# Patent

## Title
Process for producing dipeptides

## Abstract

The present invention provides a process for producing a dipeptide which comprises culturing in a medium a microorganism which has the ability to produce a protein having the activity to form the dipeptide from one or more kinds of amino acids and which has the ability to produce at least one of said one or more kinds of amino acids, allowing the dipeptide to form and accumulate in the medium, and recovering the dipeptide from the medium.

## Background
This application is a division of application Ser. No. 11/165,211 filed Jun. 24, 2005, which in turn claims benefit of JP 2004-189011, filed Jun. 25, 2004, the entire contents of both of which are incorporated herein by reference.


BACKGROUND OF THE INVENTION
The present invention relates to a process for producing a dipeptide which comprises culturing in a medium a microorganism which has the ability to produce a protein having the activity to form the dipeptide from one or more kinds of amino acids and which has the ability to produce at least one of said one or more kinds of amino acids, allowing the dipeptide to form and accumulate in the medium, and recovering the dipeptide from the medium.
At present, many of the amino acids are produced by the so-called fermentation method (Hiroshi Soda, et al., Amino Acid Fermentation, Gakkai Shuppan Center (1986) and Biotechnology 2nd ed., Vol. 6, Products of Primary Metabolism, VCH Verlagsgesellschaft mbH, Weinheim (1996)). The fermentation method as used herein refers to a method in which a microorganism is cultured in a medium comprising inexpensive substances such as glucose, acetic acid, methanol, ammonia, ammonium sulfate and corn steep liquor to obtain a desired amino acid by utilizing the metabolic activity of the microorganism. The fermentation method is excellent as a method for producing amino acids from inexpensive materials with light burdens on the environment.
As for the method for large-scale peptide synthesis, chemical synthesis methods (liquid phase method and solid phase method), enzymatic synthesis methods and biological synthesis methods utilizing recombinant DNA techniques are known. Currently, the enzymatic synthesis methods and biological synthesis methods are employed for the synthesis of long-chain peptides longer than 50 residues, and the chemical synthesis methods and enzymatic synthesis methods are mainly employed for the synthesis of dipeptides.
In the synthesis of dipeptides by the chemical synthesis methods, operations such as introduction and removal of protective groups for functional groups are necessary, and racemates are also formed. The chemical synthesis methods are thus considered to be disadvantageous in respect of cost and efficiency. They are unfavorable also from the viewpoint of environmental hygiene because of the use of large amounts of organic solvents and the like.
As to the synthesis of dipeptides by the enzymatic methods, the following methods are known: a method utilizing reverse reaction of protease (J. Biol. Chem., 119, 707-720 (1937)); methods utilizing thermostable aminoacyl t-RNA synthetase (Japanese Published Unexamined Patent Application No. 146539/83, Japanese Published Unexamined Patent Application No. 209991/83, Japanese Published Unexamined Patent Application No. 209992/83 and Japanese Published Unexamined Patent Application No. 106298/84); a method utilizing reverse reaction of proline iminopeptidase (WO03/010307 pamphlet); and methods utilizing non-ribosomal peptide synthetase (hereinafter referred to as NRPS) (Chem. Biol., 7, 373-384 (2000), FEBS Lett., 498, 42-45 (2001), U.S. Pat. No. 5,795,738 and U.S. Pat. No. 5,652,116).
However, the method utilizing reverse reaction of protease requires introduction and removal of protective groups for functional groups of amino acids used as substrates, which causes difficulties in raising the efficiency of peptide-forming reaction and in preventing peptidolytic reaction. The methods utilizing thermostable aminoacyl t-RNA synthetase have the defects that the expression of the enzyme and the prevention of side reactions forming by-products other than the desired products are difficult. The method utilizing proline iminopeptidase requires amidation of one of the amino acids used as substrates. The methods utilizing NRPS are inefficient in that the supply of coenzyme 4′-phosphopantetheine is necessary.
In addition to the above defects, these methods are disadvantageous in respect of production cost because all of them use amino acids or derivatives thereof as substrates.
On the other hand, there exist a group of peptide synthetases that have enzyme molecular weight lower than that of NRPS and do not require coenzyme 4′-phosphopantetheine; for example, γ-glutamylcysteine synthetase, glutathione synthetase, D-alanyl-D-alanine (D-Ala-D-Ala) ligase, and poly-γ-glutamate synthetase. Most of these enzymes utilize D-amino acids as substrates or catalyze peptide bond formation at the γ-carboxyl group. Because of such properties, they can not be used for the synthesis of dipeptides by peptide bond formation at the α-carboxyl group of L-amino acid.
It is reported that a protein bearing no similarity to NRPS (albC gene product) is responsible for the synthesis of the cyclo(L-phenylalanyl-L-leucine) structure in Streptomyces noursei ATCC 11455 known as a strain producing the antibiotic albonoursin and that albonoursin was detected when cyclo dipeptide oxidase was made to act on the culture broth of Escherichia coli and Streptomyces lividans into which the albC gene was introduced (Chemistry & Biol., 9, 1355-1364 (2002)). However, there is no report that the albC gene product forms a straight-chain dipeptide.
The only known example of an enzyme capable of dipeptide synthesis by the activity to form a peptide bond at the α-carboxyl group of L-amino acid is bacilysin (dipeptide antibiotic derived from a microorganism belonging to the genus Bacillus) synthetase. Bacilysin synthetase is known to have the activity to synthesize bacilysin [L-alanyl-L-anticapsin (L-Ala-L-anticapsin)] and L-alanyl-L-alanine (L-Ala-L-Ala), but there is no information about its activity to synthesize other dipeptides (J. Ind. Microbiol., 2, 201-208 (1987) and Enzyme. Microbial. Technol., 29, 400-406 (2001)).
As for the bacilysin biosynthetase genes in Bacillus subtilis 168 whose entire genome information has been clarified (Nature, 390, 249-256 (1997)), it is known that the productivity of bacilysin is increased by amplification of bacilysin operons containing ORFs ywfA-F (WO00/03009 pamphlet). However, it is not known whether an ORF encoding a protein having the activity to ligate two or more amino acids by peptide bond is contained in these ORFs, and if contained, which ORF encodes the protein.
That is, no method has so far been known for producing a dipeptide consisting of one or more kinds of amino acids by fermentation.
An object of the present invention is to provide a process for producing a dipeptide which comprises culturing in a medium a microorganism which has the ability to produce a protein having the activity to form the dipeptide from one or more kinds of amino acids and which has the ability to produce at least one of said one or more kinds of amino acids, allowing the dipeptide to form and accumulate in the medium, and recovering the dipeptide from the medium.
SUMMARY OF THE INVENTION
The present invention relates to the following (1) to (15).

    (1) A process for producing a dipeptide, which comprises: culturing in a medium a microorganism which has the ability to produce a protein having the activity to form the dipeptide from one or more kinds of amino acids and which has the ability to produce at least one of said one or more kinds of amino acids; allowing the dipeptide to form and accumulate in the medium; and recovering the dipeptide from the medium.
    (2) The process according to the above (1), wherein the protein having the activity to form the dipeptide from one or more kinds of amino acids is a protein selected from the group consisting of the following [1] to [11]:
    
        [1] a protein having the amino acid sequence shown in any of SEQ ID NOS: 1 to 8;
        [2] a protein consisting of an amino acid sequence wherein one or more amino acid residues are deleted, substituted or added in the amino acid sequence shown in any of SEQ ID NOS: 1 to 8 and having the activity to form the dipeptide from one or more kinds of amino acids;
        [3] a protein consisting of an amino acid sequence which has 65% or more homology to the amino acid sequence shown in any of SEQ ID NOS: 1 to 8 and having the activity to form the dipeptide from one or more kinds of amino acids;
        [4] a protein having an amino acid sequence which has 80% or more homology to the amino acid sequence shown in SEQ ID NO: 17 and having the activity to form the dipeptide from one or more kinds of amino acids;
        [5] a protein having the amino acid sequence shown in SEQ ID NO: 37 or 38;
        [6] a protein consisting of an amino acid sequence wherein one or more amino acid residues are deleted, substituted or added in the amino acid sequence shown in SEQ ID NO: 37 or 38 and having the activity to form the dipeptide from one or more kinds of amino acids;
        [7] a protein consisting of an amino acid sequence which has 65% or more homology to the amino acid sequence shown in SEQ ID NO: 37 or 38 and having the activity to form the dipeptide from one or more kinds of amino acids;
        [8] a protein having non-ribosomal peptide synthetase (hereinafter referred to as NRPS) activity;
        [9] a protein having the amino acid sequence shown in SEQ ID NO: 43;
        [10] a protein consisting of an amino acid sequence wherein one or more amino acid residues are deleted, substituted or added in the amino acid sequence shown in SEQ ID NO: 43 and having the activity to form the dipeptide from one or more kinds of amino acids; and
        [11] a protein consisting of an amino acid sequence which has 65% or more homology to the amino acid sequence shown in SEQ ID NO: 43 and having the activity to form the dipeptide from one or more kinds of amino acids.
    
    
    (3) The process according to the above (1) or (2), wherein the protein having the activity to form the dipeptide from one or more kinds of amino acids is a protein encoded by DNA selected from the group consisting of the following [1] to [8]:
    
        [1] DNA having the nucleotide sequence shown in any of SEQ ID NOS: 9 to 16 and 36;
        [2] DNA which hybridizes with DNA having a nucleotide sequence complementary to the nucleotide sequence shown in any of SEQ ID NOS: 9 to 16 and 36 under stringent conditions and which encodes a protein having the activity to form the dipeptide from one or more kinds of amino acids;
        [3] DNA having a nucleotide sequence which has 80% or more homology to the nucleotide sequence shown in SEQ ID NO: 18 and encoding a protein having the activity to form the dipeptide from one or more kinds of amino acids;
        [4] DNA having the nucleotide sequence shown in SEQ ID NO: 39 or 40;
        [5] DNA which hybridizes with DNA having a nucleotide sequence complementary to the nucleotide sequence shown in SEQ ID NO: 39 or 40 under stringent conditions and which encodes a protein having the activity to form the dipeptide from one or more kinds of amino acids;
        [6] DNA encoding a protein having NRPS activity;
        [7] DNA having the nucleotide sequence shown in SEQ ID NO: 44; and
        [8] DNA which hybridizes with DNA having a nucleotide sequence complementary to the nucleotide sequence shown in SEQ ID NO: 44 under stringent conditions and which encodes a protein having the activity to form the dipeptide from one or more kinds of amino acids.
    
    
    (4) The process according to the above (1), wherein the microorganism which has the ability to produce a protein having the activity to form the dipeptide from one or more kinds of amino acids is a microorganism carrying a recombinant DNA comprising the DNA selected from the group consisting of [1] to [8] of the above (3).
    (5) The process according to any of the above (1) to (4), wherein the ability to produce an amino acid is acquired by a method selected from the group consisting of the following [1] to [5]:
    
        [1] a method in which at least one of the regulation of the biosynthesis of the amino acid is reduced or eliminated;
        [2] a method in which the expression of at least one of the enzymes involved in the biosynthesis of the amino acid is enhanced;
        [3] a method in which the copy number of at least one of the enzyme genes involved in the biosynthesis of the amino acid is increased;
        [4] a method in which at least one of the metabolic pathways branching from the biosynthetic pathway of the amino acid into metabolites other than the amino acid is weakened or blocked; and
        [5] a method in which a cell strain having a higher resistance to an analogue of the amino acid as compared with a wild-type strain is selected.
    
    
    (6) The process according to any of the above (1) to (5), wherein the microorganism is a microorganism belonging to the genus Escherichia, Corynebacterium, Bacillus, Serratia, Pseudomonas or Streptomyces. 
    (7) The process according to the above (6), wherein the microorganism belonging to the genus Escherichia, Corynebacterium, Bacillus, Serratia, Pseudomonas or Streptomyces is Escherichia coli, Corynebacterium glutamicum, Corynebacterium ammoniagenes, Corynebacterium lactofermentum, Corynebacterium flavum, Corynebacterium efficiens, Bacillus subtilis, Bacillus megaterium, Serratia marcescens, Pseudomonas putida, Pseudomonas aeruginosa, Streptomyces coelicolor or Streptomyces lividans. 
    (8) The process according to any of the above (1) to (5), wherein the microorganism is a microorganism in which the activities of one or more kinds of peptidases and one or more kinds of proteins having peptide-permeating/transporting activity (hereinafter referred to also as peptide-permeating/transporting proteins) are reduced or lost.
    (9) The process according to any of the above (1) to (5), wherein the microorganism is a microorganism in which the activities of three or more kinds of peptidases are reduced or lost.
    (10) The process according to the above (8) or (9), wherein the peptidase is a protein having the amino acid sequence shown in any of SEQ ID NOS: 45 to 48, or a protein having an amino acid sequence which has 80% or more homology to the amino acid sequence shown in any of SEQ ID NOS: 45 to 48 and having peptidase activity.
    (11) The process according to the above (8) or (10), wherein the peptide-permeating/transporting protein is a protein having the amino acid sequence shown in any of SEQ ID NOS: 49 to 53, or a protein having an amino acid sequence which has 80% or more homology to the amino acid sequence shown in any of SEQ ID NOS: 49 to 53 and having peptide-permeating/transporting activity.
    (12) The process according to any of the above (8) to (11), wherein the microorganism is a microorganism belonging to the genus Escherichia, Bacillus or Corynebacterium. 
    (13) The process according to the above (12), wherein the microorganism belonging to the genus Escherichia, Bacillus or Corynebacterium is Escherichia coli, Corynebacterium glutamicum, Corynebacterium ammoniagenes, Corynebacterium lactofermentum, Corynebacterium flavum, Corynebacterium efficiens, Bacillus subtilis or Bacillus megaterium. 
    (14) The process according to any of the above (1) to (13), wherein the amino acid is an amino acid selected from the group consisting of L-alanine, L-glutamine, L-glutamic acid, glycine, L-valine, L-leucine, L-isoleucine, L-proline, L-phenylalanine, L-tryptophan, L-methionine, L-serine, L-threonine, L-cysteine, L-asparagine, L-tyrosine, L-lysine, L-arginine, L-histidine, L-aspartic acid, L-α-aminobutyric acid, L-4-hydroxyproline, L-3-hydroxyproline, L-ornithine and L-citrulline.
    (15) The process according to any of the above (1) to (14), wherein the dipeptide is a dipeptide represented by formula (I):

R1-R2  (I)

     (wherein R1 and R2, which may be the same or different, each represent an amino acid selected from the group consisting of L-alanine, L-glutamine, L-glutamic acid, glycine, L-valine, L-leucine, L-isoleucine, L-proline, L-phenylalanine, L-tryptophan, L-methionine, L-serine, L-threonine, L-cysteine, L-asparagine, L-tyrosine, L-lysine, L-arginine, L-histidine, L-aspartic acid, L-α-aminobutyric acid, L-4-hydroxyproline, L-3-hydroxyproline, L-ornithine and L-citrulline.


The present invention provides a process for producing a dipeptide which comprises culturing in a medium a microorganism which has the ability to produce a protein having the activity to form the dipeptide from one or more kinds of amino acids and which has the ability to produce at least one of said one or more kinds of amino acids, allowing the dipeptide to form and accumulate in the medium, and recovering the dipeptide from the medium.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the steps for constructing plasmid pPE43.
FIG. 2 shows the steps for constructing plasmid pQE60ywfE.
FIG. 3 shows the steps for constructing pAL-nou and pAL-alb, which are plasmid vectors for the expression of proteins having the activity to synthesize a straight-chain dipeptide.
FIG. 4 shows the steps for constructing ywfE gene expression-enhanced vector pPE56.
FIG. 5 shows the steps for constructing ywfE gene and ald gene expression vector pPE86.
FIG. 6 shows the steps for constructing desensitized pheA gene expression vector pPHEA2, and feedback-resistant pheA gene and feedback-resistant aroF gene expression plasmid vector pPHEAF2.



EXPLANATION OF SYMBOLS
ywfE: ywfE gene derived from Bacillus subtilis 168
Ptrp: Tryptophan promoter gene
PT5: T5 promoter
Ampr: Ampicillin resistance gene
lacIq Lactose repressor gene
albC: albC gene or albC-analogous gene
ald: ald gene
pheAfbr: feedback-resistant pheA gene
aroFfbr: feedback-resistant aroF gene
DETAILED DESCRIPTION OF THE INVENTION
The protein having the activity to form a dipeptide from one or more kinds of amino acids used in the production process of the present invention may be any protein that has the activity to form a dipeptide wherein the same or different amino acids are linked by peptide bond from one or more kinds of amino acids. Examples of the proteins include:

    
    
        [1] a protein having the amino acid sequence shown in any of SEQ ID NOS: 1 to 8;
        [2] a protein consisting of an amino acid sequence wherein one or more amino acid residues are deleted, substituted or added in the amino acid sequence shown in any of SEQ ID NOS: 1 to 8 and having the activity to form a dipeptide from one or more kinds of amino acids;
        [3] a protein consisting of an amino acid sequence which has 65% or more homology to the amino acid sequence shown in any of SEQ ID NOS: 1 to 8 and having the activity to form a dipeptide from one or more kinds of amino acids;
        [4] a protein having an amino acid sequence which has 80% or more homology to the amino acid sequence shown in SEQ ID NO: 17 and having the activity to form a dipeptide from one or more kinds of amino acids;
        [5] a protein having the amino acid sequence shown in SEQ ID NO: 37 or 38;
        [6] a protein consisting of an amino acid sequence wherein one or more amino acid residues are deleted, substituted or added in the amino acid sequence shown in SEQ ID NO: 37 or 38 and having the activity to form a dipeptide from one or more kinds of amino acids;
        [7] a protein consisting of an amino acid sequence which has 65% or more homology to the amino acid sequence shown in SEQ ID NO: 37 or 38 and having the activity to form a dipeptide from one or more kinds of amino acids;
        [8] a protein having NRPS activity;
        [9] a protein having the amino acid sequence shown in SEQ ID NO: 43;
        [10] a protein consisting of an amino acid sequence wherein one or more amino acid residues are deleted, substituted or added in the amino acid sequence shown in SEQ ID NO: 43 and having the activity to form a dipeptide from one or more kinds of amino acids; and
        [11] a protein consisting of an amino acid sequence-which has 65% or more homology to the amino acid sequence shown in SEQ ID NO: 43 and having the activity to form a dipeptide from one or more kinds of amino acids.
    
    


In the present invention, the amino acids are those which are produced by the microorganisms used in the production process of the present invention described below, preferably L-amino acids and glycine, more preferably L-alanine, L-glutamine, L-glutamic acid, L-valine, L-leucine, L-isoleucine, L-proline, L-phenylalanine, L-tryptophan, L-methionine, L-serine, L-threonine, L-cysteine, L-asparagine, L-tyrosine, L-lysine, L-arginine, L-histidine, L-aspartic acid, L-α-aminobutyric acid, L-4-hydroxyproline, L-3-hydroxyproline, L-ornithine, L-citrulline and glycine, further preferably L-alanine, L-glutamine, L-glutamic acid, L-valine, L-leucine, L-isoleucine, L-proline, L-phenylalanine, L-tryptophan, L-methionine, L-serine, L-threonine, L-cysteine, L-asparagine, L-tyrosine, L-lysine, L-arginine, L-histidine, L-aspartic acid, L-α-aminobutyric acid and glycine.
The above protein consisting of an amino acid sequence wherein one or more amino acid residues are deleted, substituted or added and having the activity to form a dipeptide from one or more kinds of amino acids can be obtained, for example, by introducing a site-directed mutation into DNA encoding a protein consisting of the amino acid sequence shown in any of SEQ ID NOS: 1 to 8, 37, 38 and 43 by site-directed mutagenesis described in Molecular Cloning, A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press (2001) (hereinafter referred to as Molecular Cloning, Third Edition); Current Protocols in Molecular Biology, John Wiley & Sons (1987-1997) (hereinafter referred to as Current Protocols in Molecular Biology); Nucleic Acids Research, 10, 6487 (1982); Proc. Natl. Acad. Sci. USA, 79, 6409 (1982); Gene, 34, 315 (1985); Nucleic Acids Research, 13, 4431 (1985); Proc. Natl. Acad. Sci. USA, 82, 488 (1985), etc.
The number of amino acid residues which are deleted, substituted or added is not specifically limited, but is within the range where deletion, substitution or addition is possible by known methods such as the above site-directed mutagenesis. The suitable number is 1 to dozens, preferably 1 to 20, more preferably 1 to 10, further preferably 1 to 5.
The expression “one or more amino acid residues are deleted, substituted or added in any of the amino acid sequences shown in any of SEQ ID NOS: 1 to 8, 37, 38 and 43” means that the amino acid sequence may contain deletion, substitution or addition of a single or plural amino acid residues at an arbitrary position therein.
Amino acid residues that may be substituted are, for example, those which are not conserved in all of the amino acid sequences shown in SEQ ID NOS: 1 to 8, 37 and 38, or both of the amino acid sequence of a known NRPS and that shown in SEQ ID NO: 43 when the sequences are compared using known alignment software. An example of known alignment software is alignment analysis software contained in gene analysis software Genetyx (Software Development Co., Ltd.). As analysis parameters for the analysis software, default values can be used.
Deletion or addition of amino acid residues may be contained, for example, in the N-terminal region or the C-terminal region of the amino acid sequence shown in any of SEQ ID NOS: 1 to 8, 37, 38 and 43.
Deletion, substitution and addition may be simultaneously contained in one sequence, and amino acids to be substituted or added may be either natural or not. Examples of the natural amino acids are L-alanine, L-asparagine, L-aspartic acid, L-glutamine, L-glutamic acid, glycine, L-arginine, L-histidine, L-isoleucine, L-leucine, L-lysine, L-methionine, L-phenylalanine, L-proline, L-serine, L-threonine, L-tryptophan, L-tyrosine, L-valine and L-cysteine.
The following are examples of the amino acids capable of mutual substitution. The amino acids in the same group can be mutually substituted.

    Group A: leucine, isoleucine, norleucine, valine, norvaline, alanine, 2-aminobutanoic acid, methionine, O-methylserine, t-butylglycine, t-butylalanine, cyclohexylalanine
    Group B: aspartic acid, glutamic acid, isoaspartic acid, isoglutamic acid, 2-aminoadipic acid, 2-aminosuberic acid
    Group C: asparagine, glutamine
    Group D: lysine, arginine, ornithine, 2,4-diaminobutanoic acid, 2,3-diaminopropionic acid
    Group E: proline, 3-hydroxyproline, 4-hydroxyproline
    Group F: serine, threonine, homoserine
    Group G: phenylalanine, tyrosine


In order that the protein of the present invention may have the activity to form a dipeptide from one or more kinds of amino acids, it is desirable that the homology of its amino acid sequence to the amino acid sequence shown in any of SEQ ID NOS: 1 to 8, 37, 38 and 43, preferably the amino acid sequence shown in SEQ ID NO: 1, is 65% or more, preferably 75% or more, more preferably 85% or more, further preferably 90% or more, particularly preferably 95% or more, and most preferably 98% or more.
The homology among amino acid sequences and nucleotide sequences can be determined by using algorithm BLAST by Karlin and Altschul [Proc. Natl. Acad. Sci. USA, 90, 5873 (1993)] and FASTA [Methods Enzymol., 183, 63 (1990)]. On the basis of the algorithm BLAST, programs such as BLASTN and BLASTX have been developed [J. Mol. Biol., 215, 403 (1990)]. When a nucleotide sequence is analyzed by BLASTN on the basis of BLAST, the parameters, for instance, are as follows: score=100 and wordlength=12. When an amino acid sequence is analyzed by BLASTX on the basis of BLAST, the parameters, for instance, are as follows: score=50 and wordlength=3. When BLAST and Gapped BLAST programs are used, default parameters of each program are used. The specific techniques for these analyses are known.
The amino acid sequence shown in SEQ ID NO: 17 is a region conserved among the proteins having the amino acid sequences shown in SEQ ID NOS: 1 to 7 and is also a region corresponding to the consensus sequence of proteins having Ala-Ala ligase activity derived from various microorganisms.
Proteins having an amino acid sequence which has 80% or more, preferably 90% or more, further preferably 95% or more homology to the amino acid sequence shown in SEQ ID NO: 17 and having the activity to form a dipeptide from one or more kinds of amino acids are also included in the proteins produced by the microorganisms used in the production process of the present invention.
In order that the protein having an amino acid sequence which has 80% or more, preferably 90% or more, further preferably 95% or more homology to the amino acid sequence shown in SEQ ID NO: 17 may have the activity to form a dipeptide from one or more kinds of amino acids, it is desirable that the homology of its amino acid sequence to the amino acid sequence shown in any of SEQ ID NOS: 1 to 8 is at least 80% or more, usually 90% or more, and particularly 95% or more.
The homology among amino acid sequences can be determined by using BLAST or FASTA as described above.
It is possible to confirm that the proteins of the above [1] to [11] are proteins having the activity to form a dipeptide from one or more kinds of amino acids, for example, in the following manner. That is, a transformant expressing the protein is prepared by recombinant DNA techniques, the protein of the present invention is produced using the transformant, and then the protein of the present invention, one or more kinds of amino acids and ATP are allowed to be present in an aqueous medium, followed by HPLC analysis or the like to know whether a dipeptide is formed and accumulated in the aqueous medium.
The DNA used in the production process of the present invention may be any DNA encoding a protein having the activity to form a dipeptide wherein the same or different amino acids are linked by peptide bond from one or more kinds of amino acids. Examples of the DNAs include:

    
    
        [12] DNA having the nucleotide sequence shown in any of SEQ ID NOS: 9 to 16 and 36;
        [13] DNA which hybridizes with DNA having a nucleotide sequence complementary to the nucleotide sequence shown in any of SEQ ID NOS: 9 to 16 and 36 under stringent conditions and which encodes a protein having the activity to form a dipeptide from one or more kinds of amino acids;
        [14] DNA having a nucleotide sequence which has 80% or more homology to the nucleotide sequence shown in SEQ ID NO: 18 and encoding a protein having the activity to form a dipeptide from one or more kinds of amino acids;
        [15] DNA having the nucleotide sequence shown in SEQ ID NO: 39 or 40;
        [16] DNA which hybridizes with DNA having a nucleotide sequence complementary to the nucleotide sequence shown in SEQ ID NO: 39 or 40 under stringent conditions and which encodes a protein having the activity to form a dipeptide from one or more kinds of amino acids;
        [17] DNA encoding a protein having NRPS activity;
        [18] DNA having the nucleotide sequence shown in SEQ ID NO: 44; and
        [19] DNA which hybridizes with DNA having a nucleotide sequence complementary to the nucleotide sequence shown in SEQ ID NO: 44 under stringent conditions and which encodes a protein having the activity to form a dipeptide from one or more kinds of amino acids.
    
    


The above DNA capable of hybridization under stringent conditions refers to DNA which is obtained by colony hybridization, plaque hybridization, Southern blot hybridization, or the like using a part or the whole of the DNA having a nucleotide sequence complementary to the nucleotide sequence shown in any of SEQ ID NOS: 9 to 16, 36, 39, 40 and 44 as a probe. A specific example of such DNA is DNA which can be identified by performing hybridization at 65° C. in the presence of 0.7 to 1.0 mol/l, preferably 0.9 mol/l sodium chloride using a filter with colony- or plaque-derived DNA immobilized thereon, and then washing the filter at 65° C. with a 0.1 to 2-fold conc., preferably 0.1-fold conc. SSC solution (1-fold conc. SSC solution: 150 mmol/l sodium chloride and 15 mmol/l sodium citrate). Hybridization can be carried out according to the methods described in Molecular Cloning, Third Edition; Current Protocols in Molecular Biology; DNA Cloning 1: Core Techniques, A Practical Approach, Second Edition, Oxford University (1995), etc. Specifically, the hybridizable DNA includes DNA having at least 75% or more homology, preferably 85% or more homology, further preferably 90% or more homology, particularly preferably 95% or more homology to the nucleotide sequence shown in any of SEQ ID NOS: 9 to 16, 36; 39, 40 and 44 as calculated by use of BLAST or FASTA described above based on the above parameters.
The DNA samples to be subjected to hybridization include, for example, chromosomal DNAs of microorganisms belonging to the same genus, preferably the same species as those having the nucleotide sequence shown in any of SEQ ID NOS: 9 to 16, 36, 39, 40 and 44 on their chromosomal DNAs. It is possible to confirm that the DNA which hybridizes with DNA having the nucleotide sequence shown in any of SEQ ID NOS: 9 to 16, 36, 39, 40 and 44 under stringent conditions is DNA encoding a protein having the activity to form a dipeptide from one or more kinds of amino acids, for example, by producing a protein encoded by the DNA by recombinant DNA techniques and measuring the activity of the protein as described above.
(i) Preparation of DNA Used in the Production Process of the Present Invention
The DNAs used in the production process of the present invention can be obtained by:

    (a) Southern hybridization of a chromosomal DNA library from a microorganism, preferably a microorganism belonging to the genus Bacillus, using a probe designed based on the nucleotide sequence shown in any of SEQ ID NOS: 9 to 16 and 36, or by PCR [PCR Protocols, Academic Press (1990)] using primer DNAs designed based on the nucleotide sequence shown in any of SEQ ID NOS: 9 to 16 and 36 and, as a template, the chromosomal DNA of a microorganism, preferably a microorganism belonging to the genus Bacillus; 
    (b) Southern hybridization of a chromosomal DNA library from a microorganism, preferably a microorganism belonging to the genus Streptomyces, using a probe designed based on the nucleotide sequence shown in SEQ ID NO: 39 or 40, or by PCR using primer DNAs designed based on the nucleotide sequence shown in SEQ ID NO: 3 or 4 and, as a template, the chromosomal DNA of a microorganism, preferably a microorganism belonging to the genus Streptomyces; and
    (c) Southern hybridization of a chromosomal DNA library from a microorganism, preferably a microorganism belonging to the genus Bacillus, Streptomyces, Pseudomonas or Xanthomonas, using DNA encoding known NRPS, for example, NRPS described in Eur. J. Biochem., 270, 4555 (2003), PCT National Publication No. 512835/03, U.S. Pat. No. 5,795,738 or U.S. Pat. No. 5,652,116, or a probe designed based on the nucleotide sequence shown in SEQ ID NO: 44, or by PCR using primer DNAs designed based on the nucleotide sequence of DNA encoding the above NRPS and, as a template, the chromosomal DNA of a microorganism, preferably a microorganism belonging to the genus Bacillus, Streptomyces, Pseudomonas or Xanthomonas. 


The DNA used in the production process of the present invention can also be obtained by conducting a search through various gene sequence databases for a sequence having 75% or more homology, preferably 85% or more homology, more preferably 90% or more homology, further preferably 95% or more homology, particularly preferably 98% or more homology to the nucleotide sequence of DNA encoding the amino acid sequence shown in any of SEQ ID NOS: 1 to 8, 17, 37, 38 and 43, and obtaining the desired DNA, based on the nucleotide sequence obtained by the search, from a chromosomal DNA or cDNA library of an organism having the nucleotide sequence according to the above-described method.
The obtained DNA, as such or after cleavage with appropriate restriction enzymes, is inserted into a vector by a conventional method, and the obtained recombinant DNA is introduced into a host cell. Then, the nucleotide sequence of the DNA can be determined by a conventional sequencing method such as the dideoxy method [Proc. Natl. Acad. Sci., USA, 74, 5463 (1977)] or by using a nucleotide sequencer such as 373A DNA Sequencer (Perkin-Elmer Corp.).
In cases where the obtained DNA is found to be a partial DNA by the analysis of nucleotide sequence, the full length DNA can be obtained by Southern hybridization of a chromosomal DNA library using the partial DNA as a probe.
It is also possible to prepare the desired DNA by chemical synthesis using a DNA synthesizer (e.g., Model 8905, PerSeptive Biosystems) based on the determined nucleotide sequence of the DNA.
Examples of the DNAs that can be obtained by the above-described method are DNAs having the nucleotide sequences shown in SEQ ID NOS: 9 to 16, 36, 39, 40 and 44.
Examples of the vectors for inserting the above DNA include pBluescriptII KS(+) (Stratagene), pDIRECT [Nucleic Acids Res., 18, 6069 (1990)], pCR-Script Amp SK(+) (Stratagene), pT7 Blue (Novagen, Inc.), pCR II (Invitrogen Corp.) and pCR-TRAP (Genhunter Corp.).
The above host cells include microorganisms belonging to the genus Escherichia. Examples of the microorganisms belonging to the genus Escherichia include Escherichia coli XL1-Blue, Escherichia coli XL2-Blue, Escherichia coli DH1, Escherichia coli MC1000, Escherichia coli ATCC 12435, Escherichia coli W1485, Escherichia coli JM109, Escherichia coli HB101, Escherichia coli No. 49, Escherichia coli W3110, Escherichia coli NY49, Escherichia coli MP347, Escherichia coli NM522 and Escherichia coli ME8415.
Introduction of the recombinant DNA can be carried out by any of the methods for introducing DNA into the above host cells, for example, the method using calcium ion [Proc. Natl. Acad. Sci. USA, 69, 2110 (1972)], the protoplast method (Japanese Published Unexamined Patent Application No. 248394/88) and electroporation [Nucleic Acids Res., 16, 6127 (1988)].
An example of the microorganism carrying the DNA used in the production process of the present invention obtained by the above method is Escherichia coli NM522/pPE43, which is a microorganism carrying a recombinant DNA comprising DNA having the sequence shown in SEQ ID NO: 1.
(ii) Preparation of Microorganisms Having the Ability to Produce Amino Acids
The microorganisms having the ability to produce amino acids used in the process for producing a dipeptide of the present invention include any microorganisms having the ability to produce one or more kinds of amino acids, for example, a strain isolated from nature which inherently has the ability and a microorganism to which the ability to produce at least one kind of amino acid among amino acids constituting a desired dipeptide was artificially imparted by a known method.
Examples of the known methods are:

    (a) a method in which at least one of the regulation of the biosynthesis of an amino acid is reduced or eliminated;
    (b) a method in which the expression of at least one of the enzymes involved in the biosynthesis of an amino acid is enhanced;
    (c) a method in which the copy number of at least one of the enzyme genes involved in the biosynthesis of an amino acid is increased;
    (d) a method in which at least one of the metabolic pathways branching from the biosynthetic pathway of an amino acid into metabolites other than the amino acid is weakened or blocked; and
    (e) a method in which a cell strain having a higher resistance to an analogue of an amino acid as compared with a wild-type strain is selected.


The above known methods can be used alone or in combination.
The method of the above (a) is specifically described in Agric. Biol. Chem., 43, 105-111 (1979); J. Bacteriol., 110, 761-763 (1972); Appl. Microbiol. Biotechnol., 39, 318-323 (1993), etc. The method of the above (b) is specifically described in Agric. Biol. Chem., 43, 105-111 (1979); J. Bacteriol., 110, 761-763 (1972), etc. The method of the above (c) is specifically described in Appl. Microbiol. Biotechnol., 39, 318-323 (1993); Agric. Biol. Chem., 39, 371-377 (1987), etc. The method of the above (d) is specifically described in Appl. Environ. Microbiol., 38, 181-190 (1979); Agric. Biol. Chem., 42, 1773-1778 (1978), etc. The method of the above (e) is specifically described in Agric. Biol. Chem., 36, 1675-1684 (1972); Agric. Biol. Chem., 41, 109-116 (1977); Agric. Biol. Chem., 37, 2013-2023 (1973), Agric. Biol. Chem., 51, 2089-2094 (1987), etc. Microorganisms having the ability to produce various amino acids can be prepared by referring to the above publications.
Further, as for the preparation of microorganisms having the ability to produce amino acids by the methods of the above (a) to (e), alone or in combination, many examples are described in Biotechnology 2nd ed., Vol. 6, Products of Primary Metabolism (VCH Verlagsgesellschaft mbH, Weinheim, 1996) section 14a and 14b; Advances in Biochemical Engineering/Biotechnology 79, 1-35 (2003); Hiroshi Soda, et al., Amino Acid Fermentation, Gakkai Shuppan Center (1986), etc. In addition to the above, many reports have been made on the methods for preparation of microorganisms having the ability to produce specific amino acids: for example, Japanese Published Unexamined Patent Application No. 164297/03; Agric. Biol. Chem., 39, 153-160 (1975); Agric. Biol. Chem., 39, 1149-1153 (1975); Japanese Published Unexamined Patent Application No. 13599/83; J. Gen. Appl. Microbiol., 4, 272-283 (1958); Japanese Published Unexamined Patent Application No. 94985/88; Agric. Biol. Chem., 37, 2013-2023 (1973); WO 97/15673; Japanese Published Unexamined Patent Application No. 18596/81; Japanese Published Unexamined Patent Application No. 144092/81 and PCT National Publication No. 511086/03. Microorganisms having the ability to produce one or more kinds of amino acids can be prepared by referring to the above publications.
Examples of the microorganisms having the ability to produce amino acids prepared by the above methods include. L-glutamine-producing strains (e.g. a microorganism wherein the glnE gene and/or the glnB gene are deleted), L-alanine-producing strains [e.g. a microorganism wherein the expression of alanine dehydrogenase gene (ald gene) is enhanced], and L-phenylalanine-producing microorganisms (e.g. a microorganism expressing the phenylalanine-feedback-resistant pheA gene and/or the tyrosine-feedback-resistant aroF gene).
The above microorganisms which produce amino acids include any microorganisms to which the methods of the above (a) to (e) can be applied or microorganisms having the above genotypes, preferably procaryotes, more preferably bacteria.
The procaryotes include microorganisms belonging to the genera Escherichia, Serratia, Bacillus, Brevibacterium, Corynebacterium, Microbacterium, Pseudomonas, Agrobacterium, Alicyclobacillus, Anabaena, Anacystis, Arthrobacter, Azotobacter, Chromatium, Erwinia, Methylobacterium, Phormidium, Rhodobacter, Rhodopseudomonas, Rhodospirillum, Scenedesmus, Streptomyces, Synechoccus and Zymomonas, for example, Escherichia coli, Bacillus subtilis, Bacillus megaterium, Bacillus amyloliquefaciens, Bacillus coagulans, Bacillus licheniformis, Bacillus pumilus, Brevibacterium ammoniagenes, Brevibacterium immariophilum, Brevibacterium saccharolyticum, Brevibacterium flavum, Brevibacterium lactofermentum, Corynebacterium glutamicum, Corynebacterium acetoacidophilum, Microbacterium ammoniaphilum, Serratia ficaria, Serratia fonticola, Serratia liquefaciens, Serratia marcescens, Pseudomonas aeruginosa, Pseudomonas putida, Agrobacterium radiobacter, Agrobacterium rhizogenes, Agrobacterium rubi, Anabaena cylindrica, Anabaena doliolum, Anabaena flos-aquae, Arthrobacter aurescens, Arthrobacter citreus, Arthrobacter globformis, Arthrobacter hydrocarboglutamicus, Arthrobacter mysorens, Arthrobacter nicotianae, Arthrobacter paraffineus, Arthrobacter protophormiae, Arthrobacter roseoparaffinus, Arthrobacter sulfureus, Arthrobacter ureafaciens, Chromatium buderi, Chromatium tepidum, Chromatium vinosum, Chromatium warmingii, Chromatium fluviatile, Erwinia uredovora, Erwinia carotovora, Erwinia ananas, Erwinia herbicola, Erwinia punctata, Erwinia terreus, Methylobacterium rhodesianum, Methylobacterium extorquens, Phormidium sp. ATCC 29409, Rhodobacter capsulatus, Rhodobacter sphaeroides, Rhodopseudomonas blastica, Rhodopseudomonas marina, Rhodopseudomonas palustris, Rhodospirillum rubrum, Rhodospirillum salexigens, Rhodospirillum salinarum, Streptomyces ambofaciens, Streptomyces aureofaciens, Streptomyces aureus, Streptomyces fungicidicus, Streptomyces griseochromogenes, Streptomyces griseus, Streptomyces lividans, Streptomyces olivogriseus, Streptomyces rameus, Streptomyces tanashiensis, Streptomyces vinaceus and Zymomonas mobilis. Preferred procaryotes include bacteria belonging to the genera Escherichia, Serratia, Bacillus, Brevibacterium, Corynebacterium, Pseudomonas and Streptomyces, for example, the above-mentioned species belonging to the genera Escherichia, Serratia, Bacillus, Brevibacterium, Corynebacterium, Pseudomonas and Streptomyces. More preferred bacteria include Escherichia coli, Corynebacterium glutamicum, Corynebacterium ammoniagenes, Corynebacterium lactofermentum, Corynebacterium flavum, Corynebacterium efficiens, Bacillus subtilis, Bacillus megaterium, Serratia marcescens, Pseudomonas putida, Pseudomonas aeruginosa, Streptomyces coelicolor and Streptomyces lividans, among which Escherichia coli is particularly preferred.
Specific examples of the microorganisms producing amino acids include Escherichia coli JGLE1 and Escherichia coli JGLBE1, which are L-glutamine-producing strains, Escherichia coli JM101 carrying an ald gene expression plasmid, which is an L-alanine-producing strain, Escherichia coli JM101 carrying pPHEA2 and/or an aroF gene expression plasmid, which are L-phenylalanine-producing strains, Escherichia coli JGLE1 and Escherichia coli JGLBE1 carrying an ald gene expression plasmid, which are L-glutamine- and L-alanine-producing strains, Escherichia coli JM101 carrying an ald gene expression plasmid and pPHEA2 and/or an aroF gene expression plasmid, which are L-alanine- and L-phenylalanine-producing strains, and ATCC 21277 strains carrying pPHEA and/or an aroF gene expression plasmid, which are L-threonine- and L-phenylalanine-producing strains.
Further, specific examples of the microorganisms having the ability to produce amino acids include FERM BP-5807 and ATCC 13032 strains producing L-glutamic acid, FERM P-4806 and ATCC 14751 strains producing L-glutamine, ATCC 21148, ATCC 21277 and ATCC 21650 strains producing L-threonine, FERM P-5084 and ATCC 13286 strains producing L-lysine, FERM P-5479, VKPM B-2175 and ATCC 21608 strains producing L-methionine, FERM BP-3757 and ATCC 14310 strains producing L-isoleucine, ATCC 13005 and ATCC 19561 strains producing L-valine, FERM BP-4704 and ATCC 21302 strains producing L-leucine, FERM BP-4121 and ATCC 15108 strains producing L-alanine, ATCC 21523 and FERM BP-6576 strains producing L-serine, FERM BP-2807 and ATCC 19244 strains producing L-proline, FERM P-5616 and ATCC 21831 strains producing L-arginine, ATCC 13232 strain producing L-ornithine, FERM BP-6674 and ATCC 21607 strains producing L-histidine, DSM 10118, DSM 10121, DSM 10123 and FERM BP-1777 strains producing L-tryptophan, ATCC 13281 and ATCC 21669 strains producing L-phenylalanine, ATCC 21652 strain producing L-tyrosine, W3110/pHC34 strain producing L-cysteine (PCT National Publication No. 511086/03), Escherichia coli SOLR/pRH71 producing L-4-hydroxyproline described in WO96/27669, FERM BP-5026 and FERM BP-5409 strains producing L-3-hydroxyproline, and FERM P-5643 and FERM P-1645 strains producing L-citrulline.
The above strains designated by FERM Nos., ATCC Nos., VKPM Nos. and DSM Nos. are available from International Patent Organism Depositary, National Institute of Advanced Industrial Science and Technology (Japan), American Type Culture Collection (U.S.A.), Russian National Collection of Industrial Microorganisms (Russia) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (Germany), respectively.
(iii) Preparation of Microorganisms which have the Ability to Produce a Protein Having the Activity to Form a Dipeptide from One or More Kinds of Amino Acids and which have the Ability to Produce at Least One of Said One or More Kinds of Amino Acids
The microorganisms which have the ability to produce a protein having the activity to form a dipeptide from one or more kinds of amino acids and which have the ability to produce at least one of said one or more kinds of amino acids can be prepared by the following methods:

    (a) a method of introducing DNA encoding a protein having the activity to form a dipeptide from one or more kinds of amino acids prepared by the method of the above (i) into a microorganism having the ability to produce one or more kinds of amino acids prepared by the method of the above (ii);
    (b) a method of imparting, by the method of the above (ii), the ability to produce one or more kinds of amino acids to a microorganism carrying DNA encoding a protein having the activity to form a dipeptide from one or more kinds of amino acids prepared by the method of the above (i);
    (c) a method of introducing DNA encoding a protein having the activity to form a dipeptide from one or more kinds of amino acids into a microorganism inherently having the ability to produce one or more kinds of amino acids by the method of the above (i); and
    (d) a method of imparting the ability to produce one or more kinds of amino acids to a microorganism inherently having the ability to produce a protein having the activity to form a dipeptide from one or more kinds of amino acids by the method of the above (ii).


Introduction of DNA encoding a protein having the activity to form a dipeptide from one or more kinds of amino acids prepared by the method of the above (i) into a microorganism can impart the ability to produce a protein having the activity to form a dipeptide from one or more kinds of amino acids to the microorganism. The ability to produce a protein having the activity to form a dipeptide from one or more kinds of amino acids can be imparted to a microorganism by expressing the DNA prepared by the method of the above (i) in a host cell utilizing the methods described in Molecular Cloning, Third Edition, Current Protocols in Molecular Biology, or the like, for example, in the following manner.
On the basis of the DNA prepared by the method described in the above (i), a DNA fragment of an appropriate length comprising a region encoding the protein is prepared according to need. The productivity of the protein can be enhanced by replacing a nucleotide in the nucleotide sequence of the region encoding the protein so as to make a codon most suitable for the expression in a host cell.
The DNA fragment is inserted downstream of a promoter in an appropriate expression vector to prepare a recombinant DNA.
A transformant producing the protein can be obtained by introducing the recombinant DNA into a host cell suited for the expression vector.
As the host cell, any microorganisms that are capable of expressing the desired gene can be used. Preferred are procaryotes, and more preferred are bacterial cells. Examples of the preferred procaryotes are the procaryotes mentioned in the above (ii).
The microorganism may or may not have the ability to produce one or more kinds of amino acids. When a microorganism without the ability is used as the host cell, a microorganism used in the production process of the present invention can be obtained by preparing a transformant by introducing the recombinant DNA obtained by the above method into the microorganism by the following method, and then imparting the ability to produce one or more kinds of amino acids to the transformant by the method of the above (ii).
The expression vectors that can be employed are those capable of autonomous replication or integration into the chromosome in microorganism cells and comprising a promoter at a position appropriate for the transcription of the DNA used in the production process of the present invention.
When a prokaryote is used as the host cell, it is preferred that the recombinant DNA comprising the DNA used in the production process of the present invention is a recombinant DNA which is capable of autonomous replication in the prokaryote and which comprises a promoter, a ribosome binding sequence, the DNA used in the production process of the present invention, and a transcription termination sequence. The recombinant DNA may further comprise a gene regulating the promoter.
Examples of suitable expression vectors are pBTrp2, pBTac1 and pBTac2 (products of Boehringer Mannheim GmbH), pHelix1 (Roche Diagnostics Corp.), pKK233-2 (Amersham Pharmacia Biotech), pSE280 (Invitrogen Corp.), pGEMEX-1 (Promega Corp.), pQE-8 (Qiagen, Inc.), pET-3 (Novagen, Inc.), pKYP10 (Japanese Published Unexamined Patent Application, No. 110600/83), pKYP200 [Agric. Biol. Chem., 48, 669 (1984)], pLSA1 [Agric. Biol. Chem., 53, 277 (1989)], pGEL1 [Proc. Natl. Acad. Sci. USA, 82, 4306 (1985)], pBluescript II SK(+), pBluescript II KS(−) (Stratagene), pTrS30 [prepared from Escherichia coli JM109/pTrS30 (FERM BP-5407)], pTrS32 [prepared from Escherichia coli JM109/pTrS32 (FERM BP-5408)], pPAC31 (WO98/12343), pUC19 [Gene, 33, 103 (1985)], pSTV28 (Takara Bio Inc.), pUC118 (Takara Bio Inc.), pPA1 (Japanese Published Unexamined Patent Application No. 233798/88), pWH1520 (MoBiTec), pCS299P (WO00/63388), pVLT31 [Gene, 123, 17 (1993)] and pIJ702 (Genetic Manipulation of Streptomyces: a Laboratory Manual: John Innes Foundation).
When a microorganism belonging to the genus Escherichia is used as the host cell, any promoters capable of functioning in Escherichia coli can be used as the promoter. For example, promoters derived from Escherichia coli or phage, such as trp promoter (Ptrp), lac promoter (Plac), PL promoter, PR promoter and PSE promoter, SPO1 promoter, SPO2 promoter and penP promoter can be used. Artificially designed and modified promoters such as a promoter in which two Ptrps are combined in tandem, tac promoter, lacT7 promoter and letI promoter, etc. can also be used.
Also useful are promoters such as xylA promoter for the expression in microorganisms belonging to the genus Bacillus [Appl. Microbiol. Biotechnol., 35, 594-599 (1991)], P54-6 promoter for the expression in microorganisms belonging to the genus Corynebacterium [Appl. Microbiol. Biotechnol., 53, 674-679 (2000)], tac promoter for the expression in microorganisms belonging to the genus Pseudomonas [Gene, 123, 17-24 (1993)] and xylA promoter for the expression in microorganisms belonging to the genus Streptomyces (Genetic Manipulation of Streptomyces: a Laboratory Manual: John Innes Foundation).
It is preferred to use a plasmid in which the distance between the Shine-Dalgarno sequence (ribosome binding sequence) and the initiation codon is adjusted to an appropriate length (e.g., 6 to 18 nucleotides).
In the recombinant DNA wherein the DNA used in the production process of the present invention is ligated to an expression vector, the transcription termination sequence is not essential, but it is preferred to place the transcription termination sequence immediately downstream of the structural gene.
An example of such recombinant DNA is pPE43.
Introduction of the recombinant DNA into microorganism cells can be carried out by any of the methods for introducing DNA into the cells, for example, the method using calcium ion [Proc. Natl. Acad. Sci. USA, 69, 2110 (1972)], the protoplast method (Japanese Published Unexamined Patent Application No. 248394/88) and electroporation [Nucleic Acids Res., 16, 6127 (1988)].
Examples of the microorganisms inherently having the ability to produce one or more kinds of amino acids used in the above method (c) include known strains having the ability to produce amino acids described in the above (ii).
Examples of the microorganisms inherently having the ability to produce a protein having the activity to form a dipeptide from one or more kinds of amino acids used in the above method (d) include: (A) microorganisms belonging to the genus Bacillus, more preferably, microorganisms belonging to the genus Bacillus which have bacilysin-synthesizing activity, further preferably, microorganisms belonging to a species selected from the group consisting of Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus coagulans, Bacillus licheniformis, Bacillus megaterium and Bacillus pumilus, most preferably, microorganisms selected from the group consisting of the strains Bacillus subtilis ATCC 15245, Bacillus subtilis ATCC 6633, Bacillus subtilis IAM 1213, Bacillus subtilis IAM 1107, Bacillus subtilis IAM 1214, Bacillus subtilis ATCC 9466, Bacillus subtilis IAM 1033, Bacillus subtilis ATCC 21555, Bacillus amyloliquefaciens IFO 3022 and Bacillus pumilus NRRL B-12025; and (B) microorganisms belonging to the genus Streptomyces, preferably, microorganisms belonging to the genus Streptomyces which have the ability to produce albonoursin, more preferably, microorganisms belonging to the species Streptomyces albulus or Streptomyces noursei. 
(iv) Microorganisms in which the Activities of Peptidases And Proteins Having Peptide-Permeating/Transporting Activity are Reduced or Lost
The microorganisms used in the production process of the present invention include microorganisms prepared by the method of the above (iii) in which the activities of one or more kinds of peptidases and one or more kinds of proteins having peptide-permeating/transporting activity (hereinafter referred to as peptide-permeating/transporting proteins) are reduced or lost, and those in which the activities of three or more kinds of peptidases are reduced or lost.
Such microorganisms can be obtained, for example, by the following methods: (a) a method of imparting, by the method of the above (iii), the ability to produce a protein having the activity to form a dipeptide from one or more kinds of amino acids and the ability to produce at least one of said one or more kinds of amino acids to a microorganism in which the functions of one or more kinds of peptidases and one or more kinds of peptide-permeating/transporting proteins are reduced or lost, or a microorganism in which the functions of three or more kinds of peptidases are reduced or lost; and (b) a method of reducing or causing loss of the functions of a) one or more kinds of peptidases and one or more kinds of peptide-permeating/transporting proteins or b) three or more kinds of peptidases of a microorganism having the ability to produce a protein having the activity to form a dipeptide from one or more kinds of amino acids and the ability to produce at least one of said one or more kinds of amino acids which can be prepared by the method of the above (iii).
The microorganisms in which the activities of one or more kinds of peptidases and one or more kinds of peptide-permeating/transporting proteins are reduced or lost include microorganisms in which the activities of one or more arbitrary kinds of peptidases and one or more arbitrary kinds of peptide-permeating/transporting proteins are reduced or lost provided that the microorganisms can normally grow, specifically, microorganisms in which the activities of preferably one to nine kinds, more preferably one to seven kinds, further preferably one to four kinds of peptidases and preferably one to five kinds, more preferably one to three kinds, further preferably one or two kinds, particularly preferably one kind of peptide-permeating/transporting protein are reduced or lost.
Examples of such microorganisms are microorganisms in which the activities of one or more kinds of peptidases and one or more kinds of peptide-permeating/transporting proteins are reduced or lost because the nucleotide sequences of one or more kinds of genes encoding peptidases (hereinafter referred to as peptidase genes) and one or more kinds of genes encoding peptide-permeating/transporting proteins (hereinafter referred to as peptide-permeating/transporting protein genes) among the peptidase genes and peptide-permeating/transporting protein genes existing on the genomic DNA of the microorganisms are entirely or partially deleted or said nucleotide sequences contain nucleotide substitutions or additions.
The expression “the activity of peptidase is reduced” means that the peptidolytic activity is reduced, or reduced to normally 80% or less, preferably 50% or less, more preferably 30% or less, further preferably 20% or less, particularly preferably 10% or less, most preferably 5% or less compared with peptidase having none of the above deletions, substitutions and additions of nucleotides.
The peptidolytic activity of a microorganism can be measured by allowing a peptide as a substrate and microorganism cells to be present in an aqueous medium, thereby performing peptidolytic reaction, and then determining the amount of the remaining peptide by a known method, e.g., HPLC analysis.
The above peptidases may be any proteins having peptidolytic activity. Preferred are proteins having high dipeptide-hydrolyzing activity. More preferred are dipeptidases.
Examples of peptidases include: those existing in Escherichia coli such as PepA having the amino acid sequence shown in SEQ ID NO: 45, PepB having the amino acid sequence shown in SEQ ID NO: 46, PepD having the amino acid sequence shown in SEQ ID NO: 47, PepN having the amino acid sequence shown in SEQ ID NO: 48, PepP [GenBank accession No. (hereinafter abbreviated as Genbank) AAC75946], PepQ (GenBank AAC76850), PepE (GenBank AAC76991), PepT (GenBank AAC74211), Dcp (GenBank AAC74611) and IadA (GenBank AAC77284); those existing in Bacillus subtilis such as AmpS (GenBank AF012285), PepT (GenBank X99339), YbaC (GenBank Z99104), YcdD (GenBank Z99105), YjbG (GenBank Z99110), YkvY (GenBank Z99111), YqjE (GenBank Z99116) and YwaD (GenBank Z99123); and those existing in Corynebacterium glutamicum such as proteins having the amino acid sequences represented by BAB97732, BAB97858, BAB98080, BAB98880, BAB98892, BAB99013, BAB99598 and BAB99819 (registration Nos. of DNA Data Bank of Japan). Examples of dipeptidases include PepA, PepB, PepD and PepN having the amino acid sequences shown in SEQ ID NOS: 45 to 48, PepQ, PepE and IadA. Proteins having amino acid sequences which have 80% or more, preferably 90% or more, more preferably 95% or more homology to the amino acid sequence shown in any of SEQ ID NOS: 45 to 48 and having peptidase activity are also included in the proteins having high dipeptide-hydrolyzing activity. The homology among amino acid sequences and nucleotide sequences can be determined by using BLAST, FASTA or the like described above.
The expression “the activity of a peptide-permeating/transporting protein is reduced” means that the peptide-uptaking activity is reduced, or reduced to normally 80% or less, preferably 50% or less, more preferably 30% or less, further preferably 20% or less, particularly preferably 10% or less, most preferably 5% or less compared with a peptide-permeating/transporting protein having none of the above deletions, substitutions and additions of nucleotides.
The peptide-uptaking activity of a microorganism can be measured by allowing a peptide as a substrate and microorganism cells to be present in an aqueous medium, thereby performing peptide-uptaking reaction, and then determining the amount of the remaining peptide by a known method, e.g., HPLC analysis.
The above peptide-permeating/transporting proteins may be any proteins involved in peptide permeation or transport of microorganisms, for example, proteins encoded by genes forming an operon on chromosomal DNA which form a complex on cell membrane to express peptide-uptaking activity and those which have peptide-uptaking activity as individual proteins. Preferred are proteins having high dipeptide-uptaking activity.
Examples of the peptide-permeating/transporting proteins include: those existing in Escherichia coli such as DppA having the amino acid sequence shown in SEQ ID NO: 49, DppB having the amino acid sequence shown in SEQ ID NO: 50, DppC having the amino acid sequence shown in SEQ ID NO: 51, DppD having the amino acid sequence shown in SEQ ID NO: 52, DppF having the amino acid sequence shown in SEQ ID NO: 53, OppA (GenBank AAC76569), OppB (GenBank AAC76568), OppC (GenBank AAC76567), OppD (GenBank AAC76566), OppF (GenBank AAC76565), YddO (GenBank AAC74556), YddP (GenBank AAC74557), YddQ (GenBank AAC74558), YddR (GenBank AAC74559), YddS (GenBank AAC74560), YbiK (GenBank AAC73915), MppA (GenBank AAC74411), SapA (GenBank AAC74376), SapB (GenBank AAC74375), SapC (GenBank AAC74374), SapD (GenBank AAC74373) and SapF (GenBank AAC74372); those existing in Bacillus subtilis such as DppA (GenBank CAA40002), DppB (GenBank CAA40003), DppC (GenBank CAA40004), DppD (GenBank CAA40005), DppE (GenBank CAA40006), OppA (GenBank CAA39787), OppB (GenBank CAA39788), OppC (GenBank CAA39789), OppD (GenBank CAA39790), OppF (GenBank CAA39791), AppA (GenBank CAA62358), AppB (GenBank CAA62359), AppC (GenBank CAA62360), AppD (GenBank CAA62356), AppF (GenBank CAA62357), YclF (GenBank CAB12175) and YkfD (GenBank CAB13157); and those existing in Corynebacterium glutamicum such as proteins having the amino acid sequences represented by BAB99048, BAB99383, BAB99384, BAB99385, BAB99713, BAB99714, BAB99715, BAB99830, BAB99831 and BAB99832 (registration Nos. of DNA Data Bank of Japan). Examples of the proteins having high dipeptide-uptaking activity include DppA, DppB, DppC, DppD and DppF having the amino acid sequences shown in SEQ ID NOS: 49 to 53, and proteins having amino acid sequences which have 80% or more, preferably 90% or more, more preferably 95% or more homology to the amino acid sequence shown in any of SEQ ID NOS: 49 to 53.
The homology among amino acid sequences can be determined by using programs such as BLAST and FASTA described above.
The microorganisms in which the activities of three or more kinds of peptidases are reduced or lost include microorganisms in which the activities of three or more arbitrary kinds of peptidases are reduced or lost provided that the microorganisms can normally grow, specifically, microorganisms in which the activities of preferably three to nine kinds, more preferably three to six kinds, further preferably three or four kinds of peptidases are reduced or lost.
Examples of peptidases include the above-described peptidases and dipeptidases existing in Escherichia coli, Bacillus subtilis and Corynebacterium glutamicum. Proteins consisting of amino acid sequences which have 80% or more, preferably 90% or more, more preferably 95% or more homology to the amino acid sequence shown in any of SEQ ID NOS: 45 to 48 and having peptidase activity are also included in the proteins having high dipeptide-hydrolyzing activity.
The homology among amino acid sequences can be determined by using programs such as BLAST and FASTA described above.
(v) Preparation of Microorganisms in which the Activities of Peptidases and Peptide-Permeating/Transporting Proteins are Reduced or Lost
The microorganisms in which the activities of peptidases and peptide-permeating/transporting proteins are reduced or lost may be obtained by any method capable of preparing such microorganisms. For example, they can be obtained by introducing a deletion, substitution or addition of a nucleotide into peptidase genes and peptide-permeating/transporting protein genes on chromosomal DNAs of microorganisms as described below.
The methods for introducing a deletion, substitution or addition of a nucleotide into a gene on the chromosomal DNA of a microorganism include methods utilizing homologous recombination. An example of the methods utilizing general homologous recombination is a method using a plasmid for homologous recombination prepared by ligating a mutant gene having an introduced nucleotide deletion, substitution or addition to a plasmid DNA incapable of autonomous replication in a host cell into which the nucleotide deletion or the like is to be introduced and carrying a drug resistance gene.
The plasmid for homologous recombination is introduced into a host cell by an ordinary method, followed by selection of a transformant in which the plasmid for homologous recombination has been integrated into the chromosomal DNA by homologous recombination using the drug resistance as a marker. The obtained transformant is cultured using a medium which does not contain the drug for several hours to one day, and then spread on an agar medium containing the drug and on an agar medium without the drug. By selecting a strain which does not grow on the former medium but can grow on the latter medium, the strain in which second homologous recombination occurred on the chromosomal DNA can be obtained. Introduction of a nucleotide deletion, substitution or addition into a desired gene on the chromosomal DNA can be confirmed by determining the nucleotide sequence of a region of the chromosomal DNA containing the gene into which the deletion or the like has been introduced.
By use of the above method, a nucleotide deletion, substitution or addition can be introduced into desired genes on chromosomal DNAs of microorganisms such as those belonging to the genera Escherichia, Bacillus and Corynebacterium. 
Further, a nucleotide deletion, substitution or addition can be efficiently introduced into plural genes by utilizing homologous recombination according to a method using a straight-chain DNA.
Specifically, a straight-chain DNA containing a gene into which a nucleotide deletion, substitution or addition is to be introduced is incorporated into a cell to cause homologous recombination between chromosomal DNA and the introduced straight-chain DNA. This method is applicable to any microorganisms capable of efficiently incorporating a straight-chain DNA. Preferred microorganisms are those belonging to the genera Escherichia and Bacillus. Escherichia coli is more preferred, and Escherichia coli expressing a group of recombinant proteins derived from λ phage (Red recombination system) is further preferred.
An example of Escherichia coli expressing λ Red recombination system is Escherichia coli JM101 carrying pKD46, which is a plasmid DNA comprising a λ Red recombination system gene (available from Escherichia coli Genetic Stock Center, Yale University, U.S.A.).
Examples of the DNAs useful for homologous recombination are as follows:

    (a) straight-chain DNA in which DNAs having homology to the DNAs present on the outside of a region of chromosomal DNA to be subjected to introduction of a nucleotide deletion, substitution or addition are present at both termini of a drug resistance gene;
    (b) straight-chain DNA in which DNAs having homology to the DNAs present on the outside of a region of chromosomal DNA to be subjected to introduction of a nucleotide deletion, substitution or addition are directly ligated to each other;
    (c) straight-chain DNA having a drug resistance gene and a gene that can be used for negative selection and in which DNAs having homology to the DNAs present on the outside of a region of chromosomal DNA to be subjected to introduction of a nucleotide deletion, substitution or addition are present at both termini; and
    (d) straight-chain DNA of the above (a) in which a nucleotide sequence recognized by yeast-derived Flp recombinase [Proc. Natl. Acad. Sci. USA., 82, 5875 (1985)] is additionally present between the drug resistance gene and the DNAs having homology to the DNAs present on the outside of a region of chromosomal DNA.


As the drug resistance gene, any drug resistance genes that impart resistance to a drug to which the host microorganism shows sensitivity can be used. When Escherichia coli is used as the host microorganism, examples of the drug resistance genes are kanamycin resistance gene, chloramphenicol resistance gene, gentamicin resistance gene, spectinomycin resistance gene, tetracycline resistance gene and ampicillin resistance gene.
The “gene that can be used for negative selection” refers to a gene that is fatal to a host microorganism under certain culture conditions when the gene is expressed in the host microorganism. Examples of the genes are sacB gene derived from a microorganism belonging to the genus Bacillus [Appl. Environ. Microbiol., 59, 1361-1366 (1993)] and rpsL gene derived from a microorganism belonging to the genus Escherichia [Genomics, 72, 99-104 (2001)].
The DNAs having homology to the DNAs present on the outside of a region of chromosomal DNA to be subjected to introduction of a substitution or deletion, which exist at both ends of the above straight-chain DNAs, are located in the same direction as that on the chromosomal DNA, and their length is preferably about 10 bp to 100 bp, more preferably about 20 bp to 50 bp, and further preferably about 30 bp to 40 bp.
The nucleotide sequence recognized by yeast-derived Flp recombinase is not specifically limited so long as it is a nucleotide sequence recognized by the said protein and catalyzing homologous recombination. Preferred examples are DNA having the nucleotide sequence shown in SEQ ID NO: 54, and DNA having a nucleotide sequence wherein one to several nucleotides are deleted, substituted or added in the said DNA and having a nucleotide sequence recognized by yeast-derived Flp recombinase and catalyzing homologous recombination.
The expression “having homology” means that the above straight-chain DNA has such a degree of homology that allows occurrence of homologous recombination between the subject region of chromosomal DNA and the straight-chain DNA, specifically, 80% or more homology, preferably 90% or more homology, more preferably 95% or more homology, further preferably 100% homology.
The homology among nucleotide sequences can be determined by using programs such as BLAST and FASTA described above.
The above straight-chain DNA can be prepared by PCR. The desired straight-chain DNA can also be obtained by constructing DNA containing the above straight-chain DNA on plasmid and then carrying out treatment with restriction enzymes.
Examples of the methods for introducing a nucleotide deletion, substitution or addition into the chromosomal DNA of a microorganism include the following Methods 1 to 4.
Method 1:
A method which comprises introducing the straight-chain DNA of the above (a) or (d) into a host microorganism and selecting a transformant carrying the straight-chain DNA inserted on its chromosomal DNA by homologous recombination using the drug resistance as a marker.
Method 2:
A method which comprises introducing the straight-chain DNA of the above (b) into the transformant obtained according to the above Method 1 and eliminating the drug resistance gene inserted on its chromosomal DNA by Method 1 to substitute or delete a region of the chromosomal DNA of the microorganism.
Method 3:
A method which comprises:

    [1] introducing the straight-chain DNA of the above (c) into a host microorganism and selecting a transformant carrying the straight-chain DNA inserted on its chromosomal DNA by homologous recombination using the drug resistance as a marker;
    [2] synthesizing DNA by ligating DNAs having homology to the DNAs present on the outside of a region of chromosomal DNA to be subjected to introduction of a substitution or deletion in the same direction as that on the chromosomal DNA, and introducing the synthesized DNA into the transformant obtained in the above [1]; and
    [3] culturing the transformant subjected to the operation of the above [2] under conditions such that the gene that can be used for negative selection is expressed, and selecting a strain capable of growing by the culturing as a strain in which the drug resistance gene and the gene that can be used for negative selection are eliminated from the chromosomal DNA.

Method 4:



A method which comprises:

    [1] introducing the straight-chain DNA of the above (d) into a host microorganism and selecting a transformant carrying the straight-chain DNA inserted on its chromosomal DNA by homologous recombination using the drug resistance as a marker; and
    [2] introducing a Flp recombinase gene expression plasmid into the transformant obtained in the above [1], and after expression of the gene, obtaining a strain sensitive to the drug used in the above [1].


In the above methods, introduction of the straight-chain DNA into a host microorganism can be carried out by any of the methods for introducing DNA into the microorganism, for example, the method using calcium ion [Proc. Natl. Acad. Sci. USA, 69, 2110 (1972)], the protoplast method (Japanese Published Unexamined Patent Application No. 248394/88) and electroporation [Nucleic Acids Res., 16, 6127 (1988)].
By using a straight-chain DNA in which an arbitrary gene to be inserted to chromosomal DNA is incorporated in the center part of the straight-chain DNA used in Method 2 or Method 3 [2], it is possible to eliminate the drug resistance gene and at the same time to insert an arbitrary gene to the chromosomal DNA.
The above Methods 2 to 4 are methods that leave no foreign genes such as a drug resistance gene and a gene usable for negative selection on the chromosomal DNA of the transformant to be finally obtained. Therefore, it is possible to readily produce a microorganism having nucleotide deletions, substitutions or additions in two or more different regions of the chromosomal DNA by repeating the operations of Methods 1 and 2, Method 3 [1] to [3], and Method 4 [1] and [2] using the same drug resistance gene and the same gene usable for negative selection.
(vi) Process for Producing a Dipeptide of the Present Invention
A dipeptide can be produced by culturing in a medium a microorganism obtained by the methods of the above (iii) and (v), allowing the dipeptide to form and accumulate in the culture, and recovering the dipeptide from the culture.
Culturing of the microorganism in a medium can be carried out according to an ordinary method used for culturing of a microorganism.
That is, any of natural media and synthetic media can be used insofar as it contains carbon sources, nitrogen sources, inorganic salts, etc. which can be assimilated by the microorganism and is a medium suitable for efficient culturing of the microorganism.
The medium does not necessarily contain amino acids which constitute the desired dipeptide; however, some of natural media and media for culturing an amino acid-requiring strain contain said amino acids. The medium used in the production process of the present invention may contain an amino acid in an amount required for the growth of a microorganism used in the present invention. That is, the amount of amino acid contained in an ordinary medium is very small compared with that of the amino acid produced by the microorganism used in the production process of the present invention and the presence of the amino acid contained in an ordinary medium does not affect the amount of a dipeptide produced by the present invention; consequently, the medium used in the production process of the present invention may contain the amino acid in such a degree of amount.
For example, a natural medium used in the present invention may contain the amino acid usually in an amount of less than 2.5 g/l, preferably 0.5 g/l or less, more preferably 0.1 g/l or less, further preferably 20 mg/l or less, and a synthetic medium may contain the amino acid usually in an amount of 1 g/l or less, preferably 50 mg/l or less, more preferably 1 mg/l or less, further preferably 0.5 mg/l or less. When a dipeptide consisting of two different kinds of amino acids is produced according to the production process of the present invention and the microorganism used has the ability to produce only one of the amino acids constituting the dipeptide, the other amino acid which can not be produced by the microorganism may be added to the medium used in the present invention. In this case, the amino acid is added usually in an amount of 0.5 g/l to 100 g/l, preferably 2 g/l to 50 g/l.
As the carbon sources, any carbon sources that can be assimilated by the microorganism can be used. Examples of suitable carbon sources include carbohydrates such as glucose, fructose, sucrose, molasses containing them, starch and starch hydrolyzate; organic acids such as acetic acid and propionic acid; and alcohols such as ethanol and propanol.
As the nitrogen sources, ammonia, ammonium salts of organic or inorganic acids such as ammonium chloride, ammonium sulfate, ammonium acetate and ammonium phosphate, and other nitrogen-containing compounds can be used as well as peptone, meat extract, yeast extract, corn steep liquor, casein hydrolyzate, soybean cake, soybean cake hydrolyzate, and various fermented microbial cells and digested products thereof.
Examples of the inorganic salts include potassium dihydrogenphosphate, dipotassium hydrogenphosphate, magnesium phosphate, magnesium sulfate, sodium chloride, ferrous sulfate, manganese sulfate, copper sulfate and calcium carbonate.
Culturing is usually carried out under aerobic conditions, for example, by shaking culture or submerged spinner culture under aeration. The culturing temperature is preferably 15 to 40° C., and the culturing period is usually 5 hours to 7 days. The pH is maintained at 3.0 to 9.0 during the culturing. The pH adjustment is carried out by using an organic or inorganic acid, an alkali solution, urea, calcium carbonate, ammonia, etc.
If necessary, antibiotics such as ampicillin and tetracycline may be added to the medium during the culturing.
When a microorganism transformed with an expression vector comprising an inducible promoter is cultured, an inducer may be added to the medium, if necessary. For example, in the case of a microorganism transformed with an expression vector comprising lac promoter, isopropyl-β-D-thiogalactopyranoside or the like may be added to the medium; and in the case of a microorganism transformed with an expression vector comprising trp promoter, indoleacrylic acid or the like may be added.
The dipeptides produced by the above process include dipeptides in which one or two kinds of amino acids are linked by the α-bond. Preferred are those in which the amino acids are L-amino acids or glycine. More preferred are those represented by formula (I):

R1-R2  (I)

(wherein R1 and R2, which may be the same or different, each represent an amino acid selected from the group consisting of L-alanine (L-Ala), L-glutamine (L-Gln), L-glutamic acid (L-Glu), glycine (Gly), L-valine (L-Val), L-leucine (L-Leu), L-isoleucine (L-Ile), L-proline (L-Pro), L-phenylalanine (L-Phe), L-tryptophan (L-Trp), L-methionine (L-Met), L-serine (L-Ser), L-threonine (L-Thr), L-cysteine (L-Cys), L-asparagine (L-Asn), L-tyrosine (L-Tyr), L-lysine (L-Lys), L-arginine (L-Arg), L-histidine (L-His), L-aspartic acid (L-Asp), L-α-aminobutyric acid (L-α-AB), L-4-hydroxyproline (L-4-HYP), L-3-hydroxyproline (L-3-HYP), L-ornithine (L-Orn) and L-citrulline (L-Cit). Further preferred are dipeptides wherein R1 is L-Ala, Gly, L-Met, L-Ser or L-Thr and R2 is L-Gln, L-Glu, Gly, L-Val, L-Leu, L-Ile, L-Pro, L-Phe, L-Trp, L-Met, L-Ser, L-Thr, L-Cys, L-Asn, L-Tyr, L-Lys, L-Arg, L-His, L-Asp, L-α-AB, L-4-HYP, L-3-HYP, L-Orn or L-Cit. Particularly preferred dipeptides are: dipeptides wherein R1 is L-Ala and R2 is L-Gln, Gly, L-Val, L-Leu, L-Ile, L-Phe, L-Trp, L-Met, L-Ser, L-Thr, L-Cys, L-Asn, L-Tyr, L-Lys, L-Arg, L-His, L-α-AB or L-Cit; dipeptides wherein R1 is Gly and R2 is L-Gln, Gly, L-Phe, L-Trp, L-Met, L-Ser, L-Thr, L-Cys, L-Tyr, L-Lys, L-Arg, L-α-AB or L-Cit; dipeptides wherein R1 is L-Met and R2 is L-Phe, L-Met, L-Cys, L-Tyr, L-Lys or L-His; dipeptides wherein R1 is L-Ser and R2 is L-Gln, Gly, L-Phe, L-Met, L-Ser, L-Thr, L-Tyr, L-His or L-α-AB; dipeptides wherein R1 is L-Thr and R2 is L-Gln, L-Leu, L-Phe, L-Met, L-Ser, L-Thr or L-α-AB; dipeptides wherein R1 is L-Gln and R2 is L-Phe or L-α-AB; a dipeptide wherein R1 is L-Phe and R2 is L-Gln; a dipeptide wherein R1 is L-Trp and R2 is Gly; dipeptides wherein R1 is L-Cys and R2 is L-Ala, L-Gln, Gly or L-Met; dipeptides wherein R1 is L-Lys and R2 is L-Ala, Gly or L-Met; a dipeptide wherein R1 is L-Arg and R2 is L-α-AB; a dipeptide wherein R1 is L-His and R2 is L-Met; and dipeptides wherein R1 is L-α-AB and R2 is L-Ala, L-Gln, Gly, L-Ser, L-Thr, L-Arg or L-α-AB. Most preferred are L-alanyl-L-alanine (L-Ala-L-Ala), L-alanyl-L-glutamine (L-Ala-L-Gln), L-alanyl-L-phenylalanine (L-Ala-L-Phe), L-threonyl-L-phenylalanine (L-Thr-L-Phe), L-alanyl-L-tyrosine(L-Ala-L-Tyr), L-Alanyl-L-methionine(L-Ala-L-Met), L-Alanyl-L-valine(L-Ala-L-Val), L-Alanyl-L-isoleucine(L-Ala-L-Ile), L-Alanyl-L-Leucine(L-Ala-L-Leu) and L-Serinyl-L-phenylalanine(L-Ser-L-Phe).

Recovery of the dipeptide formed and accumulated in the culture can be carried out by ordinary methods using active carbon, ion-exchange resins, etc. or by means such as extraction with an organic solvent, crystallization, thin layer chromatography and high performance liquid chromatography.
The method for obtaining DNA encoding a protein having the activity to form a dipeptide from one or more kinds of amino acids and the like are illustrated in the following experimental examples, but the method for obtaining the DNA and the like are not limited to the following experimental examples.
Experimental Example 1
Search for a Protein Having the Dipeptide-Synthesizing Activity Utilizing a Database
By using, as a query, the amino acid sequence of D-Ala-D-Ala ligase gene derived from Bacillus subtilis 168 [Nature, 390, 249-256 (1997)], a search for a gene encoding a protein having homology which is present in the genomic DNA sequences of Bacillus subtilis 168 was carried out using the homology search function of Subtilist which is a database of the genomic DNA of Bacillus subtilis 168.
From the sequences obtained as a result of the search, genes encoding the amino acid sequences shown in SEQ ID NOS: 33, 34 and 35 which are D-Ala-D-Ala ligase motifs [Biochemistry, 30, 1673 (1991)] and encoding proteins whose function had already been clarified were excluded. Of the remaining sequences, the sequence showing the highest homology (29.1%) to the D-Ala-D-Ala ligase motif was selected as a gene of unknown function, ywfE.
The nucleotide sequence of ywfE gene is shown in SEQ ID NO: 9, and the amino acid sequence of the protein encoded by the nucleotide sequence is shown in SEQ ID NO: 1.
Experimental Example 2
Construction of a Strain Expressing the ywfE Gene
On the basis of the information on the nucleotide sequence obtained in Experimental Example 1, a ywfE gene fragment of Bacillus subtilis was obtained in the following manner.
That is, Bacillus subtilis 168 (ATCC 23857) was inoculated into LB medium [10 g/l Bacto-tryptone (Difco), 5 g/l yeast extract (Difco) and 5 g/l sodium chloride] and subjected to static culture overnight at 30° C. After the culturing, the chromosomal DNA of the microorganism was isolated and purified according to the method using saturated phenol described in Current Protocols in Molecular Biology.
By using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.), DNAs having the nucleotide sequences shown in SEQ ID NOS: 19 to 22 (hereinafter referred to as primer A, primer B, primer C and primer D, respectively) were synthesized. Primer A has a sequence wherein a nucleotide sequence containing the XhoI recognition sequence is added to the 5′ end of a region of the Bacillus subtilis chromosomal DNA containing the initiation codon of ywfE gene. Primer B has a sequence wherein a nucleotide sequence containing the BamHI recognition sequence is added to the 5′ end of a nucleotide sequence complementary to a sequence containing the termination codon of ywfE gene. Primer C has a sequence wherein a nucleotide sequence containing the EcoRI recognition sequence is added to the 5′ end of the nucleotide sequence of trp promoter region of expression vector pTrS30 containing trp promoter [prepared from Escherichia coli JM109/pTrS30 (FERM BP-5407)]. Primer D has a sequence wherein a nucleotide sequence containing the XhoI recognition sequence is added to the 5′ end of a sequence complementary to the sequence of trp promoter region of expression vector pTrS30 containing trp promoter.
A ywfE gene fragment was amplified by PCR using the above primer A and primer B, and the chromosomal DNA of Bacillus subtilis as a template. A trp promoter region fragment was amplified by PCR using primer C and primer D, and pTrS30 as a template. PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 0.1 μg of the chromosomal DNA or 10 ng of pTrS30 as a template, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase (Stratagene), 4 μl of buffer for Pfu DNA polymerase (10×) (Stratagene) and 200 μmol/l each of dNTPs (dATP, dGTP, dCTP and dTTP).
One-tenth of each of the resulting reaction mixtures was subjected to agarose gel electrophoresis to confirm that a ca. 1.4 kb DNA fragment corresponding to the ywfE gene fragment and a ca. 0.3 kb DNA fragment corresponding to the trp promoter region fragment were respectively amplified in the PCR using primer A and primer B and the PCR using primer C and primer D. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform (1 vol/1 vol) saturated with TE [10 mmol/l Tris-HCl (pH 8.0), 1 mmol/l EDTA]. The resulting solution was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged to precipitate DNA, and the obtained DNA was dissolved in 20 μl of TE.
The thus obtained solutions (5 μl each) were respectively subjected to reaction to cleave the DNA amplified using primer A and primer B with restriction enzymes XhoI and BamHI and to reaction to cleave the DNA amplified using primer C and primer D with restriction enzymes EcoRI and XhoI. DNA fragments were separated by agarose gel electrophoresis, and a 1.4 kb fragment containing ywfE gene and a 0.3 kb fragment containing trp promoter region were respectively recovered using GENECLEAN II Kit (BIO 101).
Expression vector pTrS30 containing trp promoter [prepared from Escherichia coli JM109/pTrS30 (FERM BP-5407)] (0.2 μg) was cleaved with restriction enzymes EcoRI and BamHI. DNA fragments were separated by agarose gel electrophoresis and a 4.5 kb DNA fragment was recovered in the same manner as above.
The 1.4 kb fragment containing ywfE gene, the 0.3 kb fragment containing trp promoter region and the 4.5 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit (Takara Bio Inc.) at 16° C. for 16 hours.
Escherichia coli NM522 (Stratagene) was transformed using the reaction mixture according to the method using calcium ion [Proc. Natl. Acad. Sci. USA, 69, 2110 (1972)], spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from a colony of the transformant that grew on the medium according to a known method and the structure of the plasmid was analyzed using restriction enzymes, whereby it was confirmed that expression vector pPE43 containing ywfE gene ligated downstream of the trp promoter was obtained (FIG. 1).
Experimental Example 3
Production of a Dipeptide
Escherichia coli NM522 carrying pPE43 (Escherichia coli NM522/pPE43) obtained in Experimental Example 2 was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube, and cultured at 28° C. for 17 hours. The resulting culture was centrifuged to obtain wet cells.
A reaction mixture (0.1 ml) comprising 60 mg/ml (final concentration) wet cells, 120 mmol/l potassium phosphate buffer (pH 7.4), 60 mmol/1 magnesium chloride, 60 mmol/l ATP, 30 mmol/l L-Ala, 30 mmol/l L-Gln and 0.4% Nymeen S-215 was prepared, and reaction was carried out at 37° C. for 3 minutes.
After the completion of reaction, the reaction product was derivatized by the dinitrophenol method and then analyzed by HPLC. The HPLC analysis was carried out using, as a separation column, Lichrosorb-RP-18 column (Kanto Kagaku) and, as an eluent, 1% (v/v) phosphoric acid and 25% (v/v) acetonitrile at a flow rate of 0.7 ml/min. As a result, it was confirmed that 120 mg/l L-alanyl-L-glutamine (L-Ala-L-Gln) was formed and accumulated in the reaction mixture.
Formation of L-Ala-L-Gln was not observed when the reaction was carried out using cells of Escherichia coli NM522/pTrS30, which is a control strain carrying only a vector.
Experimental Example 4
Purification of C-Terminal His-Tagged Recombinant Dipeptide Synthetase
By using the above DNA synthesizer, DNAs having the nucleotide sequences shown in SEQ ID NOS: 23 and 24 (hereinafter referred to as primer E and primer F, respectively) were synthesized. Primer E has a nucleotide sequence containing a region wherein the initiation codon of ywfE gene (atg) is substituted by the NcoI recognition sequence (ccatgg). Primer F has a nucleotide sequence containing a region wherein the termination codon of ywfE gene is substituted by the BamHI recognition sequence (ggatcc).
PCR was carried out using the chromosomal DNA of Bacillus subtilis 168 (ATCC 23857) as a template and the above primer E and primer F as a set of primers. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 0.1 μg of the chromosomal DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of dNTPs.
One-tenth of the resulting reaction mixture was subjected to agarose gel electrophoresis to confirm that a ca. 1.4 kb fragment corresponding to the ywfE gene fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting solution was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
The thus obtained solution (5 μl) was subjected to reaction to cleave the amplified DNA with restriction enzymes NcoI and BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 1.4 kb DNA fragment containing ywfE gene was recovered using GENECLEAN II Kit.
C-Terminal His-tagged recombinant expression vector pQE60 (Qiagen, Inc.) (0.2 μg) was cleaved with restriction enzymes NcoI and BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 3.4 kb DNA fragment was recovered in the same manner as above.
The 1.4 kb DNA fragment containing ywfE gene and the 3.4 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using the ligation reaction mixture according to the method using calcium ion, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from a colony of the transformant that grew on the medium according to a known method and the structure of the plasmid was analyzed using restriction enzymes, whereby it was confirmed that pQE60ywfE, which is a C-terminal His-tagged ywfE gene expression vector, was obtained (FIG. 2).
Escherichia coli NM522 carrying pQE60ywfE (Escherichia coli NM522/pQE60ywfE) was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube, and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 50 ml of LB medium containing 50 μg/ml ampicillin in a 250-ml Erlenmeyer flask, and cultured at 30° C. for 3 hours. Then, isopropyl-β-D-thiogalactopyranoside (IPTG) was added to give a final concentration of 1 mmol/l, followed by further culturing at 30° C. for 4 hours. The resulting culture was centrifuged to obtain wet cells, and a His-tagged recombinant enzyme was purified from the wet cells using HisTrap (His-tagged protein purification kit, Amersham Pharmacia Biotech) according to the instructions attached thereto.
Experimental Example 5
Production of Dipeptides Using the His-Tagged Recombinant Enzyme (1)
(i) A reaction mixture (0.1 ml) comprising 0.04 mg of the purified His-tagged recombinant enzyme obtained in Experimental Example 4, 100 mmol/l Tris-HCl (pH 8.0), 60 mmol/l magnesium chloride, 60 mmol/l ATP, 30 mmol/l L-Ala and 30 mmol/l L-Gln was prepared, and reaction was carried out at 37° C. for 16 hours.
After the completion of reaction, the reaction product was analyzed in the same manner as in Experimental Example 3 above, whereby it was confirmed that 3.7 g/l L-Ala-L-Gln and 0.3 g/l L-alanyl-L-alanine (L-Ala-L-Ala) were formed and accumulated in the reaction mixture.
(ii) Reactions were carried out under the same conditions as in the above (i) using reaction mixtures having the same composition as that of the reaction mixture of the above (i) except that 0.01 mg of the enzyme was used and L-Phe, L-Met, L-Leu and L-Val, respectively, were used in place of L-Gln.
After the completion of reactions, the reaction products were analyzed in the same manner as in Experimental Example 3 above, whereby it was confirmed that the following dipeptides were formed and accumulated in the respective reaction mixtures: 7.0 g/l L-alanyl-L-phenylalanine (L-Ala-L-Phe) alone; 7.0 g/l L-alanyl-L-methionine (L-Ala-L-Met) and 0.03 g/l L-Ala-L-Ala; 5.0 g/l L-alanyl-L-leucine (L-Ala-L-Leu) and 0.2 g/l L-Ala-L-Ala; and 1.6 g/l L-alanyl-L-valine (L-Ala-L-Val) and 0.3 g/l L-Ala-L-Ala.
(iii) Reactions were carried out under the same conditions as in the above (i) using reaction mixtures having the same composition as that of the reaction mixture of the above (i) except that 0.01 mg of the enzyme was used, Gly was used in place of L-Ala, and L-Phe and L-Met, respectively, were used in place of L-Gln.
After the completion of reactions, the reaction products were analyzed in the same manner as in Experimental Example 3 above, whereby it was confirmed that 5.2 g/l glycyl-L-phenylalanine (Gly-L-Phe) and 1.1 g/l glycyl-L-methionine (Gly-L-Met) were formed and accumulated in the respective reaction mixtures.
When ATP was excluded from the compositions of the above reaction mixtures, no dipeptide was formed.
The above results revealed that the ywfE gene product has the activity to produce, in the presence of ATP, the following dipeptides: L-Ala-L-Gln plus L-Ala-L-Ala, L-Ala-L-Phe, L-Ala-L-Met plus L-Ala-L-Ala, L-Ala-L-Leu plus L-Ala-L-Ala, or L-Ala-L-Val plus L-Ala-L-Ala from L-Ala plus L-Gln, L-Phe, L-Met, L-Leu or L-Val; and Gly-L-Phe or Gly-L-Met from Gly plus L-Phe or L-Met.
Experimental Example 6
Production of Dipeptides Using the His-Tagged Recombinant Enzyme (2)
A reaction mixture (0.1 ml) comprising 0.04 mg of the purified His-tagged recombinant enzyme obtained in Experimental Example 4, 100 mmol/l Tris-HCl (pH 8.0), 60 mmol/1 magnesium chloride and 60 mmol/l ATP was prepared. To this mixture were respectively added combinations of various L-amino acids, Gly and β-Ala selected from the amino acids shown in the first row of Table 1 and in the leftmost column of Table 1 to give a concentration of 30 mmol/l each, and the resulting mixtures were subjected to reaction at 37° C. for 16 hours. After the completion of reactions, the reaction products were analyzed by HPLC, whereby it was confirmed that the dipeptides shown in Table 1 were formed.















TABLE 1








Ala
Gln
Glu
Gly
Val
Leu
Ile
Pro





Ala
AlaAla
AlaGln
AlaAla
AlaGly
AlaVal
AlaLeu
AlaIle
AlaAla




AlaAla

AlaAla
AlaAla
AlaAla
AlaAla


Gln

X
X
GlyGln
X
X
X
X






GlyGly


Glu



GlyGly


Gly



GlyGly



GlyGly


Val


Leu


Ile


Pro


Phe


Trp


Met


Ser


Thr


Cys


Asn


Tyr


Lys


Arg


His


Asp


αAB


β-Ala


Cit






Phe
Trp
Met
Ser
Thr
Cys
Asn
Tyr





Ala
AlaPhe
AlaTrp
AlaMet
AlaSer
AlaThr
AlaAla
AlaAsn
AlaTyr



AlaAla
AlaAla

AlaAla
AlaAla
◯
AlaAla
AlaAla


Gln
◯
X
MetMet
SerGln
ThrGln
◯
X
X






SerSer
ThrThr


Glu


Gly
GlyPhe
GlyGly
GlyMet
GlySer
GlyThr
GlyGly
GlyGly
GlyTyr




◯
GlyGly
GlyGly
GlyGly
◯

GlyGly






SerGly
ThrGly






SerSer
ThrThr


Val


X


Leu


MetMet

ThrLeu


Ile


MetMet


Pro


MetMet
SerSer
ThrThr


Phe


MetPhe
SerPhe
ThrPhe





MetMet

ThrThr


Trp


Met


MetMet
SerMet
ThrMet
MetMet

MetTyr







ThrThr
◯

MetMet


Ser



SerSer
SerThr


SerTyr







SerSer


SerSer







ThrSer







ThrThr


Thr




ThrThr


Cys


Asn


Tyr


Lys


Arg


His


Asp


α-AB


β-Ala


Cit




















Lys
Arg
His
Asp
α-AB
β-Ala
Cit
Azaserine
Theanine





Ala
AlaAla
AlaArg
AlaHis
AlaAla
AlaAla

AlaAla
AlaAla
AlaAla



◯
AlaAla
AlaAla

◯

◯
◯
◯


Gln
X
X
X
X
◯


Glu


Gly
GlyGly
GlyArg
GlyGly
GlyGly
GlyGly

◯



◯
GlyGly


◯


Val


Leu


Ile


Pro


Phe



X

◯


Trp


Met
MetMet

MetMet


◯



◯

◯


Ser


SerHis

SerSer







◯


Thr




ThrThr







◯


Cys


Asn


Tyr


Lys


Arg




◯


His





β-AlaHis


Asp


α-AB




◯


β-Ala


Cit





◯









The dipeptides formed by the reaction using, as substrates, two (or one) kinds of L-amino acids, Gly and β-Ala shown in the first row and the leftmost column of Table 1 are shown in the respective cells of the table. In the table, ◯ means that a dipeptide was formed though its sequence was unidentified; X means that formation of a dipeptide was not confirmed; and a blank means that reaction was not carried out.
Experimental Example 7
Production of a Dipeptide Using a Strain Expressing the His-Tagged Recombinant Enzyme
Escherichia coli NM522/pQE60ywfE obtained in Experimental Example 4 was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube, and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 50 ml of LB medium containing 50 μg/ml ampicillin in a 250-ml Erlenmeyer flask, and cultured at 30° C. for 3 hours. Then, IPTG was added to give a final concentration of 1 mmol/l, followed by further culturing at 30° C. for 4 hours. The resulting culture was centrifuged to obtain wet cells.
A reaction mixture (20 ml, pH 7.2) comprising 200 g/l wet cells, 50 g/l glucose, 5 g/l phytic acid (diluted to neutrality with 33% conc. sodium hydroxide solution), 15 g/l potassium dihydrogenphosphate, 5 g/l magnesium sulfate heptahydrate, 4 g/l Nymeen S-215, 10 ml/l xylene, 200 mmol/l L-Ala and 200 mmol/l L-Gln was put in a 50-ml beaker, and reaction was carried out at 32° C. at 900 rpm for 2 hours. During the reaction, the pH of the reaction mixture was maintained at 7.2 by using 2 mol/l potassium hydroxide.
The reaction product was analyzed by the same method as in Experimental Example 3, whereby it was confirmed that 25 mg/l L-Ala-L-Gln was accumulated.
Experimental Example 8
Cloning of Genes Corresponding to the ywfE Gene from Various Microorganisms of the Genus Bacillus and Analysis Thereof
On the basis of the nucleotide sequence shown in SEQ ID NO: 9, genes corresponding to the ywfE gene which exist in Bacillus subtilis ATCC 15245, ATCC 6633, IAM 1213, IAM 1107, IAM 1214, ATCC 9466, IAM 1033 and ATCC 21555, Bacillus amyloliquefaciens IFO 3022 and Bacillus pumilus NRRL B-12025 were obtained in the following manner.
That is, Bacillus subtilis ATCC 15245, ATCC 6633, IAM 1213, IAM 1107, IAM 1214, ATCC 9466, IAM 1033 and ATCC 21555, Bacillus amyloliquefaciens IFO 3022 and Bacillus pumilus NRRL B-12025 were respectively inoculated into LB medium and subjected to static culture overnight at 30° C. After the culturing, the chromosomal DNAs of the respective microorganisms were isolated and purified according to the method using saturated phenol described in Current Protocols in Molecular Biology.
By using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.), DNAs having the nucleotide sequences shown in SEQ ID NOS: 25 and 26 (hereinafter referred to as primer G and primer H, respectively) were synthesized. Primer G has a sequence containing a region upstream of the initiation codon of ywfE gene on the chromosomal DNA of Bacillus subtilis 168, and primer H has a sequence complementary to a sequence containing a region downstream of the termination codon of ywfE gene.
PCR was carried out using each of the chromosomal DNAs of Bacillus subtilis ATCC 15245, ATCC 6633, IAM 1213, IAM 1107, IAM 1214, ATCC 9466, IAM 1033 and ATCC 21555 and Bacillus amyloliquefaciens IFO 3022 as a template and the above primer G and primer H as a set of primers. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 0.1 μg of the chromosomal DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of dNTPs.
One-tenth of each of the resulting reaction mixtures was subjected to agarose gel electrophoresis to confirm that a ca. 1.4 kb fragment corresponding to the ywfE gene fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting solution was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
Each of the thus obtained 1.4 kb DNA fragments derived from the chromosomal DNAs of the respective strains and pCR-blunt (Invitrogen Corp.) were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using each ligation reaction mixture according to the method using calcium ion, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from a colony of each transformant that grew on the medium according to a known method and the structure of each plasmid was analyzed using restriction enzymes. As a result, it was confirmed that the following plasmids containing a gene corresponding to the ywfE gene were obtained: pYWFE1 (derived from ATCC 15245, DNA having the nucleotide sequence shown in SEQ ID NO: 36), pYWFE2 (derived from ATCC 6633, DNA having the nucleotide sequence shown in SEQ ID NO: 10), pYWFE3 (derived from IAM 1213, DNA having the nucleotide sequence shown in SEQ ID NO: 11), pYWFE4 (derived from IAM 1107, DNA having the nucleotide sequence shown in SEQ ID NO: 12), pYWFE5 (derived from IAM 1214, DNA having the nucleotide sequence shown in SEQ ID NO: 13), pYWFE6 (derived from ATCC 9466, DNA having the nucleotide sequence shown in SEQ ID NO: 9), pYWFE7 (derived from IAM 1033, DNA having the nucleotide sequence shown in SEQ ID NO: 36), pYWFE8 (derived from ATCC 21555, DNA having the nucleotide sequence shown in SEQ ID NO: 14) and pYWFE9 (derived from IFO 3022, DNA having the nucleotide sequence shown in SEQ ID NO: 15).
On the other hand, a gene corresponding to ywfE gene derived from Bacillus pumilus NRRL B-12025 (DNA having the nucleotide sequence shown in SEQ ID NO: 16) was obtained in the following manner.
PCR was carried out using the chromosomal DNA of the NRRL B-12025 strain prepared above as a template and DNAs respectively consisting of the nucleotide sequences shown in SEQ ID NOS: 27 and 28 as a set of primers. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 98° C. for 5 seconds, reaction at 55° C. for 30 seconds and reaction at 72° C. for one minute, using 50 μl of a reaction mixture comprising 0.1 μg of the chromosomal DNA, 0.5 μmol/l each of the primers, 2.5 units of Z-taq polymerase (Takara Bio Inc.), 5 μl of buffer for Z-taq polymerase (10×) (Takara Bio Inc.) and 200 μmol/l each of dNTPs.
One-tenth of the resulting reaction mixture was subjected to agarose gel electrophoresis to confirm that a ca. 0.8 kb fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
The thus obtained 0.8 kb DNA fragment and pGEM T-easy (Promega Corp.) were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli DH5a was transformed using the reaction mixture according to the method using calcium ion, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from the transformant obtained above and the nucleotide sequence of the ca. 0.8 kb DNA insert was determined, whereby a sequence from nucleotides 358 to 1160 in the nucleotide sequence shown in SEQ ID NO: 16 was confirmed.
The above plasmid was cleaved with EcoRI and then subjected to agarose gel electrophoresis to separate a DNA fragment. The DNA fragment was purified using GENECLEAN II Kit, and ca. 0.5 μg of the purified DNA fragment was DIG-labeled using DIG-High Prime DNA Labeling & Detection Starter Kit I (Roche Diagnostics Corp.) according to the instructions attached thereto.
Southern analysis of the chromosomal DNA of the NRRL B-12025 strain was carried out using the DIG-labeled DNA obtained above.
The chromosomal DNA of the NRRL B-12025 strain was completely digested with BamHI, EcoRI, HindIII, KpnI, PstI, SacI, SalI and SphI, respectively, and subjected to agarose gel electrophoresis to separate DNA fragments, followed by transfer to nylon membrane plus charge (Roche Diagnostics Corp.) according to an ordinary method.
After the DNA fragments were fixed on the nylon membrane by UV irradiation, Southern hybridization was carried out using the above probe DNA and the nylon membrane.
The hybridization was carried out by bringing the nylon membrane into contact with the probe DNA at 65° C. for 16 hours, washing the nylon membrane twice with a solution consisting of 0.1% SDS and 2×SSC at room temperature for 5 minutes, and further washing the membrane twice with a solution consisting of 0.1% SDS and 0.5×SSC at 65° C. for 15 minutes. The other operations and conditions and detection of the hybridized DNA were carried out according to the instructions attached to the above-mentioned DIG-High Prime DNA Labeling & Detection Starter Kit I.
As a result, color development was observed at around 3.5 kbp of the fragments completely digested with HindIII and PstI.
Subsequently, the chromosomal DNA of the NRRL B-12025 strain was completely digested with HindIII and PstI, respectively, and subjected to agarose gel electrophoresis to separate DNA fragments. From the respective restriction enzyme-digested DNAs, 3-4 kbp fragments were purified using GENECLEAN II Kit, followed by autocyclization using a ligation kit.
On the basis of the nucleotide sequence of the 0.8 kb DNA fragment determined above, the nucleotide sequences shown in SEQ ID NOS: 29 and 30 were designed and synthesized, and they were used in PCR using the cyclized DNA obtained above as a template. PCR was carried out by 30 cycles, one cycle consisting of reaction at 98° C. for 5 seconds, reaction at 55° C. for 30 seconds and reaction at 72° C. for 3 minutes and 30 seconds, using 50 μl of a reaction mixture comprising 10 ng of the cyclized DNA, 0.5 μmol/l each of the primers, 2.5 units of pyrobest polymerase (Takara Bio Inc.), 5 μl of buffer for pyrobest polymerase (10×) (Takara Bio Inc.) and 200 μmol/l each of dNTPs.
One-tenth of the resulting reaction mixture was subjected to agarose gel electrophoresis to confirm that a ca. 3.0 kb fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
The thus obtained DNA fragment and Zero Blunt PCR Cloning Kit (Invitrogen Corp.) were subjected to ligation reaction using a ligation kit.
Escherichia coli NM522 was transformed using the reaction mixture according to the method using calcium ion, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from a colony of the transformant that grew on the medium according to a known method and the structure of the plasmid was analyzed using restriction enzymes. As a result, it was confirmed that plasmid pYWFE10 (derived from NRRL B-12025, DNA having the nucleotide sequence shown in SEQ ID NO: 16) containing a gene corresponding to the ywfE gene was obtained.
The nucleotide sequences of the genes corresponding to the ywfE gene which are respectively contained in the plasmids pYWFE1 to pYWFE10 obtained above were determined using 373A DNA Sequencer.
The amino acid sequences of the proteins encoded by the genes respectively contained in pYWFE1, pYWFE6 and pYWFE7 were identical with the amino acid sequence of the protein encoded by the ywfE gene, whereas those of the proteins encoded by the genes respectively contained in pYWFE2, pYWFE3, pYWFE4, pYWFE5, pYWFE8, pYWFE9 and pYWFE10 were different from the amino acid sequence of the protein encoded by the ywfE gene.
The amino acid sequences of the proteins encoded by the genes corresponding to the ywfE gene which are contained in pYWFE2, pYWFE3, pYWFE4, pYWFE5, pYWFE8, pYWFE9 and pYWFE10, and pYWFE1 and pYWFE7 are shown in SEQ ID NOS: 2 to 8 and 1, respectively, and the nucleotide sequences of these genes are shown in SEQ ID NOS: 10 to 16 and 36, respectively.
Experimental Example 9
Purification of C-Terminal His-Tagged Recombinant Dipeptide Synthetase
PCR was carried out using each of the chromosomal DNAs of Bacillus subtilis ATCC 15245, ATCC 6633, IAM 1213, IAM 1107, IAM 1214, ATCC 9466, IAM 1033 and ATCC 21555 and Bacillus amyloliquefaciens IFO 3022 as a template and primer A and primer B described in Experimental Example 2 as a set of primers. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 0.1 μg of the chromosomal DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of dNTPs.
When the chromosomal DNA of Bacillus pumilus NRRL B-12025 was used as a template, PCR was carried out using DNAs respectively having the nucleotide sequences shown in SEQ ID NOS: 31 and 32 as a set of primers under the same conditions as above.
One-tenth of each of the resulting reaction mixtures was subjected to agarose gel electrophoresis to confirm that a ca. 1.4 kb DNA fragment corresponding to the ywfE gene fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
Each of the thus obtained solutions (5 μl) was subjected to reaction to cleave the amplified DNA with restriction enzymes NcoI and BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 1.4 kb DNA fragment containing a gene corresponding to the ywfE gene was recovered using GENECLEAN II Kit.
Subsequently, 0.2 μg of the C-terminal His-tagged recombinant expression vector pQE60 was cleaved with restriction enzymes NcoI and BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 3.4 kb DNA fragment was recovered in the same manner as above.
Each of the 1.4 kb DNA fragments containing a gene corresponding to the ywfE gene of Bacillus subtilis 168 and the 3.4 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using each ligation reaction mixture according to the method using calcium ion, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from a colony of each transformant that grew on the medium according to a known method and the structure of each plasmid was analyzed using restriction enzymes. As a result, it was confirmed that the following C-terminal His-tagged gene expression vectors were obtained: pQE60ywfE1 (a vector containing the gene derived from ATCC 15245), pQE60ywfE2 (a vector containing the gene derived from ATCC 6633), pQE60ywfE3 (a vector containing the gene derived from IAM 1213), pQE60ywfE4 (a vector containing the gene derived from IAM 1107), pQE60ywfE5 (a vector containing the gene derived from IAM 1214), pQE60ywfE6 (a vector containing the gene derived from ATCC 9466), pQE60ywfE7 (a vector containing the gene derived from IAM 1033), pQE60ywfE8 (a vector containing the gene derived from ATCC 21555), pQE60ywfE9 (a vector containing the gene derived from IFO 3022) and pQE60ywfE10 (a vector containing the gene derived from NRRL B-12025).
Escherichia coli NM522/pQE60ywfE1 to NM522/pQE60ywfE10 strains obtained above were respectively inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube, and cultured at 28° C. for 17 hours. Each of the resulting cultures was inoculated into 50 ml of LB medium containing 50 μg/ml ampicillin in a 250-ml Erlenmeyer flask, and cultured at 30° C. for 3 hours. Then, IPTG was added to give a final concentration of 1 mmol/l, followed by further culturing at 30° C. for 4 hours. The resulting culture was centrifuged to obtain wet cells, and His-tagged recombinant enzymes were purified from the respective wet cells using HisTrap according to the instructions attached thereto.
Experimental Example 10
Production of Dipeptides Using Purified Enzymes
Reaction mixtures (0.1 ml each) comprising 0.04 mg of the respective recombinant enzymes obtained in Experimental Example 9, 100 mmol/l Tris-HCl (pH 8.0), 60 mmol/1 magnesium chloride, 60 mmol/l ATP, 30 mmol/l L-Ala and 30 mmol/l L-Gln were prepared, and reactions were carried out at 37° C. for 16 hours.
After the completion of reactions, the reaction mixtures were analyzed by the method described in Experimental Example 3, whereby it was confirmed that 3.0 to 3.5 g/l L-Ala-L-Gln and 0.25 to 0.3 g/l L-Ala-L-Ala were formed and accumulated.
When ATP was excluded from the compositions of the above reaction mixtures, L-Ala-L-Gln or L-Ala-L-Ala was not formed at all.
The above results revealed that all of the products of the genes obtained in Experimental Example 8 have the activity to produce L-Ala-L-Gln and L-Ala-L-Ala from L-Ala and L-Gln in the presence of ATP.
Experimental Example 11
Acquisition of the albC Gene and its Analogous Gene
The albC gene and its analogous gene were obtained from Streptomyces noursei and Streptomyces albulus based on the nucleotide sequence of the albC gene of Streptomyces noursei [Chemistry & Biol., 9, 1355 (2002)] in the following manner.
Streptomyces noursei IFO15452 and Streptomyces albulus IFO14147 were inoculated into KM73 medium [2 g/l yeast extract (Difco) and 10 g/l soluble starch (Wako Pure Chemical Industries, Ltd.)] containing 1% glycine and KP medium [15 g/l glucose, 10 g/l glycerol, 10 g/l polypeptone (Nihon Pharmaceutical Co., Ltd.), 10 g/1 meat extract (Kyokuto Pharmaceutical Industrial Co., Ltd.) and 4 g/l calcium carbonate], respectively, and subjected to shaking culture overnight at 28° C. Streptomyces noursei IFO15452 and Streptomyces albulus IFO14147 were distributed by National Institute of Technology and Evaluation (NITE) Biological Resource Center (BRC) (2-5-8, Kazusakamatari, Kisarazu-shi, Chiba 292-0818 Japan).
After the culturing, the chromosomal DNAs of the respective microorganisms were isolated and purified according to the method described in Genetic Manipulation of Streptomyces: a Laboratory Manual: John Innes Foundation.
On the basis of the nucleotide sequence of the albC gene, DNAs having the nucleotide sequences shown in SEQ ID NOS: 41 and 42 (hereinafter referred to as primer J and primer K, respectively) were synthesized by using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.). Primer J has a sequence wherein a sequence containing the NcoI recognition sequence is added to the 5′ end of a region containing the initiation codon of the albC gene on the chromosomal DNA of Streptomyces noursei. Primer K has a sequence wherein a sequence containing the BglII recognition sequence is added to the 5′ end of a sequence complementary to a sequence containing the termination codon of the albC gene.
PCR was carried out using each of the chromosomal DNAs of Streptomyces noursei and Streptomyces albulus as a template and the above primer J and primer K as a set of primers. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 30 seconds and reaction at 72° C. for one minute, using 50 μl of a reaction mixture comprising 0.1 μg of the chromosomal DNA as a template, 0.5 μmol/l each of the primers, 2.5 units of Ex Taq DNA polymerase (Takara Bio Inc.), 5 μl of buffer for Ex Taq DNA polymerase (10×) (Takara Bio Inc.), 200 μmol/l each of dNTPs and 5 μl of dimethyl sulfoxide.
One-tenth of each of the resulting reaction mixtures was subjected to agarose gel electrophoresis to confirm that a ca. 0.7 kb DNA fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting solution was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged to precipitate DNA, and the obtained DNA was dissolved in 20 μl of TE.
Each of the thus obtained solutions (5 μl) was subjected to reaction to cleave the amplified DNA with restriction enzymes NcoI and BglII. DNA fragments were separated by agarose gel electrophoresis, and a 700 bp DNA fragment was recovered using GENECLEAN II Kit.
Subsequently, 0.2 μg of the expression vector pQE60 containing phage T5 promoter was cleaved with restriction enzymes NcoI and BglII. DNA fragments were separated by agarose gel electrophoresis, and a 3.4 kb DNA fragment was recovered in the same manner as above.
Each of the actinomycetes-derived 0.7 kb DNA fragments and the pQE60-derived 3.4 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using each ligation reaction mixture according to the method using calcium ion, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from a colony of each transformant that grew on the medium according to a known method, and the structure of each plasmid was analyzed using restriction enzymes. As a result, it was confirmed that expression vector pAL-nou containing the DNA derived from Streptomyces noursei at a position downstream of the phage T5 promoter and expression vector pAL-alb containing the DNA derived from Streptomyces albulus were obtained (FIG. 3).
The nucleotide sequence of each actinomycete-derived DNA inserted into the respective plasmid was determined by using a nucleotide sequencer (373A DNA Sequencer), whereby it was confirmed that pAL-alb contained DNA encoding a protein having the amino acid sequence shown in SEQ ID NO: 37, i.e. DNA having the nucleotide sequence shown in SEQ ID NO: 39, and pAL-nou contained DNA encoding a protein having the amino acid sequence shown in SEQ ID NO: 38, i.e. DNA having the nucleotide sequence shown in SEQ ID NO: 40.
Experimental Example 12
Production of Straight-Chain Dipeptides by the Use of Cells as an Enzyme Source
Escherichia coli NM522 carrying pAL-nou or pAL-alb obtained in Experimental Example 11 (Escherichia coli NM522/pAL-nou or NM522/pAL-alb) and Escherichia coli NM522 without a plasmid were respectively inoculated into 10 ml of LB medium containing 50 μg/ml ampicillin in a test tube (no addition of ampicillin in the case of a strain carrying no plasmid, hereinafter the same shall apply), and cultured at 30° C. for 17 hours. Each of the resulting cultures (0.5 ml) was inoculated into 50 ml of LB medium in a 250-ml Erlenmeyer flask and subjected to shaking culture at 30° C. for one hour. Then, IPTG was added to give a final concentration of 1 mmol/l, followed by further culturing for 4 hours. The resulting culture was centrifuged to obtain wet cells.
A reaction mixture (3.0 ml) comprising 100 mg/ml (final concentration) wet cells, 60 mmol/l potassium phosphate buffer (pH 7.2), 10 mmol/1 magnesium chloride, 10 mmol/l ATP, 1 g/l L-Leu and 1 g/l L-Phe was prepared, and reaction was carried out at 30° C. One hour after the start of the reaction, the reaction mixture was sampled and acetonitrile was added thereto to a concentration of 20% (v/v). Then, the obtained reaction product was analyzed by HPLC. The HPLC analysis was carried out by using ODS-HA column (YMC Co., Ltd.) as a separation column and 30% (v/v) acetonitrile as an eluent at a flow rate of 0.6 ml/min, and by measuring ultraviolet absorption at 215 nm.
As a result, it was confirmed that 36.7 mg/l cyclo(L-leucyl-L-phenylalanine) [cyclo(L-Leu-L-Phe)] was accumulated in the reaction mixture of Escherichia coli NM522/pAL-nou. However, no cyclo(L-Leu-L-Phe) was detected in the reaction mixture of Escherichia coli NM522. The same reaction mixtures were analyzed by HPLC under the following conditions to measure straight-chain dipeptides (hereinafter, “straight-chain dipeptide” is referred simply as “dipeptide”) L-leucyl-L-phenylalanine (L-Leu-L-Phe) and L-phenylalanyl-L-leucine (L-Phe-L-Leu).
Both the dipeptides were derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out by using ODS-HG5 (Nomura Kagaku Co., Ltd.) as a separation column and solution A (6 ml/l acetic acid and 20% (v/v) acetonitrile, pH adjusted to 4.8 with triethylamine) and solution B (6 ml/l acetic acid and 70% (v/v) acetonitrile, pH adjusted to 4.8 with triethylamine) as eluents at a flow rate of 0.6 ml/min, and by detecting the dipeptides at an excitation wavelength of 254 nm and a fluorescence wavelength of 630 nm. The ratio of solution A to solution B was 8:2 during the first 5 minutes of elution and thereafter changed with a linear gradient so that the ratio became 1:1 at 20 minutes after the start of elution.
As a result, it was confirmed that 21.9 mg/l L-Leu-L-Phe and 12.0 mg/l L-Phe-L-Leu were accumulated in the reaction mixture of Escherichia coli NM522/pAL-nou and no dipeptide was detected in the reaction mixture of Escherichia coli NM522 used as a control strain.
The above result revealed that the cyclodipeptide-synthesizing enzyme obtained in Experimental Example 11 has the ability to synthesize dipeptides.
Experimental Example 13
Production of Dipeptides Using the Purified Enzyme (1)
Escherichia coli NM522/pAL-nou was cultured in the same manner as in Experimental Example 12. After the completion of the culturing, centrifugation was carried out to obtain wet cells. The obtained wet cells were washed with a 60 mmol/l potassium phosphate buffer (pH 7.2) and suspended in a 20 mmol/l potassium phosphate buffer containing 10 mmol/l imidazole. The resulting suspension was subjected to ultrasonication at 4° C. to obtain a disrupted cell suspension. The obtained suspension (10 ml: containing 0.863 mg of protein) was passed through a His-tag purification column (Amersham Biosciences K.K.) and then 15 ml of a 20 mmol/l potassium phosphate buffer containing 10 mmol/l imidazole was passed through the column for washing to purify a His-tagged albC protein in the column. Then, 2 ml of a reaction mixture having the same composition as that in Experimental Example 12 [composition: 60 mmol/l potassium phosphate buffer (pH 7.2), 10 mmol/1 magnesium chloride, 10 mmol/l ATP, 1 g/l L-Leu, 1 g/l L-Phe] was put into the column containing the His-tagged albC protein, followed by incubation at 30° C., during which the substrates were held in the column. After 24 hours, the reaction mixture in the column was eluted with 3 ml of a reaction mixture having the same composition, and the cyclodipeptide and dipeptides in the reaction mixture were determined in the same manner as in Experimental Example 12.
As a result, it was confirmed that 6.8 mg/l cyclo(L-Leu-L-Phe), 28.7 mg/l L-Leu-L-Phe and 18.5 mg/l L-Phe-L-Leu were formed. No cyclodipeptide or dipeptide was detected in the reaction mixture when without ATP incubated in the same manner.
Experimental Example 14
Production of Dipeptides Using the Purified Enzyme (2)
Enzymatic reaction was carried out in the same manner as in Experimental Example 13 except that the amino acids as substrates were replaced by another amino acid, and the obtained product was analyzed. As the reaction mixture, a mixture having the same composition as that of Experimental Example 13 except that the amino acids as the substrates were replaced by 1 g/l L-Ala, L-Leu or L-Phe was used.
As a result, it was revealed that 9.41 mg/l L-Ala-L-Ala, 7.85 mg/l L-Leu-L-Leu and 5.20 mg/l L-Phe-L-Phe were respectively formed in 24 hours after the start of the reaction.
Experimental Example 15
Construction of Escherichia coli for Enhanced Expression of the ywfE Gene
By using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.), DNAs having the sequences shown in SEQ ID NOS: 84 to 87 (hereinafter referred to as primer L, primer M, primer N and primer 0, respectively) were synthesized. The sequence of SEQ ID NO: 84 is a sequence wherein a sequence containing the XhoI recognition sequence is added to the 5′ end of a region containing the Shine-Dalgarno sequence (ribosome binding sequence) of the ywfE gene on the plasmid pQE60ywfE. The sequence of SEQ ID NO: 85 is a sequence wherein a sequence containing the BamHI recognition sequence is added to the 5′ end of a sequence complementary to a sequence containing the termination codon of the ywfE gene. The sequence of SEQ ID NO: 86 is a sequence wherein a sequence containing the EcoRI recognition sequence is added to the 5′ end of the sequence of trp promoter region of expression vector pTrS30 containing trp promoter. The sequence of SEQ ID NO: 87 is a sequence wherein a sequence containing the XhoI recognition sequence is added to the 5′ end of a sequence complementary to the sequence of trp promoter region of expression vector pTrS30 containing trp promoter.
A ywfE gene fragment and a trp promoter region fragment were amplified by PCR using the above primers L and M, and primers N and O as a set of primers, respectively, and the plasmid pQE60ywfE as a template. PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 10 ng of pQE60ywfE, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of dNTPs.
One-tenth of each of the resulting reaction mixtures was subjected to agarose gel electrophoresis to confirm that a ca. 1.4 kb fragment corresponding to the ywfE gene fragment and a ca. 0.3 kb fragment corresponding to the trp promoter region fragment were respectively amplified in the PCR using primer L and primer M and the PCR using primer N and primer 0. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting solution was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA was dissolved in 20 μl of TE.
The thus obtained DNA solutions (5 μl each) were respectively subjected to reaction to cleave the DNA amplified using primer L and primer M with restriction enzymes XhoI and BamHI and to reaction to cleave the DNA amplified using primer N and primer O with restriction enzymes EcoRI and XhoI. DNA fragments were separated by agarose gel electrophoresis, and a 1.4 kb fragment containing the ywfE gene and a 0.3 kb fragment containing trp promoter region were respectively recovered using GENECLEAN II Kit.
Expression vector pTrs30 containing trp promoter (0.2 μg) was cleaved with restriction enzymes EcoRI and BamHI. DNA fragments were separated by agarose gel electrophoresis and a 4.5 kb DNA fragment was recovered in the same manner as above.
The 1.4 kb fragment containing the ywfE gene, the 0.3 kb fragment containing trp promoter region and the 4.5 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using the reaction mixture according to the method using calcium ion, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from a colony of the transformant that grew on the medium according to a known method, whereby expression vector pPE56 containing the ywfE gene at a position downstream of the trp promoter was obtained. The structure of the vector was confirmed by digestion with restriction enzymes (FIG. 4)
Experimental Example 16
Preparation of Strains Having Deletions of the pepD, pepN, pepB and pepA Genes and the dpp Operon
Strains in which specific genes on Escherichia coli chromosomal DNA are deleted were prepared according to the method utilizing the homologous recombination system of lambda phage [Proc. Natl. Acad. Sci. USA, 97, 6641-6645 (2000)].
Plasmids pKD46, pKD3 and pCP20 used below were prepared by extraction, according to a known method, from Escherichia coli strains carrying them which were obtained from Escherichia coli Genetic Stock Center, Yale University, U.S.A.
(1) Cloning of DNA Fragments for Gene Deletion
For the purpose of deleting the following genes existing on the chromosomal DNA of Escherichia coli K12, DNAs having nucleotide sequences homologous to 36-bp nucleotide sequences that lie upstream and downstream of the respective genes to be deleted on the chromosomal DNA of Escherichia coli K12 and the nucleotide sequence shown in SEQ ID NO: 54 which is recognized by yeast-derived Flp recombinase were synthesized using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.). The genes to be deleted are the pepD gene having the nucleotide sequence shown in SEQ ID NO: 55, the pepN gene having the nucleotide sequence shown in SEQ ID NO: 56, the pepB gene having the nucleotide sequence shown in SEQ ID NO: 57, the pepA gene having the nucleotide sequence shown in SEQ ID NO: 58, the dppA gene having the nucleotide sequence shown in SEQ ID NO: 59, the dppB gene having the nucleotide sequence shown in SEQ ID NO: 60, the dppC gene having the nucleotide sequence shown in SEQ ID NO: 61, the dppD gene having the nucleotide sequence shown in SEQ ID NO: 62 and the dppF gene having the nucleotide sequence shown in SEQ ID NO: 63. In the case of the dppA, dppB, dppC, dppD and dppF genes, which form an operon, DNAs having nucleotide sequences homologous to the nucleotide sequences that lie upstream and downstream of the operon were synthesized.
That is, DNAs consisting of the following nucleotide sequences were synthesized as respective sets of primers for amplification of DNA fragments for gene deletion: SEQ ID NOS: 64 and 65 for pepD gene deletion; SEQ ID NOS: 66 and 67 for pepN gene deletion; SEQ ID NOS: 68 and 69 for pepA gene deletion; SEQ ID NOS: 70 and 71 for pepB gene deletion; and SEQ ID NOS: 72 and 73 for dpp operon deletion.
Subsequently, PCR was carried out using each set of the above synthetic DNAs as a set of primers and pKD3 DNA as a template. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 10 ng of the plasmid DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
One-tenth of each of the resulting reaction mixtures was subjected to agarose gel electrophoresis to confirm that the desired fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE.
The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes, followed by centrifugation. By this procedure, chloramphenicol resistance gene-containing DNA fragments for deletion of the pepD, pepN, pepB and pepA genes and the dpp operon were obtained.
(2) Preparation of Escherichia coli JM101 Having pepD Gene Deletion
Escherichia coli JM101 was transformed with pKD46, spread on LB agar medium containing 100 mg/l ampicillin, and cultured at 30° C. to select Escherichia coli JM101 carrying pKD46 (hereinafter referred to as Escherichia coli JM101/pKD46).
The plasmid pKD46 carries λ Red recombinase gene the expression of which can be induced by L-arabinose. Accordingly, when Escherichia coli carrying pKD46 grown in the presence of L-arabinose is transformed using a straight-chain DNA, homologous recombination occurs with high frequency. Further, as pKD46 has a thermosensitive replication origin, curing of the plasmid can be readily caused by culturing the strain at 42° C.
The chloramphenicol resistance gene-containing DNA fragment for pepD gene deletion obtained above was introduced into Escherichia coli JM101/pKD46 obtained by culturing in the presence of 10 mmol/l L-arabinose and 50 μg/ml ampicillin by electroporation. The resulting cells were spread on LB agar medium (10 g/l Bacto-tryptone, 5 μg/l Bacto-yeast extract, 5 g/l sodium chloride and 15 g/l agar) containing 25 mg/l chloramphenicol and cultured at 30° C. to select a transformant in which the chloramphenicol resistance gene-containing DNA fragment for pepD gene deletion was integrated into the chromosomal DNA of Escherichia coli JM101 by homologous recombination.
The selected chloramphenicol-resistant strain was inoculated onto LB agar medium containing 25 mg/l chloramphenicol and cultured at 42° C. for 14 hours, followed by single colony isolation. Replicas of the obtained colonies were made on LB agar medium containing 25 mg/l chloramphenicol and LB agar medium containing 100 mg/l ampicillin, followed by culturing at 37° C. By selecting a colony showing chloramphenicol resistance and ampicillin sensitivity, a pKD46-cured strain was obtained.
The pKD46-cured strain thus obtained was transformed using pCP20, followed by selection on LB agar medium containing 100 mg/l ampicillin to obtain a pKD46-cured strain carrying pCP20.
The plasmid pCP20 carries a yeast-derived Flp recombinase gene the expression of which can be induced at a temperature of 42° C.
The chloramphenicol resistance gene-containing DNA fragments for deletion of the pepD, pepN, pepB and pepA genes and the dpp operon prepared above contain nucleotide sequences recognized by Flp recombinase at both termini of the chloramphenicol resistance gene. Therefore, the resistance gene can be readily deleted by homologous recombination catalyzed by Flp recombinase.
Further, as pCP20 has a thermosensitive replication origin, expression of Flp recombinase and curing of pCP20 can be simultaneously induced by culturing the pCP20-carrying strain at 42° C.
The pCP20-carrying pKD46-cured strain obtained above was inoculated onto drug-free LB agar medium and cultured at 42° C. for 14 hours, followed by single colony isolation. Replicas of the obtained colonies were made on drug-free LB agar medium, LB agar medium containing 25 mg/l chloramphenicol and LB agar medium containing 100 mg/l ampicillin, followed by culturing at 30° C. Then, colonies showing chloramphenicol sensitivity and ampicillin sensitivity were selected.
Chromosomal DNAs were prepared from the respective strains selected above according to an ordinary method [Seibutsukogaku Jikkensho (Experiments in Biotechnology), edited by The Society for Biotechnology, Japan, p. 97-98, Baifukan (1992)]. PCR was carried out using, as a set of primers, DNAs having the nucleotide sequences shown in SEQ ID NOS: 74 and 75 which were designed based on an inner nucleotide sequence of the pepD gene to be deleted, and using each of the chromosomal DNAs as a template. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 0.1 μg of the chromosomal DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
A strain with which no amplified DNA fragment was detected in the above PCR was identified as a strain having pepD gene deletion and was designated as Escherichia coli JPD1.
(3) Preparation of a Strain in which the pepD and pepN Genes on the Chromosomal DNA of Escherichia coli JM101 are Deleted
Escherichia coli JPD1 obtained in the above (2) was transformed with pKD46, spread on LB agar medium containing 100 mg/l ampicillin, and cultured at 30° C. to select Escherichia coli JPD1 carrying pKD46 (hereinafter referred to as Escherichia coli JPD1/pKD46). The chloramphenicol resistance gene-containing DNA fragment for pepN gene deletion was introduced into Escherichia coli JPD1/pKD46 by electroporation to obtain a transformant in which the chloramphenicol resistance gene-containing DNA fragment for pepN gene deletion was integrated into the chromosomal DNA of Escherichia coli JPD1/pKD46 by homologous recombination.
Subsequently, the same procedure as in the above (2) was carried out to obtain a strain in which the chloramphenicol resistance gene was deleted from the chromosomal DNA, which was designated as Escherichia coli JPDN2.
(4) Preparation of Strains in which the pepN, pepA or pepB Gene or the dpp Operon on the Chromosomal DNA of Escherichia coli JM101 is Deleted and Strains Having Multiple Gene Deletion
The strains having pepN, pepA or pepB gene or dpp operon deletion were prepared according to the same procedure as in the above (2) using the respective chloramphenicol resistance gene-containing DNA fragments for gene or operon deletion prepared in the above (1).
Acquisition of the strains having gene deletions by the above method was confirmed by carrying out PCR in the same manner as in the above (2) using, as sets of primers, DNAs having the nucleotide sequences shown in SEQ ID NOS: 76 to 83 which were designed and synthesized based on inner nucleotide sequences of the respective genes to be deleted. That is, DNAs having the following nucleotide sequences were used as respective sets of primers for the confirmation of gene deletion: SEQ ID NOS: 76 and 77 for pepN deletion; SEQ ID NOS: 78 and 79 for pepA deletion; SEQ ID NOS: 80 and 81 for pepB deletion; and SEQ ID NOS: 82 and 83 for dpp operon deletion.
The thus obtained dpp operon-deleted strain, pepN gene-deleted strain, pepA gene-deleted strain and pepB gene-deleted strain were designated as Escherichia coli JDPP1, Escherichia coli JPN1, Escherichia coli JPA1 and Escherichia coli JPB7, respectively.
Further, strains having multiple gene deletions, i.e., deletions of two or more genes or operon selected from the group consisting of the pepD, pepN, pepA and pepB genes and the dpp operon were prepared according to the method of the above (3). Acquisition of the strains having multiple gene deletions was confirmed by PCR similar to that in the above (2). The thus obtained double gene-deleted strain having pepD gene and dpp operon deletions was designated as Escherichia coli JPDP49, triple gene-deleted strain having pepB, pepD and pepN gene deletions as Escherichia coli JPDNB43, triple gene-deleted strain having pepD and pepN gene and dpp operon deletions as Escherichia coli JPNDDP36, quadruple gene-deleted strain having pepA, pepD and pepN gene and dpp operon deletions as Escherichia coli JPNDAP5, and quadruple gene-deleted strain having pepB, pepD and pepN gene and dpp operon deletions as Escherichia coli JPNDBP7. The genes deleted in the gene-deleted strains are shown in Table 2.










TABLE 2







Strain
Deleted gene









JM101
none



JDPP1
dpp operon



JPN1
pepN



JPA1
pepA



JPB7
pepB



JPD1
pepD



JPDN2
pepD, pepN



JPNDB43
pepB, pepD, pepN



JPDP49
pepD, dpp operon



JPNDDP36
pepD, pepN, dpp operon



JPNDAP5
pepA, pepD, pepN, dpp operon



JPNDBP7
pepB, pepD, pepN, dpp operon










Experimental Example 17
Evaluation of Productivity of L-Ala-L-Gln and L-Ala-L-Ala by Escherichia coli Strains in which Peptidase and Dipeptide-Permeating/Transporting Protein Activities are Lost
The strains having deletions of genes encoding various peptidases and dipeptide-permeating/transporting protein which were obtained in Experimental Example 16 were transformed using the plasmid pPE56 constructed in Experimental Example 15 to obtain ampicillin-resistant transformants.
Each of the obtained transformants was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube and cultured at 28° C. for 17 hours. The resulting culture was added to 8 ml of an aqueous medium [16 g/l dipotassium hydrogenphosphate, 14 g/l potassium dihydrogenphosphate, 5 g/l ammonium sulfate, 1 g/l citric acid (anhydrous), 0.5 g/l Casamino acid (Difco), 1 g/l L-Pro, 2.5 g/l L-Ala, 2.5 g/l L-Gln, 10 g/l glucose, 10 mg/l vitamin B1, 25 mg/l magnesium sulfate heptahydrate and 50 mg/l ferrous sulfate heptahydrate; pH adjusted to 7.2 with 10 mol/l sodium hydroxide solution; L-Gln was added after sterilization by filtration of a 10-fold conc. solution; glucose, vitamin B1, magnesium sulfate heptahydrate and ferrous sulfate heptahydrate were added after separate steam sterilization] containing 100 μg/ml ampicillin in a test tube in an amount of 1% and subjected to reaction at 30° C. for 24 hours. The resulting aqueous medium was centrifuged to obtain a supernatant.
The product in the supernatant was derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out using ODS-HG5 (Nomura Kagaku Co., Ltd.) as a separation column and solution A (6 ml/l acetic acid and 20% (v/v) acetonitrile, pH adjusted to 4.8 with triethylamine) and solution B (6 ml/l acetic acid and 70% (v/v) acetonitrile, pH adjusted to 4.8 with triethylamine) as eluents. The ratio of solution A to solution B was 8:2 during the first 5 minutes of elution and thereafter changed with a linear gradient so that the ratio became 1:1 at 20 minutes after the start of elution. The results of analysis are shown in Table 3.










TABLE 3







L-Ala-L-Gln
L-Ala-L-Ala


Strain
Deleted gene
(g/l)
(g/l)


















JM101
none
0
0


JDPP1
dpp operon
0.02
0.01


JPN1
pepN
0.01
0.01


JPA1
pepA
0.01
0.01


JPB7
pepB
0.01
0.01


JPD1
pepD
0.01
0.01


JPDN2
pepD, pepN
0.02
0.03


JPNDB43
pepB, pepD, pepN
0.05
0.12


JPDP49
pepD, dpp operon
0.11
0.08


JPNDDP36
pepD, pepN, dpp operon
0.16
0.21


JPNDAP5
pepA, pepD, pepN, dpp
0.28
0.26



operon


JPNDBP7
pepB, pepD, pepN, dpp
0.43
0.22



operon









As can be seen from Table 3, small amounts of dipeptides were formed and accumulated by use of the microorganisms having deletions of two or less kinds of peptidase genes or one operon encoding a peptide-permeating/transporting protein, whereas the amounts of dipeptides formed and accumulated were greatly increased by use of the microorganisms having deletions of one or more kinds of peptidase genes and one operon encoding a peptide-permeating/transporting protein or microorganisms having deletions of three or more kinds of peptidase genes.
Experimental Example 18
Evaluation of Productivity of L-Alanyl-L-valine (Hereinafter Referred to as L-Ala-L-Val) by Escherichia coli Strains in which Peptidase and Peptide-Permeating/Transporting Protein Activities are Lost
Similarly to Experimental Example 17, the Escherichia coli strains having deletions of genes encoding various peptidases and peptide-permeating/transporting protein were transformed using pPE56. Each of the obtained transformants was added to 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube and cultured at 28° C. for 17 hours. The resulting culture was added to 8 ml of an aqueous medium [16 g/l dipotassium hydrogenphosphate, 14 g/l potassium dihydrogenphosphate, 5 g/l ammonium sulfate, 1 g/l citric acid (anhydrous), 0.5 g/l Casamino acid (Difco), 1 g/l L-Pro, 2.5 g/l L-Ala, 2.5 g/l L-Val, 10 g/l glucose, 10 mg/l vitamin B1, 25 mg/l magnesium sulfate heptahydrate and 50 mg/l ferrous sulfate heptahydrate; pH adjusted to 7.2 with 10 mol/l sodium hydroxide solution; glucose, vitamin B1, magnesium sulfate heptahydrate and ferrous sulfate heptahydrate were added after separate steam sterilization] containing 100 μg/ml ampicillin in a test tube in an amount of 1% and subjected to reaction at 30° C. for 24 hours. The resulting aqueous medium was centrifuged to obtain a supernatant.
The product in the supernatant was analyzed by the method described in Experimental Example 17. The results are shown in Table 4.











TABLE 4









L-Ala-L-Val



Strain
Deleted gene
(g/l)




















JM101
none
0



JDPP1
dpp operon
0



JPN1
pepN
0



JPA1
pepA
0



JPB7
pepB
0



JPD1
pepD
0



JPDN2
pepD, pepN
0



JPNDB43
pepB, pepD, pepN
0.04



JPDP49
pepD, dpp operon
0.11



JPNDDP36
pepD, pepN, dpp operon
0.22



JPNDBP7
pepB, pepD, pepN, dpp operon
0.20










As can be seen from Table 4, the dipeptide was not produced by use of the microorganisms having deletions of two or less kinds of peptidase genes or one operon encoding a peptide-permeating/transporting protein, whereas the dipeptide was produced by use of the microorganisms having deletions of three or more kinds of peptidase genes or microorganisms having deletions of one or more kinds of peptidase genes and one operon encoding a peptide-permeating/transporting protein.
Experimental Example 19
Evaluation of Productivity of Glycyl-L-glutamine (Hereinafter Referred to as Gly-L-Gln) by Escherichia coli Strains in which Peptidase and Dipeptide-Permeating/Transporting Protein Activities are Lost
Similarly to Experimental Example 17, the strains having deletions of various peptidase genes and an operon encoding a dipeptide-permeating/transporting protein were transformed using pPE56. Each of the obtained transformants was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube and cultured at 28° C. for 17 hours.
The resulting culture was added to 8 ml of an aqueous medium [16 g/l dipotassium hydrogenphosphate, 14 g/l potassium dihydrogenphosphate, 5 g/l ammonium sulfate, 1 g/l citric acid (anhydrous), 0.5 g/l Casamino acid (Difco), 1 g/l L-Pro, 2.5 g/l Gly, 2.5 g/l L-Gln, 10 g/l glucose, 10 mg/l vitamin B1, 25 mg/l magnesium sulfate heptahydrate and 50 mg/l ferrous sulfate heptahydrate; pH adjusted to 7.2 with 10 mol/l sodium hydroxide solution; L-Gln was added after sterilization by filtration of a 10-fold conc. solution; glucose, vitamin B1, magnesium sulfate heptahydrate and ferrous sulfate heptahydrate were added after separate steam sterilization] containing 100 μg/ml ampicillin in a test tube in an amount of 1% and subjected to reaction at 30° C. for 24 hours. The resulting aqueous medium was centrifuged to obtain a supernatant.
The product in the supernatant was analyzed by the method described in Experimental Example 17. The results are shown in Table 5.











TABLE 5









Gly-L-Gln



Strain
Deleted gene
(g/l)




















JM101
none
0



JDPP1
dpp operon
0



JPDN2
pepD, pepN
0



JPNDB43
pepB, pepD, pepN
0.01



JPNDDP36
pepD, pepN, dpp operon
0.02



JPNDBP7
pepB, pepD, pepN, dpp operon
0.03










As can be seen from Table 5, the dipeptide was not produced by use of the microorganisms having deletions of two or less kinds of peptidase genes or one operon encoding a peptide-permeating/transporting protein, whereas the dipeptide was produced by use of the microorganisms having deletions of three or more kinds of peptidase genes or microorganisms having deletions of two or more kinds of peptidase genes and one operon encoding a peptide-permeating/transporting protein.
Certain embodiments of the present invention are illustrated in the following examples. These examples are not to be construed as limiting the scope of the invention.
Example 1
Preparation of a Microorganism Having Deletions of the glnE and glnB Genes Involved in the Regulation of L-Glutamine Biosynthesis
Deletion of specific genes on Escherichia coli chromosomal DNA was carried out according to the method utilizing the homologous recombination system of lambda phage [Proc. Natl. Acad. Sci. USA, 97, 6641-6645 (2000)].
(1) Cloning of Drug Resistance Gene-Containing DNA Fragments for Gene Deletion
The nucleotide sequences of the glnE gene and the glnB gene of Escherichia coli K12 were already disclosed [Science, 5331, 1453-1474 (1997)]. On the basis of the reported nucleotide sequences, DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 88 and 89 to be used as primer DNAs for glnE gene deletion and DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 90 and 91 to be used as primer DNAs for glnB gene deletion were synthesized using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.). The synthesized primer DNAs were designed based on the 36-bp nucleotide sequences that lie upstream and downstream of the respective target genes to be deleted.
PCR was carried out using each set of the above synthetic DNAs as a set of primers and pKD3 DNA as a template. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 10 ng of the plasmid DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
One-tenth of each of the resulting reaction mixtures was subjected to agarose gel electrophoresis to confirm that the desired fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE.
The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes, followed by centrifugation to precipitate DNA. Then, the DNA precipitate was dissolved in 20 μl of TE. By this procedure, chloramphenicol resistance gene-containing DNA fragments for deletion of the glnE gene and the glnB gene were obtained.
(2) Preparation of Escherichia coli JM101 in which the glnE Gene on the Chromosomal DNA is Deleted
Escherichia coli JM101 was transformed with pKD46, and Escherichia coli JM101 carrying pKD46 (hereinafter referred to as Escherichia coli JM101/pKD46) was selected on LB agar medium containing 100 mg/l ampicillin. Escherichia coli JM101/pKD46 cultured in the presence of 10 mmol/l L-arabinose and 50 μg/ml ampicillin was transformed by electroporation using the chloramphenicol resistance gene-containing DNA fragment for glnE gene deletion, and a recombinant strain in which the chloramphenicol resistance gene was inserted into the glnE gene on the chromosomal DNA of JM101 strain and the glnE structural gene was deleted was selected on LB agar medium containing 25 mg/l chloramphenicol.
Replicas of the obtained chloramphenicol-resistant strain were made on LB agar medium containing 25 mg/l chloramphenicol, followed by single colony isolation at 42° C. Then, replicas of the obtained colonies were made on LB agar medium containing 25 mg/l chloramphenicol and LB agar medium containing 100 mg/l ampicillin to select a colony showing chloramphenicol resistance and ampicillin sensitivity. The selected pKD46-cured strain was transformed using pCP20, spread on LB agar medium containing 100 mg/l ampicillin, and cultured overnight at 30° C.
Replicas of the ampicillin-resistant strain that grew on the medium were made on drug-free LB agar medium, followed by single colony isolation at 42° C. Then, replicas of the obtained colonies were made on drug-free LB agar medium, LB agar medium containing 25 mg/l chloramphenicol and LB agar medium containing 100 mg/l ampicillin to select colonies showing chloramphenicol sensitivity and ampicillin sensitivity. Chromosomal DNAs were prepared from the respective strains thus obtained according to an ordinary method [Seibutsukogaku Jikkensho (Experiments in Biotechnology), edited by The Society for Biotechnology, Japan, p. 97-98, Baifukan (1992)]. Colony PCR was carried out using primer DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 92 and 93 which were designed based on an inner nucleotide sequence of the glnE gene to be deleted. That is, colony PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising the cells in an amount obtained by contacting a 200-μl pipette tip with the colony, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
Of the strains subjected to PCR, a strain with which no gene amplification was detected was identified as a strain having glnE gene deletion and was designated as Escherichia coli JGLE1.
(3) Preparation of Escherichia coli JM101 in which the glnE and glnB Genes on the Chromosomal DNA are Deleted
Escherichia coli JGLE1 obtained in the above (2) was transformed with pKD46, spread on LB agar medium containing 100 mg/l ampicillin, and cultured overnight at 30° C. to obtain Escherichia coli JGLE1 carrying pKD46 (hereinafter referred to as Escherichia coli JGLE1/pKD46). Escherichia coli JGLE1/pKD46 was transformed by electroporation using the chloramphenicol resistance gene-containing DNA fragment for glnB gene deletion to obtain a recombinant strain in which the chloramphenicol resistance gene was inserted into the glnB gene on the chromosomal DNA and the glnB structural gene was deleted. Colony PCR was carried out under the same conditions as in the above (2) using primer DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 94 and 95 which were designed based on an inner nucleotide sequence of the glnB gene. A strain with which no gene amplification was detected in the above PCR was identified as a strain having glnB gene deletion and was designated as Escherichia coli JGLBE1.
Example 2
Construction of a Plasmid Expressing the ywfE Gene and an Alanine Dehydrogenase Gene (ald Gene) Derived from Bacillus subtilis 
On the basis of the ywfE gene expression plasmid pPE56 constructed in Experimental Example 15, an expression plasmid which constitutively expresses an alanine dehydrogenase gene (ald gene) derived from Bacillus subtilis at the same time was constructed by the method shown in FIG. 5.
By using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.), DNAs having the nucleotide sequences shown in SEQ ID NOS: 96 and 97 (hereinafter referred to as primer P and primer Q, respectively) were synthesized. The sequence shown in SEQ ID NO: 96 is a sequence wherein a sequence containing the BamHI recognition sequence is added to the 5′ end of a region containing the Shine-Dalgarno sequence (ribosome binding sequence) of the ald gene. The sequence shown in SEQ ID NO: 97 is a sequence wherein a sequence containing the BamHI recognition sequence is added to the 5′ end of a sequence complementary to a sequence containing the termination codon of the ald gene.
PCR was carried out using the chromosomal DNA of Bacillus subtilis obtained in Experimental Example 2 as a template and the above primer P and primer Q as a set of primers. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 0.1 μg of the chromosomal DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of dNTPs.
One-tenth of the resulting reaction mixture was subjected to agarose gel electrophoresis to confirm that a ca. 1.2 kb fragment corresponding to the ald gene fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
The thus obtained solution (5 μl) was subjected to reaction to cleave the amplified DNA with restriction enzyme BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 1.2 kb DNA fragment containing the ald gene was recovered using GENECLEAN II Kit.
pPE56 (0.2 μg) was cleaved with restriction enzyme BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 6.3 kb DNA fragment was recovered in the same manner as above. Dephosphorylation of the end of the 6.3 kb DNA fragment was carried out by treatment with alkaline phosphatase (E. coli C75, Takara Bio Inc.) at 60° C. for 30 minutes. The reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
The 1.2 kb DNA fragment containing the ald gene and the alkaline phosphatase-treated 6.3 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using the ligation reaction mixture according to the method using calcium ion, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from a colony of the transformant that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that a plasmid into which the ald gene was inserted in the same direction as the ywfE gene was obtained, and the plasmid was designated as pPE86 (FIG. 5).
Example 3
Construction of a Plasmid Expressing a Feedback-Resistant pheA Gene and a Feedback-Resistant aroF Gene Derived from Escherichia coli 
(1) Construction of a Plasmid Expressing a Desensitized pheA Gene
A feedback-resistant pheA gene was obtained from plasmid pE pheA 22 expressing the phenylalanine-desensitized pheA gene obtained by introduction of a phenylalanine analogue resistance mutation (Japanese Published Unexamined Patent Application No. 260892/86) and a feedback-resistant aroF gene was obtained from plasmid pE aroF 18 expressing the tyrosine-feedback-resistant aroF gene obtained by introduction of a tyrosine resistance mutation (Japanese Published Unexamined Patent Application No. 65691/87), and an expression plasmid was constructed in the following manner.
By using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.), DNAs having the nucleotide sequences shown in SEQ ID NOS: 98 and 99 (hereinafter referred to as primer R and primer S, respectively) were synthesized. The sequence shown in SEQ ID NO: 98 is a sequence wherein a sequence containing the ClaI recognition sequence is added to the 5′ end of a region containing the Shine-Dalgarno sequence (ribosome binding sequence) of the pheA gene. The sequence shown in SEQ ID NO: 99 is a sequence wherein a sequence containing the BamHI recognition sequence is added to the 5′ end of a sequence complementary to a sequence containing the termination codon of the pheA gene. PCR was carried out using the plasmid pE pheA 22 as a template and the above primer R and primer S as a set of primers. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 10 ng of the plasmid DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of dNTPs.
One-tenth of the resulting reaction mixture was subjected to agarose gel electrophoresis to confirm that a ca. 1.1 kb fragment corresponding to the pheA gene fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
The thus obtained solution (5 μl) was subjected to reaction to cleave the amplified DNA with restriction enzymes ClaI and BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 1.1 kb DNA fragment containing the pheA gene was recovered using GENECLEAN II Kit.
Expression vector pTrS30 containing trp promoter [preparable from Escherichia coli JM109/pTrS30 (FERM BP-5407)] (0.2 μg) was cleaved with restriction enzymes ClaI and BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 4.6 kb DNA fragment was recovered in the same manner as above.
The 1.1 kb DNA fragment containing the pheA gene and the 4.6 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using the ligation reaction mixture according to the method using calcium ion, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from a colony of the transformant that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that a plasmid expressing the feedback-resistant pheA gene was obtained, and the plasmid was designated as pPHEA1.
The obtained pPHEA1 (0.2 μg) was cleaved with restriction enzymes EcoRI and BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 1.5 kb DNA fragment containing the trp promoter and the desensitized pheA gene was recovered using GENECLEAN II Kit.
Then, plasmid vector pSTV28 having the replication origin of pACYC184 and containing a chloramphenicol resistance gene (Takara Bio Inc.) (0.2 μg) was cleaved with restriction enzymes EcoRI and BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 3.0 kb DNA fragment was recovered in the same manner as above.
The 1.5 kb DNA fragment containing the trp promoter and the feedback-resistant pheA gene and the 3.0 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using the ligation reaction mixture according to the method using calcium ion, spread on LB agar medium containing 30 μg/ml chloramphenicol, and cultured overnight at 30° C.
A plasmid was extracted from a colony of the transformant that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that a vector expressing the feedback-resistant pheA gene was obtained, and the plasmid was designated as pPHEA2 (FIG. 6).
(2) Construction of a Plasmid Expressing the Feedback-Resistant pheA Gene and the Feedback-Resistant aroF Gene
By using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.), DNAs having the nucleotide sequences shown in SEQ ID NOS: 100 and 101 (hereinafter referred to as primer T and primer U, respectively) were synthesized. The sequence shown in SEQ ID NO: 100 is a sequence wherein a sequence containing the BglII recognition sequence is added to the 5′ end of a region containing the Shine-Dalgarno sequence (ribosome binding sequence) of the aroF gene. The sequence shown in SEQ ID NO: 101 is a sequence wherein a sequence containing the BamHI recognition sequence is added to the 5′ end of a sequence complementary to a sequence containing the termination codon of the aroF gene. PCR was carried out using the plasmid pE aroF 18 as a template and the above primer T and primer U as a set of primers. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 10 ng of the plasmid pE aroF 18, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of dNTPs.
One-tenth of the resulting reaction mixture was subjected to agarose gel electrophoresis to confirm that a ca. 1.1 kb fragment corresponding to the aroF gene fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
The thus obtained solution (5 μl) was subjected to reaction to cleave the amplified DNA with restriction enzymes BglII and BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 1.1 kb DNA fragment containing the desensitized aroF gene was recovered using GENECLEAN II Kit.
The plasmid pPHEA2 expressing the feedback-resistant pheA gene obtained in the above (1) (0.2 μg) was cleaved with restriction enzyme BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 4.5 kb DNA fragment was recovered in the same manner as above. Dephosphorylation of the end of the 4.5 kb DNA fragment was carried out by treatment with alkaline phosphatase at 60° C. for 30 minutes. The reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
The 1.1 kb DNA fragment containing the feedback-resistant aroF gene and the alkaline phosphatase-treated 4.5 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using the ligation reaction mixture according to the method using calcium ion, spread on LB agar medium containing 30 μg/ml chloramphenicol, and cultured overnight at 30° C.
A plasmid was extracted from a colony of the transformant that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that a plasmid expressing the feedback-resistant aroF gene and the feedback-resistant pheA gene in which the feedback-resistant aroF gene was inserted in the same direction as the feedback-resistant pheA gene was obtained, and the plasmid was designated as pPHEAF2 (FIG. 6).
Example 4
Construction of a Plasmid Expressing an aroF-tyrA Operon which Exhibits Tyrosine Resistance Derived from Escherichia coli 
(1) Construction of a Plasmid Expressing an aroF-tyrA Operon which Exhibits Tyrosine Resistance
An aroF-tyrA operon exhibiting tyrosine resistance was obtained from plasmid pKm1aroFm-18 expressing the aroF-tyrA operon obtained by introduction of a tyrosine resistance mutation (Japanese Published Unexamined Patent Application No. 034197/85) and an expression plasmid was constructed in the following manner.
By using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.), DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 102 and 103 were synthesized. The sequence shown in SEQ ID NO: 102 is a sequence wherein a sequence containing the ClaI recognition sequence is added to the 5′ end of a region containing the Shine-Dalgarno sequence (ribosome binding sequence) of the aroF gene. The sequence shown in SEQ ID NO: 103 is a sequence wherein a sequence containing the SphI recognition sequence is added to the 5′ end of a sequence complementary to a sequence containing the termination codon of the tyrA gene.
PCR was carried out using the plasmid pKm1aroFm-18 as a template and the DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 102 and 103 as a set of primers. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 10 ng of the plasmid DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of dNTPs.
One-tenth of the resulting reaction mixture was subjected to agarose gel electrophoresis to confirm that a ca. 2.2 kb fragment corresponding to the aroF-tyrA gene fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
The thus obtained solution (5 μl) was subjected to reaction to cleave the amplified DNA with restriction enzymes ClaI and SphI. DNA fragments were separated by agarose gel electrophoresis, and a 2.2 kb DNA fragment containing the aroF-tyrA operon was recovered using GENECLEAN II Kit.
Expression vector pTrS30 containing trp promoter [preparable from Escherichia coli JM109/pTrS30 (FERM BP-5407)] (0.2 μg) was cleaved with restriction enzymes ClaI and SphI. DNA fragments were separated by agarose gel electrophoresis, and a 4.6 kb DNA fragment was recovered in the same manner as above.
The 2.2 kb DNA fragment containing the aroF-tyrA operon and the 4.6 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using the ligation reaction mixture according to the method using calcium ion, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from a colony of the transformant that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that a plasmid expressing the aroF-tyrA operon which exhibits tyrosine resistance was obtained, and the plasmid was designated as pTY1.
The obtained pTY1 (0.2 μg) was cleaved with restriction enzymes EcoRI and SphI. DNA fragments were separated by agarose gel electrophoresis, and a 2.6 kb DNA fragment containing the trp promoter and the aroF-tyrA operon exhibiting tyrosine resistance was recovered using GENECLEAN II Kit.
Then, plasmid vector pSTV28 having the replication origin of pACYC184 and containing a chloramphenicol resistance gene (Takara Bio Inc.) (0.2 μg) was cleaved with restriction enzymes EcoRI and SphI. DNA fragments were separated by agarose gel electrophoresis, and a 3.0 kb DNA fragment was recovered in the same manner as above.
The 2.6 kb DNA fragment containing the trp promoter and the aroF-tyrA operon exhibiting tyrosine resistance and the 3.0 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using the ligation reaction mixture according to the method using calcium ion, spread on LB agar medium containing 30 μg/ml chloramphenicol, and cultured overnight at 30° C.
A plasmid was extracted from a colony of the transformant that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that a vector expressing the aroF-tyrA operon which exhibits tyrosine resistance was obtained, and the plasmid was designated as pTY2.
Example 5
Preparation of a Strain Having metJ Gene Deletion
(1) Cloning of a Drug Resistance Gene-Containing DNA Fragment for metJ Gene Deletion
The nucleotide sequence of the metJ gene of Escherichia coli K12 was already disclosed [Science, 5331, 1453-1474 (1997)].
The metJ gene encodes a repressor of the L-methionine biosynthesis system of Escherichia coli and it is known that L-methionine producing-ability is enhanced by introducing a mutation to inhibit production of the repressor (Japanese Published Unexamined Patent Application No. 139471/00).
On the basis of the reported nucleotide sequence, DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 104 and 105 to be used as primer DNAs for preparation of a strain having metJ gene deletion were synthesized using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.).
The DNAs have nucleotide sequences homologous to 36-bp nucleotide sequences that lie upstream and downstream of the target gene to be deleted.
PCR was carried out using the DNAs as a set of primers and pKD3 DNA as a template to amplify a chloramphenicol resistance gene-containing DNA fragment for preparation of a strain having metJ gene deletion. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 10 ng of the plasmid DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
One-tenth of the resulting reaction mixture was subjected to agarose gel electrophoresis to confirm that the desired fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
(2) Preparation of Escherichia coli JM101 in which the Drug Resistance Gene is Inserted into the metJ Gene on the Chromosomal DNA
By using Escherichia coli JM101 and the chloramphenicol resistance gene-containing DNA fragment for preparation of a strain having metJ gene deletion obtained in the above (1), a recombinant in which the chloramphenicol resistance gene was inserted into the metJ gene on the chromosomal DNA of Escherichia coli JM101 was prepared in the same manner as in Example 1 (2).
Insertion of the chloramphenicol resistance gene into the chromosome was confirmed by carrying out colony PCR in the same manner as in Example 1 (2) using, as a set of primers, DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 106 and 107, i.e., the nucleotide sequences located approximately 400 bp upstream and downstream of the site to which the chloramphenicol resistance gene was inserted.
Of the strains subjected to colony PCR, a strain with which a ca. 2 kb fragment containing the chloramphenicol resistance gene was amplified was identified as a strain having metJ gene deletion. Then, by using pCP20 expressing Flp recombinase, a strain in which the chloramphenicol resistance gene was cured from the chromosomal DNA was prepared in the same manner as in Example 7 (3), and was designated as Escherichia coli JMJ1.
Example 6
Construction of a Plasmid Expressing the ywfE Gene and a Feedback-Resistant 3-Phosphoglycerate Dehydrogenase Gene (serA Gene) Derived from Escherichia coli 
It is known that mutation of the Escherichia coli-derived 3-phosphoglycerate dehydrogenase gene (serA gene) to substitute the codon at positions 1096-1098 of the structural gene by the termination codon (TAA) produces a gene encoding a mutant 3-phosphoglycerate dehydrogenase in which the C-terminal 45 amino acid residues are deleted and the substantial inhibition by serine is alleviated (hereinafter referred to as the feedback-resistant serA gene) (Japanese Patent No. 2584409).
As the primers for amplification of the feedback-resistant serA gene, DNA consisting of the nucleotide sequence shown in SEQ ID NO: 108 and DNA consisting of the nucleotide sequence shown in SEQ ID NO: 109 containing the codon-substituted mutant sequence were used.
The nucleotide sequence shown in SEQ ID NO: 108 is a sequence wherein a sequence containing the ClaI recognition sequence is added to the 5′ end of a region containing the Shine-Dalgarno sequence (ribosome binding sequence) of the serA gene. The sequence shown in SEQ ID NO: 109 is a sequence wherein a sequence containing the SphI recognition sequence is added to the 5′ end of a sequence complementary to a sequence containing the termination codon to delete the C-terminal 45 amino acid residues of the serA gene.
PCR was carried out to amplify the feedback-resistant serA gene using the above synthetic DNAs as a set of primers and the chromosomal DNA of Escherichia coli W3110 as a template. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 0.1 μg of the chromosomal DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
One-tenth of the resulting reaction mixture was subjected to agarose gel electrophoresis to confirm that a ca. 1.1 kb fragment corresponding to the feedback-resistant serA gene fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
The thus obtained solution (5 μl) was subjected to reaction to cleave the amplified DNA with restriction enzymes ClaI and SphI. DNA fragments were separated by agarose gel electrophoresis, and a 1.1 kb DNA fragment containing the serA gene was recovered using GENECLEAN II Kit.
Expression vector pTrS30 containing trp promoter [preparable from Escherichia coli JM109/pTrS30 (FERM BP-5407)] (0.2 μg) was cleaved with restriction enzymes ClaI and SphI. DNA fragments were separated by agarose gel electrophoresis, and a 4.3 kb DNA fragment was recovered in the same manner as above.
The 1.1 kb DNA fragment containing the serA gene and the 4.3 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using the ligation reaction mixture according to the method using calcium ion, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from a colony of the transformant that grew on the medium according to a known method and was designated as pSE15. The structure of the plasmid was confirmed by restriction enzyme digestion.
Amplification of a feedback-resistant serA gene fragment was carried out using the above-obtained plasmid pSE15 expressing the feedback-resistant serA gene derived from Escherichia coli as a template and DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 110 and 109 as a set of primers.
Separately, amplification of a ywfE gene fragment containing trp promoter was carried out using the plasmid pPE56 expressing the ywfE gene constructed in Experimental Example 15 as a template, and DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 111 and 112 as a set of primers. Both PCRs were carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 10 ng of the plasmid DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
One-tenth of each of the resulting reaction mixtures was subjected to agarose gel electrophoresis to confirm that the desired fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE. The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes. The resulting solution was centrifuged, and the obtained DNA precipitate was dissolved in 20 μl of TE.
By the above procedure, a feedback-resistant serA gene fragment and a ywfE gene fragment containing trp promoter were obtained. The feedback-resistant serA gene fragment was cleaved with restriction enzymes BglII and SphI. The ywfE gene fragment containing trp promoter was cleaved with restriction enzymes EcoRI and BamHI. DNA fragments were separated by agarose gel electrophoresis, and a 1.1 kb DNA fragment containing the serA gene and a 1.8 kb DNA fragment containing trp promoter and the ywfE gene were recovered using GENECLEAN II Kit.
Expression vector pTrS30 containing trp promoter (0.2 μg) was cleaved with restriction enzymes EcoRI and SphI. DNA fragments were separated by agarose gel electrophoresis, and a 3.9 kb DNA fragment was recovered in the same manner as above.
The 1.6 kb DNA fragment containing the serA gene, the 1.8 kb DNA fragment containing trp promoter and the ywfE gene and the 3.9 kb DNA fragment obtained above were subjected to ligation reaction using a ligation kit at 16° C. for 16 hours.
Escherichia coli NM522 was transformed using the ligation reaction mixture according to the method using calcium ion, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C.
A plasmid was extracted from a colony of the transformant that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that a plasmid into which the feedback-resistant serA gene was inserted in the same direction as the ywfE gene was obtained, and the plasmid was designated as pPE212.
Example 7
Preparation of a Strain Having ilvL Gene Deletion and a Strain Having Revertant ilvG Gene Substitution
(1) Cloning of a Drug Resistance Gene-Containing DNA Fragment for Preparation of a Strain Having ilvL Gene Deletion and a DNA Fragment for Preparation of a Strain Having Revertant ilvG Gene Substitution
The nucleotide sequences of the ilvL gene and the ilvG gene of Escherichia coli K12 were already disclosed [Science, 5331, 1453-1474 (1997)].
The attenuator region which regulates the expression of the ilvGMEDA operon of Escherichia coli K12 is located in the 5′ upstream region of the operon and its nucleotide sequence is disclosed in Nucleic Acids Res., 15, 2137 (1987). It is known that removal of the attenuator region deactivates the attenuation function, which leads to constitutive expression of the ilvGMEDA operon (Japanese Published Unexamined Patent Application No. 473979/96). On the basis of this information, Escherichia coli K12 which constitutively expresses ilvGMEDA operon was prepared in the following manner.
As wild-type Escherichia coli K12 has the ilvG gene having a frameshift mutation, it does not express active acetohydroxy acid synthase isozyme II (AHASII) [Proc. Natl. Acad. Sci. USA, 78, 922 (1981)]. Escherichia coli K12 in which the activity of acetohydroxy acid synthase is restored was prepared in the following manner by introduction of a mutation to restore the frame by inserting two nucleotides (AA) between the 981st nucleotide and the 982nd nucleotide of the ilvG gene of Escherichia coli K12 by referring to the sequence of the ilvG gene existing on the chromosomal DNA of Escherichia coli 0157:H7 in which AHASII is normally functioning.
On the basis of the reported nucleotide sequence, DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 113 and 114 were synthesized as a set of primers to amplify a drug resistance gene-containing DNA fragment for preparation of a strain having ilvL gene deletion using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.).
The DNAs have nucleotide sequences homologous to 36-bp nucleotide sequences that lie upstream and downstream of the target gene to be deleted.
Separately, DNA consisting of the nucleotide sequence shown in SEQ ID NO: 115 and DNA consisting of the nucleotide sequence shown in SEQ ID NO: 116 containing the two nucleotides-inserted mutant sequence were synthesized as a set of primers for amplification of an upstream region of the revertant ilvG gene, and DNA consisting of the nucleotide sequence shown in SEQ ID NO: 117 containing the two nucleotides-inserted mutant sequence and DNA consisting of the nucleotide sequence shown in SEQ ID NO: 118 were synthesized as a set of primers for amplification of a downstream region of the revertant ilvG gene.
PCR was carried out, using each set of the above DNAs as a set of primers, to amplify a chloramphenicol resistance gene-containing DNA fragment for deletion of the ilvL gene using pKD3 DNA as a template, and to amplify upstream and downstream regions of the revertant ilvG gene using the chromosomal DNA of Escherichia coli W3110 as a template. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 0.1 μg of the chromosomal DNA or 10 ng of the plasmid DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
One-tenth of each of the resulting reaction mixtures was subjected to agarose gel electrophoresis to confirm that the desired fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE.
The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes, followed by centrifugation to precipitate DNA. Then, the DNA precipitate was dissolved in 20 μl of TE. By this procedure, a chloramphenicol resistance gene-containing DNA fragment for preparation of a strain having ilvL gene deletion, an upstream region of the revertant ilvG gene and a downstream region of the revertant ilvG gene were obtained.
Then, crossover PCR [A. J. Link, D. Phillips, G. M. Church, J. Bacteriol., 179, 6228-6237 (1997)] was carried out using the upstream region of the revertant ilvG gene and the downstream region of the revertant ilvG gene as templates and DNAs having the nucleotide sequences shown in SEQ ID NOS: 115 and 118 as a set of primers. PCR was carried out under the same conditions as above.
The above PCR produced a DNA fragment for preparation of a revertant ilvG gene-substituted strain in which the upstream region of the revertant ilvG gene and the downstream region of the revertant ilvG gene are ligated.
(2) Preparation of Escherichia coli JM101 in which the ilvG Gene on the Chromosomal DNA is Substituted by the Revertant ilvG Gene
Escherichia coli JM101 was transformed with pKD46 according to a known method, spread on LB agar medium containing 100 mg/l ampicillin, and cultured overnight at 30° C. to obtain Escherichia coli JM101 carrying pKD46 (hereinafter referred to as Escherichia coli JM101/pKD46).
Escherichia coli JM101/pKD46 cultured in the presence of 10 mmol/l L-arabinose and 50 μg/ml ampicillin was transformed by electroporation using the DNA fragment for preparation of a revertant ilvG gene-substituted strain obtained in the above (1), and a strain in which the ilvG gene on the chromosomal DNA was substituted by the revertant ilvG gene was selected on agar medium containing M9 medium and glucose, containing 200 mg/l L-valine.
Replicas of the obtained L-valine-resistant strain were made on agar medium containing M9 medium and glucose, containing 200 mg/l L-valine, followed by single colony isolation at 42° C. Then, replicas of the obtained colonies were made on agar medium containing M9 medium and glucose, containing 200 mg/l L-valine and LB agar medium containing 100 mg/l ampicillin to select a colony showing L-valine resistance and ampicillin sensitivity. The obtained revertant ilvG gene-substituted strain was designated as Escherichia coli JM101G+1.
(3) Preparation of Escherichia coli JM101 in which the ilvG Gene on the Chromosomal DNA is Substituted by the Revertant ilvG Gene and the ilvL Gene is Deleted
Escherichia coli JM101G+1 obtained in the above (2) was transformed with pKD46, spread on LB agar medium containing 100 mg/l ampicillin, and cultured overnight at 30° C. to obtain Escherichia coli JM101G+1 carrying pKD46 (hereinafter referred to as Escherichia coli JM101G+1/pKD46).
Escherichia coli JM101G+1/pKD46 was transformed by electroporation using the chloramphenicol resistance gene-containing DNA fragment for preparation of a strain having ilvL gene deletion obtained in the above (1), and a recombinant strain in which the chloramphenicol resistance gene was inserted into the ilvL gene on the chromosomal DNA of JM101 strain was selected on LB agar medium containing 25 mg/l chloramphenicol.
Replicas of the obtained chloramphenicol-resistant strain were made on LB agar medium containing 25 mg/l chloramphenicol, followed by single colony isolation at 42° C. Then, replicas of the obtained colonies were made on LB agar medium containing 25 mg/l chloramphenicol and 100 mg/l ampicillin to select a pKD46-cured strain showing chloramphenicol resistance and ampicillin sensitivity.
The structure of the chromosomal DNA of the transformant obtained above was confirmed by synthesizing the nucleotide sequences shown in SEQ ID NOS: 119 and 120, i.e., the nucleotide sequences located approximately 400 bp upstream and downstream of the site to which the chloramphenicol resistance gene was inserted on the chromosomal DNA of Escherichia coli, and then carrying out colony PCR using the synthetic DNAs as a set of primers. Colony PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising the cells in an amount obtained by contacting a 200-μl pipette tip with the colony, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
Of the strains subjected to colony PCR, a strain with which a ca. 2 kb fragment containing the chloramphenicol resistance gene was amplified was identified as a strain having ilvL gene deletion and was designated as Escherichia coli JILG+Cm1.
The above-obtained Escherichia coli JILG+Cm1 was transformed using pCP20, followed by selection on LB agar medium containing 100 mg/l ampicillin to obtain Escherichia coli JILG+Cm1 carrying pCP20.
The plasmid pCP20 carries a yeast-derived Flp recombinase gene the expression of which can be induced at a temperature of 42° C.
The chloramphenicol resistance gene-containing DNA fragment for preparation of a strain having ilvL gene deletion prepared in the above (1) contains nucleotide sequences recognized by Flp recombinase at both termini of the chloramphenicol resistance gene. Therefore, the resistance gene can be readily deleted by homologous recombination catalyzed by Flp recombinase.
Further, as pCP20 has a thermosensitive replication origin, expression of Flp recombinase and curing of pCP20 can be simultaneously induced by culturing the pCP20-carrying strain at 42° C.
Escherichia coli JILG+Cm1 obtained above was inoculated onto drug-free LB agar medium and cultured at 42° C. for 14 hours, followed by single colony isolation. Replicas of the obtained colonies were made on drug-free LB agar medium, LB agar medium containing 25 mg/l chloramphenicol and LB agar medium containing 100 mg/l ampicillin, followed by culturing at 30° C. Then, colonies showing chloramphenicol sensitivity and ampicillin sensitivity were selected.
Each of the colonies selected above was subjected to colony PCR using DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 119 and 120 as a set of primers. Colony PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising the cells in an amount obtained by contacting a 200-μl pipette tip with the colony, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
Of the strains subjected to colony PCR, a strain with which a ca. 0.7 kb chloramphenicol resistance gene-cured fragment was amplified was identified as a strain having ilvL gene deletion and was designated as Escherichia coli JILG+1.
Example 8
Preparation of a Strain Having Feedback-Resistant ilvA Gene Substitution
(1) Cloning of a Drug Resistance Gene-Containing DNA Fragment for Preparation of a Strain Having ilvA Gene Deletion and a DNA Fragment for Preparation of a Strain Having Feedback-Resistant ilvA Gene Substitution
The nucleotide sequence of the ilvA gene of Escherichia coli K12 was already disclosed [Science, 5331, 1453-1474 (1997)].
It is known that the ilvA 219 gene encoding threonine deaminase of which the inhibition by L-isoleucine is substantially eliminated (hereinafter referred to as feedback-resistant ilvA gene) has a mutation in which leucine 447 is substituted by phenylalanine [Biochemistry, 34, 9403 (1995)].
On the basis of the reported nucleotide sequence, DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 121 and 122 were synthesized as primer DNAs to amplify a drug resistance gene-containing DNA fragment for preparation of a strain having ilvA gene deletion using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.).
The DNAs have nucleotide sequences homologous to 36-bp nucleotide sequences that lie upstream and downstream of the target gene to be deleted.
Separately, DNA consisting of the nucleotide sequence shown in SEQ ID NO: 123 and DNA consisting of the nucleotide sequence shown in SEQ ID NO: 124 containing the codon-substituted mutant sequence were synthesized as a set of primers for amplification of an upstream region of the feedback-resistant ilvA gene, and DNA consisting of the nucleotide sequence shown in SEQ ID NO: 125 containing the codon-substituted mutant sequence and DNA consisting of the nucleotide sequence shown in SEQ ID NO: 126 were synthesized as a set of primers for amplification of a downstream region of the feedback-resistant ilvA gene.
PCR was carried out, using each set of the above DNAs as a set of primers, to amplify a chloramphenicol resistance gene-containing DNA fragment for preparation of a strain having ilvA gene deletion using pKD3 DNA as a template, and to amplify upstream and downstream regions of the feedback-resistant ilvA gene using the chromosomal DNA of Escherichia coli W3110 as a template. That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 0.1 μg of the chromosomal DNA or 10 ng of the plasmid DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
One-tenth of each of the resulting reaction mixtures was subjected to agarose gel electrophoresis to confirm that the desired fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE.
The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes, followed by centrifugation to precipitate DNA. Then, the DNA precipitate was dissolved in 20 μl of TE. By this procedure, a chloramphenicol resistance gene-containing DNA fragment for deletion of the ilvA gene, an upstream region of the feedback-resistant ilvA gene and a downstream region of the feedback-resistant ilvA gene were obtained.
Then, crossover PCR was carried out using, of the above PCR-amplified fragments, the upstream region of the feedback-resistant ilvA gene and the downstream region of the feedback-resistant ilvA gene as templates and using DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 123 and 126 as a set of primers. PCR was carried out under the same conditions as above.
The above PCR produced a DNA fragment for preparation of a feedback-resistant ilvA gene-substituted strain in which the upstream region of the feedback-resistant ilvA gene and the downstream region of the feedback-resistant ilvA gene are ligated.
(2) Preparation of Escherichia coli JM110 in which the Drug Resistance Gene is Inserted into the ilvA Gene on the Chromosomal DNA of Escherichia coli 
Escherichia coli JM101/pKD46 cultured in the presence of 10 mmol/l L-arabinose and 50 μg/ml ampicillin was transformed by electroporation using the chloramphenicol resistance gene-containing DNA fragment for deletion of the ilvA gene obtained in the above (1). A recombinant strain in which the chloramphenicol resistance gene was inserted into the ilvA gene on the chromosomal DNA of Escherichia coli JM101 and the ilvA structural gene was deleted was selected on LB agar medium containing 25 mg/l chloramphenicol.
Replicas of the obtained chloramphenicol-resistant strain were made on LB agar medium containing 25 mg/l chloramphenicol, followed by single colony isolation at 30° C. Then, replicas of the obtained colonies were made on LB agar medium containing 25 mg/l chloramphenicol and 100 mg/l ampicillin to select colonies showing chloramphenicol resistance and ampicillin resistance.
Colony PCR was carried out on the obtained strains using, as a set of primers, DNAs having the nucleotide sequences shown in SEQ ID NOS: 123 and 126, i.e., the nucleotide sequences located approximately 400 bp upstream and downstream of the site to which the chloramphenicol resistance gene was inserted on the chromosomal DNA. That is, colony PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising the cells in an amount obtained by contacting a 200-μl pipette tip with the colony, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
Of the strains subjected to colony PCR, a strain with which a ca. 2 kb fragment containing the chloramphenicol resistance gene was amplified was identified as a strain having ilvA gene deletion and was designated as Escherichia coli JIACm1/pKD46.
(3) Preparation of Escherichia coli JM101 in which the ilvA Gene on the Chromosomal DNA is Substituted by the Feedback-Resistant ilvA Gene
Escherichia coli JIACm1/pKD46 prepared in the above (2) was cultured in the presence of 10 mmol/l L-arabinose and 50 μg/ml ampicillin and then transformed by electroporation using the DNA fragment for preparation of an feedback-resistant ilvA gene-substituted strain obtained in the above (1). A strain in which the ilvA gene on the chromosomal DNA of JIACm1 strain was substituted by the feedback-resistant ilvA gene was selected on agar medium containing M9 medium and glucose using recovery of isoleucine requirement as a marker.
Replicas of the ampicillin-resistant strain which grew were made on drug-free agar medium containing M9 medium and glucose, followed by single colony isolation at 42° C. Then, replicas of the obtained colonies were made on drug-free LB agar medium, LB agar medium containing 25 mg/l chloramphenicol and LB agar medium containing 100 mg/l ampicillin to select a colony showing chloramphenicol sensitivity and ampicillin sensitivity. It was confirmed that the obtained strain was the inhibition-released ilvA gene-substituted strain, which was designated as Escherichia coli JIA1.
(4) Preparation of Escherichia coli JILG+1 in which the ilvA Gene on the Chromosomal DNA is Substituted by the Inhibition-Released ilvA Gene
The procedures of the above (1) to (3) were carried out using, as a parent strain, Escherichia coli JILG+1 prepared in Example 7 in place of Escherichia coli JM101 to obtain a strain in which the ilvL gene was deleted, the ilvG gene was substituted by the revertant ilvG gene and the ilvA gene was substituted by the feedback-resistant ilvA gene. The obtained strain was designated as Escherichia coli JILG+IA1.
Example 9
Preparation of a Strain Having Mutant leuA Gene Substitution
(1) Cloning of a Drug Resistance Gene-Containing DNA Fragment for Preparation of a Strain Having leuA Gene Deletion and a DNA Fragment for Preparation of a Strain Having Mutant leuA Substitution
The nucleotide sequence of the leuA gene of Escherichia coli K12 was already disclosed [Science, 5331, 1453-1474 (1997)].
Escherichia coli FERM BP-4704 is a leucine-producing strain selected by leucine analogue (4-azaleucine) resistance (Japanese Published Unexamined Patent Application No. 70879/96) and is considered to have the mutant leuA gene encoding isopropyl malate synthase substantially released from the inhibition by L-leucine.
On the basis of the reported nucleotide sequence, DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 127 and 128 were synthesized as a set of primers to amplify a drug resistance gene-containing DNA-fragment for preparation of a strain having leuA gene deletion using a DNA synthesizer (Model 8905, PerSeptive Biosystems, Inc.).
The DNAs have nucleotide sequences homologous to 36-bp nucleotide sequences that lie upstream and downstream of the target gene to be deleted.
Separately, DNA having the nucleotide sequence shown in SEQ ID NO: 129, i.e., the nucleotide sequence located approximately 200 bp upstream of the initiation codon of the leuA gene, and DNA having the nucleotide sequence shown in SEQ ID NO: 130, i.e., the nucleotide sequence located approximately 200 bp downstream of the termination codon of the leuA gene in reverse orientation were synthesized as a set of primers to amplify a DNA fragment for preparation of a strain having mutant leuA gene substitution.
PCR was carried out, using each set of the above DNAs as a set of primers, to amplify a chloramphenicol resistance gene-containing DNA fragment for preparation of a strain having leuA gene deletion using pKD3 DNA as a template, and to amplify a DNA fragment for preparation of a strain having mutant leuA gene substitution using the chromosomal DNA of FERM BP-4704 strain prepared by an ordinary method as a template.
That is, PCR was carried out by 30 cycles, one cycle consisting of reaction at 94° C. for one minute, reaction at 55° C. for 2 minutes and reaction at 72° C. for 3 minutes, using 40 μl of a reaction mixture comprising 0.1 μg of the chromosomal DNA or 10 ng of the plasmid DNA, 0.5 μmol/l each of the primers, 2.5 units of Pfu DNA polymerase, 4 μl of buffer for Pfu DNA polymerase (10×) and 200 μmol/l each of deoxyNTPs.
One-tenth of each of the resulting reaction mixtures was subjected to agarose gel electrophoresis to confirm that the desired fragment was amplified. Then, the remaining reaction mixture was mixed with an equal amount of phenol/chloroform saturated with TE.
The resulting mixture was centrifuged, and the obtained upper layer was mixed with a two-fold volume of cold ethanol and allowed to stand at −80° C. for 30 minutes, followed by centrifugation to precipitate DNA. Then, the DNA precipitate was dissolved in 20 μl of TE. By this procedure, a chloramphenicol resistance gene-containing DNA fragment for preparation of a strain having leuA gene deletion and a DNA fragment for preparation of a strain having mutant leuA gene substitution were obtained.
(2) Preparation of Escherichia coli JM101 in which the Drug Resistance Gene is Inserted into the leuA Gene on the Chromosomal DNA
A mutant strain of Escherichia coli in which the chloramphenicol resistance gene was inserted into the leuA gene on the chromosomal DNA of Escherichia coli JM101 was prepared by the same procedure as in Example 8 (2).
Insertion of the chloramphenicol resistance gene into the chromosomal DNA was confirmed by carrying out colony PCR using, as a set of primers, DNAs consisting of the nucleotide sequences shown in SEQ ID NOS: 131 and 132, i.e., the nucleotide sequences located approximately 200 bp upstream and downstream of the site to which the chloramphenicol resistance gene was inserted.
PCR was carried out under the same conditions as in Example 8 (2). Of the strains subjected to colony PCR, a strain with which a ca. 2 kb fragment containing the chloramphenicol resistance gene was amplified was identified as a strain having leuA gene deletion in which the chloramphenicol resistance gene was inserted into the leuA gene, and was designated as Escherichia coli JLACm1/pKD46.
(3) Preparation of Escherichia coli JM101 in which the leuA Gene on the Chromosomal DNA is Substituted by the Mutant Gene Derived from Escherichia coli H-9070
The same procedure as in Example 8 (3) was carried out using the DNA fragment for preparation of a strain having mutant leuA gene substitution obtained in the above (1) and Escherichia coli JLACm1/pKD46 obtained in the above (2) to obtain a recombinant strain in which the leuA gene into which the chloramphenicol resistance gene was inserted on the chromosomal DNA of Escherichia coli JLACm1/pKD46 was substituted by the mutant leuA gene. The obtained strain was designated as Escherichia coli JLA1.
(4) Preparation of Escherichia coli JILG+1 in which the leuA Gene on the Chromosomal DNA is Substituted by the mutant leuA Gene
The procedures of the above (1) to (3) were carried out using, as a parent strain, Escherichia coli JILG+1 prepared in Example 7 in place of Escherichia coli JM101 to obtain a strain in which the ilvL gene was deleted, the ilvG gene was substituted by the revertant ilvG gene and the leuA gene was substituted by the mutant leuA gene. The obtained strain was designated as Escherichia coli JILG+LA1.
Example 10
Fermentative Production of L-Ala-L-Ala Using a Microorganism Having the Ability to Produce L-Alanine
Escherichia coli JM101 was transformed with the plasmid pPE86 expressing the ywfE gene and the ald gene both derived from Bacillus subtilis obtained in Example 2, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C. A plasmid was extracted from the strain that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that Escherichia coli JM101 carrying the plasmid pPE86 (hereinafter referred to as Escherichia coli JM101/pPE86) was obtained. Escherichia coli JM101 carrying the plasmid pTrS30 (hereinafter referred to as Escherichia coli JM101/pTrS30) and Escherichia coli JM101 carrying the plasmid pPE56 (hereinafter referred to as Escherichia coli JM101/pPE56) were also obtained in the same manner.
Each of the obtained transformants was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 8 ml of a production medium [16 g/l dipotassium hydrogenphosphate, 14 g/l potassium dihydrogenphosphate, 5 g/l ammonium sulfate, 1 g/l citric acid (anhydrous), 5 g/l Casamino acid (Difco), 10 g/l glucose, 10 mg/l vitamin B1, 25 mg/l magnesium sulfate heptahydrate and 50 mg/l ferrous sulfate heptahydrate; pH adjusted to 7.2 with 10 mol/l sodium hydroxide; glucose, vitamin B1, magnesium sulfate heptahydrate and ferrous sulfate heptahydrate were added after separate steam sterilization] containing 100 μg/ml ampicillin in a test tube in an amount of 1% and cultured at 30° C. for 24 hours. The resulting culture was centrifuged to obtain a culture supernatant.
The product in the culture supernatant was derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out in the same manner as in Experimental Example 17. The results are shown in Table 6.










TABLE 6







L-Ala-L-Ala (mg/l)
L-Ala (mg/l)




















JM101/pTrS30
0
0



JM101/pPE56
0
1



JM101/pPE86
7
667










Example 11
Fermentative Production of L-Ala-L-Gln Using a Microorganism Having the Ability to Produce L-Ala and L-Gln
Escherichia coli JGLBE1 having double deletions of the glnE gene and the glnB gene obtained in Example 1 was transformed with the plasmid pPE86 obtained in Example 2, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C. A plasmid was extracted from a colony that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that Escherichia coli JGLBE1 carrying the plasmid pPE86 was obtained, and the strain was designated as Escherichia coli JGLBE1/pPE86. Escherichia coli JGLBE1 carrying the plasmid pTrS30 (hereinafter referred to as Escherichia coli JGLBE1/pTrS30) and Escherichia coli JGLBE1 carrying the plasmid pPE56 (hereinafter referred to as Escherichia coli JGLBE1/pPE56) were also obtained in the same manner.
Each of the obtained transformants was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 8 ml of the production medium described in Example 10 containing 100 μg/ml ampicillin in a test tube in an amount of 1% and cultured at 30° C. for 24 hours. The resulting culture was centrifuged to obtain a culture supernatant.
The product in the culture supernatant was derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out in the same manner as in Experimental Example 17. The results are shown in Table 7.










TABLE 7







L-Ala-L-Gln (mg/l)
L-Gln (mg/l)




















JGLBE1/pTrS30
0
183



JGLBE1/pPE56
6
1063



JGLBE1/pPE86
72
311










Example 12
Fermentative Production of L-Ala-L-Phe Using a Microorganism Having the Ability to Produce L-Ala and L-Phe
Escherichia coli JM101/pPE86 obtained in Example 10 was transformed with each of the plasmid pPHEA2 expressing the feedback-resistant pheA gene derived from Escherichia coli and the plasmid pPHEAF2 expressing the feedback-resistant pheA gene and feedback-resistant aroF gene derived from Escherichia coli constructed in Example 3, spread on LB agar medium containing 50 μg/ml ampicillin and 30 μg/ml chloramphenicol, and cultured overnight at 30° C. A plasmid was extracted from a colony of each strain that grew on the medium according to a known method, and it was confirmed that Escherichia coli JM101/pPE86 strains respectively carrying pPHEA2 and pPHEAF2 (hereinafter referred to as Escherichia coli JM101/pPE86/pPHEA2 and Escherichia coli JM101/pPE86/pPHEAF2, respectively) were obtained. In the same manner, Escherichia coli JM101/pTrS30 and Escherichia coli JM101/pPE56 obtained in Example 10 were transformed with each of pPHEA2 and pPHEAF2 to obtain Escherichia coli JM101/pTrS30 carrying pPHEA2 (hereinafter referred to as Escherichia coli JM101/pTrS30/pPHEA2), Escherichia coli JM101/pTrS30 carrying pPHEAF2 (hereinafter referred to as Escherichia coli JM101/pTrS30/pPHEAF2), Escherichia coli JM101/pPE56 carrying pPHEA2 (hereinafter referred to as Escherichia coli JM101/pPE56/pPHEA2) and Escherichia coli JM101/pPE56 carrying pPHEAF2 (hereinafter referred to as Escherichia coli JM101/pPE56/pPHEAF2).
Each of the obtained transformants was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin and 30 μg/ml chloramphenicol in a test tube and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 8 ml of the production medium described in Example 10 containing 100 μg/ml ampicillin and 50 μg/ml chloramphenicol in a test tube in an amount of 1% and cultured at 30° C. for 24 hours. The resulting culture was centrifuged to obtain a culture supernatant.
The product in the culture supernatant was derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out in the same manner as in Experimental Example 17. The results are shown in Table 8.










TABLE 8







L-Ala-L-Phe (mg/l)
L-Phe (mg/l)




















JM101/pTrS30/pPHEA2
0
37



JM101/pTrS30/pPHEAF2
0
77



JM101/pPE56/pPHEA2
129
54



JM101/pPE56/pPHEAF2
294
104



JM101/pPE86/pPHEA2
277
91



JM101/pPE86/pPHEAF2
340
118










Example 13
Fermentative Production of L-Threonyl-L-phenylalanine (L-Thr-L-Phe) Using a Microorganism Having the Ability to Produce L-Thr and L-Phe
Escherichia coli βIM-4 (ATCC 21277) exhibiting proline-, methionine-, isoleucine- and thiamine-requirement, imparted with α-amino-β-hydroxyvaleric acid resistance and having the ability to produce L-Thr was transformed with the Bacillus subtilis-derived ywfE expression-enhanced plasmid pPE56 obtained in Experimental Example 15, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C. A plasmid was extracted from a colony that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that Escherichia coli ATCC 21277 carrying pPE56 (hereinafter referred to as Escherichia coli ATCC 21277/pPE56) was obtained.
Then, Escherichia coli ATCC 21277/pPE56 was transformed with each of pSTV28 (Takara Bio Inc.), and pPHEA2 and pPHEAF2 obtained in Example 3, spread on LB agar medium containing 50 μg/ml ampicillin and 30 μg/ml chloramphenicol, and cultured overnight at 30° C. A plasmid was extracted from a colony of each strain that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that Escherichia coli ATCC 21277/pPE56 strains respectively carrying pSTV28, pPHEA2 and pPHEAF2 (hereinafter referred to as Escherichia coli ATCC 21277/pPE56/pSTV28, Escherichia coli ATCC 21277/pPE56/pPHEA2 and Escherichia coli ATCC 21277/pPE56/pPHEAF2, respectively) were obtained. In the same manner, Escherichia coli ATCC 21277 carrying pTrS30 and pSTV28 (hereinafter referred to as Escherichia coli ATCC 21277/pTrS30/pSTV28), Escherichia coli ATCC 21277 carrying pTrS30 and pPHEA2 (hereinafter referred to as Escherichia coli ATCC 21277/pTrS30/pPHEA2) and Escherichia coli ATCC 21277 carrying pTrS30 and pPHEAF2 (hereinafter referred to as Escherichia coli ATCC 21277/pTrS30/pPHEAF2) were obtained.
Each of the obtained transformants was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin and 30 μg/ml chloramphenicol in a test tube and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 8 ml of the production medium described in Example 10 containing 100 μg/ml ampicillin and 50 μg/ml chloramphenicol in a test tube in an amount of 1% and cultured at 30° C. for 24 hours. The resulting culture was centrifuged to obtain a culture supernatant.
The product in the culture supernatant was derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out in the same manner as in Experimental Example 17. The results are shown in Table 9.











TABLE 9







L-Thr-L-Phe
L-Thr
L-Phe



(mg/l)
(mg/l)
(mg/l)



















ATCC21277/pTrS30/pSTV28
0
180
80


ATCC21277/pTrS30/pPHEA2
0
30
210


ATCC21277/pTrS30/pPHEAF2
0
30
170


ATCC21277/pPE56/pSTV28
230
300
70


ATCC21277/pPE56/pPHEA2
410
250
110


ATCC21277/pPE56/pPHEAF2
460
270
0









Example 14
Fermentative Production of L-Ala-L-Tyr Using a Microorganism Having the Ability to Produce L-Ala and L-Tyr
Escherichia coli JM101/pPE86 obtained in Example 10 was transformed with the plasmid pTY2 expressing the tyrosine-resistant mutant aroF-tyrA operon derived from Escherichia coli constructed in Example 4, spread on LB agar medium containing 50 μg/ml ampicillin and 30 μg/ml chloramphenicol, and cultured overnight at 30° C. A plasmid was extracted from a colony of the strain that grew on the medium according to a known method, and it was confirmed that Escherichia coli JM101/pPE86 carrying pTY2 (hereinafter referred to as Escherichia coli JM101/pPE86/pTY2) was obtained. In the same manner, Escherichia coli JM101/pTrS30 and Escherichia coli JM101/pPE56 obtained in Example 10 were transformed with pTY2 to obtain Escherichia coli JM101/pTrS30 carrying pTY2 (hereinafter referred to as Escherichia coli JM101/pTrS30/pTY2) and Escherichia coli JM101/pPE56 carrying pTY2 (hereinafter referred to as Escherichia coli JM101/pPE56/pTY2).
Each of the obtained transformants was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin and 30 μg/ml chloramphenicol in a test tube and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 8 ml of the production medium described in Example 10 containing 100 μg/ml ampicillin and 50 μg/ml chloramphenicol in a test tube in an amount of 1% and cultured at 30° C. for 24 hours. The resulting culture was centrifuged to obtain a culture supernatant.
The product in the culture supernatant was derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out in the same manner as in Experimental Example 17. The results are shown in Table 10.










TABLE 10







L-Ala-L-Tyr (mg/l)
L-Tyr (mg/l)




















JM101/pTrS30/pTY2
0
1



JM101/pPE56/pTY2
51
6



JM101/pPE86/pTY2
63
7










Example 15
Fermentative Production of L-Alanyl-L-methionine (L-Ala-L-Met) Using a Microorganism Having the Ability to Produce L-Ala and L-Met
Escherichia coli JMJ1 obtained in Example 5 was transformed with pPE86 obtained in Example 2, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C. A plasmid was extracted from a colony of the strain that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that Escherichia coli JMJ1 carrying pPE86 was obtained, and the strain was designated as Escherichia coli JMJ1/pPE86. In the same manner, Escherichia coli JMJ1 carrying pTrS30 (hereinafter referred to as Escherichia coli JMJ1/pTrS30) and Escherichia coli JMJ1 carrying pPE56 (hereinafter referred to as Escherichia coli JMJ1/pPE56) were obtained.
Each of the obtained transformants was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 8 ml of the production medium described in Example 10 containing 100 μg/ml ampicillin in a test tube in an amount of 1% and cultured at 30° C. for 24 hours. The resulting culture was centrifuged to obtain a culture supernatant.
The product in the culture supernatant was derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out in the same manner as in Experimental Example 17. The results are shown in Table 11.










TABLE 11







L-Ala-L-Met (mg/l)
L-Met (mg/l)




















JMJ1/pTrS30
0
16



JMJ1/pPE56
0
61



JMJ1/pPE86
113
180










The results shown in Examples 10 to 15 revealed that a microorganism which has the ability to produce a protein having the activity to form a dipeptide from one or more kinds of amino acids and the ability to produce one or more kinds of amino acids forms and accumulates the dipeptide in a medium when cultured therein, and the ability to produce the dipeptide of a microorganism which has the ability to produce two amino acids is higher than that of a microorganism which has the ability to produce one amino acids in the above microorganism.
Example 16
Fermentative Production of L-Ala-L-Ala Using a Microorganism Having the Ability to Produce L-Ala and Having Deletions of Peptidase Genes and a Dipeptide-Permeating/Transporting Protein Operon
Escherichia coli JPNDDP36 having deletions of the pepD and pepN genes and the dpp operon obtained in Experimental Example 16 (4) was transformed with each of pTrS30, and pPE56 and pPE86 obtained in Example 2, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C. A plasmid was extracted from a colony of each strain that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that Escherichia coli JPNDDP36 strains respectively carrying pTrS30, pPE56 and pPE86 (hereinafter referred to as Escherichia coli JPNDDP36/pTrS30, Escherichia coli JPNDDP36/pPE56 and Escherichia coli JPNDDP36/pPE86, respectively) were obtained.
Each of the obtained transformants was cultured in the same manner as in Example 10 and the product in the culture supernatant was analyzed in the same manner as in Experimental Example 17. The results are shown in Table 12.










TABLE 12







L-Ala-L-Ala (mg/l)
L-Ala (mg/l)




















JPNDDP36/pTrS30
0
0



JPNDDP36/pPE56
0
1



JPNDDP36/pPE86
10
2










Example 17
Fermentative Production of L-Ala-L-Gln Using a Microorganism Having the Ability to Produce L-Ala and L-Gln and Having Deletions of Peptidase Genes and a Dipeptide-Permeating/Transporting Protein Operon
(1) Construction of a Microorganism Having the Ability to Produce L-Ala and L-Gln and Having Deletions of Peptidase Genes and a Dipeptide-Permeating/Transporting Protein Operon
According to the same procedure as in Example 1, deletions of the glnE gene and the glnB gene were introduced into Escherichia coli JPNDDP36 obtained in Experimental Example 16 (4) to obtain Escherichia coli JPNDDPGBE1 having the ability to produce L-Ala and L-Gln and having deletions of peptidase genes and a dipeptide-permeating/transporting protein operon.
(2) Fermentative Production of L-Ala-L-Gln
Escherichia coli JPNDDPGBE1 obtained in the above (1) was transformed with each of pTrS30, pPE56 and pPE86 in the same manner as in Example 16 to obtain Escherichia coli JPNDDPGBE1 strains carrying the respective plasmids (hereinafter referred to as Escherichia coli JPNDDPGBE1/pTrS30, Escherichia coli JPNDDPGBE1/pPE56 and Escherichia coli JPNDDPGBE1/pPE86, respectively). Each of the obtained transformants was cultured in the same manner as in Example 10 and the product in the culture supernatant was analyzed in the same manner as in Experimental Example 17. The results are shown in Table 13.










TABLE 13







L-Ala-L-Gln (mg/l)
L-Gln (mg/l)




















JPNDDPGBE1/pTrS30
0
1329



JPNDDPGBE1/pPE56
400
1625



JPNDDPGBE1/pPE86
1053
504










Example 18
Fermentative Production of L-Ala-L-Tyr Using a Microorganism Having the Ability to Produce L-Ala and L-Tyr and Having Deletions of Peptidase Genes and a Dipeptide-Permeating/Transporting Protein Operon
Escherichia coli JPNDDP36 obtained in Experimental Example 16 was transformed with pPE86 obtained in Example 2, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C. A plasmid was extracted from a colony of the strain that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that Escherichia coli JPNDDP36 carrying pPE86 was obtained, and the strain was designated as Escherichia coli JPNDDP36/pPE86. In the same manner, Escherichia coli JPNDDP36 carrying pTrS30 (hereinafter referred to as Escherichia coli JPNDDP36/pTrS30) and Escherichia coli JPNDDP36 carrying pPE56 (hereinafter referred to as Escherichia coli JPNDDP36/pPE56) were obtained.
The obtained transformants were transformed with pTY2 obtained in Example 4 to obtain the following transformants carrying pTY2: Escherichia coli JPNDDP36/pTrS30/pTY2, Escherichia coli JPNDDP36/pPE56/pTY2 and Escherichia coli JPNDDP36/pPE86/pTY2.
Each of the obtained transformants was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 8 ml of the production medium described in Example 10 containing 100 μg/ml ampicillin in a test tube in an amount of 1% and cultured at 30° C. for 24 hours. The resulting culture was centrifuged to obtain a culture supernatant.
The product in the culture supernatant was derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out in the same manner as in Experimental Example 17. The results are shown in Table 14.










TABLE 14







L-Ala-L-Tyr
L-Tyr



(mg/l)
(mg/l)




















JPNDDP36/pTrS30/pTY2
0
41



JPNDDP36/pPE56/pTY2
301
16



JPNDDP36/pPE86/pTY2
367
8










Example 19
Fermentative Production of L-Ala-L-Val Using a Microorganism Having the Ability to Produce L-Ala and L-Val and Having Deletions of Peptidase Genes and a Dipeptide-Permeating/Transporting Protein Operon
Escherichia coli JPNDDPILG+1 in which the ilvL gene was deleted and the frameshift mutation of the ilvG gene reverted was prepared using, as a parent strain, the mutant strain having deletions of peptidase genes and a peptide-permeating/transporting protein operon obtained in Experimental Example 16 according to the method described in Example 7.
Escherichia coli JPNDDPILG+1 was transformed with pPE86 obtained in Example 2, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C. A plasmid was extracted from the strain that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that Escherichia coli JPNDDPILG+1 carrying the plasmid pPE86 (hereinafter referred to as Escherichia coli JPNDDPILG+1/pPE86) was obtained. In the same manner, Escherichia coli JPNDDPILG+1 carrying the plasmid pTrS30 (hereinafter referred to as Escherichia coli JPNDDPILG+1/pTrS30) and Escherichia coli JPNDDPILG+1 carrying the plasmid pPE56 (hereinafter referred to as Escherichia coli JPNDDPILG+1/pPE56) were obtained.
Each of the obtained transformants was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 8 ml of a medium [16 g/l dipotassium hydrogenphosphate, 14 g/l potassium dihydrogenphosphate, 5 g/l ammonium sulfate, 1 g/l citric acid (anhydrous), 5 g/l Casamino acid (Difco), 10 g/l glucose, 10 mg/l vitamin B1, 25 mg/l magnesium sulfate heptahydrate and 50 mg/l ferrous sulfate heptahydrate; pH adjusted to 7.2 with 10 mol/l sodium hydroxide; glucose, vitamin B1, magnesium sulfate heptahydrate and ferrous sulfate heptahydrate were added after separate steam sterilization] containing 100 μg/ml ampicillin in a test tube in an amount of 1% and cultured at 30° C. for 24 hours. The resulting culture was centrifuged to obtain a culture supernatant.
The product in the culture supernatant was derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out in the same manner as in Experimental Example 17. The results are shown in Table 15.










TABLE 15







L-Ala-L-Val
L-Val



(mg/l)
(mg/l)




















JPNDDPILG + 1/pTrS30
0
220



JPNDDPILG + 1/pPE56
62
171



JPNDDPILG + 1/pPE86
300
240










Example 20
Fermentative Production of L-Ala-L-Ile Using a Microorganism Having the Ability to Produce L-Ala and L-Ile and Having Deletions of Peptidase Genes and a Dipeptide-Permeating/Transporting Protein Operon
Escherichia coli JPNDDPILG+IA1 in which the ilvL gene was deleted, the frameshift mutation of the ilvG gene reverted and the ilvA gene was substituted by the inhibition-released ilvA gene was prepared using, as a parent strain, Escherichia coli JPNDDP36, the mutant strain having deletions of peptidase genes and a peptide-permeating/transporting protein operon obtained in Experimental Example 16 according to the methods described in Examples 7 and 8.
Escherichia coli JPNDDPILG+IA1 was transformed with pPE86 obtained in Example 2, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C. A plasmid was extracted from a colony of the strain that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that Escherichia coli JPNDDPILG+IA1 carrying pPE86 was obtained, and the strain was designated as Escherichia coli JPNDDPILG+IA1/pPE86. In the same manner, Escherichia coli JPNDDPILG+IA1 carrying pTrS30 (hereinafter referred to as Escherichia coli JPNDDPILG+IA1/pTrS30) and Escherichia coli JPNDDPILG+IA1 carrying pPE56 (hereinafter referred to as Escherichia coli JPNDDPILG+IA1/pPE56) were obtained.
Each of the obtained transformants was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 8 ml of the production medium described in Example 10 containing 100 μg/ml ampicillin in a test tube in an amount of 1% and cultured at 30° C. for 24 hours. The resulting culture was centrifuged to obtain a culture supernatant.
The product in the culture supernatant was derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out in the same manner as in Experimental Example 17. The results are shown in Table 16.










TABLE 16







L-Ala-L-Ile
L-Ile



(mg/l)
(mg/l)




















JPNDDPILG + IA1/pTrS30
0
124



JPNDDPILG + IA1/pPE56
21
212



JPNDDPILG + IA1/pPE86
159
189










Example 21
Fermentative Production of L-Ala-L-Leu Using a Microorganism Having the Ability to Produce L-Ala and L-Leu and Having Deletions of Peptidase Genes and a Dipeptide-Permeating/Transporting Protein Operon
Escherichia coli JPNDDPILG+LA1 in which the ilvL gene was deleted, the frameshift mutation of the ilvG gene reverted and the leuA gene was substituted by the mutant leuA gene was prepared using, as a parent strain, Escherichia coli JPNDDP36, the mutant strain having deletions of peptidase genes and a peptide-permeating/transporting protein operon obtained in Experimental Example 16 according to the methods described in Examples 7 and 9. The obtained strain was transformed with pPE86 obtained in Example 2, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C. A plasmid was extracted from a colony of the strain that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that Escherichia coli JPNDDPILG+LA1 carrying pPE86 was obtained, and the strain was designated as Escherichia coli JPNDDPILG+LA1/pPE86. In the same manner, Escherichia coli JPNDDPILG+LA1 carrying pTrS30 (hereinafter referred to as Escherichia coli JPNDDPILG+LA1/pTrS30) and Escherichia coli JPNDDPILG+LA1 carrying pPE56 (hereinafter referred to as Escherichia coli JPNDDPILG+LA1/pPE56) were obtained.
Each of the obtained transformants was inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin in a test tube and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 8 ml of the production medium described in Example 10 containing 100 μg/ml ampicillin in a test tube in an amount of 1% and cultured at 30° C. for 24 hours. The resulting culture was centrifuged to obtain a culture supernatant.
The product in the culture supernatant was derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out in the same manner as in Experimental Example 17. The results are shown in Table 17.










TABLE 17







L-Ala-L-Leu
L-Leu



(mg/l)
(mg/l)




















JPNDDPILG + LA1/pTrS30
0
12



JPNDDPILG + LA1/pPE56
78
66



JPNDDPILG + LA1/pPE86
110
25










Example 22
Fermentative Production of L-Ser-L-Phe Using a Microorganism Having the Ability to Produce L-Ser and L-Phe and Having Deletions of Peptidase Genes and a Dipeptide-Permeating/Transporting Protein Operon
Escherichia coli JPNDDP36 obtained in Experimental Example 16 was transformed with pSE15 or pPE212 obtained in Example 3, spread on LB agar medium containing 50 μg/ml ampicillin, and cultured overnight at 30° C. A plasmid was extracted from a colony of each of the strains that grew on the medium according to a known method. By restriction enzyme digestion, it was confirmed that Escherichia coli JPNDDP36 carrying pSE15 and Escherichia coli JPNDDP36 carrying pPE212 were obtained, and the strain was designated as Escherichia coli JPNDDP36/pSE15 and Escherichia coli JPNDDP36/pPE212, respectively.
The obtained transformants were transformed with the plasmid pPHEAF2 expressing the feedback-resistant pheA gene and feedback-resistant aroF gene derived from Escherichia coli constructed in Example 3 to obtain the following transformants carrying pPHEAF2: Escherichia coli JPNDDP36/pSE15/pPHEAF2 and Escherichia coli JPNDDP36/pPE212/pPHEAF2.
Escherichia coli JPNDDP36/pSE15/pPHEAF2 and Escherichia coli JPNDDP36/pPE212/pPHEAF2 were inoculated into 8 ml of LB medium containing 50 μg/ml ampicillin and 30 μg/ml chloramphenicol in a test tube, respectively and cultured at 28° C. for 17 hours. The resulting culture was inoculated into 8 ml of the production medium described in Example 10 containing 100 μg/ml ampicillin in a test tube in an amount of 1% and cultured at 30° C. for 24 hours. The resulting culture was centrifuged to obtain a culture supernatant.
The product in the culture supernatant was derivatized by the F-moc method and then analyzed by HPLC. The HPLC analysis was carried out in the same manner as in Experimental Example 17. The results are shown in Table 18.











TABLE 18







L-Ala-L-Tyr
L-Ser
L-Tyr



(mg/l)
(mg/l)
(mg/l)



















JPNDDP36/pSE15/pPHEAF2
0
7
31


JPNDDP36/pSE212/pPHEAF2
7
7
10









The results shown in Examples 16 to 22 revealed that a microorganism which has the ability to produce a protein having the activity to form a dipeptide from one or more kinds of amino acids, which has the ability to produce one or more kinds of amino acids, and in which the activities of one or more kinds of peptidases and one or more kinds of peptide-permeating/transporting proteins are lost, or in which the activities of three or more kinds of peptidases are lost forms and accumulates the dipeptide in a medium when cultured therein, and the ability to produce the dipeptide of said microorganism is higher than that of a microorganism which has the ability to produce the protein having the activity to form the dipeptide from one or more kinds of amino acids and the ability to produce one or more kinds of amino acids, but in which the activities of any peptidase and peptide-permeating/transporting protein are not lost.
Sequence Listing Free Text
SEQ ID NO: 19—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 20—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 21—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 22—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 23—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 24—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 25—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 26—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 27—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 28—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 29—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 30—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 31—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 32—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 33—Description of Artificial Sequence: Amino acid sequence used in database search
SEQ ID NO: 34—Description of Artificial Sequence: Amino acid sequence used in database search
SEQ ID NO: 35—Description of Artificial Sequence: Amino acid sequence used in database search
SEQ ID NO: 41—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 42—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 54—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 64—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 65—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 66—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 67—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 68—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 69—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 70—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 71—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 72—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 73—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 74—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 75—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 76—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 77—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 78—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 79—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 80—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 81—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 82—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 83—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 84—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 85—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 86—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 87—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 88—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 89—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 90—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 91—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 92—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 93—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 94—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 95—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 96—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 97—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 98—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 99—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 100—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 101—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 102—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 103—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 104—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 105—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 106—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 107—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 108—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 109—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 110—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 111—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 112—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 113—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 114—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 115—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 116—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 117—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 118—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 119—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 120—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 121—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 122—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 123—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 124—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 125—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 126—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 127—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 128—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 129—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 130—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 131—Description of Artificial Sequence: Synthetic DNA
SEQ ID NO: 132—Description of Artificial Sequence: Synthetic DNA

## Claims

1. A process for producing a dipeptide represented by formula (I):


R1-R2  (I)

wherein R1 is L-alanine, glycine, L-methionine, L-serine, L-threonine, β-alanine, L-cysteine or L-α-aminobutyric acid, and R2 is L-alanine, L-glutamine, L-glutamic acid, glycine, L-valine, L-leucine, L-isoleucine, L-proline, L-phenylalanine, L-tryptophan, L-methionine, L-serine, L-threonine, L-cysteine, L-asparagine, L-tyrosine, L-lysine, L-arginine, L-histidine, L-aspartic acid, L-α-aminobutyric acid, β-alanine, L-azaserine, L-theanine, L-4-hydroxyproline, L-3-hydroxyproline, L-ornithine, L-citrulline or L-6-diazo-5-oxo-norleucine, provided that both R1 and R2 cannot be L-alanine at the same time, said method comprising:
culturing in a medium a microorganism which produces a protein comprising the amino acid sequence of SEQ ID NO:2, or a protein consisting of an amino acid sequence which has 95% or more homology to the amino acid sequence of SEQ ID NO:2 and having the activity of forming said dipeptide, and which has the ability to produce at least one of R1 or R2;
allowing the dipeptide to form and accumulate in the medium; and
recovering the dipeptide from the medium.

2. The process according to claim 1, wherein the protein is encoded by DNA selected from the group consisting of the following [1] to [3]:
[1] DNA comprising the nucleotide sequence of SEQ ID NO ID NO:10;
[2] DNA encoding a protein comprising the amino acid sequence of SEQ ID NO:2 or a protein consisting of an amino acid sequence which has 95% or more homology to the amino acid sequence of SEQ ID NO:2 and having the activity of forming the dipeptide from R1 and R2; and
[3] DNA which hybridizes with DNA having a nucleotide sequence completely complementary to the nucleotide sequence shown in SEQ ID NO:10 at 65° C. in the presence of 0.7 to 1.0 mol/l sodium chloride followed by washing at 65° C. with a 0.1 to 2-fold concentrated SSC solution, and which encodes a protein having the activity to form the dipeptide from R1 and R2.

3. The process according to claim 1, wherein the microorganism is transformed with a recombinant DNA comprising the DNA selected from the group consisting of [1] to [3];
[1] DNA comprising the nucleotide sequence of SEQ ID NO:10;
[2] DNA encoding a protein comprising the amino acid sequence of SEQ ID NO:2 or a protein consisting of an amino acid sequence which has 95% or more homology to the amino acid sequence of SEQ ID NO:2 and having the activity of forming the dipeptide from R1 and R2; and
[3] DNA which hybridizes with DNA having a nucleotide sequence completely complementary to the nucleotide sequence shown in SEQ ID NO:10 at 65° C. in the presence of 0.7 to 1.0 mol/l sodium chloride followed by washing at 65° C. with a 0.1 to 2-fold concentrated SSC solution, and which encodes a protein having the activity to form the dipeptide from R1 and R2.

4. The process according to claim 3, wherein the microorganism belongs to the genus Escherichia, Corynebacterium, Bacillus, Serratia, Pseudomonas or Streptomyces.

5. The process according to claim 4, wherein the microorganism is Escherichia coli, Corynebacterium glutamicum, Corynebacterium ammoniagenes, Corynebacterium lactofermentum, Corynebacterium flavum, Corynebacterium efficiens, Bacillus subtilis, Bacillus megaterium, Serratia marcescens, Pseudomonas putida, Pseudomonas aeruginosa, Streptomyces coelicolor or Streptomyces lividans.

6. The process according to claim 1, wherein the microorganism belongs to the genus Bacillus.

7. The process according to claim 6, wherein the microorganism is Bacillus subtilis.

8. The process according to claim 1, wherein the protein consists of said amino acid sequence which has 95% or more homology to the amino acid sequence of SEQ ID NO:2 and having the activity of forming a dipeptide from R1 and R2.

9. The process according to claim 2, wherein the DNA comprises SEQ ID NO:10.

10. The process according to claim 3, wherein the DNA comprises SEQ ID NO:10.

11. The process according to claim 1, wherein the protein comprises SEQ ID NO:2.