US20050202543A1

US20050202543A1 - Method for producing L-amino acid

Info

Publication number: US20050202543A1
Application number: US11/116,286
Authority: US
Inventors: Vitaliy Livshits; Natalia Zakataeva; Kazuo Nakanishi; Vladimir Aleshin; Petr Troshin; Irina Tokhmakova
Original assignee: Individual
Current assignee: Individual
Priority date: 1998-12-30
Filing date: 2005-04-28
Publication date: 2005-09-15
Also published as: KR20070034024A; BR9906287A; MXPA00000177A; CA2291895A1; EP1598416A1; CN1332021C; CN1737119A; US20080050785A1; JP4221862B2; EP1589096B1; US7524656B2; SK187099A3; KR20070034023A; CN100410366C; US20080050784A1; EP1016710B1; AU764189B2; EP1589096A1; ATE456648T1; DE69942160D1

Abstract

A bacterium belonging to the genus Escherichia which has an ability to produce an L-amino acid, wherein the ability to produce the L-amino acid is increased by increasing expression of an L-amino acid excretion protein is described. A method for producing the L-amino acid using the bacterium is also described.

Description

This application claims the benefit as a continuation application under 35 U.S.C. §120 to application Ser. No. 09/459,573.

FIELD OF THE INVENTION

The present invention relates to a method for producing an amino acid. In particular, the present invention relates to an L-amino acid-producing bacterium belonging to the genus Escherichia and a method for producing L-amino acids using the bacterium, more specifically, L-glutamic acid, L-lysine, L-threonine, L-alanine, L-histidine, L-proline, L-arginine, L-valine, and L-isoleucine.

BRIEF DESCRIPTION OF THE RELATED ART

To improve production of L-amino acids by fermentation, strains isolated from nature or artificial mutants thereof have been used. For example, many artificial mutants which produce L-lysine are known, and most of them are resistant to S-2-aminoethylcysteine (AEC) and belong to the genus Brevibacterium, Corynebacterium, Bacillus, or Escherichia. Also, various techniques have been proposed to increase amino acid production, such as using a strain which has been transformed with recombinant DNA (U.S. Pat. No. 4,278,765).
The reported techniques are largely based on enhancing an activity of an enzyme involved in an amino acid biosynthetic pathway, conversion of the enzyme to one that is desensitized in inhibition, and the like (As to bacterium belonging the genus Escherichia, see Japanese Patent Application Laid-Open No. 56-18596 (1981) and International Publication No. WO 95/16042).
Alternatively, a bacterium belonging to the genus Corynebacterium in which the L-lysine excretion gene lysE is enhanced is known, and is an example of improving amino acid productivity by enhancing an amino acid excretion protein. However, as to bacteria belonging to the genus Escherichia, it is unknown whether an L-amino acid excretion protein exists or not. Therefore, it is unknown whether or not enhancing an L-amino acid excretion protein would be effective for L-amino acid production when using a bacterium belonging to the genus Escherichia.
Although the entire nucleotide sequence of E. coli strain K-12 has been determined (Science, 277, 1453-1474(1997)), there are a large number of proteins for which their functions remain unknown.

SUMMARY OF THE INVENTION

An object of the present invention is to obtain a protein which participates in excretion of an L-amino acid, and thereby provide a strain which has improved L-amino acid productivity. Another object of the present invention is to provide an improved method for producing an L-amino acid by fermentation.
The inventors have conducted screening for a protein which participates in excretion of an L-amino acid. As a result, the present inventors have found that the yield of an L-amino acid based on consumed sugar increases when a particular gene is enhanced. On the basis of this finding, the present invention has been completed.
Thus, the present invention provides a bacterium belonging to the genus Escherichia (hereinafter “the bacterium of the present invention”) which has an ability to produce an L-amino acid, wherein the ability to produce the L-amino acid increases by increasing the expression of at least one protein selected from the group consisting of:
(A) a protein comprising an amino acid sequence shown in SEQ ID NO: 10;
(B) a protein comprising an amino acid sequence of SEQ ID NO: 10, and which includes deletion, substitution, insertion, addition, or inversion of one or several amino acids in said amino acid sequence, and which has an activity of increasing the ability of the bacterium having the protein to produce the L-amino acid;
(C) a protein comprising an amino acid sequence shown in SEQ ID NO: 12;
(D) a protein comprising an amino acid sequence of SEQ ID NO: 12, and which includes deletion, substitution, insertion, addition, or inversion of one or several amino acids in said amino acid sequence, and which has an activity of increasing the ability of the bacterium having the protein to produce the L-amino acid;
(E) a protein comprising an amino acid sequence shown in SEQ ID NO: 14;
(F) a protein comprising an amino acid sequence of SEQ ID NO: 14, and which includes deletion, substitution, insertion, addition, or inversion of one or several amino acids in said amino acid sequence, and which has an activity of increasing the ability of the bacterium having the protein to produce the L-amino acid;
(G) a protein comprising an amino acid sequence shown in SEQ ID NO: 16; or
(H) a protein comprising an amino acid sequence of SEQ ID NO: 16, and which includes deletion, substitution, insertion, addition, or inversion of one or several amino acids in said amino acid sequence, and which has an activity of increasing the ability of the bacterium having the protein to produce the L-amino acid.
The bacterium of the present invention is preferably an L-lysine-producing bacterium in which expression of at least one protein selected from the group consisting of the proteins (A) to (D), (G) and (H) is increased; an L-glutamic acid-producing bacterium in which expression of at least one protein selected from the group consisting of the proteins (A) to (H) is increased; an L-alanine-producing bacterium in which expression of at least one protein selected from the group consisting of the proteins (C) and (D) is increased; an L-valine-producing bacterium in which expression of at least one protein selected from the group consisting of the proteins (C) and (D) is increased; an L-histidine-producing bacterium in which expression of at least one protein selected from the group consisting of said proteins (C) to (F) is increased; an L-proline-producing bacterium in which expression of at least one protein selected from the group consisting of said proteins (A) to (F) is increased; an L-threonine-producing bacterium in which expression of at least one protein selected from the group consisting of said proteins (E) and (F) is increased; an L-arginine-producing bacterium in which expression of at least one protein selected from the group consisting of said proteins (G) and (H) is increased; or an L-isoleucine-producing bacterium in which expression of at least one protein selected from the group consisting of said proteins (C) and (D) is increased.
Preferably, in the bacterium of the present invention, the copy number of a DNA coding for said protein is increased. The DNA is preferably carried on a multicopy vector or on a transposon in the cell.
The present invention also provides a method for producing an L-amino acid comprising cultivating the bacterium of the present invention in a culture medium, and recovering the L-amino acid from the medium (hereinafter also referred to as “the method of the present invention”).
The method of the present invention is preferably an L-lysine production method using an L-lysine-producing bacterium in which expression of at least one protein selected from the group consisting of the proteins (A) to (D), (G) and (H) is increased; an L-glutamic acid production method using an L-glutamic acid-producing bacterium in which expression of at least one protein selected from the group consisting of the proteins (A) to (H) is increased; an L-alanine production method using an L-alanine-producing bacterium in which expression of at least one protein selected from the group consisting of the proteins (C) and (D) is increased; an L-valine production method using an L-valine-producing bacterium in which expression of at least one protein selected from the group consisting of the proteins (C) and (D) is increased; an L-histidine production method using an L-histidine-producing bacterium in which expression of at least one protein selected from the group consisting of said proteins (C) to (F) is increased; an L-proline production method using an L-proline-producing bacterium in which expression of at least one protein selected from the group consisting of said proteins (A) to (F) is increased; an L-threonine production method using an L-threonine-producing bacterium in which expression of at least one protein selected from the group consisting of said proteins (E) and (F) is increased; an L-arginine production method using an L-arginine-producing bacterium in which expression of at least one protein selected from the group consisting of said proteins (G) and (H) is increased; or an L-isoleucine production method using an L-isoleucine-producing bacterium in which expression of at least one protein selected from the group consisting of said proteins (C) and (D) is increased.
Preferably, in the method of the present invention, a copy number of a DNA coding for said protein in the bacterium is increased. The DNA is preferably carried on a multicopy vector or on a transposon in the cell.
According to the present invention, an ability of a bacterium belonging to the genus Escherichia to produce an L-amino acid is increased. Also, a method for producing an L-amino acid is improved by increasing the production rate of the L-amino acid.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

The present invention will be explained in detail below. Hereinafter, an amino acid is of L-configuration unless otherwise noted.
<1> Bacterium of the present invention
The bacterium of the present invention is a bacterium belonging to the genus Escherichia which has an ability to produce an amino acid. The ability to produce the amino acid is increased by increasing expression of a protein which has an activity of increasing the ability to produce the amino acid of the bacterium, or an activity of increasing resistance to an amino acid or amino acid analogue. Hereinafter, the protein is referred to as “amino acid excretion protein”. However, the term does not mean that function of the protein is limited to amino acid excretion.
Examples of the amino acid excretion protein include a protein having an amino acid sequence shown in SEQ ID NO: 10, a protein having an amino acid sequence shown in SEQ ID NO: 12, a protein having an amino acid sequence shown in SEQ ID NO: 14, and a protein having an amino acid sequence shown in SEQ ID NO: 16.
The amino acid excretion protein may be selective for a particular amino acid. An amino acid excretion protein appropriate for each amino acid can be determined by expressing the protein in an Escherichia bacterium which has the ability to produce the amino acid, and measuring the increased yield of the amino acid, or measuring the increased minimum inhibition concentration (MIC) of the amino acid or an amino acid analogue.
For example, for lysine, a protein having an amino acid sequence shown in SEQ ID NO: 10, 12, or 16 is effective; for glutamic acid, a protein having an amino acid sequence shown in SEQ ID NO: 10, 12, 14, or 16 is effective; for alanine, a protein having an amino acid sequence shown in SEQ ID NO: 12 is effective; for valine, a protein having an amino acid sequence shown in SEQ ID NO: 12 is effective; for histidine, a protein having an amino acid sequence shown in SEQ ID NO: 12 or 14; for proline, a protein having an amino acid sequence shown in SEQ ID NO: 10, 12, or 14 is effective; for threonine, a protein having an amino acid sequence shown in SEQ ID NO: 14 is effective; for arginine, a protein having an amino acid sequence shown in SEQ ID NO: 16 is effective; for isoleucine, a protein having an amino acid sequence shown in SEQ ID NO: 12 is effective.
The phrase “expression is increased” used herein usually means that the expression amount is larger than that in a wild-type strain of E. coli, such as the strains MG1655 or W3110. The phrase also means that when a strain is modified by genetic engineering techniques or the like, the expression amount is larger than that prior to the modification. Expression of the amino acid excretion protein may be determined directly by measuring the protein amount, or indirectly by measuring the MIC of the amino acid or an amino acid analogue, or measuring the amino acid productivity of the Escherichia bacterium.
The method for increasing expression of the amino acid excretion protein is exemplified by increasing a copy number of a DNA encoding the amino acid excretion protein in the bacterium.
To increase the copy number in the cell, a DNA fragment coding for the amino acid excretion protein may be ligated to a vector which functions in the chosen Escherichia bacterium to produce a recombinant DNA, which is introduced into a host to transform it. The copy number of the gene coding for the amino acid excretion protein (amino acid excretion protein gene) in the cell of the transformant strain increases, thereby increasing the expression amount of the amino acid excretion protein. The vector is preferably a multicopy vector.
The increase of the copy number in the cell can be achieved by allowing plural copies of the amino acid excretion protein gene to exist on the chromosomal DNA of the host. The introduction of plural copies of the amino acid excretion protein gene to the chromosomal DNA of the Escherichia bacterium, may be achieved via homologous recombination using a target sequence of which plural copies exist on the chromosomal DNA. As said target sequence, a repetitive DNA and an inverted repeat present in a terminal portion of a transposable element may be used. Alternatively, as disclosed in Japanese Patent Application Laid-Open No. 2-109985 (1990), plural copies can be introduced to the chromosomal DNA by carrying the amino acid excretion protein gene on a transposon and allowing the transposon to be transposed, which is preferred. According to any of the above-mentioned methods, the copy number of the amino acid excretion protein gene in the transformant strain increases, thereby increasing expression of the amino acid excretion protein.
The multicopy vector is exemplified by plasmid vectors such as pBR322, pMW118, pUC19, or the like, and phage vectors such as λ1059, λBF101, M13mp9, or the like. The transposon is exemplified by Mu, Tn10, Tn5, or the like.
To introduce a DNA into an Escherichia bacterium, for example, the method of D. M. Morrison (Methods in Enzymology 68, 326 (1979)), or a method in which recipient bacterial cells are treated with calcium chloride to increase permeability of DNA (Mandel, M. and Higa, A., J. Mol. Biol., 53, 159 (1970)), and the like can be used.
Besides the above-mentioned gene amplification, increasing expression of the amino acid excretion protein can be also achieved by replacing an expression regulatory sequence, such as a promoter of the amino acid excretion protein gene, with stronger one (see Japanese Patent Application Laid-Open No. 1-215280 (1989)). For example, lac promoter, trp promoter, tac promoter, P_Rpromoter and P_Lpromoter of lambda phage, and the like are known as a strong promoters. Replacing the promoter enhances expression of the amino acid excretion protein, thereby increasing expression of the amino acid excretion protein. Enhancing the expression regulatory sequence may be combined with increasing the copy number of the amino acid excretion protein.
In the bacterium of the present invention, expression of plural amino acid excretion proteins may be increased.
The amino acid excretion protein is encoded by genes which are known as the yahN gene, yeaS gene, yfiK gene, and yggA gene. The functions of these genes are unknown. Therefore, the DNA encoding the amino acid excretion protein can be obtained by synthesizing primers based on the known sequences (for example, the entire nucleotide sequence of the chromosome of Escherichia coli strain K-12 has been determined (Science, 277, 1453-1474(1997))), and amplifying by PCR using chromosomal DNA of an Escherichia bacterium as a template. Also, the object DNA fragment can be selected by hybridization from an Escherichia bacterium chromosomal DNA library by preparing a probe based on the known sequences. Alternatively, the DNA encoding the amino acid excretion protein may be synthesized based on the known sequences. The nucleotide sequence of the DNA encoding the amino acid excretion protein is exemplified by those shown in SEQ ID NOs: 9, 11, 13, or 15.
Methods for preparation of a chromosomal DNA, preparation of a chromosomal DNA library, hybridization, PCR, preparation of plasmid DNA, digestion and ligation of DNA, transformation, selection of an oligonucleotide as a primer, and the like may be performed by ordinary methods well known to those skilled in the art. These methods are described in Sambrook, J., Fritsch, E. F., and Maniatis, T., “Molecular Cloning A Laboratory Manual, Second Edition”, Cold Spring Harbor Laboratory Press (1989) and the like.
The amino acid excretion protein may include substitution, deletion, insertion, addition, or inversion of one or several amino acids at one or a plurality of positions, provided that the activity of increasing the ability of the Escherichia bacterium having the protein to produce the amino acid is not deteriorated. The number intended by the term “several” may vary depending on the position in the steric structure of the protein and the kind of amino acid residue. This is because some amino acids such as isoleucine and valine are highly similar, and interchanging such amino acids does not largely affect the steric structure of the protein.
The DNA which codes for substantially the same protein as the amino acid excretion protein as described above, may be obtained, for example, by modifying the nucleotide sequence, for example, by means of site-directed mutagenesis so that one or more amino acid residues at a specified site are substituted, deleted, inserted, added, or inverted. The DNA modified as described above may be obtained by a conventionally known mutation treatment. Such a mutation treatment includes treating a DNA coding for the amino acid excretion protein in vitro, for example, with hydroxylamine, and treating a microorganism, for example, a bacterium belonging to the genus Escherichia, harboring a DNA coding for the amino acid excretion protein with ultraviolet irradiation or a mutating agent, such as N-methyl-N′-nitro-N-nitrosoguanidine (NG) and nitrous acid, which are usually used for mutation treatments.
The substitution, deletion, insertion, addition, or inversion of one or more amino acid residues includes a naturally-occurring mutation or variation which results from differences between individual microorganisms having the amino acid excretion protein, and differences between species, strains, or the like.
The DNA which codes for substantially the same protein as the amino acid excretion protein can be obtained by allowing a DNA having the mutation as described above to be expressed in an appropriate Escherichia bacterium, and investigating the increase of amino acid productivity of the cell.
Also, the DNA which codes for substantially the same protein as the amino acid excretion protein can be obtained by isolating a DNA which hybridizes with, for example, a nucleotide sequence shown in SEQ ID NO: 9, 11, 13, or 15 under stringent conditions, and which DNA codes for a protein having the activity of increasing the ability of the bacterium belonging to the genus Escherichia to produce the amino acid, from DNAs encoding the amino acid excretion proteins having mutations or cells containing the DNAs. The term “stringent conditions” referred to herein means conditions under which a specific hybrid is formed, and a non-specific hybrid is not formed. It is difficult to clearly express this condition by using any numerical value. However, for example, the stringent conditions include conditions under which DNAs having high homology, for example, DNAs having homology of not less than 70% with each other are hybridized, and DNAs having homology with each other lower than the above are not hybridized, or conditions comprising washing in a salt concentration corresponding to 60° C., 1×SSC, 0.1% SDS, preferably 0.1×SSC, 0.1% SDS, which is ordinary washing conditions for Southern hybridization.
Although there may be a gene in which a stop codon is located in the middle, or a gene encoding a protein which has lost activity due to mutation of the active center among the genes which hybridize under such the condition, such genes can be easily eliminated by ligating the genes to a commercially available activity-expression vector and determining the activity of the bacterium belonging to the genus Escherichia to increase the ability to produce the amino acid as described above.
The term “DNA coding for a protein” used herein means a DNA of which one of strands codes for the protein when the DNA is double-stranded.
By increasing expression of an amino acid excretion protein in an amino acid-producing Escherichia bacterium as described above, the amount of the amino acid produced can be increased. As the Escherichia bacterium which has increased expression of the amino acid excretion protein, strains which have abilities to produce desired amino acids (amino acid productivities) are used. Besides, an ability to produce an amino acid may be imparted to a bacterium in which expression of the amino acid excretion protein is increased. Examples of amino acid-producing bacteria belonging to the genus Escherichia include E. coli AJ13199 (FR patent No. 2747689), and those obtainable from known materials (e.g., E. coli W3110 (tyrA)/pCABD2, E. coli VL614, E. coli VL2054, E. coli VL2160, E. coli VL2151, E. coli W3350 argE::Tn10/pKA10 as described in the Examples below).
For reference, the amino acid excretion protein according to the present invention was identified for the first time as described below.
The present inventors have identified rhtB and rhtC as threonine excretion protein genes of a bacterium belonging to the genus Escherichia. The present inventors searched databases based on a hypothesis that amino acid excretion proteins may share a common structure. Namely, BLAST and PSI-BLAST search (Altschul, S. F. et al., Nucleic Acids Res., 25, 3389-3402(1997)) for homology of a protein encoded by rhtB was performed in GenBank CDS, PDB, SWISS-PROT, Spupdate, and PIR. Tblastn search was performed in unfinished microbial genomes. BLITZ search (Sturrock, S. S., and Collins, J. F., Mpsch version 1.3. Biocomputing research unit University of Edinburgh, UK (1993)) was performed in SWALL database. SMART search (Ogiwara, I. et al., Protein Sci., 5, 1991-1999 (1996)) was performed in the databases of translations and SWISS-PROT. From the samples of more than 60 sequences found, YeaS (corresponding to f212 of ACCESSION No. AE000274 in GenBank), YahN (corresponding to f223 of ACCESSION No. AE000140 in GenBank), YfiK (corresponding to o195 of ACCESSION No. AE000344 in GenBank) and YggA (corresponding to f211 of ACCESSION No. AE000375 in GenBank) remained among those originating from E. coli as proteins which may have similar function to RhtB. Since the function of any of these genes was unknown, the genes were actually obtained, and effects thereof on MIC of amino acids and amino acid analogues and on amino acid production were examined by enhancing the activities thereof. As a result, an effect of increasing MIC of some amino acids and analogues was found with respect to YeaS, YfiK, YahN and YggA. Further examination has revealed that proteins encoded by these genes exhibit an effect of increasing accumulation of an amino acid, although they may have some amino acid selectivities.
<2> Method of the present invention
The method of the present invention includes the steps of cultivating the bacterium of the present invention in a culture medium to produce and accumulate the amino acid in the medium, and recovering the amino acid from the medium.
Suitable amino acids include lysine, glutamic acid, alanine, valine, histidine, proline, threonine, arginine, and isoleucine.
In the method of present invention, the cultivation of the Escherichia bacterium, and the collection and purification of an amino acid from the liquid medium may be performed in a manner similar to conventional methods for producing an amino acid by fermentation using a bacterium. A medium used in cultivation may be either a synthetic medium or a natural medium, so long as the medium includes a carbon and a nitrogen source and minerals and, if necessary, nutrients which the chosen bacterium requires for growth in appropriate amounts. The carbon source may include various carbohydrates such as glucose and sucrose, and various organic acids. Depending on the assimilatory ability of the chosen bacterium, alcohols including ethanol and glycerol may be used. As the nitrogen source, ammonia, various ammonium salts such as ammonium sulfate, other nitrogen compounds such as amines, a natural nitrogen source such as peptone, soybean hydrolyte and digested fermentative microbe are used. As minerals, monopotassium phosphate, magnesium sulfate, sodium chloride, ferrous sulfate, manganese sulfate, and calcium carbonate are used.
The cultivation is preferably under aerobic conditions such as by shaking, aeration, and/or stirring. The temperature of the culture is usually 20 to 40° C., preferably 30 to 38° C. The pH of the culture is usually between 5 and 9, preferably between 6.5 and 7.2. The pH of the culture can be adjusted with ammonia, calcium carbonate, various acids, various bases, and buffers. Usually, a 1 to 3-day cultivation leads to the accumulation of the target amino acid in the medium.
Recovering the amino acid can be performed by removing solids such as cells from the medium by centrifugation or membrane filtration after cultivation, and then collecting and purifying the target amino acid by ion exchange, concentration, crystalline fraction methods, and the like.

EXAMPLES

The present invention will be more concretely explained below with reference to the following non-limiting Examples.
Example 1. Preparation of the DNA fragments which code for amino acid excretion proteins.
The entire nucleotide sequence of the chromosome of E. coli strain K-12 has been determined (Science, 277, 1453-1474, 1997). Based on the reported nucleotide sequence, primers were synthesized and the genes yahN, yfiK, yeaS and yggA were amplified by PCR.
(1). Chromosomal DNA of the E. coli strain MG1655 was used as a template.
The chromosomal DNA was prepared by an ordinary method (Sambrook, J., Fritsch E. F. and Maniatis T. (1989) Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.). In the PCR reaction, a standard condition described in “PCR protocols. Current methods and applications”. (White, B. A., ed. Humana Press, Totowa, N.J., 1993) was used. The obtained PCR products were purified by an ordinary method and digested with restriction enzymes as described below.
The yahN gene was amplified by using primers No. 1 and No. 2.
Primer No. 1: gtgtggaaccgacgccggat (a sequence complementary to a sequence from nucleotide numbers 1885 to 1904 in the nucleotide sequence registered under ACCESSION No. AE000140 in GenBank; SEQ ID NO: 17), and
Primer No. 2: tgttgtatggtacggggttcgag (a sequence from nucleotide numbers 223 to 245 in the same; SEQ ID NO: 18).
The obtained PCR product after purification was digested with restriction enzymes PstI and StuI and ligated to vector pUC21 (Vieira, Messing, Gene, 100, 189-194, 1991), and digested with the enzymes PstI and EcoRV by using a ligation kit. Then, transformation of competent cells of E. coli TG1 (Sambrook, J., Fritsch E. F. and Maniatis T. (1989) Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.) with the product was conducted and the cells were spread on L medium (10 g/l Bacto trypton, 5 g/l Yeast extract, 5 g/l NaCl, 15 g/l agar, pH 7.0) containing 10 μg/ml IPTG (isopropyl-β-D-thiogalactopyranoside) and 40 μg/ml X-gal (5-bromo-4-chloro-3-indolyl-β-D-galactoside) and 100 μg/ml ampicillin, and cultured overnight. White colonies which appeared were picked up and subjected to single colony isolation to obtain transformants. A plasmid was prepared from the transformants using an alkali extraction method and designated as pYAHN.
The yeaS gene was amplified by using primers No. 3 and No. 4.
Primer No. 3: ctttgccaatcccgtctccc (a sequence complementary to a sequence from nucleotide numbers 7683 to 7702 in a nucleotide sequence registered under ACCESSION No AE000274 in GenBank; SEQ ID NO: 19);
Primer No. 4: gccccatgcataacggaaag (a sequence from nucleotide numbers 5542 to 5561 in the same; SEQ ID NO: 20).
The obtained PCR product after purification was digested with a restriction enzyme AvaI and ligated to vector pUC 19. After transformation of E. coli TG1 as above, a plasmid was obtained and designated pYEAS.
The yfiK gene was amplified by using primers No. 5 and No. 6.
Primer No. 5: gaagatcttgtaggccggataaggcg (a sequence from nucleotide numbers 4155 to 4177 in a nucleotide sequence registered under ACCESSION No AE000344 in GenBank, with a restriction enzyme BglII site added at the 5′-end thereof; SEQ ID NO: 21)
Primer No. 6: tggttttaccaattggccgc (a sequence complementary to a sequence from nucleotide numbers 6307 base to 6326 in the same; SEQ ID NO: 22).
The PCR product obtained after purification was digested with restriction enzymes BglII and MunI and ligated to vector pUC21 digested with restriction enzymes BglII and EcoRI. After transformation of E. coli TG1 as above, the plasmid designated pYFIK was obtained.
The yggA gene was amplified by using primers No. 7 and No. 8.
Primer No. 7: acttctcccgcgagccagttc (a sequence complementary to a sequence from nucleotide numbers 9606 to 9626 in a nucleotide sequence registered under ACCESSION No AE000375 in GenBank; SEQ ID NO: 23).
Primer No. 8: ggcaagcttagcgcctctgtt (a sequence from nucleotide numbers 8478 to 8498 in the same; SEQ ID NO: 24).
The PCR product obtained after purification was digested with restriction enzymes HindIII and ClaI and ligated to vector pOK12 (Vieira, Messing, Gene, 100, 189-194, 1991) digested with the same restriction enzymes. After transformation of E. coli TG1 as above, a plasmid was obtained and designated pYGGA.
(2). Chromosomal DNA of the E. coli strain W3110 was used as a template.
The yahN gene was amplified by using primers No. 9 (SEQ ID NO 1) and No. 10 (SEQ ID NO.2)
The yeaS gene was amplified by using primers No. 11 (SEQ ID NO 3) and No. 12 (SEQ ID NO 4)
The yfiK gene was amplified by using primers No. 13 (SEQ ID NO 5) and No. 14 (SEQ ID NO 6).
The yggA gene was amplified by using primers No. 15 (SEQ ID NO 7) and No. 16 (SEQ ID NO 8)
The obtained PCR product was purified, digested with restriction enzymes SacI and XbaI (EcoRI and PstI for yggA), and ligated to plasmid pMW118 (Nippon Gene). The plasmid into which a DNA fragment with an identical sequence to the reported sequence was inserted was designated as follows:

- Plasmid carrying yahN: pMW118::yahN
- Plasmid carrying yeaS: pMW118::yeaS Plasmid carrying yfiK: pMW118::yfiK
- Plasmid carrying yggA: pMW118::yggA

Example 2. Effect of amplification of the yahN, yeaS, yfiK, and yggA DNA fragments on the E. coli TG1 resistance to some amino acids and amino acid analogues.
The homology of the yeaS, yfiK, yahN, and yggA gene products with the lysine transporter, LysE, of Corynebacterium glutamicum (Vrljic et al., Mol. Microbiol.,22, 815-826, 1996) and RhtB protein involved in homoserine excretion, indicates functional analogues for these proteins. It is well known that the increased expression of genes involved in antibiotic and heavy metal efflux increases the level of resistance to the drugs (Nikaido, H. J. Bacteriology, 178, 5853-5859, 1996). Therefore, the effect of the pYEAS, pYAHN, pYFIK, and pYGGA plasmids on susceptibility of the strain TG1 to some amino acids and amino acid analogues was tested. Overnight cultures of the E. coli strains TG1/pYEAS, TG1/pYAHN, TG1/pYFIK, TG1/pYGGA and of the control strains TG1/pUC21, TG1/pUC19 and TG1/pOK12 grown in M9 minimal medium with an appropriate antibiotic on a rotary shaker (10⁹cfu/ml) were diluted 1:100 in M9 minimal medium and grown for 5 h in the same medium. Then the log phase cultures thus obtained were diluted and about 10⁴live cells were applied to well-dried test plates with M9 agar containing doubling increments of amino acids or analogues. Thus, the minimum inhibition concentration (MIC) of these compounds was examined.

The results are shown in Table 1. It follows from the Table 1 that multiple copies of the yfiK gene conferred increased resistance to proline, homoserine, histidine, threonine, glutamate, lysine, α-amino-β-hydroxyvaleric-acid (AHVA), S-(2-aminoethyl)-L-cysteine (AEC), and α-aminobutyric acid; multiple copies of yahN gene conferred increased resistance to proline, multiple copies of the yeaS gene conferred increased resistance to threonine, homoserine, lysine, glutamate, histidine, proline, and α-aminobutyric acid; multiple copies of yggA gene conferred increased resistance to S-(2-aminoethyl)-L-cysteine (AEC), lysine, and arginine. These results indicate that except for YahN, all of the presumed transporters have specificity to several substrates (amino acids and amino acid analogues), or may show non-specific effects as a result of amplification.

	TABLE 1


	MIC (μg/ml) for E. coli TG1, harboring the
	plasmid

Substrate	pUC21	pYFIK	pYAHN	pYEAS	pYGGA

L-homoserine	500	1000	500	1000	500
L-threonine	30000	40000	30000	50000	30000
L-lysine	5000	7500	5000	7500	15000
L-glutamate (Na salt)	5000	10000	5000	20000	5000
L-histidine	5000	10000	5000	30000	5000
L-valine	0.5	0.5	0.5	0.5	0.5
L-proline	1000	5000	2000	2000	1000
L-arginine	10000	10000	10000	10000	20000
AHVA	100	200	100	100	100
AEC	5	10	5	5	200
α-aminobutyric acid	2500	5000	2500	>10000	2500
4-aza-DL-leucine	100	100	100	100	100

Example 3. Effect of amplification of the yeaS, yahN, and yfiK DNA fragments on glutamic acid production.
The E. coli strain AJ13199 (FR patent No. 2747689) was transformed with the vector pUC21 and each of the plasmids pYAHN, pYEAS and pYFIK. Thus the strains AJ13199/pUC21 (VKPM B-7728), AJ13199/pYAHN (VKPM B-7729), AJ13199/pYEAS (VKPM B-7731), and AJ13199/pYFIK (VKPM B-7730) were obtained.
These strains were each cultivated at 37° C. for 18 hours in a nutrient broth with 100 mg/l ampicillin, and 0.3 ml of the obtained culture was inoculated into 3 ml of a fermentation medium containing 100 mg/l ampicillin, in a 20×200 mm test tube, and cultivated at 37° C. for 48 hours on a rotary shaker. After the cultivation, the amount of glutamic acid which had accumulated in the medium was determined by a known method.

The composition of the fermentation medium (g/l):



	Glucose	80
	(NH₄)₂SO₄	22
	K₂HPO₄	2
	NaCl	0.8
	MgSO₄.7H₂O	0.8
	FeSO₄.7H₂O	0.02
	MnSO₄.5H₂O	0.02
	Thiamine HCl	0.0002
	Yeast extract	1.0
	CaCO₃	30.0
		(dry-heat-sterilized
		at 180° C. for 2 h)

	(Glucose and K₂HPO₄separately sterilized)

The results are shown in Table 2. As shown in Table 2, the strains AJ13199/pYAHN, AJ13199/pYEAS, and AJ13199/pYFIK yielded glutamic acid in a larger amount than the strain AJ 13199/pUC21, in which expression of amino acid excretion proteins was not enhanced.

TABLE 2

Strain Glutamic acid, g/l

AJ13199/pUC21 21.9

AJ13199/pYAHN 27.9

AJ13199/pYEAS 29.7

AJ13199/pYFIK 28.4
Example 4. Effect of amplification of yeaS, yahN, and yfiK DNA fragments on lysine production.
(1) As the lysine-producing bacterium belonging to the genus Escherichia, E. coli strain W3110 (TyrA) described in European Patent Publication No. 488424, and which contains plasmid pCABD2, described in International Publication No. WO 95/16042, was used. Specifically, plasmid pCABD2, and each of the plasmid pMW118::yahN, pMW118::yeaS, pMW118::yfiK and pMW118 were introduced into E. coli strain W3110 (TyrA) to obtain the following strains:

- W3110 (tyrA)/pCABD2+pMW118::yahN
- W3110 (tyrA)/pCABD2+pMW118::yeaS
- W3110 (tyrA)/pCABD2+pMW118::yfik
- W3110 (tyrA)/pCABD2+pMW118.

Lysine productivity of these strains was estimated by culturing. The composition of the medium was as follows (g/l):

Glucose 40.0

MgSO₄.7H₂O 1.0

(NH₄)₂SO₄ 16.0

K₂HPO₄ 1.0

FeSO₄.7H₂O 0.01

MnSO₄.7H₂O 0.01

Yeast extract (Difco) 2.0

Tyrosine 0.1
Adjusted to pH 7.0 and autoclaved at 115° C. for 10 minutes. (Glucose and MgSO₄ ^.7H₂O separately sterilized)
Pharmacopeial CaCO₃25 g/l (dry-heat-sterilized at 180° C. for 2 h)

As antibiotics, 20 mg/l of streptomycin and 50 mg/l of ampicillin were added depending on the plasmid. Cultivation was conducted at 37° C. for 30 hours with agitation at 115 rpm. The results are shown in Table 3.

TABLE 3


	Lysine,	Yield,
Strain	g/l	(%)

W3110(tyrA)	0.08	0.2
W3110(tyrA)/pCABD2 + pMW118	12.2	30.5
W3110(tyrA)/pCABD2 + pMW118::yahN	13.8	34.5
W3110(tyrA)/pCABD2 + pMW118::yeaS	12.7	31.8
W3110(tyrA)/pCABD2 + pMW118::yfiK	12.2	30.5

Table 3 shows that the amount produced and the yield based on consumed sugar of lysine is increased by enhancing YahN and YeaS.
(2) As the lysine-producing bacterium belonging to the genus Escherichia, E. coli strain VL614 was used. This strain is a derivative of the known E. coli strain VL613 (SU Patent No. 1354458). In turn, the strain VL613 was obtained from the known strain Gif102 (Theze, J. and Saint Girons. J.Bacteriol., 118, 990-998, 1974) in the three steps:
In the first step, the mutants resistant to 2 mg/ml S-(2-aminoethyl)-L-cysteine were selected, and among them strain VL611 was found able to produce L-lysine.
In the second step, the genes involved in sucrose utilization and located on the transposon Tn2555 (Doroshenko et al., Mol. Biologiya, 22, 645-658, 1988), were introduced into VL611 using phage P1-mediated transduction giving the strain VL612.
In the third step, the mutation rhtA23 from the strain VKPM B-3996, conferring resistance to threonine and homoserine (U.S. Pat. No. 5,175,107) was introduced into VL612 by phage P1 transduction giving the strain VL613.
The E. coli strain VL614 was obtained by transduction of the wild-type allele of the rhtA gene from the E. coli strain VKPM B-6204 (MG1655 zbi3058::Tn10) to VL613. Transductants were selected on L-medium containing 10 mg/l tetracyclin, and among them the strain VL614 (rhtA⁺) sensitive to 10 g/l homoserine was found.
The strain VL614 was transformed with the pYGGA plasmid or with the pOK12 vector to obtain strains VL614/pYGGA (VKPM B-7719) and VL614/pOK12 (VKPM B-7722).
These strains were each cultivated at 37° C. for 18 hours in a nutrient broth with 50 mg/l kanamycin, and 0.3 ml of the obtained culture was inoculated into 3 ml of a fermentation medium (Example 3) containing 0.3 g/l threonine, 0.3 g/l methionine and 50 mg/l kanamycin, in a 20×200 mm test tube, and cultivated at 37° C. for 48 hours on a rotary shaker. After the cultivation, the amount of lysine and glutamate which accumulated in the medium was each determined by a known method.
The results are shown in Table 4.

TABLE 4

Strain Lysine, g/l Glutamate, g/l

VL614/pOK12 2.6 0.8

VL614/pYGGA 3.6 2.2
As shown in Table 4, the strain VL614/pYGGA yielded lysine in a larger amount than the strain VL614/pOK12, in which the yggA gene was not enhanced. Besides, the strain VL614/pYGGA yielded more glutamic acid than the strain VL614/pOK12.
Example 5. Effect of amplification of yeaS, yahN, and yfiK DNA fragments on threonine, alanine, valine, and isoleucine production.
As the threonine-producing bacterium belonging to the genus Escherichia, the E. coli strain VL2054 was used. This strain was derived from the known E. coli strain VKPM B-3996 (U.S. Pat. No. 5,175,107) as follows.
Initially, a new recipient strain was constructed in several steps:

- The plasmidless derivative of the strain VKPM B-3996 was selected after spontaneous elimination of pVIC40 plasmid.
- The wild-type allele of the rhtA gene from the E. coli strain VKPM B-6204 (MG1655 zbi3058::Tn10) was introduced into the thus obtained strain by phage P1 mediated transduction as in the Example 4.
- A mutation inactivating kan gene of the Tn5 transposon inserted into the tdh gene was obtained after NG mutagenesis and selection of kanamycin-sensitive cells still unable to degrade threonine. Thus the strain VL2053 was obtained.

On the other hand, the threonine operon from pVIC40 was cloned into integrative Mud vector under the P_Rpromoter of the phage lambda. In addition, the cat gene of Tn9 conferring the resistance to chloramphenicol was cloned into the same vector. The construct thus obtained was inserted into the chromosome of the E. coli strain C600 by use of a known method (U.S. Pat. No. 5,595,889) and transduced from the thus obtained strain to VL2053, giving the new plasmidless threonine-producing strain VL2054. This strain was able to yield alanine, valine and isoleucine in the culture broth.
The strain VL2054 was transformed with each of the plasmids pYEAS, pYFIK, and with the vector pUC21 to obtain E. coli strains VL2054/pYEAS (VKPM B-7707), VL2054/pYFIK (VKPM B-7712), and VL2054/pUC21 (VKPM B-7708).
These strains were each cultivated at 37° C. for 18 hours in a nutrient broth with 100 mg/l ampicillin, and 0.3 ml of the obtained culture was inoculated into 3 ml of a fermentation medium (Example 3) containing 100 mg/l ampicillin, in a 20×200 mm test tube, and cultivated at 37° C. for 48 hours with a rotary shaker. After the cultivation, threonine, alanine, valine and isoleucine each accumulated in the medium, and the amount of each was determined by a known method.
The results are shown in Table 5.
As shown in Table 5, the strain VL2054/pYFIK yielded threonine in a larger amount than the strain VL2054/pUC21 in which the yfiK gene was not enhanced. Besides, the strain VL2054/pYEAS yielded more alanine, valine, and isoleucine than the strain VL2054/pUC21, in which the yeaS gene was not enhanced.

TABLE 5

Amino acid accumulation, g/l

Strain Threonine Alanine Valine Isoleucine

VL2054/pUC21 5.8 0.4 0.31 0.15

VL2054/pYEAS 5.2 1.4 0.52 0.45

VL2054/pYFIK 8.8 0.5 0.22 0.14
Example 6. Effect of amplification of yeaS and yfiK DNA fragments on histidine production.
As the histidine-producing bacterium belonging to the genus Escherichia, the strain E. coli VL2160 was used. This strain was obtained based on the known strain NK5526 hisG::Tn10 (VKPM B-3384) by phage P1-mediated transduction of the hisG^Rmutation desensitizing ATP-phosphoribosyltransferase from the strain CC46 (Astvatsaturianz et al., Genetika, 24, 1928-1934, 1988). The strain E. coli VL2160 was transformed with each of the plasmids pYEAS, pYFIK, and with the vectors pUC21 to obtain E. coli strains VL2160/pYEAS (VKPM B-7753), E. coli VL2160/pYFIK (VKPM B-7754), E. coli VL2160/pUC21 (VKPM B-7752).
These strains were each cultivated at 37° C. for 18 hours in a nutrient broth with 100 mg/l ampicillin, and 0.3 ml of the obtained culture was inoculated into 3 ml of the fermentation medium (Example 3) containing an increased amount of yeast extract (3 g/l) and 100 mg/l ampicillin, in a 20×200 mm test tube, and cultivated at 34° C. for 68 hours on a rotary shaker.
After the cultivation, the amount of histidine which had accumulated in the medium was determined by a known method. The results are shown in Table 6.

TABLE 6

Strain Histidine, g/l

VL2160/pUC21 1.2

VL2160/pYEAS 1.8

VL2160/pYFIK 1.4
As shown in Table 6, the strains E. coli VL2160/pYEAS and E. coli VL2160/pYFIK yielded histidine in a larger amount than the strain E. coli VL2160/pUC21, in which the yeaS and yfiK genes were not enhanced.
Example 7. Effect of amplification of yahN, yfiK and yeaS DNA fragments on proline production.
As the proline-producing bacterium belonging to the genus Escherichia, the strain VL2151 (W3350 proB* ΔputAP Tn10) was used. This strain was obtained by transduction into W3350 of ΔputAP mutation linked to Tn10 and selecting tetracycline-resistant transductants unable to utilize proline as a sole carbon source. The thus obtained strain W3350 ΔputAP Tn10 was mutagenized with NG and mutants resistant to 20 mg/l of 3,4-dehydro-DL-proline were selected. Among them the strain VL2151 (W3350proB* ΔputAP Tn10) was found able to produce proline.
The strain E. coli VL2151 was transformed with each of the plasmids pYEAS, pYFIK, pYAHN and with the vector pUC21 to obtain E. coli strains VL2151/pYEAS (VKPM B-7714), VL2151/pYFIK (VKPM B-7713), VL2151/pYAHN (VKPM B-7748) and E. coli VL2151/pUC21 (VKPM B-7715).
These strains were each cultivated at 37° C. for 18 hours in a nutrient broth with 100 mg/l ampicillin, and 0.3 ml of the obtained culture was inoculated into 3 ml of a fermentation medium (Example 3) containing 100 mg/l ampicillin, in a 20×200 mm test tube, and cultivated at 37° C. for 48 hours on a rotary shaker. After the cultivation, the amount of proline which had accumulated in the medium was determined by a known method. The results are shown in Table 7.

TABLE 7

Strain Proline, g/l

VL2151/pUC21 1.8

VL2151/pYAHN 2.2

VL2151/pYEAS 2.1

VL2151/pYFIK 2.5
As shown in Table 7, the strains E. coli VL2151/pYFIK, E. coli VL2151/pYAHN and E. coli VL2151/pYEAS yielded proline in a larger amount than the strain E. coli VL2151/pUC21, in which the yfiK, yahN and yeaS genes were not enhanced. The amplification of the yfiK gene had the most pronounced effect.
Example 8. Effect of amplification of yggA DNA fragments on arginine production.
As arginine-producing bacterium belonging to the genus Escherichia, the strain W3350 argE::Tn10/pKA10 was used. This strain harbors a plasmid, pKA10, which contains a DNA region from Corynebacterium (Brevibacterium) flavum which complements at least argA and argE mutations in the recipient strain of E. coli K-12 (Kharitonov A. and Tarasov A. P. Molecular Genetics, Microbiology and Virology. No. 9, 29-33, 1986).
The strain E. coli W3350 argE::Tn10/pKA10 was transformed with the plasmid pYGGA, or with the vector pOK12 to obtain the strains E. coli W3350 argE::Tn10/pKA10, pYGGA (VKPM B-7716) and E. coli W3350 argE::Tn10/pKA10, pOK12 (VKPM B-7718).
The thus obtained transformants were each cultivated at 37° C. for 18 hours in a nutrient broth with 100 mg/l ampicillin and 50 mg/l kanamycin, and 0.3 ml of the obtained culture was inoculated into 3 ml of a fermentation medium (Example 3) containing 100 mg/l ampicillin and 50 mg/l kanamycin, in a 20×200 mm test tube, and cultivated at 37° C. for 48 hours on a rotary shaker. After the cultivation, the amount of arginine which had accumulated in the medium was determined by a known method.
The results are shown in Table 8.

TABLE 8

Strain Arginine, g/l

W3350 argE::Tn10/pKA10, pOK12 0.11

W3350 argE::Tn10/pKA10, pYGGA 0.46
As shown in Table 8, the strains E. coli W3350 argE::Tn10/pKA10, pYGGA yielded arginine in a larger amount than the strain E. coli W3350 argE::Tn10/pKA10, pUC21 in which the yggA gene was not enhanced.
The following E. coli strains have been deposited according to the Budapest Treaty in the Russian National Collection of Industrial Microorganisms (VKPM) on Dec. 29, 1998 under the accession numbers shown in parenthesis.

- AJ13199/pUC21 (VKPM B-7728)
- AJ13199/pYAHN (VKPM B-7729)
- AJ13199/pYEAS (VKPM B-7731)
- AJ13199/pYFIK (VKPM B-7730)
- VL614/pYGGA (VKPM B-7719)
- VL614/pOK12 (VKPM B-7722)
- VL2054/pYEAS (VKPM B-7707)
- VL2054/pYFIK (VKPM B-7712)
- VL2054/pUC21 (VKPM B-7708)
- VL2160/pYEAS (VKPM B-7753)
- VL2160/pYFIK (VKPM B-7754)
- VL2160/pUC21 (VKPM B-7752)
- VL2151/pYFIK (VKPM B-7713)
- VL2151 /pYEAS (VKPM B-7714)
- VL2151/pYAHN (VKPM B-7748)
- VL2151/pUC21 (VKPM B-7715)
- W3350 argE::Tn10/pKA10, pYGGA (VKPM B-7716)
- W3350 argE::Tn10/pKA10, pOK12 (VKPM B-7718)

While the invention has been described in detail with reference to preferred embodiments thereof, it will be apparent to one skilled in the art that various changes can be made, and equivalents employed, without departing from the scope of the invention. Each of the aforementioned documents, including the foreign priority document, is incorporated by reference herein in its entirety.

Claims

1. A method for producing an L-amino acid selected from the group consisting of L-glutamic acid, L-proline, and L-lysine comprising:

cultivating a bacterium in a culture medium,

and recovering the L-amino acid from the medium,

wherein said bacterium belongs to the genus Escherichia and wherein expression of at least one protein selected from the group consisting of:

(A) a protein having an amino acid sequence shown in SEQ ID NO: 10; and

(B) a protein which is encoded by a DNA which hybridizes with a polynucleotide having the nucleotide sequence shown in SEQ ID NO: 9 under stringent conditions comprising 60° C., 1×SSC, and 0.1% SDS, and which has an activity of producing L-proline, L-lysine, and L-glutamic acid,

is increased relative to the expression of said protein in a wild-type strain by increasing the copy number of a DNA coding for said protein in said bacterium or by replacing the native promoter with a stronger promoter.

2. The method of claim 1, wherein the copy number of a DNA coding for said protein in a bacterium is increased.

3. The method of claim 2, wherein said DNA is carried on a multicopy vector in the bacterium.

4. The method of claim 2, wherein said DNA is carried on a transposon in the bacterium.

5. The method of claim 1, wherein production of said protein of (A) is increased.

6. The method of claim 1, wherein production of said protein of (B) is increased.

7. The method of claim 1, wherein the L-amino acid is L-glutamic acid.

8. The method of claim 1, wherein the L-amino acid is L-proline.

9. A method for producing an L-amino acid selected from the group consisting of L-glutamic acid, L-proline, and L-lysine comprising

cultivating a bacterium in a culture medium,

and recovering the L-amino acid from the medium,

(A) a protein having an amino acid sequence shown in SEQ ID NO: 10; and

(B) a protein which is encoded by a DNA which hybridizes with a polynucleotide having the nucleotide sequence shown in SEQ ID NO: 9 under stringent conditions comprising 60° C., 1×SSC, and 0.1% SDS, and which has at least an activity of producing an L-amino acid selected from the group consisting of L-glutamic acid, L-proline, and L-lysine,

10. The method of claim 9, wherein the copy number of a DNA coding for said protein in a bacterium is increased.

11. The method of claim 10, wherein said DNA is carried on a multicopy vector in the bacterium.

12. The method of claim 10, wherein said DNA is carried on a transposon in the bacterium.

13. The method of claim 9, wherein production of said protein of (A) is increased.

14. The method of claim 9, wherein production of said protein of (B) is increased.

15. The method of claim 9, wherein the L-amino acid is L-glutamic acid.

16. The method of claim 9, wherein the L-amino acid is L-proline.