# Patent

## Title
Alleles of the aceA gene from coryneform bacteria

## Abstract

The invention relates to alleles of the aceA gene from coryneform bacteria coding for isocitrate lyases and processes for the fermentative production of L-lysine using bacteria that contain these alleles.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
The present application claims priority to German application no. 102 10 527.8, filed Mar. 9, 2002, which is incorporated in its entirety herein by reference.
FIELD OF THE INVENTION
The present invention relates to alleles of the aceA gene from coryneform bacteria that code for variants of isocitrate lyase and processes for the production of L-lysine using bacteria that contain these alleles.
PRIOR ART
The amino acid L-lysine is widely used in human medicine and in the pharmaceutical industry, in the foodstuffs industry, and most especially in animal nutrition.
It is known to produce amino acids by fermentation of strains of coryneform bacteria, in particular Corynebacterium glutamicum. On account of their great importance efforts are constantly being made to improve the production processes. Process improvements may relate to fermentation technology measures, such as for example stirring and provision 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, for example by ion exchange chromatography, or the intrinsic performance properties of the microorganism itself.
Methods involving mutagenesis, selection and mutant choice are employed in order to improve the performance properties of these microorganisms. In this way strains are obtained that are resistant to antimetabolites or that are auxotrophic for regulatorily important metabolites, and that produce amino acids. A known antimetabolite is the lysine analogue S-(2-aminoethyl)-L-cysteine (AEC).
For some years methods of recombinant DNA technology have also been used to improve the strain of corynebacterium strains producing L-amino acid by amplifying individual amino acid biosynthesis genes and investigating the effect on the amino acid production.
The nucleotide sequence of the Corynebacterium glutamicum gene coding for isocitrate lyase may be found in patent application WO 01/00844 as Sequence No. 591 and as Sequence No. 589, as well as in patent application U.S. Pat. No. 5,439,822 as Sequence No. 3.
Furthermore, the nucleotide sequence of the Corynebacterium glutamicum gene coding for isocitrate lyase may be found in patent application EP-A-1108790 as Sequence No. 3489 and as Sequence No. 7067, as well as in patent application U.S. Pat. No. 5,700,661 as Sequence No. 3.
The nucleotide sequence is also deposited in the databank of the National Center for Biotechnology Information (NCBI) of the National Library of Medicine (Bethesda, Md., USA) under the Accession Nos. X75504, AX065465, AX065463, I86191, I13693, AX127151, AX123573 and L28760.
OBJECT OF THE INVENTION
The inventors have been concerned with the object of providing new ways for the improved production of L-lysine.
SUMMARY OF THE INVENTION
Wherever L-lysine or lysine are mentioned hereinafter, this is understood to denote not only the bases but also the salts, such as for example lysine monohydrochloride or lysine sulfate.
The present invention provides nucleotide sequences (DNA) derived from coryneform bacteria, in particular Corynebacterium glutamicum, that are capable of replication and code for the enzyme isocitrate lyase, wherein the associated amino acid sequences in SEQ ID No. 2 contain at least at Position 332 each proteinogenic amino acid with the exception of L-alanine.
The invention furthermore provides a nucleotide sequence (DNA) derived from coryneform bacteria, in particular Corynebacterium glutamicum, that is capable of replication and codes for the enzyme isocitrate lyase, wherein the associated amino acid sequence contains L-threonine at least at Position 332, shown in SEQ ID No. 4.
The invention also provides a nucleotide sequence (DNA) derived from coryneform bacteria, in particular Corynebacterium glutamicum, that is capable of replication and codes for the enzyme isocitrate lyase, whose base sequence contains adenine at Position 994, shown in SEQ ID No. 3.
The invention furthermore provides plasmids (vectors) that contain the nucleotide sequences according to the invention and that optionally replicate in coryneform bacteria.
The invention in addition provides bacteria, in particular coryneform bacteria, that contain the nucleotide sequences according to the invention and in which the nucleotide sequences coding for isocitrate lyase are over-expressed, wherein in the associated amino acid sequences a different proteinogenic amino acid is contained at least at Position 332 of SEQ ID No. 2.
DETAILED DESCRIPTION OF THE INVENTION
The bacteria may be bacteria that contain the nucleotide sequences according to the invention in isolated form. Furthermore the bacteria may be mutants that are produced and isolated using conventional in vivo mutagenesis methods and that contain the nucleotide sequences according to the invention or the mutation accordingly at their natural position in the chromosome. Finally, the bacteria may also be recombinant bacteria.
Over-expression is understood to mean an increase in the intracellular concentration or activity of the isocitrate lyases according to the invention.
By means of the over-expression measures the activity or concentration of the corresponding protein is increased in general by at least 10%, 25%, 50%, 75%, 100%, 150%, 200%, 300%, 400% or 500%, at most up to 1000% or 2000%, referred to the activity or concentration of the protein in the starting microorganism.
In order to achieve an over-expression the number of copies of the corresponding gene can be increased, or the promoter and regulation region or the ribosome binding site, which is located upstream of the structure gene, can be mutated. Expression cassettes that are incorporated upstream of the structure gene act in the same way. By means of inducible promoters it is also possible to increase the expression in the course of the fermentative L-lysine production. The expression is similarly improved by measures aimed at increasing the lifetime of the m-RNA. Furthermore, the enzyme activity is similarly enhanced by preventing the breakdown of the enzyme protein. The genes or gene constructs may either be present in plasmids with different numbers of copies, or may be integrated in the chromosome and amplified. Alternatively, an over-expression of the relevant genes can also be achieved by altering the composition of the media and culture conditions.
In order to increase the number of copies of the aceA-alleles according to the invention, plasmids that are replicated in coryneform bacteria are suitable. Numerous known plasmid vectors such as for example pZ1 (Menkel et al., Applied and Environmental Microbiology (1989) 64: 549–554), pEKEx 1 (Eikmanns et al., Gene 102:93–98 (1991)) or pHS2-1 (Sonnen et al., Gene 107:69–74 (1991)) are based on the cryptic plasmids pHM1519, pBL1 or pGA1. Other plasmid vectors such as for example those that 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 be used in a similar way.
Furthermore, the process of chromosomal gene amplification may be used to increase the number of copies, as has been described for example by Reinscheid et al. (Applied and Environmental Microbiology 60, 126–132 (1994)) for the duplication or amplification of the hom-thrB operon. In this method the complete gene or allele is cloned in a plasmid vector that can replicate 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 (Schäfer et al., Gene 145, 69–73 (1994)), pGEM-T (Promega Corporation, Madison, Wis., USA), pCR2.1-TOPO (Shuman, Journal of Biological Chemistry 269:32678–84 (1994); U.S. Pat. No. 5,487,993), pCR® Blunt (Invitrogen, Groningen, Netherlands; Bernard et al., Journal of Molecular Biology, 234: 534–541 (1993)), pEM1 (Schrumpf et al., Journal of Bacteriology 173:4510–4516 (1991)) or pBGS8 (Spratt et al., Gene 41: 337–342 (1986)). The plasmid vector that contains the gene or allele to be amplified is then transferred by conjugation or transformation into the desired strain of C. glutamicum. The method of conjugation has been described for example by Schäfer et al. (Applied and Environmental Microbiology 60, 756–759 (1994)). Methods of transformation are described for example by Thierbach et al. (Applied Microbiology and Biotechnology 29, 356–362 (1988)), Dunican and Shivnan (Bio/Technology 7, 1067–1070 (1989)) and Tauch et al. (FEMS Microbiological Letters 123, 343–347 (1994)). After homologous recombination by means of a crossover event the resulting strain contains at least two copies of the relevant gene or allele.
The present invention provides preferably endogenous nucleotide sequences (DNA) derived from coryneform bacteria that are capable of replication and code for the enzyme isocitrate lyase, wherein in the associated amino acid sequences the L-alanine at Position 332 of SEQ ID No. 2 is replaced by another proteinogenic amino acid, in particular L-threonine, shown in SEQ ID No 4. The present invention also provides preferably endogenous nucleotide sequences (DNA) derived from coryneform bacteria that are capable of replication and code for the enzyme isocitrate lyase, whose associated base sequence contains adenine at Position 994, as shown in SEQ ID No. 3.
The present invention also provides those nucleotide sequences that are substantially identical to the afore-described nucleotide sequences. Such sequences include nucleotide sequences that code for variants of isocitrate lyase and that in addition to the afore-described change at Position 332 of SEQ ID No. 2 contain at least one further, in particular conservative amino acid replacement. Also, such sequences include nucleotide sequences that code for variants of isocitrate lyase and that a change at any Position of SEQ ID No. 2 of at least one conservative amino acid replacement.
With aromatic amino acids conservative replacements are referred to if phenylalanine, tryptophan and tyrosine are replaced by one another. With hydrophobic amino acids conservative replacements are referred to if leucine, isoleucine and valine are replaced with one another. With polar amino acids conservative replacements are referred to if glutamine and asparagine are replaced by one another. With basic amino acids conservative replacements are referred to if arginine, lysine and histidine are replaced by one another. With acidic amino acids conservative replacements are referred to if aspartic acid and glutamic acid are replaced by one another. With amino acid containing hydroxyl groups conservative replacements are referred to if serine and threonine are replaced by one another.
With regard to substantially identical nucleic acids, these also include those nucleotide sequences that code for variants of isocitrate lyase and that in addition to the described change at Position 332 of SEQ ID No. 2, contain at the N-terminus or C-terminus an extension or shortening of at least one (1) amino acid. This extension or shortening involves not more than 50, 40, 30, 20, 10, 5, 3 or 2 amino acids or amino acid radicals.
The present invention likewise provides nucleic acids that are derived from or have their origin in the genus Corynebacterium, in particular of the species Corynebacterium glutamicum, and code for an isocitrate lyase, and that contain an amino acid sequence corresponding to Positions 327 to 337, or Positions 322 to 342 or 312 to 352 according to SEQ ID No. 4.
The terms “endogenous genes” or “endogenous nucleotide sequences” are understood to mean the genes or nucleotide sequences or alleles present in the population of a species.
The invention also relates to vectors (plasmids) that contain the aforementioned nucleotide sequences and replicate in coryneform bacteria.
Also claimed are bacteria, in particular coryneform bacteria, in which the aforementioned nucleotide sequence(s) coding for the enzyme isocitrate lyase are present. These are typically over-expressed.
The present invention provides a process for the production of L-lysine or feedstuffs additives containing L-lysine, in which the following steps are carried out:

    a) fermentation of coryneform bacteria that contain the endogenous nucleotide sequences coding for the enzyme isocitrate lyase, wherein in the associated amino acid sequences at least the L-alanine at Position 332 is replaced by another proteinogenic amino acid, preferably L-threonine.
    
        The alleles of the endogenous isocitrate lyase gene are possibly over-expressed under conditions that are suitable for the formation of the enzyme isocitrate lyase.
    
    
    b) Enrichment of the L-lysine in the fermentation broth,
    c) isolation of the L-lysine or feedstuffs additive containing L-lysine from the fermentation broth, optionally
    d) with constituents from the fermentation broth and/or from the biomass (>0 to 100%).


Proteinogenic amino acids are understood to mean all amino acids that are constituents of proteins or polypeptides. These include in particular: L-aspartic acid, L-asparagine, L-threonine, L-serine, L-glutamic acid, L-glutamine, glycine, L-alanine, L-cysteine, L-valine, L-methionine, L-isoleucine, L-leucine, L-tyrosine, L-phenylalanine, L-histidine, L-lysine, L-tryptophan, L-proline and L-arginine.
The wild form of the aceA gene is contained in wild type strains of coryneform bacteria, in particular of the genus Corynebacterium. The sequence of the wild type gene of Corynebacterium glutamicum is shown in SEQ ID No. 1. The wild type protein is shown in SEQ ID No. 2.
In connection with the genus Corynebacterium, the species Corynebacterium glutamicum known to specialists in the field should in particular be mentioned. Known wild type strains of the species Corynebacterium glutamicum are for example

    
    
        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.
    
    


In order to produce the aceA alleles according to the invention that code for variants of isocitrate lyase, characterized by an amino acid replacement at least at Position 332 of SEQ ID No. 2, mutagenesis methods described in the prior art are used. In this way strains can be produced and isolated that contain the afore-described mutation in the aceA gene or the nucleotide sequences according to the invention.
For the mutagenesis conventional in vivo mutagenesis methods with cell populations may be employed, using mutagenic substances such as for example N-methyl-N′-nitro-N-nitrosoguanidine or ultraviolet light.
In addition in vitro methods may be used for the mutagenesis, such as for example a treatment with hydroxylamine (Miller, J. H.: A Short Course in Bacterial Genetics. A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1992) or mutagenic oligonucleotides (T. A. Brown: Gentechnologie für Einsteiger, Spektrum Akademischer Verlag, Heidelberg, 1993) or the polymerase chain reaction (PCR) as described in the handbook by Newton and Graham (PCR, Spektrum Akademischer Verlag, Heidelberg, 1994).
Further details and instructions for producing mutations may be obtained from the prior art and known textbooks on genetics and molecular biology, such as for example 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).
When using in vitro methods the aceA gene described in the prior art is amplified by means of the polymerase chain reaction starting from isolated whole DNA of a wild type strain, possibly cloned in suitable plasmid vectors, and the DNA is then subjected to the mutagenesis process. The person skilled in the art can find details and instructions on the amplification of DNA sequences by means of the polymerase chain reaction (PCR) in, inter alia, the handbook by Gait: Oligonucleotide Synthesis: A Practical Approach (IRL Press, Oxford, UK, 1984) and in Newton and Graham: PCR (Spektrum Akademischer Verlag, Heidelberg, Germany, 1994). Suitable aceA alleles are then selected and investigated with the afore-described processes.
The present invention accordingly provides a new aceA allele coding for a variant of isocitrate lyase, which is shown in SEQ ID No. 3.
The aceA alleles according to the invention may be transferred into suitable strains by the process of gene replacement, as described by Schwarzer and Pühler (Bio/Technology 9, 84–87 (1991)) or Peters-Wendisch et al. (Microbiology 144, 915–927 (1998)). The corresponding aceA allele is in this connection cloned in a vector that is non-replicative for C. glutamicum, such as for example pK18mobsacB or pK19mobsacB (Jäger et al., Journal of Bacteriology 174: 5462–65 (1992)) or pCR® Blunt (Invitrogen, Groningen, Netherlands; Bernard et al., Journal of Molecular Biology, 234: 534–541 (1993)) and this is then transferred by transformation or conjugation into the desired host of C. glutamicum. The incorporation of the mutation in the target gene or in the target sequence is achieved after homologous recombination by means of a first crossover event effecting integration and a second crossover event effecting an excision, and a recombinant bacterium is obtained.
Also it may be advantageous for the production of L-amino acids, in addition to the use of the aceA alleles according to the invention, at the same time also to enhance, in particular over-express, one or more enzymes of the respective biosynthesis pathway, glycolysis, anaplerosis, the citric acid cycle, the pentose phosphate cycle, amino acid export and possibly regulatory proteins. The use of endogenous genes is generally preferred.
The term “enhancement” describes in this connection the raising of the intracellular activity or concentration of one or more enzymes or proteins in a microorganism that are coded by the corresponding DNA, by for example increasing the number of copies of the gene or allele, or genes or alleles, by using a strong promoter or using a gene or allele that codes for a corresponding enzyme or protein having a high activity, and optionally by combining these measures.
By these enhancement measures, in particular over-expression, the activity or concentration of the corresponding protein is generally increased by at least 10%, 25%, 50%, 75%, 100%, 150%, 200%, 300%, 400% or 500%, at most up to 1000% or 2000%, referred to that of the wild type protein or to the activity or concentration of the protein in the starting microorganism.
Thus, for the production of L-lysine, in addition to the use of the alleles of the aceA gene according to the invention, at the same time one or more of the genes selected from the following group may be enhanced, in particular over-expressed:

    
    
        the dapA gene coding for dihydrodipicolinate synthase (EP-B 0 197 335),
        the gap gene coding for glyceraldehyde-3-phosphate dehydrogenase (Eikmanns (1992), Journal of Bacteriology 174:6076–6086),
        the eno gene coding for enolase (DE: 19947791.4),
        the tpi gene coding for triose phosphate isomerase (Eikmanns (1992), Journal of Bacteriology 174:6076–6086),
        the pgk gene coding for 3-phosphoglycerate kinase (Eikmanns (1992), Journal of Bacteriology 174:6076–6086),
        the zwf gene coding for glucose-6-phosphate dehydrogenase (JP-A-09224661, EP-A-1108790),
        the pyc gene coding for pyruvate carboxylase (DE-A-198 31 609, EP-A-1108790),
        the mqo gene coding for malate-quinone oxidoreductase (Molenaar et al., European Journal of Biochemistry 254, 395–403 (1998)),
        the lysc gene coding for a feedback-resistant aspartate kinase (Accession No. P26512; EP-B-0387527; EP-A-0699759; WO 00/63388),
        the lysE gene coding for the lysine export protein (DE-A-195 48 222),
        the zwa1 gene coding for the Zwa1 protein (DE: 19959328.0, DSM 13115)
        the gnd gene coding for 6-phosphogluconate dehydrogenase (WO 01/71012),
        the opcA gene coding for a subunit of glucose-6-phosphate dehydrogenase (Sequence No. 79 from WO 01/00844; WO 01/04322).
    
    


The enhancement of 6-phosphogluconate dehydrogenase may be achieved inter alia also by amino acid replacements, such as for example by replacing L-proline by L-serine, L-leucine, L-isoleucine or L-threonine at Position 158 of the enzyme protein and/or by replacing L-serine by L-phenylalanine or L-tyrosine at Position 361 of the enzyme protein.
The enhancement of the subunit of glucose-6-phosphate dehydrogenase for which the opcA gene codes may be achieved inter alia also by amino acid replacements, such as for example by replacing L-serine by L-phenylalanine or L-tyrosine at Position 312 of the enzyme protein.
Moreover, it may be advantageous for the production of L-lysine, in addition to the use of the alleles of the aceA gene according to the invention, at the same time to attenuate, in particular to reduce the expression, of one or more of the endogenous genes selected from the group:

    
    
        the pck gene coding for phosphoenol pyruvate carboxykinase (DE 199 50 409.1, DSM 13047),
        the pgi gene coding for glucose-6-phosphate isomerase (U.S. Ser. No. 09/396,478, DSM 12969),
        the poxB gene coding for pyruvate oxidase (DE: 1995 1975.7, DSM 13114),
        the Zwa2 gene coding for the Zwa2 protein (DE: 19959327.2, DSM 13113),
        the fda gene coding for fructose-1,6-bisphosphate aldolase (Accession No. X17313; von der Osten et al., Molecular Microbiology 3 (11), 1625–1637 (1989)),
        the hom gene coding for homoserine dehydrogenase (EP-A-0131171),
        the thrB gene coding for homoserine kinase (Peoples, O. W., et al., Molecular Microbiology 2 (1988): 63–72) and
        the pfkB gene coding for phosphofructokinase (Sequence No. 57 from WO 01/00844).
    
    


The term “attenuation” describes in this connection the reduction or switching off of the intracellular activity of one or more enzymes (proteins) in a microorganism that are coded by the corresponding DNA, by using for example a weak promoter, or using a gene or allele that codes for a corresponding enzyme with a low activity, or inactivating the corresponding gene or enzyme (protein), and optionally combining these measures.
By means of these attenuation measures the activity or concentration of the corresponding protein is generally reduced to 0 to 75%, 0 to 50%, 0 to 25%, 0 to 10% or 0 to 5% of the activity or concentration of the wild type protein, or the activity or concentration of the protein in the starting microorganism.
The attenuation of the phosphofructokinase may also be achieved inter alia by amino acid replacements, such as for example by replacing L-leucine by L-alanine, L-glycine or L-proline at Position 109 of the enzyme protein.
The microorganisms produced according to the invention are also covered by the invention and may be cultivated continuously or batchwise in the batch process (batch cultivation) or in the fed batch process (feed process) or in the repeated fed batch process (repetitive feed process) for the purposes of producing L-amino acids. A summary of known cultivation methods is described in the textbook by Chmiel (Bioprozesstechnik 1. Einführung in die Bioverfahrenstechnik (Gustav Fischer Verlag, Stuttgart, 1991)) or in the textbook by Storhas (Bioreaktoren und periphere Einrichtungen (Vieweg Verlag, Brunswick, Wiesbaden, 1994)).
The culture medium to be used must appropriately satisfy the requirements of the respective strains. Descriptions of culture media of various microorganisms are contained in the handbook “Manual of Methods for General Bacteriology” of the American Society for Bacteriology (Washington D.C., USA, 1981).
As carbon source, sugars and carbohydrates such as for example glucose, sucrose, lactose, fructose, maltose, molasses, starch and cellulose, oils and fats such as for example soya bean oil, sunflower oil, groundnut oil and coconut oil, fatty acids such as for example palmitic acid, stearic acid and linoleic acid, alcohols such as for example glycerol and ethanol, and organic acids such as for example acetic acid, may be used. These substances may be used individually or as a mixture.
As nitrogen source, organic nitrogen-containing compounds such as peptones, yeast extract, meat extract, malt extract, corn steep liquor, soya bean flour and urea, or inorganic compounds such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate and ammonium nitrate may be used. The nitrogen sources may be used individually or as a mixture.
As phosphorus source, phosphoric acid, potassium dihydrogen phosphate or dipotassium hydrogen phosphate or the corresponding sodium-containing salts may be used. The culture medium must furthermore contain salts of metals, such as for example magnesium sulfate or iron sulfate, that are necessary for growth. Finally, essential growth promoters such as amino acids and vitamins may be used in addition to the aforementioned substances. Suitable precursors may furthermore be added to the culture medium. The afore-mentioned starting substances may be added to the culture in the form of a single batch or may be metered in in an appropriate manner during the cultivation.
In order to regulate the pH of the culture basic compounds such as sodium hydroxide, potassium hydroxide, ammonia or ammonia water, or acidic compounds such as phosphoric acid or sulfuric acid are used as appropriate. In order to control foam formation antifoaming agents such as for example fatty acid polyglycol esters may be used. In order to maintain the stability of plasmids, suitable selectively acting substances, for example antibiotics, may be added to the medium. In order to maintain aerobic conditions, oxygen or oxygen-containing gas mixtures such as for example air are fed into the culture. The temperature of the culture is normally 20° C. to 45° C., and preferably 25° C. to 40° C. Cultivation is continued until a maximum amount of the desired product has been formed. This target is normally achieved within 10 hours to 160 hours.
The following microorganism was deposited as a pure culture on 07.02.2003 at the Deutsche Sammlung für Mikroorganismen und Zellkulturen (DSMZ=German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany) in accordance with the Budapest Treaty:

    
    
        Corynebacterium glutamicum DSM5715_aceA_A332T as DSM 15431.
    
    


Methods for determining L-amino acids are known from the prior art. The analysis may be carried out for example by anion exchange chromatography followed by ninhydrin derivation, as described by Spackman et al. (Analytical Chemistry, 30, (1958), 1190), or by reversed phase HPLC, as described by Lindroth et al. (Analytical Chemistry (1979) 51: 1167–1174).
The process according to the invention can be used for the fermentative production of L-lysine.
The concentration of L-lysine may optionally be adjusted to the desired value by the addition of L-lysine.
EXAMPLE 1
Isolation and Sequencing of the DNA of the aceA Allele from the Strain DM1547.
The Corynebacterium glutamicum strain DM1547 was prepared from C. glutamicum ATCC13032 by multiple non-directed mutagenesis, selection and mutant choice. The strain is resistant to the lysine analogue S-(2-aminoethyl)-L-cysteine and methionine-sensitive.
Chromosomal DNA is isolated from the strain DM1547 by the conventional methods (Eikmanns et al., Microbiology 140, 1817–1828 (1994)). The polymerase chain reaction is used to amplify a DNA segment carrying the aceA gene or allele. The following oligonucleotide primers are chosen for the PCR on the basis of the sequence of the aceA gene which is known for C. glutamicum (Sequence No. 591 from Patent application WO 01/00844; Sequence No. 3489 and 7067 from Patent application No. EP-A—1108790; Genebank Accession Number X75504):
aceA–A1 (SEQ ID No. 8):
5′ tac atc cgt act agc aac tc 3′
aceA–A2 (SEQ ID No. 9):
5′ atc cgt tgt aca gat gta gg 3′
The primers shown are synthesized by MWG Biotech (Ebersberg, Germany) and the PCR is carried out by the standard method of Innis et al. (PCR protocols. A Guide to Methods and Applications, 1990, Academic Press). The primers enable the amplification of an approximately 1.6 kb DNA segment carrying the aceA allele.
The amplified DNA fragment of approximately 1.6 kb, carrying the aceA allele of the strain DM1547, is identified by electrophoresis in 0.8% agarose gel, isolated from the gel and purified by the conventional methods (QIAquick Gel Extraction Kit, Qiagen, Hilden).
The nucleotide sequence of the amplified DNA fragment or PCR product is determined by GATC Biotech AG (Konstanz, Germany) by sequencing. The sequence of the PCR product is shown in SEQ ID No. 5. The sequence of the coding region is reproduced in SEQ ID No. 3. The amino acid sequence of the corresponding isocitrate lyase protein, found with the help of the Patentin program, is shown in SEQ ID No. 6 and SEQ ID No. 4.
Located in position 994 of the nucleotide sequence of the coding region of the aceA allele from the strain DM1547, i.e. in position 1251 of the nucleotide sequence shown in SEQ ID No. 5, is the base adenine. Located in the corresponding position of the wild-type gene is the base guanine (SEQ ID No. 1).
Located in position 332 of the amino acid sequence of the isocitrate lyase from the strain DM1547 is the amino acid threonine (SEQ ID No. 6 and SEQ ID No. 4). Located in the corresponding position of the wild-type protein is the amino acid alanine (SEQ ID No. 2).
The aceA allele, which contains the base adenine in position 994 of the coding region and accordingly codes for an isocitrate lyase containing the amino acid threonine in position 332 of the amino acid sequence, is called the aceA_A332T allele hereafter. In the name “aceA_A332T”, A represents L-alanine, T represents L-threonine and 332 indicates the position of the amino acid replacement (cf. SEQ ID No. 2 and 4).
EXAMPLE 2
Replacement of the aceA Wild-Type Gene from the Strain DSM5715 with the aceA_A332T Allele
2.1 Preparation of a DNA Fragment Containing the Region of the aceA_A332T Allele in which the A332T Mutation is Located
Chromosomal DNA is isolated from the strain DM1547 by the conventional methods (Eikmanns et al., Microbiology 140, 1817–1828 (1994)). The polymerase chain reaction is used to amplify a DNA segment carrying the part of the aceA allele which contains the mutation A332T. The following oligonucleotide primers are chosen for the PCR on the basis of the sequence of the aceA gene which is known for C. glutamicum (Sequence No. 591 from Patent application WO 01/00844; Sequence No. 3489 and 7067 from Patent application No. EP-A—1108790; Genebank Accession Number X75504):
aceA_XL-A1 (SEQ ID No. 10):
5′ ga tct aga ttg gcg cac tca ccg gta ac 3′
aceA_XL-A2 (SEQ ID No. 11):
5′ ga tct aga cgc tac gga atc gca gat cg 3′
The primers shown are synthesized by MWG Biotech (Ebersberg, Germany) and the PCR is carried out by the standard method of Innis et al. (PCR protocols. A Guide to Methods and Applications, 1990, Academic Press). The primers enable the amplification of an approximately 1.6 kb DNA segment carrying a region of the aceA_A332T—allele which contains the A332T mutation (SEQ ID No. 7). The primers also contain the sequences for cleavage sites of the restriction endonuclease XbaI, which are underlined in the nucleotide sequence shown above.
The amplified DNA fragment of approximately 1.6 kb, carrying the aceA allele of the strain DM1547, is cleaved with the restriction endonuclease XbaI, identified by electrophoresis in 0.8% agarose gel, isolated from the gel and purified by the conventional methods (QIAquick Gel Extraction Kit, Qiagen, Hilden).
2.2 Construction of the Replacement Vector pK18mobsacB_aceA_A332T
The approximately 1.6 kb DNA fragment described in Example 2.1, cleaved with the restriction endonuclease XbaI and containing the aceA_A332T allele, is incorporated into the chromosome of the C. glutamicum strain DSM5715 by means of replacement mutagenesis with the aid of the sacB system described in Schäfer et al. (Gene 14, 69–73 (1994)). This system makes it possible to prepare or select allele replacements that take place through homologous recombination.
The mobilizable cloning vector pK18mobsacB is digested with the restriction enzyme XbaI and the ends are dephosphorylated with alkaline phosphatase (Boehringer Mannheim, Germany). The vector prepared in this way is mixed with the approximately 1.6 kb aceA_A332T fragment digested with the restriction enzyme XbaI, and the mixture is treated with T4 DNA ligase (Amersham-Pharmacia, Freiburg, Germany).
The E. coli strain S17-1 (Simon et al., Bio/Technologie 1, 784–791, 1993) is then transformed with the ligation mixture (Hanahan, in: DNA Cloning. A Practical Approach. Vol. 1, ILR-Press, Cold Spring Harbor, N.Y., 1989). The plasmid-carrying cells are selected by plating the transformation mixture on LB agar (Sambrook et al., Molecular Cloning: A Laboratory Manual. 2nd edition. Cold Spring Harbor, N.Y., 1989) supplemented with 25 mg/l of kanamycin.
Plasmid DNA is isolated from a transformant with the aid of the QIAprep Spin Miniprep Kit from Qiagen and checked by restriction cleavage with the enzyme BglII followed by agarose gel electrophoresis. The plasmid is called pK18mobsacB_aceA_A332T and is shown in FIG. 1.
2.3 Alleles Replacement
The vector pK18mobsacB_aceA_A332T mentioned in Example 2.2 is transferred to the C. glutamicum strain DSM5715 (EP-B-0435 132) by conjugation using a protocol of Schäfer et al. (Journal of Microbiology 172, 1663–1666 (1990)). The vector cannot replicate independently in DSM5715 and is only retained in the cell when it is integrated in the chromosome as the result of a recombination event. Transconjugants, i.e. clones with integrated pK18mobsacB_aceA_A332T, are selected by plating the conjugation mixture on LB agar (Sambrook et al., Molecular Cloning: A Laboratory Manual. 2nd edition. Cold Spring Harbor, N.Y., 1989) supplemented with 15 mg/l of kanamycin and 50 mg/l of nalidixic acid. Kanamycin-resistant transconjugants are streaked on plates of LB agar supplemented with 25 mg/l of kanamycin, and incubated for 24 hours at 33° C. To select mutants in which excision of the plasmid has taken place as the result of a second recombination event, the clones are cultivated non-selectively in LB liquid medium for 30 hours and then streaked on LB agar supplemented with 10% of sucrose, and incubated for 24 hours.
Like the starting plasmid pK18mobsacB, plasmid pK18mobsacB_aceA_A332T contains not only the kanamycin resistance gene but also a copy of the sacB gene coding for the levan sucrase from Bacillus subtilis. Expression inducible by sucrose leads to the formation of levan sucrase, which catalyses the synthesis of the product levan, toxic to C. glutamicum. Therefore, the only clones that grow on LB agar supplemented with sucrose are those in which the integrated pK18mobsacB_aceA_A332T has excised as the result of a second recombination event. Depending on the location of the second recombination event in relation to the mutation site, allele replacement or incorporation of the mutation takes place in the excision or the original copy remains in the chromosome of the host.
20 clones with the phenotype “growth in the presence of sucrose” and “non-growth in the presence of kanamycin” are examined by sequencing a region containing the mutation A332T of the aceA-gene, starting from the sequencing primer GATC-10790. The synthesis of the primer GATC-10790 and the sequencing is progressed by GATC Biotech AG (Konstanz, Germany) to identify clones carrying the aceA_A332T allele.
GATC-10790 (SEQ ID No. 12):
5′ ACCGCAGAAGGCTACTACCA 3′
A clone containing the base adenine in position 994 of the coding region, and hence possessing the aceA_A332T allele, was identified in this way.
The strain was called C. glutamicum DSM5715_aceA_A332T.
EXAMPLE 3
Preparation of Lysine
The C. glutamicum strain DSM5715_aceA_A332T obtained in Example 2 is cultivated in a nutrient medium suitable for the production of lysine, and the lysine content is determined in the culture supernatant.
To do this, the strain is first incubated on an agar plate for 24 hours at 33° C. This agar plate culture is used to inoculate a preculture (10 ml of medium in a 100 ml conical flask). MM medium is used as the medium for the preculture.
The preculture is incubated on a shaker at 240 rpm for 24 hours at 33° C. This preculture is used to inoculate a main culture so that the initial OD (660 nm) of the main culture is 0.1. MM medium is also used for the main culture.










MM medium



















CSL
5
g/l



MOPS
20
g/l



Glucose (separately autoclaved)
50
g/l



Salts:



(NH4)2SO4
25
g/l



KH2PO4
0.1
g/l



MgSO4.7H2O
1.0
g/l



CaCl2.2H2O
10
mg/l



FeSO4.7H2O
10
mg/l



MnSO4.H2O
5.0
mg/l



Biotin (sterile-filtered)
0.3
mg/l



Thiamine.HCl (sterile-filtered)
0.2
mg/l



L-homoserine (sterile-filtered)
0.4
g/l



CaCO3
25
g/l










The CSL (corn steep liquor), the MOPS (morpholinopropanesulfonic acid) and the salt solution are adjusted to pH 7 with aqueous ammonia and autoclaved. The sterile substrate and vitamin solutions and the dry-autoclaved CaCO3 are then added.
Cultivation is carried out on a volume of 10 ml in a 100 ml conical flask with baffles at 33° C. and 80% atmospheric humidity.
After 48 hours the OD at a measurement wavelength of 660 nm is determined with a Biomek 1000 (Beckman Instruments GmbH, Munich). The amount of lysine formed is determined with an amino acid analyzer from Eppendorf-BioTronik (Hamburg, Germany) by means of ion exchange chromatography and post-column derivation with ninhydrin detection.
Table 1 shows the result of the experiment.











TABLE 1








OD
Lysine-HCl



Strain
(660 nm)
g/l









DSM5715
8.2
15.3



DSM5715_aceA_A332T
7.4
16.2













BRIEF DESCRIPTION OF THE FIGURE
FIG. 1: Map of plasmid pK18mobsacB_aceA_A332T



The abbreviations and symbols used have the meanings given below. The numbers of base pairs indicated are approximate values obtained within the limits of reproducibility of the measurements.
















KanR:
kanamycin resistance gene



′aceA:
cloned DNA fragment containing a 3′-terminal




region of the aceA_A332T allele and the




downstream region



sacB:
sacB gene



RP4mob:
mob region with the origin of replication




for the transfer (oriT)



oriV:
origin of replication V



BglII:
cleavage site of the restriction enzyme




BglII



XbaI:
cleavage site of the restriction enzyme




XbaI

## Claims

1. A process for the production of L-lysine or feedstuffs additives containing L-lysine, comprising:
a) fermenting coryneform bacteria in which alleles of the endogenous aceA gene are over-expressed under conditions that are suitable for the formation of the aceA gene product isocitrate lyase, and wherein said isocitrate lyase comprises the amino acid sequence of SEQ ID NO:2 in which the alanine residue at position 332 is replaced with threonine; and
b) isolating said L-lysine or the feedstuffs additive containing L-lysine from the fermentation broth, optionally
c) with constituents from the fermentation broth and/or biomass (>0 up to 100%).

2. The process of claim 1, wherein said L-lysine or said feedstuffs additive containing L-lysine is isolated with constituents from the fermentation broth and/or biomass (>0 up to 100%).

3. The process of claim 1, wherein coryneform bacteria are used in which, in addition to the over-expression of said aceA gene, further genes of the biosynthesis pathway of L-lysine are over-expressed.

4. The process of claim 1, wherein coryneform bacteria are used in which the metabolic pathways that reduce the formation of L-lysine are at least partially switched off.

5. A process for the production of L-lysine or feedstuffs additives containing L-lysine, comprising:
a) fermenting coryneform bacteria that contain endogenous nucleotide sequences coding for the enzyme isocitrate lyase, wherein in the associated amino acid sequences the L-alanine at position 332 is replaced by L-threonine,
b) optionally enriching the L-lysine in the fermentation broth,
c) isolating the L-lysine or the feedstuffs additive containing L-lysine from the fermentation broth, optionally
d) with constituents from the fermentation broth and/or from the biomass (>0 up to 100%).

6. The process of claim 5, wherein the endogenous nucleotide sequences coding for the enzyme isocitrate lyase are over-expressed under conditions that are suitable for the formation of the aceA gene product isocitrate lyase.

7. The process of either claim 1 or 5, wherein the Corynebacterium glutamicumstrain DSM5715_aceA_A332T is employed.

8. The process of any one of claims 1–6, wherein said isocitrate lyase is encoded by DNA with the nucleotide sequence of SEQ ID NO:3.

9. The process of any one of claims 1–6, wherein said isocitrate lyase consists of the amino acid sequence of SEQ ID NO:2 in which the alanine residue at position 332 is replaced with threomne.

10. The process of either claim 1 or 5, wherein the activity of said isocitrate lyase is increased by at least 50%.