 successive nucleotides of the sequence according to claim 1. 19. Process according to one or more of the preceding claims, wherein microorganisms of the genus Corynebacterium are employed. ■20. Process for discovering RNA, cDNA and DNA in order to isolate nucleic acids, or polynucleotides or genes which code for the transcription regulator CitB or have a high similarity with the sequence of the citB gene, wherein the polynucleotide sequences according to claim 1 to 4 are employed as hybridization probes. 21. Process according to claim 20, wherein arrays, micro arrays or DNA chips are employed. 1/1 Figure 1: Plasmid pCR2. IcitBint

Inventors: FARWICK MIKE, HERMANN THOMAS, MARX ACHIM, MOECKEL BETTINA, PFEFFERLE WALTER, FARWICK, MIKE, HERMANN, THOMAS, MARX, ACHIM, MOECKEL, BETTINA, PFEFFERLE, WALTER
Applicants: DEGUSSA, DEGUSSA AG
Application year: 2001
Main classification: C12N15
IPC codes: C07K14, C12N15, C12P13