# Patent

## Title
Methylophilus methylotrophus having enhanced dihydrodipicolinate synthase and/or aspartokinase activity for L-amino acid production

## Abstract

An L-amino acid is produced by culturing a Methylophilus bacterium which can grow by using methanol as a main carbon source and has L-amino acid-producing ability, for example, a Methylophilus bacterium in which dihydrodipicolinate synthase activity and aspartokinase activity are enhanced by transformation through introduction into cells, of a DNA coding for dihydrodipicolinate synthase that does not suffer feedback inhibition by L-lysine and a DNA coding for aspartokinase that does not suffer feedback inhibition by L-lysine, or a Methylophilus bacterium made to be casamino acid auxotrophic, in a medium containing methanol as a main carbon source, to produce and accumulate an L-amino acid in culture, and collecting the L-amino acid from the culture.

## Background
TECHNICAL FIELD
The present invention relates to techniques in the field of microbial industry. In particular, the present invention relates to a method for producing an L-amino acid by fermentation, and a microorganism used in the method.
BACKGROUND ART
Amino acids such as L-lysine, L-glutamic acid, L-threonine, L-leucine, L-isoleucine, L-valine and L-phenylalanine are industrially produced by fermentation by using microorganisms that belong to the genus Brevibacterium, Corynebacterium, Bacillus, Escherichia, Streptomyces, Pseudomonas, Arthrobacter, Serratia, Penicillium, Candida or the like. In order to improve the productivity, strains isolated from nature or artificial mutants thereof have been used as these microorganisms. Various techniques have been disclosed for enhancing activities of L-glutamic acid biosynthetic enzymes by using recombinant DNA techniques, to increase the L-glutamic acid-producing ability.
The productivity of L-amino acids has been considerably increased by breeding of microorganisms such as those mentioned above and the improvement of production methods. However, in order to meet further increase in the demand in future, development of methods for more efficiently producing L-amino acids at lower cost have still been desired.
As methods for producing amino acids by fermentation of methanol which is a fermentation raw material available in a large amount at a low cost, there have conventionally known methods using microorganisms that belong to the genus Achromobacter or Pseudomonas (Japanese Patent Publication (Kokoku) No. 45-25273/1970), Protaminobacter (Japanese Patent Application Laid-open (Kokai) No. 49-125590/1974), Protaminobacter or Methanomonas (Japanese Patent Application Laid-open (Kokai) No. 50-25790/1975), Microcyclus (Japanese Patent Application Laid-open (Kokai) No. 52-18886/1977), Methylobacillus (Japanese Patent Application Laid-open (Kokai) No. 4-91793/1992), Bacillus (Japanese Patent Application Laid-open (Kokai) No. 3-505284/1991) and so forth.
So far, however, no method has been known for producing L-amino acids by using Methylophilus bacteria. Although methods described in EP 0 035 831 A, EP 0 037 273 A and EP 0 066 994 A have been known as methods for transforming Methylophilus bacteria by using recombinant DNA, applying recombinant DNA techniques to improvement of amino acid productivity of Methylophilus bacteria has not been known.
DISCLOSURE OF THE INVENTION
The object of the present invention is to provide a novel L-amino acid-producing bacterium and a method for producing an L-amino acid by using the L-amino acid-producing bacterium.
As a result of the present inventors' efforts devoted to achieve the aforementioned object, they found that Methylophilus bacteria were suitable for producing L-amino acids. Further, although it has conventionally been considered difficult to obtain auxotrophic mutants of Methylophilus bacteria (FEMS Microbiology Rev. 39, 235–258 (1986) and Antonie van Leeuwenhoek 53, 47–53 (1987)), the present inventors have succeeded in obtaining auxotrophic mutants of said bacteria. Thus, the present invention has been accomplished.
That is, the present invention provides the followings.
(1) A Methylophilus bacterium having L-amino acid-producing ability.
(2) The Methylophilus bacterium according to (1), wherein the L-amino acid is L-lysine, L-valine, L-leucine, L-isoleucine or L-threonine.
(3) The Methylophilus bacterium according to (1), which has resistance to an L-amino acid analogue or L-amino acid auxotrophy.
(4) The Methylophilus bacterium according to (1), wherein L-amino acid biosynthetic enzyme activity is enhanced.
(5) The Methylophilus bacterium according to (1), wherein dihydrodipicolinate synthase activity and aspartokinase activity are enhanced, and the bacterium has L-lysine-producing ability.
(6) The Methylophilus bacterium according to (1), wherein dihydrodipicolinate synthase activity is enhanced, and the bacterium has L-lysine-producing ability.
(7) The Methylophilus bacterium according to (1), wherein aspartokinase activity is enhanced, and the bacterium has L-lysine-producing ability.
(8) The Methylophilus bacterium according to any one of (5) to (7), wherein an activity or activities of one, two or three of enzymes selected from aspartic acid semialdehyde dehydrogenase, dihydrodipicolinate reductase and diaminopimelate decarboxylase is/are enhanced.

(9) The Methylophilus bacterium according to (5), wherein the dihydrodipicolinate synthase activity and the aspartokinase activity are enhanced by transformation through introduction into cells, of a DNA coding for dihydrodipicolinate synthase that does not suffer feedback inhibition by L-lysine and a DNA coding for aspartokinase that does not suffer feedback inhibition by L-lysine.

(10) The bacterium according to (1), wherein activities of aspartokinase, homoserine dehydrogenase, homoserine kinase and threonine synthase are enhanced, and the bacterium has L-threonine-producing ability.

(11) The bacterium according to any one of (1) to (10), wherein the Methylophilus bacterium is Methylophilus methylotrophus. 

(12) A method for producing an L-amino acid, which comprises culturing a Methylophilus bacterium as defined in any one of the above (1) to (11) in a medium to produce and accumulate an L-amino acid in culture and collecting the L-amino acid from the culture.

(13) The method according to (12), wherein the medium contains methanol as a main carbon source.

(14) A method for producing bacterial cells of a Methylophilus bacterium with an increased content of an L-amino acid, which comprises culturing a Methylophilus bacterium as defined in any one of the above (1) to (11) in a medium to produce and accumulate an L-amino acid in bacterial cells of the bacterium.

(15) The method for producing bacterial cells of the Methylophilus bacterium according to (14), wherein the L-amino acid is L-lysine, L-valine, L-leucine, L-isoleucine or L-threonine.

(16) A DNA which codes for a protein defined in the following (A) or (B):

(A) a protein which has the amino acid sequence of SEQ ID NO: 6, or

(B) a protein which has an amino acid sequences of SEQ ID NO: 6 including substitution, deletion, insertion, addition or inversion of one or several amino acids, and has aspartokinase activity.

(17) The DNA according to (16), which is a DNA defined in the following (a) or (b):

(a) a DNA which has a nucleotide sequence comprising the nucleotide sequence of the nucleotide numbers 510 to 1736 of SEQ ID NO: 5; or

(b) a DNA which is hybridizable with a probe having the nucleotide sequence of the nucleotide numbers 510 to 1736 of SEQ ID NO: 5 or a part thereof under a stringent condition, and codes for a protein having aspartokinase activity.

(18) A DNA which codes for a protein defined in the following (C) or (D):

(C) a protein which has the amino acid sequence of SEQ ID NO: 8, or

(D) a protein which has an amino acid sequences of SEQ ID NO: 8 including substitution, deletion, insertion, addition or inversion of one or several amino acids, and has aspartic acid semialdehyde dehydrogenase activity.

(19) The DNA according to (18), which is a DNA defined in the following (c) or (d):

(c) a DNA which has a nucleotide sequence comprising the nucleotide sequence of the nucleotide numbers 98 to 1207 of SEQ ID NO: 7; or

(d) a DNA which is hybridizable with a probe having the nucleotide sequence of the nucleotide numbers 98 to 1207 of SEQ ID NO: 7 or a part thereof under a stringent condition, and codes for a protein having aspartic acid semialdehyde dehydrogenase activity.

(20) A DNA which codes for a protein defined in the following (E) or (F):

(E) a protein which has the amino acid sequence of SEQ ID NO: 10, or

(F) a protein which has an amino acid sequences of SEQ ID NO: 10 including substitution, deletion, insertion, addition or inversion of one or several amino acids, and has dihydrodipicolinate synthase activity.

(21) The DNA according to (20), which is a DNA defined in the following (e) or (f):

(e) a DNA which has a nucleotide sequence comprising the nucleotide sequence of the nucleotide numbers 1268 to 2155 of SEQ ID NO: 9; or

(f) a DNA which is hybridizable with a probe having the nucleotide sequence of the nucleotide numbers 1268 to 2155 of SEQ ID NO: 9 or a part thereof under a stringent condition, and codes for a protein having dihydrodipicolinate synthase activity.

(22) A DNA which codes for a protein defined in the following (G) or (H):

(G) a protein which has the amino acid sequence of SEQ ID NO: 12, or

(H) a protein which has an amino acid sequences of SEQ ID NO: 12 including substitution, deletion, insertion, addition or inversion of one or several amino acids, and has dihydrodipicolinate reductase activity.

(23) The DNA according to (22), which is a DNA defined in the following (g) or (h):

(g) a DNA which has a nucleotide sequence comprising the nucleotide sequence of the nucleotide numbers 2080 to 2883 of SEQ ID NO: 11; or

(h) a DNA which is hybridizable with a probe having the nucleotide sequence of the nucleotide numbers 2080 to 2883 of SEQ ID NO: 11 or a part thereof under a stringent condition, and codes for a protein having dihydrodipicolinate reductase activity.

(24) A DNA which codes for a protein defined in the following (I) or (J):

(I) a protein which has the amino acid sequence of SEQ ID NO: 14, or

(J) a protein which has an amino acid sequences of SEQ ID NO: 14 including substitution, deletion, insertion, addition or inversion of one or several amino acids, and has diaminopimelate decarboxylase activity.

(25) The DNA according to (24), which is a DNA defined in the following (i) or (j):

(i) a DNA which has a nucleotide sequence comprising the nucleotide sequence of the nucleotide numbers 751 to 1995 of SEQ ID NO: 13; or

(j) a DNA which is hybridizable with a probe having the nucleotide sequence of the nucleotide numbers 751 to 1995 of SEQ ID NO: 13 or a part thereof under a stringent condition, and codes for a protein having diaminopimelate decarboxylase activity.

In the present specification, “L-amino acid-producing ability” refers to ability to accumulate a significant amount of an L-amino acid in a medium or to increase the amino acid content in the microbial cells when a microorganism of the present invention is cultured in the medium.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the production process of plasmid RSF24P having a mutant dapA. The “dapA*24” refers to a mutant dapA that codes for a mutant DDPS wherein the 118-histidine residue is replaced with a tyrosine residue.
FIG. 2 shows the production process of plasmid RSFD80 having a mutant dapA and a mutant lysC. The “lysC*80” refers to a mutant lysC that codes for a mutant AKIII wherein the 352-threonine residue is replaced with an isoleucine residue.
FIG. 3 shows aspartokinase activity of transformant E. coli strains containing an ask gene.
FIG. 4 shows aspartic acid semialdehyde dehydrogenase activity of transformant E. coli strains containing an asd gene.
FIG. 5 shows dihydrodipicolinate synthase activity of transformant E. coli strains containing a dapA gene.
FIG. 6 shows dihydrodipicolinate reductase activity of a transformant E. coli strain containing a dapB gene.
FIG. 7 shows diaminopimelate decarboxylase activity of transformant E. coli strains containing a lysA gene.



BEST MODE FOR CARRYING OUT THE INVENTION
<1> Microorganism of the Present Invention
The microorganism of the present invention is a bacterium belonging to the genus Methylophilus and having L-amino acid-producing ability. The Methylophilus bacterium of the present invention includes, for example, Methylophilus methylotrophus AS1 strain (NCIMB10515) and so forth. The Methylophilus methylotrophus AS1 strain (NCIMB10515) is available from National Collections of Industrial and Marine Bacteria (Address: NCIMB Lts., Torry Research Station 135, Abbey Road, Aberdeen AB9 8DG, United Kingdom).
L-Amino acids produced according to the present invention include L-lysine, L-glutamic acid, L-threonine, L-valine, L-leucine, L-isoleucine, L-tryptophan, L-phenylalanine, L-tyrosine and so forth. One or more types of such amino acids may be produced.
Methylophilus bacteria having L-amino acid-producing ability can be obtained by imparting L-amino acid-producing ability to wild strains of Methylophilus bacteria. In order to impart L-amino acid-producing ability, there can be used methods conventionally adopted for breeding coryneform bacteria, Escherichia bacteria or the like, such as those methods for obtaining auxotrophic mutant strains, strains resistant to L-amino acid analogues or metabolic control mutant strains, and methods for producing recombinant strains wherein L-amino acid biosynthetic enzyme activities are enhanced (see “Amino Acid Fermentation”, the Japan Scientific Societies Press [Gakkai Shuppan Center], 1st Edition, published on May 30, 1986, pp. 77 to 100). In breeding of amino acid-producing bacteria, the characteristic such as auxotrophy, L-amino acid analogue resistance and metabolic control mutation may be imparted alone or in combination of two or more. The L-amino acid biosynthetic enzyme activity may be enhanced alone or in combination of two or more. Further, imparting of the characteristic such as auxotrophy, L-amino acid analogue resistance and metabolic control mutation may be combined with enhancement of the L-amino acid biosynthesis enzyme activity.
For example, L-lysine-producing bacteria are bred as mutants exhibiting auxotrophy for L-homoserine or L-threonine and L-methionine (Japanese Patent Publication (Kokoku) Nos. 48-28078/1973 and 56-6499/1981), mutants exhibiting auxotrophy for inositol or acetic acid (Japanese Patent Application Laid-open (Kokai) Nos. 55-9784/1980 and 56-8692/1981), or mutants that are resistant to oxalysine, lysine hydroxamate, S-(2-aminoethyl)-cysteine, γ-methyllysine, α-chlorocaprolactam, DL-α-amino-ε-caprolactam, α-amino-lauryllactam, aspartic acid analogue, sulfa drug, quinoid or N-lauroylleucine.
Further, L-glutamic acid-producing bacteria can be bred as mutants exhibiting auxotrophy for oleic acid or the like. L-Threonine-producing bacteria can be bred as mutants resistant to α-amino-β-hydroxyvaleric acid. L-Homoserine-producing bacteria can be bred as mutants exhibiting auxotrophy for L-threonine or mutants resistant to L-phenylalanine analogues. L-Phenylalanine-producing bacteria can be bred as mutants exhibiting auxotrophy for L-tyrosine. L-Isoleucine-producing bacteria can be bred as mutants exhibiting auxotrophy for L-leucine. L-Proline-producing bacteria can be bred as mutants exhibiting auxotrophy for L-isoleucine.
Furthermore, as mentioned in the examples hereinafter, strains that produce one or more kinds of branched amino acids (L-valine, L-leucine and L-isoleucine) can be obtained as strains exhibiting auxotrophy for casamino acid.
In order to obtain mutants from Methylophilus bacteria, the inventors of the present invention first examined details of an optimal mutagenesis condition by using emergence frequency of streptomycin resistant strains as an index. As a result, the maximum emergence frequency of streptomycin resistant strains was obtained when the survival rate after mutagenesis was about 0.5%, and they succeeded in obtaining auxotrophic strains under this condition. They also succeeded in obtaining auxotrophic strains, which had been considered difficult, by largely scaling up the screening of mutants compared with that previously conducted for E. coli and so forth.
As described above, since it has been revealed that mutants can be obtained by mutagenizing Methylophilus bacteria under a suitable condition, it has become possible to readily obtain desired mutants by suitably setting such a condition that the survival rate after the mutagenesis should become about 0.5%, depending on the mutagenesis method.
Mutagenesis methods for obtaining mutants from Methylophilus bacteria include UV irradiation and treatments with mutagenesis agents used for usual mutatagenesis treatments such as N-methyl-N′-nitro-N-nitrosoguanidine (NTG) and nitrous acid. Methylophilus bacteria having L-amino acid-producing ability can also be obtained by selecting naturally occurring mutants of Methylophilus bacteria.
L-Amino acid analogue-resistant mutants can be obtained by, for example, inoculating mutagenized Methylophilus bacteria to an agar medium containing an L-amino acid analogue at a variety of concentrations and selecting strains that form colonies.
Auxotrophic mutants can be obtained by allowing Methylophilus bacteria to form colonies on an agar medium containing a target nutrient (for example, L-amino acid), replicating the colonies to an agar medium not containing said nutrient, and selecting strains that cannot grow on the agar medium not containing the nutrient.
Methods for imparting or enhancing L-amino acid-producing ability by enhancing L-amino acid biosynthetic enzyme activity will be exemplified below.
[L-Lysine]
L-Lysine-producing ability can be imparted by, for example, enhancing dihydrodipicolinate synthase activity and/or aspartokinase activity.
The dihydrodipicolinate synthase activity and/or the aspartokinase activity in Methylophilus bacteria can be enhanced by ligating a gene fragment coding for dihydrodipicolinate synthase and/or a gene fragment coding for aspartokinase with a vector that functions in Methylophilus bacteria, preferably a multiple copy type vector, to create a recombinant DNA, and introducing them into a Methylophilus bacterium host to transform the host. As a result of the increase in the copy numbers of the gene coding for dihydrodipicolinate synthase and/or the gene coding for aspartokinase in cells of the transformant strain, the activity or activities thereof is/are enhanced. Hereafter, dihydrodipicolinate synthase, aspartokinase and aspartokinase III are also referred with abbreviations of DDPS, AK and AKIII, respectively.
As a microorganism providing a gene that codes for DDPS and a gene that codes for AK, any microorganisms can be used so long as they have genes enabling expression of DDPS activity and AK activity in microorganisms belonging to the genus Methylophilus. Such microorganisms may be wild strains or mutant strains derived therefrom. Specifically, examples of such microorganisms include E. coli (Escherichia coli) K-12 strain, Methylophilus methylotrophus AS1 strain (NCIMB10515) and so forth. Since nucleotide sequences of a gene coding for DDPS (dapA, Richaud, F. et al., J. Bacteriol., 297, (1986)) and a gene coding for AKIII (lysC, Cassan, M., Parsot, C., Cohen, G. N. and Patte, J. C., J. Biol. Chem., 261, 1052 (1986)) derived from Escherichia bacteria have been both revealed, these genes can be obtained by PCR using primers synthesized based on the nucleotide sequences of these genes and chromosome DNA of microorganism such as E. coli K-12 or the like as a template. As specific examples, dapA and lysC derived from E. coli will be explained below. However, genes used for the present invention are not limited to them.
It is preferred that DDPS and AK used for the present invention do not suffer feedback inhibition by L-lysine. It has been known that wild-type DDPS derived from E. coli suffers feedback inhibition by L-lysine, and that wild-type AKIII derived from E. coli suffers suppression and feedback inhibition by L-lysine. Therefore, dapA and lysc to be introduced into Methylophilus bacteria preferably code for DDPS and AKIII having a mutation that desensitizes the feedback inhibition by L-lysine. Hereafter, DDPS having a mutation that desensitizes the feedback inhibition by L-lysine is also referred to as “mutant DDPS”, and DNA coding for the mutant DDPS is also referred to as “mutant dapA”. AKIII derived from E. coli having a mutation that desensitizes the feedback inhibition by L-lysine is also referred to as “mutant AKIII”, and DNA coding for the mutant AKIII is also referred to as “mutant lysC”.
According to the present invention, DDPS and AK are not necessarily required to be a mutant. It has been known that, for example, DDPS derived from Corynebacterium bacteria originally does not suffer feedback inhibition by L-lysine.
A nucleotide sequence of wild-type dapA derived from E. coli is exemplified by SEQ ID NO: 1. The amino acid sequence of wild-type DDPS coded by said nucleotide sequence is exemplified by SEQ ID NO: 2. A nucleotide sequence of wild-type lysC derived from E. coli is exemplified by SEQ ID NO: 3. The amino acid sequence of wild-type ATIII coded by said nucleotide sequence is exemplified by SEQ ID NO: 4.
The DNA coding for mutant DDPS that does not suffer feedback inhibition by L-lysine includes a DNA coding for DDPS having the amino acid sequence described in SEQ ID NO: 2 wherein the 118-histidine residue is replaced with a tyrosine residue. The DNA coding for mutant AKIII that does not suffer feedback inhibition by L-lysine includes a DNA coding for AKIII having an amino sequence described in SEQ ID NO: 4 wherein the 352-threonine residue is replaced with an isoleucine residue.
The plasmid used for gene cloning may be any plasmid so long as it can replicate in microorganisms such as Escherichia bacteria or the like, and specifically include pBR322, pTWV228, pMW119, pUC19 and so forth.
The vector that functions in Methylophilus bacteria is, for example, a plasmid that can autonomously replicate in Methylophilus bacteria. Specifically, there can be mentioned RSF1010, which is a broad host spectrum vector, and derivatives thereof, for example, pAYC32 (Chistorerdov, A. Y., Tsygankov, Y. D. Plasmid, 16, 161–167, (1986)), pMFY42 (Gene, 44, 53, (1990)), pRP301, pTB70 (Nature, 287, 396, (1980)) and so forth.
In order to prepare a recombinant DNA by ligating dapA and lysC to a vector that functions in Methylophilus bacteria, the vector is digested with a restriction enzyme that corresponds to the terminus of DNA fragment containing dapA and lysc. Ligation is usually performed by using ligase such as T4 DNA ligase. dapA and lysC may be individually incorporated into separate vectors or into a single vector.
As a plasmid containing a mutant dapA coding for mutant DDPS and a mutant lysC coding for mutant AKIII, a broad host spectrum plasmid RSFD80 has been known (WO95/16042). E. coli JM109 strain transformed with this plasmid was designated as AJ12396, and deposited at National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology, Ministry of International Trade and Industry (postal code 305-8566, 1-3 Higashi 1-chome, Tsukuba-shi, Ibaraki-ken, Japan) on Oct. 28, 1993 and received an accession number of FERM P-13936, and it was transferred to an international deposition under the provisions of the Budapest Treaty on Nov. 1, 1994, and received an accession number of FERM BP-4859. RSFD80 can be obtained from the AJ12396 strain in a known manner.
The mutant dapA contained in RSFD80 has a nucleotide sequence of wild-type dapA of SEQ ID NO: 1 including replacement of C at the nucleotide number 623 with T. The mutant DDPS encoded thereby has an amino acid sequence of SEQ ID NO: 2 including replacement of the 118-histidine residue with a tyrosine residue. The mutant lysC contained in RSFD80 has a nucleotide sequence of wild-type lysC of SEQ ID NO: 3 including replacement of C at the nucleotide number 1638 with T. The mutant AKIII encoded thereby has an amino acid sequence of SEQ ID NO: 4 including replacement of the 352-threonine residue with an isoleucine residue.
In order to introduce a recombinant DNA prepared as described above into Methylophilus bacteria, any method can be used so long as it provides sufficient transformation efficiency. For example, electroporation can be used (Canadian Journal of Microbiology, 43, 197 (1997)).
The DDPS activity and/or the AK activity can also be enhanced by the presence of multiple copies of dapA and/or lysC on chromosome DNA of Methylophilus bacteria. In order to introduce multiple copies of dapA and/or lysC into chromosome DNA of Methylophilus bacteria, homologous recombination is performed by using, as a target, a sequence that is present on chromosome DNA of Methylophilus bacteria in a multiple copy number. As the sequence present on chromosome DNA in the multiple copy number, a repetitive DNA, inverted repeats present at the end of a transposable element, or the like can be used. Alternatively, as disclosed in Japanese Patent Application Laid-open (Kokai) No. 2-109985/1990, multiple copies of dapA and/or lysC can be introduced into chromosome DNA by mounting them on a transposon to transfer them. In both of the methods, as a result of increased copy number of dapA and/or lysC in transformed strains, the DDPS activity and the AK activity should be amplified.
Besides the above gene amplification, the DDPS activity and/or the AK activity can be amplified by replacing an expression control sequence such as promoters of dapA and/or lysc with stronger ones (Japanese Patent Application Laid-open (Kokai) No. 1-4 215280/1989). As such strong promoters, there have been known, for example, lac promoter, trp promoter, trc promoter, tac promoter, PR promoter and PL promoter of lambda phage, tet promoter, amyE promoter, spac promoter and so forth. Substitution of these promoters enhances expression of dapA and/or lysC, and thus the DDPS activity and the AK activity are amplified. Enhancement of expression control sequences can be combined with increase of the copy numbers of dapA and/or lysc.
In order to prepare a recombinant DNA by ligating a gene fragment and a vector, the vector is digested with a restriction enzyme corresponding to the terminus of the gene fragment. Ligation is usually performed by ligase such as T4 DNA ligase. As methods for digestion, ligation and others of DNA, preparation of chromosome DNA, PCR, preparation of plasmid DNA, transformation, design of oligonucleotides used as primers and so forth, usual methods well known to those skilled in the art can be used. Such methods are described in Sambrook, J., Fritsch, E. F., and Maniatis, T., “Molecular Cloning: A Laboratory Manual, 2nd Edition”, Cold Spring Harbor Laboratory Press, (1989) and so forth.
In addition to the enhancement of the DDPS activity and/or the AK activity, activity of another enzyme involved in the L-lysine biosynthesis may also be enhanced. Such enzymes include diaminopimelate pathway enzymes such as dihydrodipicolinate reductase, diaminopimelate decarboxylase, diaminopimelate dehydrogenase (WO96/40934 for all of the foregoing enzymes), phosphoenolpyruvate carboxylase (Japanese Patent Application Laid-open (Kokai) No. 60-87788/1985), aspartate aminotransferase (Japanese Patent Publication (Kokoku) No. 6-102028/1994), diaminopimelate epimerase, aspartic acid semialdehyde dehydrogenase and so forth, or aminoadipate pathway enzymes such as homoaconitate hydratase and so forth. Preferably, activity of at least one enzyme of aspartic acid semialdehyde dehydrogenase, dihydrodipicolinate reductase and diaminopimelate decarboxylase is enhanced.
Aspartokinase, aspartic acid semialdehyde dehydrogenase, dihydrodipicolinate synthase, dihydrodipicolinate reductase and diaminopimelate decarboxylase derived form Methylophilus methylotrophus will be described later.
Further, the microorganisms of the present invention may be decreased in activity of an enzyme that catalyzes a reaction for generating a compound other than L-lysine by branching off from the biosynthetic pathway of L-lysine, or may be deficient in such an enzyme. The enzyme that catalyzes the reaction for generating the compound other than L-lysine by branching off from the biosynthetic pathway L-lysine include homoserine dehydrogenase (see WO95/23864).
The aforementioned techniques for enhancing activity of an enzyme involved in the L-lysine biosynthesis can be similarly used for other amino acids mentioned below.
[L-Glutamic Acid]
L-Glutamic acid-producing ability can be imparted to Methylophilus bacteria by, for example, introducing a DNA that codes for any one of enzymes including glutamate dehydrogenase (Japanese Patent Application Laid-open (Kokai) 61-268185/1986), glutamine synthetase, glutamate synthase, isocitrate dehydrogenase (Japanese Patent Application Laid-open (Kokai) Nos. 62-166890/1987 and 63-214189/1988), aconitate hydratase (Japanese Patent Application Laid-open (Kokai) No. 62-294086/1987), citrate synthase (Japanese Patent Application Laid-open (Kokai) Nos. 62-201585/1987 and 63-119688/1988), phosphoenolpyruvate carboxylase (Japanese Patent Application Laid-open (Kokai) Nos. 60-87788/1985 and 62-55089/1987), pyruvate dehydrogenase, pyruvate kinase, phosphoenolpyruvate synthase, enolase, phosphoglyceromutase, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase, triose phosphate isomerase, fructose bisphosphate aldolase, phosphofructokinase (Japanese Patent Application Laid-open (Kokai) No. 63-102692/1988), glucose phosphate isomerase, glutamine-oxoglutarate aminotransferase (WO99/07853) and so forth.
Further, the microorganisms of the present invention may be decreased in activity of an enzyme that catalyzes a reaction for generating a compound other than L-glutamic acid by branching off from the biosynthetic pathway of L-glutamic acid, or may be deficient in such an enzyme. The enzyme that catalyzes the reaction for generating the compound other than L-glutamic acid by branching off from the biosynthetic pathway L-glutamic acid include α-ketoglutarate dehydrogenase (αKGDH), isocitrate lyase, phosphate acetyltransferase, acetate kinase, acetohydroxy acid synthase, acetolactate synthase, formate acetyltransferase, lactate dehydrogenase, glutamate decarboxylase, 1-pyrroline dehydrogenase and so forth.
[L-Threonine]
L-Threonine-producing ability can be imparted or enhanced by, for example, enhancing activities of aspartokinase, homoserine dehydrogenase, homoserine kinase and threonine synthase. The activities of these enzymes can be enhanced by, for example, transforming Methylophilus bacteria using a recombinant plasmid containing a threonine operon (Japanese Patent Application Laid-open (Kokai) Nos. 55-131397/1980, 59-31691/1984 and 56-15696/1981 and Japanese Patent Application Laid-open (Kohyo) No. 3-501682/1991).
The production ability can also be imparted or enhanced by amplifying or introducing a threonine operon having a gene coding for aspartokinase of which feedback inhibition by L-threonine is desensitized (Japanese Patent Publication (Kokoku) No. 1-29559/1989), a gene coding for homoserine dehydrogenase (Japanese Patent Application Laid-open (Kokai) No. 60-012995/1985) or a gene coding for homoserine kinase and homoserine dehydrogenase (Japanese Patent Application Laid-open (Kokai) No. 61-195695/1986).
Further, L-threonine-producing ability can be improved by introducing a DNA coding for a mutant phosphoenolpyruvate carboxylase having a mutation for desensitizing feedback inhibition by aspartic acid.
[L-Valine]
L-Valine-producing ability can be imparted by, for example, introducing into Methylophilus bacteria an L-valine biosynthesis gene whose control mechanism has been substantially desensitized. There may also be introduced a mutation that substantially desensitizes a control mechanism of an L-valine biosynthesis gene carried by a microorganism belonging to the genus Methylophilus. 
Examples of the L-valine biosynthesis gene include, for example, the ilvGMEDA operon of E. coli. Threonine deaminase encoded by an ilvA gene catalyzes the deamination reaction converting L-threonine into 2-ketobutyric acid, which is the rate-determining step of L-isoleucine biosynthesis. Therefore, in order to attain efficient progression of the L-valine synthesis reactions, it is preferable to use an operon that does not express threonine deaminase activity. Examples of the ilvGMEDA operon that does not express such threonine deaminase activity include an ilvGMEDA operon wherein a mutation for eliminating threonine deaminase activity is introduced into ilvA, or ilvA is disrupted, and an ilvGMED operon wherein ilvA is deleted.
Since the ilvGMEDA operon suffers expression control of operon (attenuation) by L-valine and/or L-isoleucine and/or L-leucine, the region required for the attenuation is preferably removed or mutated to desensitize the suppression of expression by L-valine.
An ilvGMEDA operon which does not express threonine deaminase activity and in which attenuation is desensitized as described above can be obtained by subjecting a wild-type ilvGMEDA operon to a mutagenesis treatment or modifying it by means of gene recombination techniques (see WO96/06926).
[L-Leucine]
L-Leucine-producing ability is imparted or enhanced by, for example, introducing into a microorganism belonging to the genus Methylophilus an L-leucine biosynthesis gene whose control mechanism has been substantially desensitized, in addition to the above characteristics required for the production of L-valine. It is also possible to introduce such a mutation that the control mechanism of an L-leucine biosynthesis gene in a microorganism belonging to the genus Methylophilus should be substantially eliminated. Examples of such a gene include, for example, an leuA gene which provides an enzyme in which inhibition by L-leucine is substantially eliminated.
[L-Isoleucine]
L-Isoleucine-producing ability can be imparted by, for example, introducing a thrABC operon containing a thrA gene coding for aspartokinase I/homoserine dehydrogenase I derived from E. coli wherein inhibition by L-threonine has been substantially desensitized and an ilvGMEDA operon which contains an ilvA gene coding for threonine deaminase wherein inhibition by L-isoleucine is substantially desensitized and whose region required for attenuation is removed (Japanese Patent Application Laid-open (Kokai) No. 8-47397/1996).
[Other Amino Acids]
Biosyntheses of L-tryptophan, L-phenylalanine, L-tyrosine, L-threonine and L-isoleucine can be enhanced by increasing phosphoenolpyruvate-producing ability of Methylophilus bacteria (WO97/08333).
The production abilities for L-phenylalanine and L-tyrosine are improved by amplifying or introducing a desensitized chorismate mutase-prephenate dehydratase (CM-PDT) gene (Japanese Patent Application Laid-open (Kokai) Nos. 5-236947/1993 and 62-130693/1987) and a desensitized 3-deoxy-D-arabinoheptulonate-7-phosphate synthase (DS) gene (Japanese Patent Application Laid-open (Kokai) Nos. 5-236947/1993 and 61-124375/1986).
The producing ability of L-tryptophan is improved by amplifying or introducing a tryptophan operon containing a gene coding for desensitized anthranilate synthase (Japanese Patent Application Laid-open (Kokai) Nos. 57-71397/1982, 62-244382/1987 and U.S. Pat. No. 4,371,614).
In the present specification, the expression that enzyme “activity is enhanced” usually refers to that the intracellular activity of the enzyme is higher than that of a wild type strain, and when a strain in which the activity of the enzyme is enhanced is obtained by modification using gene recombinant techniques or the like, the intracellular activity of the enzyme is higher than that of the strain before the modification. The expression that enzyme “activity is decreased” usually refers to that the intracellular activity of the enzyme is lower than that of a wild type strain, and when a strain in which the activity of the enzyme is decreased is obtained by modification using gene recombinant techniques or the like, the intracellular activity of the enzyme is lower than that of the strain before the modification.
L-Amino acids can be produced by culturing Methylophilus bacteria having L-amino acid-producing ability obtained as described above in a medium to produce and accumulate L-amino acids in the culture, and collecting the L-amino acids from the culture.
Bacterial cells of Methylophilus bacteria with an increased L-amino acid content compared with wild strains of Methylophilus bacteria can be produced by culturing Methylophilus bacteria having L-amino acid-producing ability in a medium to produce and accumulate L-amino acids in bacterial cells of the bacteria.
Microorganisms used for the present invention can be cultured by methods usually used for culturing microorganisms having methanol-assimilating property. The medium used for the present invention may be a natural or synthetic medium so long as it contains a carbon source, a nitrogen source, inorganic ions and other trace amount organic constituents as required.
By using methanol as a main carbon source, L-amino acids can be prepared at a low cost. When methanol is used as a main carbon source, it is usually added to a medium in an amount of 0.001 to 30%. As the nitrogen source, ammonium sulfate or the like is used by adding it to the medium. Other than these, there are usually added small amounts of the trace amount constituents such as potassium phosphate, sodium phosphate, magnesium sulfate, ferrous sulfate and manganese sulfate.
The culture is usually performed under an aerobic condition obtained by, for example, shaking or stirring for aeration, at pH 5 to 9 and a temperature of 20 to 45° C., and it is usually completed within 24 to 120 hours.
Collection of L-amino acids from culture can be usually attained by a combination of known methods such as those using ion exchange resin, precipitation and others.
Further, Methylophilus bacterium cells can be separated from the medium by usual methods for separating microbial cells.
<2> Gene of the Present Invention
The DNA of the present invention is a gene which codes for one of the enzymes, aspartokinase (henceforth also abbreviated as “AK”), aspartic acid semialdehyde dehydrogenase (henceforth also abbreviated as “ASD”), dihydrodipicolinate synthase (henceforth also abbreviated as “DDPS”), dihydrodipicolinate reductase (henceforth also abbreviated as “DDPR”), and diaminopimelate decarboxylase (henceforth also abbreviated as “DPDC”) derived from Methylophilus methylotrophus. 
The DNA of the present invention can be obtained by, for example, transforming a mutant strain of a microorganism deficient in AK, ASD, DDPS, DDPR or DPDC using a gene library of Methylophilus methylotrophus, and selecting a clone in which auxotrophy is recovered.
A gene library of Methylophilus methylotrophus can be produced as follows, for example. First, total chromosome DNA is prepared from a Methylophilus methylotrophus wild strain, for example, the Methylophilus methylotrophus AS1 strain (NCIMB10515), by the method of Saito et al. (Saito, H. and Miura, K., Biochem. Biophys. Acta 72, 619–629, (1963)) or the like, and partially digested with a suitable restriction enzyme, for example, Sau3AI or AluI, to obtain a mixture of various fragments. By controlling the degree of the digestion through adjustment of digestion reaction time and so forth, a wide range of restriction enzymes can be used.
Subsequently, the digested chromosome DNA fragments are ligated to vector DNA autonomously replicable in Escherichia coli cells to produce recombinant DNA. Specifically, a restriction enzyme producing the same terminal nucleotide sequence as that produced by the restriction enzyme used for the digestion of chromosome DNA is allowed to act on the vector DNA to fully digest and cleave the vector. Then, the mixture of chromosome DNA fragments and the digested and cleaved vector DNA are mixed, and a ligase, preferably T4 DNA ligase, is allowed to act on the mixture to obtain recombinant DNA.
A gene library solution can be obtained by transforming Escherichia coli, for example, the Escherichia coli JM109 strain or the like, using the obtained recombinant DNA, and preparing recombinant DNA from the culture broth of the transformant. This transformation can be performed by the method of D. M. Morrison (Methods in Enzymology 68, 326 (1979)), the method of treating recipient cells with calcium chloride so as to increase the permeability of DNA (Mandel, M. and Higa, A., J. Mol. Biol., 53, 159 (1970)) and so forth. In the examples mentioned hereinafter, electroporation was used.
As examples of the aforementioned vector, there can be mentioned pUC19, pUC18, pUC118, pUC119, pBR322, pHSG299, pHSG298, pHSG399, pHSG398, RSF1010, pMW119, pMW118, pMW219, pMW218, pSTV28, pSTV29 and so forth. Phage vectors can also be used. Since pUC118 and pUC119 contain an ampicillin resistance gene, and pSTV28 and pSTV29 contain a chloramphenicol resistance gene, for example, only transformants which harbor a vector or a recombinant DNA can be grown by using a medium containing ampicillin or chloramphenicol.
As the method for culturing the transformants and collecting recombinant DNA from bacterial cells, the alkali SDS method and the like can be mentioned.
A mutant microbial strain deficient in AK, ASD, DDPS, DDPR or DPDC is transformed by using the gene library solution of Methylophilus methylotrophus obtained as described above, and clones whose auxotrophy is recovered are selected.
Examples of a mutant microbial strain deficient in AK include E. coli GT3 deficient in three kinds of genes coding for AK (thrA, metLM, lysC). Examples of a mutant microbial strain deficient in ASD include E. coli Hfr3000 U482 (CGSC 5081 strain). Examples of a mutant microbial strain deficient in DDPS include E. coli AT997 (CGSC 4547 strain). Examples of a mutant microbial strain deficient in DDPR include E. coli AT999 (CGSC 4549 strain). Examples of a mutant microbial strain deficient in DPDC include E. coli AT2453 (CGSC 4505 strain). These mutant strains can be obtained from E. coli Genetic Stock Center (the Yale University, Department of Biology, Osborn Memorial Labs., P.O. Box 6666, New Haven 06511-7444, Conn., U.S.).
Although all of the aforementioned mutant strains cannot grow in M9 minimal medium, transformant strains which contain a gene coding for AK, ASD, DDPS, DDPR or DPDC can grow in M9 minimal medium because these genes function in the transformants. Therefore, by selecting transformant strains that can grow in the minimal medium and collecting recombinant DNA from the strains, DNA fragments containing a gene that codes for each enzyme can be obtained. E. coli AT999 (CGSC 4549 strain) shows extremely slow growth rate even in a complete medium such as L medium when diaminopimelic acid is not added to the medium. However, normal growth can be observed for its transformant strains which contain a gene coding for DDPR derived from Methylophilus methylotrophus, because of the function of the gene. Therefore, a transformant strain that contains a gene coding for DDPR can also be obtained by selecting a transformant strain normally grown in L medium.
By extracting an insert DNA fragment from the obtained recombinant DNA and determining its nucleotide sequence, an amino acid sequence of each enzyme and nucleotide sequence of the gene coding for it can be determined.
The gene coding for AK of the present invention (henceforth also referred to “ask”) codes for AK which has the amino acid sequence of SEQ ID NO: 6 shown in Sequence Listing. As a specific example of the ask gene, there can be mentioned a DNA having the nucleotide sequence which consists of nucleotides of SEQ ID NO: 5. The ask gene of the present invention may have a sequence in which codon corresponding to each of the amino acids is replaced with equivalent codon so long as it codes for the same amino acid sequence as the amino acid sequence of SEQ ID NO: 6.
The gene which codes for ASD of the present invention (henceforth also referred to as “asd”) codes for ASD which has the amino acid sequence of SEQ ID NO: 8 shown in Sequence Listing. As a specific example of the asd gene, a DNA which contains the nucleotide sequence consisting of the nucleotides of the nucleotide numbers 98–1207 in SEQ ID NO: 7 can be mentioned. The asd gene of the present invention may have a sequence in which codon corresponding to each of the amino acids is replaced with equivalent codon so long as it codes for the same amino acid sequence as the amino acid sequence of SEQ ID NO: 8.
The gene which codes for DDPS of the present invention (henceforth also referred to as “dapA”) codes for DDPS which has the amino acid sequence of SEQ ID NO: 10 shown in Sequence Listing. As a specific example of the dapA gene, a DNA which has the nucleotide sequence consisting of the nucleotides of the nucleotide numbers 1268–2155 in SEQ ID NO: 9 can be mentioned. The dapA gene of the present invention may have a sequence in which codon corresponding to each of the amino acids is replaced with equivalent codon so long as it codes for the same amino acid sequence as the amino acid sequence of SEQ ID NO: 10.
The gene which codes for DDPR of the present invention (henceforth also referred to as “dapB”) codes for DDPR which has the amino acid sequence of SEQ ID NO: 12 shown in Sequence Listing. As a specific example of the dapB gene, a DNA which has the nucleotide sequence consisting of the nucleotides of the nucleotide numbers 2080–2883 in SEQ ID NO: 11 can be mentioned. The dapB gene of the present invention may have a sequence in which codon corresponding to each of the amino acids is replaced with equivalent codon so long as it codes for the same amino acid sequence as the amino acid sequence of SEQ ID NO: 12.
The gene which codes for DPDC of the present invention (henceforth also referred to as “lysA”) codes for DPDC which has the amino acid sequence of SEQ ID NO: 14 shown in Sequence Listing. As a specific example of the lysA gene, a DNA which has the nucleotide sequence consisting of the nucleotides of the nucleotide numbers 751–1995 in SEQ ID NO: 13 can be mentioned. The lysA gene of the present invention may have a sequence in which codon corresponding to each of the amino acids is replaced with equivalent codon so long as it codes for the same amino acid sequence as the amino acid sequence of SEQ ID NO: 14.
The gene for each enzyme of the present invention may have an amino acid sequence corresponding to each amino acid sequence of SEQ ID NO: 6, 8, 10, 12 or 14 including substitution, deletion, insertion, addition or inversion of one or several amino acids, and may code a protein having activity of AK, ASD, DDPS, DDPR or DPDC. The expression “one or several” used herein preferably means a number of 1 to 10, more preferably a number of 1 to 5, more preferably a number of 1 to 2.
The DNA which codes for the substantially same protein as AK, ASD, DDPS, DDPR or DPDC such as those mentioned above can be obtained by modifying each nucleotide sequence so that the amino acid sequence should contain substitution, deletion, insertion, addition or inversion of an amino acid residue or residues at a particular site by, for example, site-specific mutagenesis. Such a modified DNA as mentioned above may also be obtained by a conventional mutagenesis treatment. Examples of the mutagenesis treatment include in vitro treatment of DNA coding for AK, ASD, DDPS, DDPR or DPDC with hydroxylamine or the like, treatment of a microorganism such as Escherichia bacteria containing a gene coding for AK, ASD, DDPS, DDPR or DPDC by UV irradiation or with mutagenesis agents used for usual mutagenesis treatment such as N-methyl-N′-nitro-N-nitrosoguanidine (NTG) and nitrous acid.
The aforementioned substitution, deletion, insertion, addition or inversion of nucleotides includes naturally occurring mutations (mutant or variant) such as those observed depending difference between species or strains of microorganisms containing AK, ASD, DDPS, DDPR or DPDC and so forth.
The DNA which codes for substantially the same protein as AK, ASD, DDPS, DDPR or DPDC can be obtained by allowing expression of a DNA having such a mutation as mentioned above in a suitable cell, and examining AK, ASD, DDPS, DDPR or DPDC activity of the expression product. The DNA which codes for substantially the same protein as AK, ASD, DDPS, DDPR or DPDC can also be obtained by isolating, from DNAs coding for AK, ASD, DDPS, DDPR or DPDC which have mutations or cells containing each of them, a DNA hybridizable with a probe containing a nucleotide sequence comprising the nucleotide sequence of the nucleotide numbers 510–1736 of SEQ ID NO: 5, a nucleotide sequence comprising the nucleotide sequence of the nucleotide numbers 98–1207 of SEQ ID NO: 7, a nucleotide sequence comprising the nucleotide sequence of the nucleotide numbers 1268–2155 of SEQ ID NO: 9, a nucleotide sequence comprising the nucleotide sequence of the nucleotide numbers 2080–2883 of SEQ ID NO: 11, or a nucleotide sequence comprising the nucleotide sequence of the nucleotide numbers 751–1995 of SEQ ID NO: 13, or a part of those nucleotide sequences under a stringent condition, and coding for a protein having AK, ASD, DDPS, DDPR or DPDC activity. In the present specification, to have a nucleotide sequence or a part thereof means to have the nucleotide sequence or the part thereof, or a nucleotide complementary thereto.
The term “stringent condition” used herein means a condition that allows formation of so-called specific hybrid and does not allow formation of non-specific hybrid. This condition may vary depending on the nucleotide sequence and length of the probe. However, it may be, for example, a condition that allows hybridization of highly homologous DNA such as DNA having homology of 40% or higher, but does not allow hybridization of DNA of lower homology than defined above, or a condition that allows hybridization under a washing condition of usual Southern hybridization, of a temperature of 60° C. and salt concentrations corresponding to 1×SSC and 0.1% SDS, preferably 0.1×SSC and 0.1% SDS.
A partial sequence of each gene can also be used as the probe. Such a probe can be produced by PCR (polymerase chain reaction) using oligonucleotides produced based on a nucleotide sequence of each gene as primers and a DNA fragment containing each gene as a template. When a DNA fragment having a length of about 300 bp is used as the probe, washing condition for hybridization may be, for example, 50° C., 2×SSC and 0.1% SDS.
Genes that hybridize under such a condition as mentioned above also include those having a stop codon occurring in its sequence and those encoding an enzyme no longer having its activity due to a mutation of active center. However, such genes can readily be eliminated by ligating the genes to a commercially available activity expression vector, and measuring AK, ASD, DDPS, DDPR or DPDC activity.
Since the nucleotide sequences of the genes that codes for AK, ASD, DDPS, DDPR and DPDC derived from Methylophilus methylotrophus were revealed by the present invention, DNA sequences which code for AK, ASD, DDPS, DDPR and DPDC can be obtained from a Methylophilus methylotrophus gene library by hybridization using oligonucleotide probes produced based on the sequences. Moreover, DNA sequences which code for these enzymes can also be obtained by amplifying them from Methylophilus methylotrophus chromosome DNA by PCR using oligonucleotide primers produced based on the aforementioned nucleotide sequences.
The aforementioned genes can suitably be utilized to enhance L-lysine-producing ability of Methylophilus bacteria.
EXAMPLES
The present invention will further specifically be explained with reference to the following examples hereafter.
The reagents used were obtained from Wako Pure Chemicals or Nakarai Tesque unless otherwise indicated. The compositions of the media used in each example are shown below. pH was adjusted with NaOH or HCl for all media.










(L medium)


















Bacto trypton (DIFCO)
10 g/L 



Yeast extract (DIFCO)
5 g/L



NaCl
5 g/L







[steam-sterilized at 120° C. for 20 minutes]
















(L agar medium)


















L medium




Bacto agar (DIFCO)
15 g/L







[steam-sterilized at 120° C. for 20 minutes]
















(SOC medium)


















Bacto trypton (DIFCO)
20 g/L



Yeast extract (DTFCO)
 5 g/L



 10 mM
NaCl



2.5 mM
KCl



 10 mM
MgSO4



 10 mM
MgCl2



 20 mM
Glucose







[The constituents except for magnesium solution and glucose were steam-sterilized (120° C., 20 minutes), then 2 M magnesium stock solution (1 M MgSO4, 1 M MgCl2) and 2 M glucose solution, which solutions had been passed through a 0.22-μm filter, were added thereto, and the mixture was passed through a 0.22-μm filter again.]
















(121M1 medium)



















K2HPO4
1.2
g/L



KH2PO4
0.62
g/L



NaCl
0.1
g/L



(NH4)2SO4
0.5
g/L



MgSO4•7H2O
0.2
g/L



CaCl2•6H2O
0.05
g/L



FeCl3•6H2O
1.0
mg/L



H3BO3
10
μg/L



CuSO4•5H2O
5
μg/L



MnSO4•5H2O
10
μg/L



ZnSO4•7H2O
70
μg/L



NaMoO4•2H2O
10
μg/L



CoCl2•6H2O
5
μg/L



Methanol 1% (vol/vol),
pH
7.0







[The constituents except for methanol were steam-sterilized at 121° C. for 15 minutes. After the constituents sufficiently cooled, methanol was added.]
















(Composition of 121 production medium)



















Methanol
2%




Dipotassium phosphate
0.12%



Potassium phosphate
0.062%



Calcium chloride hexahydrate
0.005%



Magnesium sulfate heptahydrate
0.02%



Sodium chloride
0.01%



Ferric chloride hexahydrate
1.0
mg/L



Ammonium sulfate
0.3%



Cupric sulfate pentahydrate
5
μg/L



Manganous sulfate pentahydrate
10
μg/L



Sodium molybdate dihydrate
10
μg/L



Boric acid
10
μg/L



Zinc sulfate heptahydrate
70
μg/L



Cobaltous chloride hexahydrate
5
μg/L



Calcium carbonate (Kanto Kagaku)
3%



(pH 7.0)




















(121M1 Agar medium)


















121M1 medium




Bacto agar (DIFCO)
15 g/L







[The constituents except for methanol were steam-sterilized at 121° C. for 15 minutes. After the constituents sufficiently cooled, methanol was added.]
















(M9 minimal medium)



















Na2HPO4•12H2O
16
g/L



KH2PO4
3
g/L



NaCl
0.5
g/L



NH4Cl
1
g/L



MgSO4•7H2O
246.48
mg/L



Glucose
2
g/L



pH 7.0







[MgSO4 and glucose were separately sterilized (120° C., 20 minutes) and added. A suitable amount of amino acids and vitamins were added as required.]
















(M9 minimal agar medium)


















M9 minimal medium




Bacto agar (DIFCO)
15 g/L










Example 1
Creation of L-Lysine-Producing Bacterium (1)
(1) Introduction of Mutant lysC and Mutant dapA into Methylophilus Bacterium
A mutant lysC and a mutant dapA were introduced into a Methylophilus bacterium by using a known plasmid RSFD80 (see WO95/16042) containing them. RSFD80 is a plasmid pVIC40 (International Publication WO90/04636, Japanese Patent Application Laid-open (Kohyo) No. 3-501682/1991) derived from a broad host spectrum vector plasmid pAYC32 (Chistorerdov, A. Y., Tsygankov, Y. D., Plasmid, 16, 161–167, (1986)), which is a derivative of RSF1010, in which a mutant dapA and a mutant lysc derived from E. coli are located in this order downstream of the promoter (tetP) of the tetracycline resistance gene of pVIC40 so that the transcription directions of the genes are ordinary with respect to tetP. The mutant dapA coded for a mutant DDPS in which the 118-histidine residue was replaced with a thyrosine residue. The mutant lysC coded for a mutant AKIII in which the 352-threonine residue was replaced with an isoleucine residue.
RSFD80 was constructed as follows. The mutant dapA on a plasmid pdapAS24 was ligated to pVIC40 at a position downstream of the promoter of the tetracycline resistance gene to obtain RSF24P as shown in FIG. 1. Then, the plasmid RSFD80 which had the mutant dapA and a mutant lysc was prepared from RSF24P and pLLC*80 containing the mutant lysC as shown in FIG. 2. That is, while pVIC40 contains a threonine operon, this threonine operon is replaced with a DNA fragment containing the mutant dapA and a DNA fragment containing the mutant lysC in RSFD80.
The E. coli JM109 strain transformed with the RSFD80 plasmid was designated as AJ12396, and deposited at National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology, Ministry of International Trade and Industry (postal code 305-8566, 1-3 Higashi 1-chome, Tsukuba-shi, Ibaraki-ken, Japan) on Oct. 28, 1993 and received an accession number of FERM P-13936, and it was transferred to an international deposition under the provisions of the Budapest Treaty on Nov. 1, 1994, and received an accession number of FERM BP-4859.
The E. coli AJ1239 strain was cultured in 30 ml of LB medium containing 20 mg/L of streptomycin at 30° C. for 12 hours, and the RSFD80 plasmid was purified from the obtained cells by using Wizard® Plus Midipreps DNA Purification System (sold by Promega).
The RSFD80 plasmid produced as described above was introduced into the Methylophilus methylotrophus AS1 strain (NCIMB10515) by electroporation (Canadian Journal of Microbiology, 43, 197 (1997)). As a control, a DNA region coding for the threonine operon was deleted from the pVIC40 plasmid used for producing the RSFD80 plasmid to produce a pRS plasmid comprising only the vector region (see Japanese Patent Application Laid-open (Kohyo) No. 3-501682/1991), and the pRS plasmid was introduced into the AS1 strain in the same manner as that used for RSFD80.
(2) AKIII Activity of Methylophilus Bacterium Containing Mutant lysC and Mutant dapA Derived from E. coli 
Cell-free extracts were prepared from the Methylophilus methylotrophus AS1 strain containing the RSFD80 plasmid (also referred to as “AS1/RSFD80” hereinafter) and the Methylophilus methylotrophus AS1 strain containing the pRS plasmid (also referred to as “AS1/pRS” hereinafter), and AK activity was measured. The cell-free extracts (crude enzyme solutions) were prepared as follows. The AS1/RSFD80 strain and AS1/pRS strain were each inoculated to 121 production medium of the above composition containing 20 mg/L of streptomycin, cultured at 37° C. for 34 hours with shaking, and then calcium carbonate was removed and cells were harvested.
The bacterial cells obtained as described above were washed with 0.2% KCl under a condition of 0° C., suspended in 20 mM potassium phosphate buffer (pH 7) containing 10 mM MgSO4, 0.8 M (NH4)2SO4 and 0.03 M β-mercaptoethanol, and disrupted by sonication (0° C., 200 W, 10 minutes). The sonicated cell suspension was centrifuged at 33,000 rpm for 30 minutes under a condition of 0° C., and the supernatant was separated. To the supernatant, ammonium sulfate was added to 80% saturation, and the mixture was left at 0° C. for 1 hour, and centrifuged. The pellet was dissolved in 20 mM potassium phosphate buffer (pH 7) containing 10 mM MgSO4, 0.8 M (NH4)2SO4 and 0.03 M β-mercaptoethanol.
The measurement of AK activity was performed in accordance with the method of Stadtman (Stadtman, E. R., Cohen, G. N., LeBras, G., and Robichon-Szulmajster, H., J. Biol. Chem., 236, 2033 (1961)). That is, a reaction solution of the following composition was incubated at 30° C. for 45 minutes, and color development was caused by adding a FeCl3 solution (2.8 N HCl: 0.4 ml, 12% TCA: 0.4 ml, 5% FeCl3.6H2O/0.1 N HCl: 0.7 ml). The reaction solution was centrifuged, and absorbance of the supernatant was measured at 540 nm. The activity was represented in terms of the amount of hydroxamic acid produced in 1 minute (1 U=1 μmol/minute). The molar extinction coefficient was set to be 600. The reaction solution not containing potassium aspartate was used as a blank. When the enzymatic activity was measured, L-lysine was added to the enzymatic reaction solution at various concentrations to examine degree of inhibition by L-lysine. The results are shown in Table 1.










(Composition of reaction solution)


















Reaction mixture *1
0.3 ml



Hydroxylamine solution *2
0.2 ml



0.1 M Potassium aspartate (pH 7.0)
0.2 ml



Enzyme solution
0.1 ml



Water (balance)
Total 1 ml







*1 1 M Tris-HCl (pH 8.1): 9 ml, 0.3 M MgSO4: 0.5 ml and 0.2 M ATP (pH 7.0): 5 ml



*2 8 M Hydroxylamine solution neutralized with KOH immediately before use
















TABLE 1






AK activity
Specific
Desensitization



(Specific
activity with
degree of


Strain
activity*1)
5 mM L-lysine
inhibition*2 (%)


















AS1/pRS
7.93
9.07
114


AS1/RSFD80
13.36
15.33
115





*1nmol/minute/mg protein


*2Activity retention ratio in the presence of 5 mM L-lysine






As shown in Table 1, AK activity was increased by about 1.7 times by the introduction of the RSFD80 plasmid. Further, it was confirmed that the inhibition by L-lysine was completely desensitized in AK derived from E. coli that was encoded by the RSFD80 plasmid. Moreover, it was found that AK that was originally retained by the AS1 strain was not inhibited by L-lysine alone. The inventors of the present invention have discovered that the AK derived from the AS1 strain was inhibited by 100% when 2 mM for each of L-lysine and L-threonine were present in the reaction solution (concerted inhibition).
(3) Production of L-Lysine by Methylophilus Bacterium Containing Mutant lysC and Mutant dapA Derived from E. coli 
Then, the AS1/RSFD80 strain and the AS1/pRS strain were inoculated to 121 production medium containing 20 mg/L of streptomycin, and cultured at 37° C. for 34 hours with shaking. After the culture was completed, the bacterial cells and calcium carbonate were removed by centrifugation, and L-lysine concentration in the culture supernatant was measured by an amino acid analyzer (JASCO Corporation [Nihon Bunko], high performance liquid chromatography). The results are shown in Table 2.










TABLE 2








Production amount of L-lysine



Strain
hydrochloride (g/L)



















AS1/pRS
0



AS1/RSFD80
0.3










Example 2
Creation of L-Lysine-Producing Bacterium (2)
(1) Introduction of tac Promoter Region into Broad Host Spectrum Vector
In order to produce a large amount of enzyme involved in the biosynthesis of L-lysine (Lys) in Methylophilus methylotrophus, tac promoter was used for gene expression of the target enzyme. The promoter is frequently used in E. coli. 
The tac promoter region was obtained by amplification through PCR using DNA of pKK233-3 (Pharmacia) as a template, DNA fragments having the nucleotide sequences of SEQ ID NOS: 15 and 16 as primers, and a heat-resistant DNA polymerase. The PCR was performed with a cycle of 94° C. for 20 seconds, 60° C. for 30 seconds, and 72° C. for 60 seconds, which was repeated 30 times. Then, the amplified DNA fragment was collected and treated with restriction enzymes EcoRI and PstI. On the other hand, a broad host spectrum vector pRS (see Japanese Patent Application Laid-open (Kohyo) No. 3-501682/1991) was also digested with the same restriction enzymes, and the aforementioned DNA fragment which contained the tac promoter region was introduced into the restriction enzyme digestion termini to construct pRS-tac.
(2) Preparation of dapA Gene (Dihydrodipicolinate Synthase Gene) Expression Plasmid pRS-dapA24 and lysC Gene (Aspartokinase Gene) Expression Plasmid pRS-lysC80
A mutant gene (dapA*24) coding for dihydrodipicolinate synthase whose feedback inhibition for the enzyme activity by Lys was partially desensitized was introduced into the plasmid pRS-tac which was prepared by the method described in the above (1).
First, the dapA*24 gene region was obtained by amplification through PCR using DNA of RSFD80 (see Example 1) as a template, and DNA fragments having the nucleotide sequences of SEQ ID NOS: 17 and 18 as primers. The PCR was performed with a cycle of 94° C. for 20 seconds, 60° C. for 30 seconds, and 72° C. for 90 seconds, which was repeated 30 times. Then, the fragment was treated with restriction enzymes Sse8387I and XbaI to prepare a dapA*24 gene fragment having corresponding cleaved termini. On the other hand, pRS-tac was also treated with Sse8387I and partially digested with XbaI in the same manner as described above. To this digested plasmid, the aforementioned dapA*24 gene fragment was ligated by using T4 ligase to obtain pRS-dapA24.
Similarly, a gene (lysC*80) coding for aspartokinase whose feedback inhibition for the enzyme activity by Lys was partially desensitized was obtained by PCR using DNA of RSFD80 as a template, and DNA fragments having the nucleotide sequences of SEQ ID NOS: 19 and 20 as primers. The PCR was performed with a cycle of 94° C. for 20 seconds, 60° C. for 30 seconds, and 72° C. for 90 seconds, which was repeated 30 times. Then, the obtained DNA fragment was treated with restriction enzymes Sse8387I and SapI. On the other hand, the vector pRS-tac was also treated with Sse8387I and SapI. To this digested plasmid, the aforementioned lysC*80 gene fragment was ligated by using T4 ligase to obtain pRS-lysC80.
(3) Introduction of pRS-dapA24 or pRS-lysC80 into Methylophilus methylotrophus and Evaluation of Culture
Each of pRS-dapA24 and pRS-lysC80 obtained as described above was introduced into the Methylophilus methylotrophus AS1 strain (NCIMB10515) by electroporation to obtain AS1/pRS-dapA24 and AS1/pRS-lysC80, respectively. Each strain was inoculated to 121 production medium containing 20 mg/L of streptomycin, and cultured at 37° C. for 48 hours with shaking. As a control strain, AS1 strain harboring pRS was also cultured in a similar manner. After the culture was completed, the cells and calcium corbonate were removed by centrifugation, and L-lysine concentration in the culture supernatant was measured by an amino acid analyzer (JASCO Corporation [Nihon Bunko], high performance liquid chromatography). The results are shown in Table 3.










TABLE 3








Production amount of L-lysine



Strain
hydrochloride (g/L)



















AS1/pRS
<0.01



AS1/pRS-lysC80
0.06



AS1/pRS-dapA24
0.13










Example 3
Creation of L-Lysine-Producing Bacterium (3)
The Methylophilus methylotrophus AS1 strain (NCIMB10515) was inoculated to 121M1 medium and cultured at 37° C. for 15 hours. The obtained bacterial cells were treated with NTG in a conventional manner (NTG concentration: 100 mg/L, 37° C., 5 minutes), and spread onto 121M1 agar medium containing 7 g/L of S-(2-aminoethyl)-cysteine (AEC) and 3 g/L of L-threonine. The cells were cultured at 37° C. for 2 to 8 days, and the formed colonies were picked up to obtain AEC-resistant strains.
The aforementioned AEC-resistant strains were inoculated to 121 production medium, and cultured at 37° C. for 38 hours under an aerobic condition. After the culture was completed, the cells and calcium carbonate were removed from the medium by centrifugation, and L-lysine concentration in the culture supernatant was measured by an amino acid analyzer (JASCO Corporation [Nihon Bunko], high performance liquid chromatography). A strain showing improved L-lysine-producing ability compared with the parent strain was selected, and designated as Methylophilus methylotrophus AR-166 strain. The L-lysine production amounts of the parent strain (AS1 strain) and the AR-166 strain are shown in Table 4.










TABLE 4








Production amount of L-lysine



Strain
hydrochloride (mg/L)



















AS1
5.8



AR-166
80










The Methylophilus methylotrophus AR-166 strain was given a private number of AJ13608, and was deposited at National Institute of Bioscience and Human-Technology, Agency of Industrial science and Technology, Ministry of International Trade and Industry (postal code 305-8566, 1-3 Higashi 1-chome, Tsukuba-shi, Ibaraki-ken, Japan) on Jun. 10, 1999 and received an accession number of FERM P-17416, and it was transferred to an international deposition under the provisions of the Budapest Treaty on Mar. 31, 2000, and received an accession number of FERM BP-7112.
Example 4
Creation of L-Threonine-Producing Bacterium
(1) Introduction of Threonine Operon Plasmid into Methylophilus Bacterium
A plasmid pVIC40 (International Publication WO90/04636, Japanese Patent Application Laid-open (Kohyo) No. 3-501682/1991) containing a threonine operon derived from E. coli was introduced into the Methylophilus methylotrophus AS1 strain (NCIMB10515) by electroporation (Canadian Journal of Microbiology, 43, 197 (1997)) to obtain AS1/pVIC40 strain. As a control, pRS (Japanese Patent Application Laid-open (Kohyo) No. 3-501682/1991) having only the vector region was obtained by deleting the DNA region coding for the threonine operon from the pVIC40 plasmid, and it was introduced into the AS1 strain in the same manner as used for pVIC40 to obtain AS1/pRS strain.
(2) Production of L-Threonine by Methylophilus Bacterium Containing Threonine Operon Derived from E. coli 
Each of the AS1/pVIC40 and AS1/pRS strains was inoculated to 121 production medium containing 20 mg/L of streptomycin, 1 g/l of L-valine and 1 g/l of L-leucine, and cultured at 37° C. for 50 hours with shaking. After the culture was completed, the cells and calcium carbonate were removed by centrifugation, and L-threonine concentration in the culture supernatant was measured by an amino acid analyzer (JASCO Corporation [Nihon Bunko], high performance liquid chromatography). The results are shown in Table 5.










TABLE 5








Production amount of



Strain
L-threonine (mg/L)



















AS1/pRS
15



AS1/pVIC40
30










Example 5
Creation of Branched Chain Amino Acid-Producing Bacterium
The Methylophilus methylotrophus AS1 strain (NCIMB10515) was inoculated to 121M1 medium and cultured at 37° C. for 15 hours. The obtained bacterial cells were treated with NTG in a conventional manner (NTG concentration: 100 mg/L, 37° C., 5 minutes), and spread onto 121M1 agar medium containing 0.5% of casamino acid (DIFCO). The cells were cultured at 37° C. for 2 to 8 days, and allowed to form colonies. The formed colonies were picked up, and inoculated to 121M1 agar medium and 121M1 agar medium containing 0.5% of casamino acid. Strains exhibiting better growth on the latter medium compared with on the former medium were selected as casamino acid auxotrophic strains. In this way, 9 leaky casamino acid auxotrophic strains were obtained from NTG-treated 500 strains. From these casamino acid auxotrophic strains, one strain that accumulated more L-valine, L-leucine and L-isoleucine in the medium compared with its parent strain was obtained. This strain was designated as Methylophilus methylotrophus C138 strain.
The Methylophilus methylotrophus C138 strain was given a private number of AJ13609, and was deposited at National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology, Ministry of International Trade and Industry (postal code 305-8566, 1-3 Higashi 1-chome, Tsukuba-shi, Ibaraki-ken, Japan) on Jun. 10, 1999 and received an accession number of FERM P-17417, and it was transferred to an international deposition under the provisions of the Budapest Treaty on Mar. 31, 2000, and received an accession number of FERM BP-7113.
The parent strain (AS1 strain) and the C138 strain were inoculated to 121 production medium, and cultured at 37° C. for 34 hours under an aerobic condition. After the culture was completed, the cells and calcium carbonate were removed from the medium by centrifugation, and concentrations of L-valine, L-leucine and L-isoleucine in the culture supernatant were measured by an amino acid analyzer (JASCO Corporation [Nihon Bunko], high performance liquid chromatography). The results are shown in Table 6.












TABLE 6








L-valine
L-leucine
L-isoleucine



Strain
(mg/L)
(mg/L)
(mg/L)





















AS1
7.5
5.0
2.7



C138
330
166
249










Example 6
Preparation of Chromosome DNA Library of Methylophilus methylotrophus AS1 Strain
(1) Preparation of Chromosome DNA of Methylophilus methylotrophus AS1 Strain
One platinum loop of the Methylophilus methylotrophus AS1 strain (NCIMB10515) was inoculated to ml of 121M1 medium in a test tube, and cultured at 37° C. overnight with shaking. The obtained culture broth was inoculated to 50 ml of 121M1 medium in a 500 ml-volume Sakaguchi flask in an amount of 1%, and cultured at 37° C. overnight with shaking. Then, the cells were harvested by centrifugation, and suspended in 50 ml of TEN solution (solution containing 50 mM Tris-HCl (pH 8.0), 10 mM EDTA and 20 mM NaCl (pH 8.0)). The cells were collected by centrifugation, and suspended again in 5 ml of the TEN solution containing 5 mg/ml of lysozyme and 10 μg/ml of RNase A. The suspension was maintained at 37° C. for 30 minutes, and then proteinase K and sodium laurylsulfate were added thereto to final concentrations of 10 μg/ml and 0.5% (wt/vol), respectively.
The suspension was maintained at 70° C. for 2 hours, and then an equal amount of a saturated solution of phenol (phenol solution saturated with 10 mM Tris-HCl (pH 8.0)) was added and mixed. The suspension was centrifuged, and the supernatant was collected. An equal amount of phenol/chloroform solution (phenol:chloroform:isoamyl alcohol=25:24:1) was added and mixed, and the mixture was centrifuged. The supernatant was collected, and an equal amount of chloroform solution (chloroform:isoamyl alcohol=24:1) was added thereto to repeat the same extraction procedure. To the supernatant, a 1/10 volume of 3 M sodium acetate (pH 4.8) and 2.5-fold volume of ethanol were added to precipitate chromosome DNA. The precipitates were collected by centrifugation, washed with 70% ethanol, dried under reduced pressure, and dissolved in a suitable amount of TE solution (10 mM Tris-HCl, 1 mM EDTA (pH 8.0)).
(2) Preparation of Gene Library
A 50 μl portion of the chromosome DNA (1 μg/μl) obtained in the above (1), 20 μl of H buffer (500 mM Tris-HCl, 100 mM MgCl2, 10 mM dithiothreitol, 1000 mM NaCl (pH 7.5)) and 8 units of a restriction enzyme Sau3AI (Takara Shuzo) were allowed to react at 37° C. for 10 minutes in a total volume of 200 μl, and then 200 μl of the phenol/chloroform solution was added and mixed to stop the reaction. The reaction mixture was centrifuged, and the upper layer was collected and separated on a 0.8% agarose gel. DNA corresponding to 2 to 5 kilobase pair (henceforth abbreviated as “kbp”) was collected by using ConcertTM Rapid Gel Extraction System (DNA collecting kit, GIBCO BRL Co.). In this way, 50 μl of a solution of DNA with fractionated size was obtained.
On the other hand, 2.5 μg of plasmid pUC118 (Takara Shuzo), 2 μl of K buffer (200 mM Tris-HCl, 100 mM MgCl2, 10 mM dithiothreitol, 1000 mM KCl (pH 8.5)) and 10 units of restriction enzyme BamHI (Takara Shuzo) were allowed to react at 37° C. for 2 hours in a total volume of 20 μl, then 20 units of calf small intestine alkaline phosphatase (Takara Shuzo) was added and mixed, and the mixture was allowed to react for further 30 minutes. The reaction mixture was mixed with an equal amount of the phenol/chloroform solution, and the mixture was centrifuged. The supernatant was collected, and an equal amount of the chloroform solution was added thereto to repeat a similar extraction procedure. To the supernatant, a 1/10 volume of 3 M sodium acetate (pH 4.8) and 2.5-fold volume of ethanol were added to precipitate DNA. The DNA was collected by centrifugation, washed with 70% ethanol, dried under reduced pressure, and dissolved in a suitable amount of TE solution.
A Sau3AI digestion product of the chromosome DNA prepared as described above and a BamHI digestion product of pUC118 were ligated by using a Ligation Kit ver. 2 (Takara Shuzo). To the reaction mixture, a 1/10 volume of 3 M sodium acetate (pH 4.8) and 2.5-fold volume of ethanol were added to precipitate DNA. The DNA was collected by centrifugation, washed with 70% ethanol, dried under reduced pressure, and dissolved in TE solution (Ligase solution A).
In the same manner as in the above procedure, fragments obtained by partial digestion of the chromosome DNA with a restriction enzyme AluI (Takara Shuzo) and a SmaI digestion product of plasmid pSTV29 (Takara Shuzo) were ligated (Ligase solution B).
One platinum loop of E. coli JM109 was inoculated to 5 ml of L medium in a test tube, and cultured at 37° C. overnight with shaking. The obtained culture broth was inoculated to 50 ml of L medium in a 500 ml-volume Sakaguchi flask in an amount of 1%, cultured at 37° C. until OD660 of the culture became 0.5 to 0.6, and cooled on ice for 15 minutes. Then, the cells were harvested by centrifugation at 4° C. The cells were suspended in 50 ml of ice-cooled water and centrifuged to wash the cells. This operation was repeated once again, and the cells were suspended in 50 ml of ice-cooled 10% glycerol solution, and centrifuged to wash the cells. The cells were suspended in 10% glycerol solution of the same volume as the cells, and divided into 50 μl aliquots. To the cells in the 50 μl volume, 1 μl of Ligase solution A or Ligase solution B prepared above was added. Then, the mixture was put into a special cuvette (0.1 cm width, preliminarily ice-cooled) for an electroporation apparatus of BioRad.
The setting of the apparatus was 1.8 kV and 25 μF, and the setting of pulse controller was 200 ohms. The cuvette was mounted on the apparatus and pulses were applied thereto. Immediately after the application of pulse, 1 ml of ice-cooled SOC medium was added thereto, and the mixture was transferred into a sterilized test tube, and cultured at 37° C. for 1 hour with shaking. Each cell culture broth was spread onto L agar medium containing an antibiotic (100 μg/ml of ampicillin when Ligase solution A was used, or 20 μg/ml of chloramphenicol when Ligase solution B was used), and incubated at 37° C. overnight. The colonies emerged on each agar medium were scraped, inoculated to 50 ml of L medium containing respective antibiotic in a 500 ml-volume Sakaguchi flask, and cultured at 37° C. for 2 hours with shaking. Plasmid DNA was extracted from each culture broth by the alkali SDS method to form Gene library solution A and Gene library solution B, respectively.
Example 7
Cloning of Lysine Biosynthesis Gene of Methylophilus methylotrophus AS1 Strain
(1) Cloning of Gene Coding for Aspartokinase (AK)
E. coli GT3 deficient in the three genes coding for AK (thrA, metLM and lysC) was transformed with Gene library solution B by the same electroporation procedure as mentioned above. SOC medium containing 20 μg/ml of diaminopimelic acid was added to the transformation solution, and cultured at 37° C. with shaking. Then, the culture broth was spread onto L medium containing 20 μg/ml of diaminopimelic acid and 20 μg/ml of chloramphenicol to obtain emerged colonies. This was replicated as a master plate to M9 agar medium containing 20 μg/ml of chloramphenicol, and the replicate was incubated at 37° C. for 2 to 3 days. The host could not grow in M9 minimal medium that did not contain diaminopimelic acid since it did not have AK activity. In contrast, it was expected that the transformant strain that contained the gene coding for AK derived from Methylophilus methylotrophus could grow in M9 minimal medium because of the function of the gene.
Two transformants out of about 3000 transformants formed colonies on M9 medium. Plasmids were extracted from the colonies emerged on M9 medium and analyzed. As a result, the presence of an inserted fragment on the plasmids was confirmed. The plasmids were designated as pMMASK-1 and pMMASK-2, respectively. By using these plasmids, E. coli GT3 was transformed again. The obtained transformants could grow on M9 minimal medium. Further, the transformant which contained each of these plasmids was cultured overnight in L medium containing 20 μg/ml of chloramphenicol, and the cells were collected by centrifugation of the culture broth. Cell-free extracts were prepared by sonicating the cells, and AK activity was measured according to the method of Miyajima et al. (Journal of Biochemistry (Tokyo), vol. 63, 139–148 (1968)) (FIG. 3: pMMASK-1, pMMASK-2). In addition, a GT3 strain harboring the vector pSTV29 was similarly cultured in L medium containing 20 μg/ml of diaminopimelic acid and 20 μg/ml of chloramphenicol, and AK activity was measured (FIG. 3: Vector). As a result, increase in AK activity was observed in two of the clones containing the inserted fragments compared with the transformant harboring only the vector. Therefore, it was confirmed that the gene that could be cloned on pSTV29 was a gene coding for AK derived from Methylophilus methylotrophus. This gene was designated as ask.
The DNA nucleotide sequence of the ask gene was determined by the dideoxy method. It was found that pMMASK-1 and pMMASK-2 contained a common fragment. The nucleotide sequence of the DNA fragment containing the ask gene derived from Methylophilus methylotrophus is shown in SEQ ID NO: 5. An amino acid sequence that can be encoded by the nucleotide sequence is shown in SEQ ID NOS: 5 and 6.
(2) Cloning of Gene Coding for Aspartic Acid Semialdehyde Dehydrogenase (ASD)
E. coli Hfr3000 U482 (CGSC 5081 strain) deficient in the asd gene was transformed by electroporation using Gene library solution B in the same manner as described above. To the transformation solution, SOC medium containing 20 μg/ml of diaminopimelic acid was added and the mixture was cultured at 37° C. with shaking. The cells were harvested by centrifugation. The cells were washed by suspending them in L medium and centrifuging the suspension. The same washing operation was repeated once again, and the cells were suspended in L medium. Then, the suspension was spread onto L agar medium containing 20 μg/ml of chloramphenicol, and incubated overnight at 37° C. The host showed extremely slow growth in L medium not containing diaminopimelic acid since it was deficient in the asd gene. In contrast, it was expected that normal growth would be observed for a transformant strain which contained the gene coding for ASD derived from Methylophilus methylotrophus even in L medium because of the function of the gene. Further, the host E. coli could not grow in M9 minimal medium, but a transformant strain that contained the gene coding for ASD derived from Methylophilus methylotrophus was expected to be able to grow in M9 minimal medium because of the function of the gene. Therefore, colonies of transformants that normally grew on L medium were picked up, streaked and cultured on M9 agar medium. As a result, growth was observed. Thus, it was confirmed that the gene coding for ASD functioned in these transformant strains as expected.
Plasmids were extracted from the three transformant strains emerged on M9 medium, and the presence of an inserted fragment in the plasmids was confirmed. The plasmids were designated as pMMASD-1, pMMASD-2 and pMMASD-3, respectively. When the E. coli Hfr3000 U482 was transformed again by using these plasmids, each transformant grew in M9 minimal medium. Further, each transformant was cultured overnight in L medium containing 20 μg/ml of chloramphenicol, and the cells were collected by centrifugation of the culture broth. The cells were sonicated to prepare a crude enzyme solution, and ASD activity was measured according to the method of Boy et al. (Journal of Bacteriology, vol. 112 (1), 84–92 (1972)) (FIG. 4: pMMASD-1, pMMASD-2, pMMASD-3). In addition, the host harboring the vector was similarly cultured in L medium containing 20 μg/ml of diaminopimelic acid and 20 μg/ml of chloramphenicol, and ASD activity was measured as a control experiment (FIG. 4: Vector). As a result, the enzymatic activity could not be detected for the transformant harboring only the vector, whereas the ASD activity could be detected in three of the clones having an insert fragment. Therefore, it was confirmed that the obtained gene was a gene coding for ASD derived from Methylophilus methylotrophus (designated as asd).
The DNA nucleotide sequence of the asd gene was determined by the dideoxy method. It was found that all of the three obtained clones contained a common fragment. The nucleotide sequence of the DNA fragment containing the asd gene derived from Methylophilus methylotrophus is shown in SEQ ID NO: 7. An amino acid sequence that can be encoded by the nucleotide sequence is shown in SEQ ID NOS: 7 and 8.
(3) Cloning of Gene Coding for Dihydrodipicolinate Synthase (DDPS)
E. coli AT997 (CGSC 4547 strain) deficient in the dapA gene was transformed by the same electroporation procedure using Gene library solution A. To the transformation solution, SOC medium containing 20 μg/ml of diaminopimelic acid was added, and the mixture was cultured at 37° C. with shaking. Then, the culture broth was spread onto L medium containing 20 μg/ml of diaminopimelic acid and 100 μg/ml of ampicillin to obtain emerged colonies. This was replicated as a master plate to M9 minimal agar medium containing 100 μg/ml of ampicillin, and the replicate was incubated at 37° C. for 2 to 3 days. The host could not grow in M9 minimal medium that did not contain diaminopimelic acid since it was deficient in dapA gene. In contrast, it was expected that a transformant strain that contained the gene coding for DDPS derived from Methylophilus methylotrophus could grow in M9 minimal medium because of the function of that gene.
Plasmids were extracted from the colonies of two strains emerged on M9 medium, and analyzed. As a result, the presence of an inserted fragment in the plasmids was confirmed. The plasmids were designated as pMMDAPA-1 and pMMDAPA-2, respectively. When E. coli AT997 was transformed again by using these plasmids, each transformant was grown in M9 minimal medium. Further, each transformant containing each plasmid was cultured overnight in L medium containing 100 μg/ml of ampicillin, and the cells were collected by centrifugation of the culture both. The cells were sonicated to prepare a cell extract, and DDPS activity was measured according to the method of Yugari et al. (Journal of Biological Chemistry, vol. 240, and p. 4710 (1965)) (FIG. 5: pMMDAPA-1, pMMDAPA-2). In addition the host harboring the vector was similarly cultured in L medium containing 20 μg/ml of diaminopimelic acid and 100 μg/ml of ampicillin, and DDPS activity was measured as a control experiment (FIG. 5: Vector). As a result, the enzymatic activity could not be detected for the transformant harboring only the vector, whereas the DDPS activity could be detected in each of the transformants harboring the plasmids having the insert fragment. Therefore, it was confirmed that the obtained gene was a gene coding for DDPS derived from Methylophilus methylotrophus (designated as dapA).
The DNA nucleotide sequence of the dapA gene was determined by the dideoxy method. It was found that two of the inserted fragments contained a common fragment. The nucleotide sequence of the DNA fragment containing the dapA gene derived from Methylophilus methylotrophus is shown in SEQ ID NO: 9. An amino acid sequence that can be encoded by the nucleotide sequence is shown in SEQ ID NOS: 9 and 10.
(4) Cloning of Gene Coding for Dihydrodipicolinate Reductase (DDPR)
E. coli AT999 (CGSC 4549 strain) deficient in the dapB gene was transformed by the same electroporation procedure as described above using Gene library solution A. To the transformation solution, SOC medium containing 20 μg/ml of diaminopimelic acid was added, and the mixture was cultured at 37° C. with shaking. Then, the cells were harvested by centrifugation. The cells were washed by suspending them in L medium and centrifuging the suspension. The same washing operation was repeated once again, and the cells were suspended in L medium. Then, the suspension was spread onto L agar medium containing 100 μg/ml of ampicillin, and incubated overnight at 37° C. The host showed extremely slow growth in L medium not containing diaminopimelic acid since it was deficient in the dapB gene. In contrast, it was expected that normal growth could be observed for a transformant strain that contained the gene coding for DDPR derived from Methylophilus methylotrophus even in L medium because of the function of the gene. Further, the host E. coli could not grow in M9 minimal medium, but it was expected that a transformant strain which contained the gene coding for DDPR derived from Methylophilus methylotrophus could grow in M9 minimal medium because of the function of the gene.
Therefore, a colony of transformant that normally grew on L medium was streaked and cultured on M9 agar medium. Then, growth was also observed on M9 medium. Thus, it was confirmed that the gene coding for DDPR functioned in the transformant strain. A plasmid was extracted from the colony emerged on M9 medium, and the presence of an inserted fragment in the plasmid was confirmed. When E. coli AT999 was transformed again by using the plasmid (pMMDAPB), the transformant grew in M9 minimal medium. Further, the transformant containing the plasmid was cultured overnight in L medium, and the cells were collected by centrifugation of the culture broth. The cells were sonicated to prepare a cell extract, and DDPR activity was measured according to the method of Tamir et al. (Journal of Biological Chemistry, vol. 249, p. 3034 (1974)) (FIG. 6: pMMDAPB). In addition, the host harboring the vector was similarly cultured in L medium containing 20 μg/ml diaminopimelic acid and 100 μg/ml of ampicillin, and DDPR activity was measured as a control experiment (FIG. 6: Vector). As a result, the enzymatic activity could not be detected for the transformant harboring only the vector, whereas the DDPR activity could be detected for the transformant harboring pMMDAPB. Therefore, it was confirmed that the obtained gene was a gene coding for DDPR derived from Methylophilus methylotrophus (designated as dapB).
The DNA nucleotide sequence of the dapB gene was determined by the dideoxy method. The nucleotide sequence of the DNA fragment containing the dapB gene derived from Methylophilus methylotrophus is shown in SEQ ID NO: 11. An amino acid sequence that can be encoded by the nucleotide sequence is shown in SEQ ID NOS: 11 and 12.
(5) Cloning of Gene Coding for Diaminopimelate Decarboxylase (DPDC)
E. coli AT2453 (CGSC 4505 strain) deficient in the lysA gene was transformed by the same electroporation procedure as described above using Gene library solution A. The transformation solution, SOC medium was added, and the mixture was cultured at 37° C. with shaking. The cells were harvested by centrifugation. The cells were washed by suspending them in 5 ml of sterilized water and centrifuging the suspension. The same washing operation was repeated once again, and the cells were suspended in 500 μl of sterilized water. Then, the suspension was spread onto M9 minimal agar medium containing 20 μg/ml of chloramphenicol, and incubated at 37° C. for 2 to 3 days. The host could not grow in M9 minimal medium not containing lysine since it was deficient in the lysA gene. In contrast, it was expected that a transformant strain that contained the gene coding for DPDC derived from Methylophilus methylotrophus could grow in M9 minimal medium because of the function of the gene.
Therefore, plasmids were extracted from the three transformant strains emerged on M9 medium, and analyzed. As a result, the presence of an inserted fragment in the plasmids was confirmed. The plasmids were designated as pMMLYSA-1, pMMLYSA-2 and pMMLYSA-3, respectively. When E. coli AT2453 was transformed again by using each of these plasmids, each transformant grew in M9 minimal medium. Further, each transformant containing each plasmid was cultured overnight in L medium containing 20 μg/ml of chloramphenicol, and the cells were collected by centrifugation of the culture broth. The cells were sonicated to prepare a cell extract, and DPDC activity was measured according to the method of Cremer et al. (Journal of General Microbiology, vol. 134, 3221–3229 (1988)) (FIG. 7: pMMLYSA-1, pMMLYSA-2, pMMLYSA-3). In addition, the host harboring the vector was similarly cultured in L medium containing 20 μg/ml of chloramphenicol, and DPDC activity was measured as a control experiment (FIG. 7: Vector). As a result, the enzymatic activity could not be detected for the transformant harboring only the vector, whereas the DPDC activity could be detected in three of the clones having an insert fragment. Therefore, it was confirmed that the obtained gene was a gene coding for DPDC derived from Methylophilus methylotrophus (designated as lysA).
The DNA nucleotide sequence of the lysA gene was determined by the dideoxy method. It was found that all of the three inserted fragments contained a common DNA fragment. The nucleotide sequence of the DNA fragment containing the lysA gene derived from Methylophilus methylotrophus is shown in SEQ ID NO: 13. An amino acid sequence that can be encoded by the nucleotide sequence is shown in SEQ ID NOS: 13 and 14.
INDUSTRIAL APPLICABILITY
According to the present invention, there are provided a Methylophilus bacterium having L-amino acid-producing ability, a method for producing an L-amino acid using the Methylophilus bacterium, and Methylophilus bacterial cells with increased content of an L-amino acid. By the method of the present invention, it is enabled to produce an L-amino acid using methanol as a raw material. Moreover, novel L-lysine biosynthesis enzyme genes derived from Methylophilus bacteria are provided by the present invention.

## Claims

1. An isolated strain of Methylophilus methylotrophus having L-lysine-producing ability, wherein dihydrodipicolinate synthase activity is enhanced as compared to a wild-type Methylophilus methylotrophus strain, and wherein said dihydrodipicolinate synthase is selected from the group consisting of:
a) a protein encoded by a DNA comprising nucleotides 1268 to 2155 of SEQ ID NO:9; and
b) a protein having dihydrodipicolinate synthase activity and encoded by a DNA comprising nucleotide numbers 1268 to 2155 of SEQ ID NO:9, except that substitution, deletion, or addition of one to 10 amino acids is present in the amino acid sequence of said protein,
and wherein said activity is enhanced by a method selected from the group consisting of:
i) increasing the copy number of said DNA in said strain,
ii) placing multiple copies of said DNA on the chromosome of said strain, and

iii) replacing a native promoter with a stronger promoter upstream of said DNA.

2. An isolated strain of Methylophilus methylotrophus having L-lysine-producing ability, wherein dihydrodipicolinate synthase activity and aspartokinase activity are enhanced as compared to a wild-type Methylophilus methylotrophus strain, and wherein said dihydrodipicolinate synthase is selected from the group consisting of:
a) a protein encoded by a DNA comprising nucleotides 1268 to 2155 of SEQ ID NO:9; and
b) a protein having dihydrodipicolinate synthase activity and encoded by a DNA comprising nucleotides 1268 to 2155 of SEQ ID NO:9, except that substitution, deletion, or addition of one to 10 amino acids is present in the amino acid sequence of said protein,
and wherein said aspartokinase is selected from the group consisting of:
a) a protein encoded by a DNA comprising nucleotides 510 to 1736 of SEQ ID NO:5; and
b) a protein having aspartokinase activity and encoded by a DNA comprising nucleotides 510 to 1736 of SEQ ID NO:5, except that substitution, deletion, addition, or inversion of one to 10 amino acids is present in the amino acid sequence of said protein,
and wherein said activity is enhanced by a method selected from the group consisting of:
i) increasing the copy number of said DNA in said strain,
ii) placing multiple copies of said DNA on the chromosome of said strain, and

iii) replacing a native promoter with a stronger promoter upstream of said DNA.

3. An isolated strain of Methylophilus methylotrophus having L-amino acid-producing ability, wherein aspartokinase activity is enhanced as compared to wild-type Methylophilus methylotrophus strain, and wherein said aspartokinase is selected from the group consisting of:
a) a protein encoded by a DNA comprising nucleotides 510 to 1736 of SEQ ID NO:5; and
b) a protein having aspartokinase activity and encoded by a DNA comprising nucleotides 510 to 1736 of SEQ ID NO:5, except that substitution, deletion, or addition of one to 10 amino acids is present in the amino acid sequence of said protein
and wherein said activity is enhanced by a method selected from the group consisting of:
i) increasing the copy number of said DNA in said strain,
ii) placing multiple copies of said DNA on the chromosome of said strain, and

iii) replacing a native promoter with a stronger promoter upstream of said DNA.

4. The isolated strain according to claim 3, wherein the L-amino acid is L-lysine.

5. The isolated strain according to claim 2, wherein an activity or activities of one, two, or three enzymes selected from the group consisting of aspartic acid semialdehyde dehydrogenase, dihydrodipicolinate reductase, and diaminopimelate decarboxylase is/are enhanced as compared to a wild-type Methylophilus methylotrophus strain by a method selected from the group consisting of:
i) increasing the copy number(s) of a DNA(s) encoding said one, two, or three enzyme(s) in said strain,
ii) placing multiple copies of said DNA(s) on the chromosome of said strain, and
iii) replacing a native promoter with a stronger promoter upstream of said DNA(s).

6. The isolated strain according to claim 2, wherein the dihydrodipicolinate synthase activity and the aspartokinase activity are enhanced as compared to a wild-type Methylophilus methylotrophus strain by transformation with a DNA coding for said dihydrodipicolinate synthase and a DNA coding for said aspartokinase.

7. The isolated strain according to claim 3, wherein activities of homoserine dehydrogenase, homoserine kinase and threonine synthase are enhanced as compared to wild-type Methylophilus methylotrophus strain by a method selected from the group consisting of:
i) increasing the copy numbers of DNAs encoding homoserine dehydrogenase, homoserine kinase, and threonine synthase in said strain,
ii) placing multiple copies of said DNAs on the chromosome of said strain, and
iii) replacing a native promoter with a stronger promoter upstream of said DNAs, and wherein said isolated strain has L-threonine-producing ability.

8. A method for producing L-lysine, which comprises culturing said strain as defined in claim 1 in a medium, accumulating said L-lysine in said medium, and collecting the L-lysine from said medium.

9. The method according to claim 8, wherein the medium contains methanol as a main carbon source.

10. The isolated strain according to claim 1, wherein an activity or activities of one, two, or three of enzymes selected from the group consisting of aspartic acid semialdehyde dehydrogenase, dihydrodipicolinate reductase and diaminopimelate decarboxylase is/are enhanced as compared to a wild-type Methylophilus methylotrophus strain by a method selected from the group consisting of:
i) increasing the copy number(s) of a DNA(s) encoding said one, two, or three enzyme(s) in said strain,
ii) placing multiple copies of said DNA(s) on the chromosome of said strain, and
iii) replacing a native promoter with a stronger promoter upstream of said DNA(s).

11. The isolated strain according to claim 4, wherein an activity or activities of one, two, or three of enzymes selected from the group consisting of aspartic acid semialdehyde dehydrogenase, dihydrodipicolinate reductase and diaminopimelate decarboxylase is/are enhanced as compared to a wild-type Methylophilus methylotrophus strain by a method selected from the group consisting of:
i) increasing the copy number(s) of a DNA(s) encoding said one, two, or three enzyme(s) in said strain,
ii) placing multiple copies of said DNA(s) on the chromosome of said strain, and
iii) replacing a native promoter with a stronger promoter upstream of said DNA(s).

12. A method for producing L-lysine, which comprises culturing said strain as defined in claim 2 in a medium, accumulating said L-lysine in said medium, and collecting the L-lysine from said medium.

13. The method according to claim 12, wherein the medium contains methanol as a main carbon source.

14. A method for producing an L-amino acid, which comprises culturing said strain as defined in claim 3 in a medium, accumulating said L-amino acid in said medium, and collecting the L-amino acid from said medium.

15. The method according to claim 14, wherein the medium contains methanol as a main carbon source.

16. A method for producing L-lysine, which comprises culturing said strain as defined in claim 5 in a medium, accumulating L-lysine in said medium, and collecting L-lysine from said medium.

17. A method for producing L-lysine, which comprises culturing said strain as defined in claim 6 in a medium, accumulating L-lysine in said medium, and collecting L-lysine from said medium.

18. A method for producing L-lysine, which comprises culturing said strain as defined in claim 10 in a medium, accumulating L-lysine in said medium, and collecting L-lysine from said medium.

19. A method for producing L-lysine, which comprises culturing said strain as defined in claim 11 in a medium, accumulating L-lysine in said medium, and collecting L-lysine from said medium.

20. A method for producing L-threonine, which comprises culturing said strain as defined in claim 7 in a medium, accumulating L-threonine in said medium, and collecting L-threonine from said medium.

21. An isolated DNA which codes for a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence of SEQ ID NO: 6, and
(B) a protein comprising the amino acid sequence of SEQ ID NO:6 except that substitution, deletion, insertion, or addition of one to 10 amino acids in said amino acid sequence is present, and wherein said protein has aspartokinase activity.

22. The DNA according to claim 21, wherein said DNA is selected from the group consisting of:
(a) a DNA comprising the nucleotides 510 to 1736 of SEQ ID NO:5; and
(b) a DNA having the nucleotides 510 to 1736 of SEQ ID NO:5, except that substitution, deletion, or addition of one to 10 amino acids is present in the amino acid sequence of a protein encoded by said DNA, and wherein said DNA codes for a protein having aspartokinase activity.

23. An isolated DNA which codes for a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence of SEQ ID NO:10, and
(B) a protein comprising the amino acid sequence of SEQ ID NO:10 except that substitution, deletion, insertion, or addition of one to 10 amino acids in said amino acid sequence is present, and wherein said protein has dihydrodipicolinate synthase activity.

24. The DNA according to claim 23, wherein said DNA is selected from the group consisting of:
(a) a DNA comprising the nucleotides 1268 to 2155 of SEQ ID NO:9; and
(b) a DNA having the nucleotides 1268 to 2155 of SEQ ID NO:9 except that substitution, deletion, or addition of one to 10 amino acids is present in the amino acid sequence of a protein encoded by said DNA, and wherein said DNA codes for a protein having dihydrodipicolinate synthase activity.