Method of Producing L-Amino Acid
An L-amino acid is produced by culturing a microorganism belonging to the family Enterobacteriaceae having an L-amino acid-producing ability and modified so that glycerol dehydrogenase and dihydroxyacetone kinase activities are increased, in a medium containing glycerol as a carbon source to produce and accumulate an L-amino acid in the medium or cells, and collecting the L-amino acid from the medium or the cells.
This application is a Continuation of, and claims priority under 35 U.S.C. §120 to, U.S. patent application Ser. No. 12/545,966, filed Aug. 24, 2009, which was a Continuation of, and claims priority under 35 U.S.C. §120 to, PCT Patent Application No. PCT/JP2008/053020, filed Feb. 22, 2008, which claims priority under 35 U.S.C. §119 to Japanese Patent Application No. 2007-041724, filed on Feb. 22, 2007, which are incorporated in their entireties by reference. The Sequence Listing in electronic format filed herewith is also hereby incorporated by reference in its entirety (File Name: 2013-07-10T_US-405C_Seq_List; File Size: 438 KB; Date Created: Jul. 10, 2013).
BACKGROUND OF THE INVENTION1. Field of the Invention
The present invention is related to the field of fermentation, and more specifically to the production of L-amino acids via the fermentation of microorganisms.
2. Brief Description of the Related Art
L-Amino acids are industrially produced by fermentation using microorganisms belonging to the genus Brevibacterium, Corynebacterium, Escherichia, or the like. In such production methods, strains are used which are isolated from nature, or artificial variants of such strains. Furthermore, microorganism strains can be used which are modified by a recombinant DNA technique to increase activity of a basic L-amino acid biosynthesis enzyme, and so forth (EP 0643135 B, EP 0733712 B, EP 1477565 A, EP 0796912 A, EP 0837134 A, WO01/53459, EP 1170376 A, WO2005/010175, and WO96/17930).
When amino acids are produced using microorganisms, sugars are generally used as a main component of substrate, but glycerol can also be used as a substrate (EP 1715055 A and EP 1715056 A).
It is known that Escherichia coli has a plurality of genes which participate in glycerol metabolism. However, it has been revealed that, since a mutant strain deficient in glpK, which is a gene coding for glycerol kinase, or glpD, which is a gene coding for glycerol-3-phosphate dehydrogenase, cannot grow in a medium when glycerol is the sole carbon source, the major glycerol assimilation pathway of E. coli consists of glycerol kinase and glycerol-3-phosphate dehydrogenase (J. Bacteriol., 23 (2006) 8259-8271).
It is known that glycerol dehydrogenase of E. coli is also one of the enzymes which participate in glycerol metabolism, and it recovers a mutant strain deficient in the three genes of glpK, glpD and glpR, which is a gene of repressor of the glp regulon, from lethality thereof in a medium containing glycerol as a sole carbon source in screening using that strain (J. Bacteriol., 131 (1977) 1026-1028).
The pathway via glycerol-3-phosphate including glycerol kinase and glycerol-3-phosphate dehydrogenase is thought to be the main glycerol assimilation pathway of microorganisms belonging to the family Enterobacteriaceae as described above, and the glycerol assimilation pathway via dihydroxyacetone is an unnecessary pathway for glycerol assimilation of microorganisms belonging to the family Enterobacteriaceae.
SUMMARYAn aspect of the present invention is to provide a method for producing an L-amino acid by fermentation using a substrate containing glycerol, which is improved compared with conventional techniques.
It has been found that enhancing either glycerol dehydrogenase or dihydroxyacetone kinase, which are enzymes of the glycerol assimilation pathway via dihydroxyacetone, was not effective for production of L-amino acids from glycerol. However, enhancing both glycerol dehydrogenase and dihydroxyacetone kinase markedly improved the production of L-amino acids from glycerol.
It is an aspect of the present invention to provide a method for producing an L-amino acid by (A) modifying a microorganism belonging to the family Enterobacteriaceae having an L-amino acid-producing ability to increase glycerol dehydrogenase and dihydroxyacetone kinase activities, (B) culturing said microorganism in a medium containing glycerol as a carbon source to produce and accumulate an L-amino acid in the medium or cells, and (C) collecting the L-amino acid from the medium or the cells.
It is a further aspect of the present invention to provide the method as described above,
wherein the glycerol dehydrogenase and dihydroxyacetone kinase activities are increased by increasing copy numbers of genes coding for glycerol dehydrogenase and dihydroxyacetone kinase, or modifying expression control sequences of the genes.
It is a further aspect of the present invention to provide the method as described above, wherein the dihydroxyacetone kinase uses ATP as a phosphate donor.
It is a further aspect of the present invention to provide the method as described above, wherein the microorganism is further modified to increase glycerol uptake activity.
It is a further aspect of the present invention to provide the method as described above, wherein the microorganism is further modified to increase the activity or activities of an enzyme selected from the group consisting of triosephosphate isomerase, fructose bisphosphate aldolase, fructose-1,6-bisphosphatase, fructose-6-phosphate aldolase, and combinations thereof.
It is a further aspect of the present invention to provide the method as described above, wherein the microorganism is further modified to reduce the activity or activities of glycerol kinase and/or membrane-binding type glycerol-3-phosphate dehydrogenase.
It is a further aspect of the present invention to provide the method as described above, wherein the microorganism belonging to the family Enterobacteriaceae is an Escherichia bacterium, or a Pantoea bacterium.
It is a further aspect of the present invention to provide the method as described above, wherein the L-amino acid is selected from the group consisting of L-glutamic acid, L-lysine, L-leucine, L-isoleucine, L-valine, L-tryptophan, L-phenylalanine, L-tyrosine, L-threonine, L-methionine, L-cysteine, L-arginine, L-serine, L-proline, L-asparatic acid, L-asparagine, L-glutamine, and L-histidine.
DETAILED DESCRIPTION OF EXEMPLARY EMBODIMENTSHereafter, the present invention will be explained in detail.
<1> Microorganism
Exemplary microorganisms of the present invention include a microorganism belonging to the family Enterobacteriaceae, which has an ability to produce an L-amino acid and is modified to increase glycerol dehydrogenase and dihydroxyacetone kinase activities. The ability to produce an L-amino acid (L-amino acid-producing ability) can mean an ability of exemplary microorganisms of the present invention to produce and accumulate an L-amino acid in a medium or cells when cultured in the medium. An exemplary microorganism of the present invention may have an ability to produce two or more kinds of L-amino acids. Although the microorganism having L-amino acid-producing ability may inherently have L-amino acid-producing ability, the microorganism can also be obtained by modifying such microorganisms as mentioned below using a recombinant DNA technique so that they have L-amino acid-producing ability.
Although the type of L-amino acid is not particularly limited, examples include basic amino acids such as L-lysine, L-ornithine, L-arginine, L-histidine and L-citrulline, aliphatic amino acids such as L-isoleucine, L-alanine, L-valine, L-leucine and L-glycine, amino acids which are hydroxy-monoaminocarboxylic acids such as L-threonine and L-serine, cyclic amino acids such as L-proline, aromatic amino acids such as L-phenylalanine, L-tyrosine and L-tryptophan, sulfur-containing amino acids such as L-cysteine, L-cystine and L-methionine, acidic amino acids such as L-glutamic acid and L-aspartic acid, and amino acids with amide group at the side chain such as L-glutamine and L-asparagine. An exemplary microorganism of the present invention may have an ability to produce two or more kinds of L-amino acids.
Microorganisms belonging to the family Enterobacteriaceae include Escherichia bacteria and Pantoea bacteria. Other examples of microorganisms belonging to the family Enterobacteriaceae include microorganisms belonging to γ-proteobacteria such as those of the genus Enterobacter, Klebsiella, Serratia, Erwinia, Salmonella, Morganella or the like.
“Glycerol dehydrogenase” can mean an enzyme which reversibly catalyzes the following oxidation reaction that converts glycerol into dihydroxyacetone by using NAD as a coenzyme (EC:1.1.1.6).
Glycerol+NAD=Dihydroxyacetone+NADH+H+
The phrase “to increase the glycerol dehydrogenase activity” can mean that the number of the glycerol dehydrogenase molecules per cell can be increased compared with that of a wild-type strain or non-modified strain, or that the activity of the glycerol dehydrogenase per molecule can be improved compared with that of a wild-type strain or non-modified strain. Moreover, when the enzyme activity is undetectable in a wild-type strain, and it is improved to a detectable level, this can also be included in the state of “the activity increases”. The glycerol dehydrogenase activity can be at any level so long as it can be detected, but the modification is preferably performed so that the glycerol dehydrogenase activity is 0.05 U/mg or higher, in another example 0.25 U/mg or higher, and in another example 0.5 U/mg or higher. Examples of wild-type strains of the microorganism belonging to the family Enterobacteriaceae which can serve as a reference for comparison include the Escherichia coli MG1655 strain (ATCC No. 47076) and W3110 strain (ATCC No. 27325), Pantoea ananatis AJ13335 strain (FERM BP-6615), and so forth. The glycerol dehydrogenase activity can be measured by referring to the method of Ansis, R. E. et al. (J. Biol. Chem., 2-3, 153-159 (1953))
“Dihydroxyacetone kinase” is an enzyme which reversibly catalyzes the following reaction that converts dihydroxyacetone into dihydroxyacetone phosphate, and one uses ATP as a phosphate donor (EC 2.7.1.29), and one uses PEP as a phosphate donor (EC 2.7.1.29) (Cell. Mol. Life. Sci., 63 (2006) 890-900; Biochemistry, 43 (2004) 13037-13045)
ATP+dihydroxyacetone=ADP+dihydroxyacetone phosphate (EC 2.7.1.29)
Phosphoenolpyruvate+Dihydroxyacetone=Pyruvate+Dihydroxyacetone phosphate (EC2.7.1.29)
In one example, dihydroxyacetone kinase can use ATP as a phosphate donor.
The phrase “to increase the dihydroxyacetone kinase activity” can mean that number of dihydroxyacetone kinase molecules per cell can be increased compared with that of a wild-type strain or non-modified strain, or that the activity of the dihydroxyacetone kinase per molecule can be improved compared with that of a wild-type strain or non-modified strain. The modification is preferably performed so that the dihydroxyacetone kinase activity per cell can be improved to 150% or more, in another example 200% or more, in another example 300% or more, of the activity of a wild-type strain or non-modified strain. Examples of wild-type strains of the microorganism belonging to the family Enterobacteriaceae which can serve as a reference for the comparison include the Escherichia coli MG1655 strain (ATCC No. 47076) and W3110 strain (ATCC No. 27325), Pantoea ananatis AJ13335 strain (FERM BP-6615), and so forth. The dihydroxyacetone kinase activity can be measured by referring to the method of Johnson E. A. (J. Bacteriol., 1984 October; 160(1):55-60).
Examples of the gene coding for glycerol dehydrogenase include the gldA gene, and one example is the gldA gene derived from a microorganism belonging the family Enterobacteriaceae. Examples of the microorganism belonging the family Enterobacteriaceae include Escherichia coli. Examples of the gene of Escherichia coli include, for example, the gldA gene of SEQ ID NO: 1 (complementary strand of the nucleotide numbers 4135955 . . . 4137058 of GenBank Accession No. NC—000913).
Furthermore, homologues of the gene coding for glycerol dehydrogenase can be those cloned on the basis of homology to the gene exemplified above from a bacterium of the genus Escherichia, Enterobacter, Klebsiella, Serratia, Erwinia, Yersinia, Shigella, Salmonella, Vibrio, Aeromonas, Bacillus, Staphylococcus, Lactobacillus, Enterococcus, Clostridium, Pseudomonas, Agrobacterium, Citrobacter, Corynebacterium, or the like. Examples of the gene which show high homology to the gldA gene of Escherichia coli and can be used as the gene coding for glycerol dehydrogenase are mentioned in Table 1.
Homology (identity etc.) of amino acid sequences and nucleotide sequences can be determined by using, for example, the algorithm BLAST of Karlin and Altschul (Pro. Natl. Acad. Sci. USA, 90, 5873 (1993)) or FASTA of Pearson (Methods Enzymol., 183, 63 (1990)). Programs called BLASTN and BLASTX have been developed on the basis of this algorithm BLAST (refer to www.ncbi.nlm.nih.gov).
As the gene coding for dihydroxyacetone kinase, the genes designated dhaKLM gene, dak1 gene, dhaK gene and dhbK gene can be used. Examples of the gene coding for the enzyme using PEP as a phosphate donor include those genes derived from Escherichia coli, such as the dhaK gene of SEQ ID NO: 34 (complementary strand of the nucleotide numbers 1248991 . . . 1250061 of GenBank Accession No. NC—000913), the dhaL gene of SEQ ID NO: 36 (complementary strand of the nucleotide numbers 1248348.1248980 of GenBank Accession No. NC—000913), and the dhaM gene of SEQ ID NO: 38 (complementary strand of the nucleotide numbers 1246919 . . . 1248337 of GenBank Accession No. NC—000913).
The gene coding for dihydroxyacetone kinase which uses ATP as a phosphate donor can be used, and includes the dak1 gene derived from yeast, the dhbK gene derived from Agrobacterium bacteria, and the dhaK gene derived from Citrobacter bacteria. Examples of the dak1 gene derived from yeast include the dak1 gene of SEQ ID NO: 3 derived from Saccharomyces cerevisiae (GenBank Accession No NP—013641.1 GI: 6323570), examples of the dhbK gene derived from Agrobacterium bacteria include the dhbK gene of SEQ ID NO: 5 derived from Agrobacterium tumefaciens (GenBank Accession No. NP—357070.1 GI: 15891398), and examples of the dhaK gene derived from Citrobacter bacteria include the dhaK gene of SEQ ID NO: 7 derived from Citrobacter freundii (GenBank Accession No. U09771).
Furthermore, homologues of the gene coding for dihydroxyacetone kinase can be those cloned on the basis of homology to the gene exemplified above from a bacterium such as those of the genus Escherichia, Enterobacter, Klebsiella, Serratia, Erwinia, Yersinia, Shigella, Salmonella, Vibrio, Aeromonas, Bacillus, Staphylococcus, Lactobacillus, Enterococcus, Clostridium, Agrobacterium, Citrobacter, and Mycobacterium, yeast such as those of the genus Saccharomyces, Schizosaccharomyces or Pichia, or the like.
In particular, as the gene coding for dihydroxyacetone kinase which uses ATP as a phosphate donor, the following sequences can be used. Genes coding for dihydroxyacetone kinase and showing high homology to the dak1 gene derived from Saccharomyces cerevisiae are shown in Table 2, dihydroxyacetone kinase genes showing high homology to the dhbK gene derived from Agrobacterium tumefaciens are shown in Table 3, and dihydroxyacetone kinase genes showing high homology to the dhaK gene derived from Citrobacter freundii are shown in Table 4.
“Homologues” of the aforementioned genes mean mutant genes derived from other microorganisms, or natural or artificial mutant genes, which show high structural similarity to the aforementioned genes and are able to improve the glycerol dehydrogenase activity and dihydroxyacetone kinase activity when they are introduced into a host or amplified. Homologues of glycerol dehydrogenase and dihydroxyacetone kinase genes mean genes coding for a protein showing a homology of 80% or more, in another example 90% or more, in another example 95% or more, in another example 98% or more, to the total amino acid sequence of SEQ ID NO: 2, 4, 6 or 8 or any of the amino acid sequences encoded by the sequences mentioned in Tables 1 to 4, and having a function of glycerol dehydrogenase or dihydroxyacetone kinase. Whether a gene codes for a protein having glycerol dehydrogenase activity or dihydroxyacetone kinase activity can be confirmed by expressing the gene in a host cell and examining whether the enzymatic activity is increased compared with a non-modified strain according to the aforementioned enzymatic activity measurement method. Moreover, whether a gene is a homologue or not can be confirmed by preparing a gene-disrupted strain in which the corresponding wild-type gene is disrupted, introducing the gene into the disrupted strain, and examining whether the gene complements the function of the wild-type gene, for example, whether the enzymatic activity reduced by the gene disruption is restored.
Furthermore, the genes coding for glycerol dehydrogenase and dihydroxyacetone kinase are not limited to wild-type genes, and they may be mutant or artificially modified genes coding for a protein having an amino acid sequence of SEQ ID NO: 2, 4, 6 or 8 or any of the amino acid sequences mentioned in Table 1 to 4, and which can include substitution, deletion, insertion, addition or the like of one or more amino acid residues at one or more positions so long as the function of encoded glycerol dehydrogenase or dihydroxyacetone kinase is not reduced. Although the number of the “one or several” amino acid residues may differ depending on positions in the three-dimensional structure or types of amino acid residues of the protein, it may be specifically 1 to 20, in another example 1 to 10, in another example 1 to 5, and in another example 1 to 3. These substitutions can be conservative substitutions. The conservative substitution is a mutation wherein substitution takes place mutually among Phe, Trp and Tyr, if the substitution site is an aromatic amino acid; among Leu, Ile and Val, if it is a hydrophobic amino acid; between Gln and Asn, if it is a polar amino acid; among Lys, Arg and His, if it is a basic amino acid; between Asp and Glu, if it is an acidic amino acid; and between Ser and Thr, if it is an amino acid having a hydroxyl group. Examples of the conservative substitution include substitution of Ser or Thr for Ala, substitution of Gln, His or Lys for Arg, substitution of Glu, Gln, Lys, His or Asp for Asn, substitution of Asn, Glu or Gln for Asp, substitution of Ser or Ala for Cys, substitution of Asn, Glu, Lys, His, Asp or Arg for Gln, substitution of Gly, Asn, Gln, Lys or Asp for Glu, substitution of Pro for Gly, substitution of Asn, Lys, Gln, Arg or Tyr for His, substitution of Leu, Met, Val or Phe for Be, substitution of Be, Met, Val or Phe for Leu, substitution of Asn, Glu, Gln, His or Arg for Lys, substitution of Be, Leu, Val or Phe for Met, substitution of Trp, Tyr, Met, Ile or Leu for Phe, substitution of Thr or Ala for Ser, substitution of Ser or Ala for Thr, substitution of Phe or Tyr for Trp, substitution of His, Phe or Trp for Tyr, and substitution of Met, Ile or Leu for Val. The aforementioned amino acid substitution, deletion, insertion, addition, inversion or the like may be the result of a naturally-occurring mutation due to an individual difference or difference of species (mutant or variant) of a microorganism having the genes coding for glycerol dehydrogenase and dihydroxyacetone kinase.
The genes coding for glycerol dehydrogenase and dihydroxyacetone kinase may also be a DNA which is able to hybridize with a sequence complementary to the nucleotide sequence of SEQ ID NO: 2, 4, 6 or 8 or any of the nucleotide sequences mentioned in Table 1 to 4, or a probe that can be prepared from the nucleotide sequences, under stringent conditions, and codes for a protein having the glycerol dehydrogenase activity or the dihydroxyacetone kinase activity. The “stringent conditions” are conditions under which a so-called specific hybrid is formed, and a non-specific hybrid is not formed. Examples of the stringent condition include those under which highly homologous DNAs hybridize to each other, for example, DNAs not less than 80% homologous, in another example not less than 90% homologous, in another example not less than 95% homologous, and in another example not less than 98% homologous, hybridize to each other, and DNAs less homologous than the above do not hybridize to each other, or conditions of washing of typical Southern hybridization, i.e., washing once, preferably 2 or 3 times, at a salt concentration and temperature corresponding to 1×SSC, 0.1% SDS at 60° C., in another example 0.1×SSC, 0.1% SDS at 60° C., in another example 0.1×SSC, 0.1% SDS at 68° C.
The phrase “intracellular activity of an enzyme increases” can mean when the intracellular activity of the enzyme is increased compared with a wild-type strain (for example, Escherichia coli W3110 and MG1655 strains), or a parent strain (strain in which intracellular activities of all the enzymes specified in the present invention are not enhanced), and also includes when the cells have the activity that a wild-type strain or the parent strain does not have.
Examples of the means for increasing the intracellular activity include the following means and combinations thereof. However, the means are not limited to these. As the means for increasing the activities of glycerol dehydrogenase and dihydroxyacetone kinase, any of (1) to (5) can be used, and the same or different means may be used.
(1) Increase in copy number of a gene coding for each protein by transformation using a vector containing the gene.
(2) Increase in copy number of a gene coding for each protein by integration of the gene into chromosome.
(3) Increase in expression amount of a gene coding for each protein by modification of an expression control region of the gene.
(4) Increase in expression amount by modification of a factor which affects on expression control.
(5) Increase in enzymatic activity by introduction of a mutation into a coding region of a gene coding for each protein.
(6) Increase in amount of protein by improvement of translation efficiency.
Henceforth the genes coding for glycerol dehydrogenase and dihydroxyacetone kinase can be each referred to as an objective gene.
(1) Increase in Copy Number of Gene Coding for Each Protein by Transformation Using Vector Containing the Gene
For example, a DNA fragment containing an objective gene can be ligated to a vector which functions in a host microorganism, for example, a vector of multi-copy type, to prepare a recombinant DNA, and the recombinant DNA can be introduced into a microorganism to transform it. The objective gene can be obtained by PCR (polymerase chain reaction, refer to White, T. J. et al., Trends Genet., 5, 185 (1989)) using chromosomal DNA of Escherichia coli, yeast, Citrobacter bacterium, Agrobacterium bacterium or the like as a template. The objective genes derived from other microorganisms can also be obtained from the chromosomal DNA or a chromosomal DNA library of each microorganism by PCR using, as primers, oligonucleotides prepared based on a known objective gene of the microorganism or sequence information of the objective gene or the protein of a microorganism of other species, or hybridization using an oligonucleotide prepared based on such sequence information as mentioned above as a probe. A chromosomal DNA can be prepared from a microorganism that serves as a DNA donor by the method of Saito and Miura (refer to Saito H. and Miura K., Biochem. Biophys. Acta, 72, 619 (1963); Experimental Manual for Biotechnology, edited by The Society for Biotechnology, Japan, pp. 97-98, Baifukan Co., Ltd., 1992) or the like.
Then, the objective gene amplified by PCR can be ligated to a vector DNA which can function in the cell of a host microorganism to prepare a recombinant DNA. Examples of the vector which can function in a cell of host microorganism include vectors which are autonomously replicable in cells of the host microorganism.
Examples of vectors which are autonomously replicable in microorganisms belonging to the family Enterobacteriaceae include pUC19, pUC18, pHSG299, pHSG399, pHSG398, pACYC184, (pHSG and pACYC series vectors are available from Takara Bio), RSF1010 (Gene, vol. 75(2), p271-288, 1989), pBR322, pMW219, pMW119 (pMW series vectors are available form Nippon Gene), pSTV28, pSTV29 (Takara Bio) and so forth. A phage DNA vector can also be used.
To prepare recombinant DNA by ligating any of the genes to the above-mentioned vector, the vector is digested with a restriction enzyme corresponding to termini of a DNA fragment containing the objective gene. Ligation is generally performed by using a ligase such as T4 DNA ligase. As methods for digesting and ligating DNA, preparation of chromosomal DNA, PCR, preparation of plasmid DNA, transformation, design of oligonucleotides to be used as primers and so forth, methods well known to a person skilled in the art can be employed. These methods are described in Sambrook, J., Fritsch, E. F., and Maniatis, T., “Molecular Cloning A Laboratory Manual, Second Edition”, Cold Sprig Harbor Laboratory Press, (1989), and so forth.
The recombinant DNA prepared as described above may be introduced into a bacterium in accordance with a conventional known transformation method. Examples include electroporation (Canadian Journal of Microbiology, 43, 197 (1997)). It is also possible to use a method of increasing the DNA permeability by treating recipient cells with calcium chloride, which is reported for Escherichia coli K-12 (Mandel, M. and Higa, A., J. Mol. Biol., 53, 159 (1970), or a method of introducing a DNA into a competent cell prepared from a cell at proliferation stage, which is reported for Bacillus subtilis (Duncan, C. H., Wilson, G. A and Young, F. E, Gene, 1, 153 (1977)).
(2) Increase in Copy Number of Gene Coding for Each Protein by Integration of the Gene into Chromosome
Increase of intracellular activity of each enzyme can be achieved by increasing the copy number of the objective gene by introducing the objective gene into chromosomal DNA of the microorganism. Introduction of the objective gene into the chromosomal DNA of the microorganism can be attained by homologous recombination using a target sequence present on the chromosomal DNA in multiple copies. As such a sequence present on a chromosomal DNA in multiple copies, a repetitive DNA or an inverted repeat present on the termini of a transposing element can be used. Alternatively, as disclosed in Japanese Patent Laid-open (Kokai) No. 2-109985, the objective gene can be introduced into the chromosomal DNA by inserting the gene into a transposon, and transferring it so that the gene is integrated into the chromosomal DNA. Moreover, it is also possible to introduce an objective gene into a chromosome by using the Red driven integration method (WO2005/010175). An objective gene can also be introduced into a chromosome by transduction using a phage such as P1 phage, or by using a vector for conjugative transfer. Transfer of a gene to a chromosome can be confirmed by performing Southern hybridization using a part of the gene as a probe. Amplification of copy number can be confirmed by Southern hybridization using a probe complementary to the objective gene. Although the copy number may be amplified to any extent so long as it is amplified by one or more copies, the gene coding for glycerol dehydrogenase can be amplified by two or more copies, in another example three or more copies, in another example five or more copies, and the gene coding for dihydroxyacetone kinase can be amplified by two or more copies, in another example three or more copies, in another example five or more copies. When the gene is not native to the chosen host microorganism, any number of copies can be introduced, so long as one or more copies are introduced.
(3) Increase in Expression Amount of Gene Coding for Each Protein by Modification of Expression Control Region of the Gene
Furthermore, besides increasing the copy number of objective gene mentioned above, increasing the intracellular activity of each enzyme can be achieved by replacing an expression regulatory sequence such as a promoter of the gene on a chromosomal DNA or on a plasmid with a stronger promoter by the method described in WO00/18935. As strong promoters, for example, there are known the lac promoter, trp promoter, trc promoter, lambda phage PR promoter, PL promoter, 1 pp promoter, T7 promoter, tet promoter, and so forth. To amplify glycerol dehydrogenase, the tacM promoter (SEQ ID NO: 10) is one example. dhaK, dhaL and dhaM coding for dihydroxyacetone kinase of Escherichia coli take an operon structure, and expression amounts of all the three genes are improved by enhancing the promoter locating upstream of dhaK.
Moreover, it is also possible to introduce nucleotide substitution or the like into a promoter region of an objective gene to modify it into a stronger promoter. Methods for evaluating potency of promoters and examples of potent promoters are described in the paper of Goldstein et al. (Prokaryotic promoters in biotechnology, Biotechnol. Annu. Rev., 1995, 1, 105-128), and so forth. Furthermore, it is known that substitution of several nucleotides in the spacer region between the ribosome binding site (RBS) and the start codon, in particular, in the region immediately upstream of the start codon, significantly affects the translation efficiency of mRNA, and such a region can also be modified. Expression of the objective gene is enhanced by such substitution or modification of promoter.
As for substitution of a stronger promoter for a promoter on a chromosome, a promoter located upstream of the objective gene on a genome can be replaced with a stronger promoter by transforming a microorganism belonging to the family Enterobacteriaceae with a DNA containing the stronger promoter amplified by PCR or the like to cause recombination of the stronger promoter and the wild-type promoter on the genome. For such gene substitution utilizing homologous recombination, there can be utilized a method called Red-driven integration (Datsenko, K. A, and Wanner, B. L., Proc. Natl. Acad. Sci. USA, 97:6640-6645 (2000)), a method of using a linear DNA such as a method utilizing the Red driven integration in combination with an excisive system derived from λ phage (Cho, E. H., Gumport, R. I., Gardner, J. F., J. Bacteriol., 184:5200-5203 (2002)) (refer to WO2005/010175), a method of using a plasmid containing a temperature sensitive replication origin (Datsenko, K. A, and Wanner, B. L., Proc. Natl. Acad. Sci. USA, 97:6640-6645 (2000), U.S. Pat. No. 6,303,383, Japanese Patent Laid-open No. 05-007491), and so forth.
(4) Increase in Expression Amount by Modification of Factor which Affects on Expression Control
Increase in expression amount by modification of a factor which affects on expression control can be attained by amplifying a gene coding for an activator which increases expression of the genes coding for glycerol dehydrogenase and dihydroxyacetone kinase, or by deleting or attenuating a gene coding for a regulator which reduces expression of the genes. Examples of the activator of dhaKLM coding for dihydroxyacetone kinase include, for example, dhaR (SEQ ID NO: 66, the nucleotide numbers 1250289.1252208 of GenBank Accession No. NC—000913), and expression amount of dhaKLM coding for dihydroxyacetone kinase is increased by a mutation of the dhaR gene (1: EMBO J., 2005 Jan. 26, 24(2):283-93). The expression amount of dhaKLM coding for dihydroxyacetone kinase is also increased by disruption of the ptsI gene (SEQ ID NO: 86, the nucleotide numbers 2532088.2533815 of GenBank Accession No. NC—000913) (Microbiology, 147 (2001) 247-253)
(5) Increase in Enzymatic Activity by Introduction of Mutation into Coding Region of Gene Coding for Each Protein
Furthermore, increase of the activities of glycerol dehydrogenase and dihydroxyacetone kinase can also be achieved by introducing a mutation which increases specific activities of the proteins or improves substrate specificities of the enzymes into the coding regions of the objective genes.
Such a gene coding for each enzyme having a mutation can be obtained by, for example, modifying the nucleotide sequence of the SEQ ID NO: 1, 3, 5 or 7, or a coding region in any of the nucleotide sequences mentioned in Tables 1 to 4, so that amino acid residues of a specific part of the encoded protein include substitution, deletion, insertion, addition or the like of amino acid residues. Furthermore, it can also be obtained by the conventionally known mutagenizing treatments described below. As for the mutagenizing treatments, by a method of treating the nucleotide sequence of the SEQ ID NO: 1, 3, 5 or 7, any of the nucleotide sequences mentioned in Tables 1 to 4, or a coding region sequence in any of these with hydroxylamine or the like in vitro, a method of treating a microorganism such as microorganisms belonging to the family Enterobacteriaceae containing the gene with ultraviolet radiation or a mutagenizing agent used for usual mutagenizing treatment such as N-methyl-N′-nitro-N-nitrosoguanidine (NTG) or ethyl methanesulfonate (EMS), error-prone PCR (Cadwell, R. C., PCR Meth. Appl., 2, 28 (1992)), DNA shuffling (Stemmer, W. P., Nature, 370, 389 (1994)), or StEP-PCR (Zhao, H., Nature Biotechnol., 16, 258 (1998)), a mutation can be artificially introduced into the genes coding for glycerol dehydrogenase and dihydroxyacetone kinase by gene recombination to obtain genes coding for highly active glycerol dehydrogenase and dihydroxyacetone kinase. Whether such mutant enzymes code for glycerol dehydrogenase and dihydroxyacetone kinase can be confirmed by, for example, introducing the genes into a microorganism belonging to the family Enterobacteriaceae and having an L-amino acid-producing ability, culturing it in a medium containing glycerol as a carbon source, and confirming whether the L-amino acid-producing ability is improved, or measuring the enzyme activities by the aforementioned methods.
(6) Increase in Amount of Protein by Improvement of Translation Efficiency
An increase in the amount of protein by improvement of translation efficiency can be attained by increasing the tRNA corresponding to codons less frequently used in the host, or by modifying the objective gene so that it has optimal codons according to frequency of use of codons in the host (Gene 85, 109-114 (1989), Biochemistry, 31, 2598-2608 (1992), J. Bacteriol., 175, 716-722 (1993), Protein Expression and Purification, 50, 49-57 (2006)). An increase in the amount of the objective protein compared with a non-modifying strain or wild-type strain can be confirmed by, for example, detection by Western blotting using antibodies (Molecular Cloning (Cold Spring Harbor Laboratory Press, Cold spring Harbor (USA), 2001)).
The microorganism can be modified to increase glycerol uptake activity, in addition to enhancing glycerol dehydrogenase and dihydroxyacetone kinase. The glycerol uptake activity can mean an activity for incorporating glycerol into cytoplasm, and a glycerol facilitator which is a membrane protein is also involved. Examples of the gene coding for the glycerol facilitator include, for example, the glpF gene of Escherichia coli (SEQ ID NO: 16, complementary strand of the nucleotide numbers 4115268.4116113 of GenBank Accession No. NC—000913).
The gene coding for the glycerol facilitator may be a DNA which hybridizes with a complementary sequence of the nucleotide sequence of SEQ ID NO: 16 or a probe which can be prepared from the complementary sequence under a stringent condition, and codes for a protein having the glycerol uptake activity. Examples also include a DNA coding for the protein of SEQ ID NO: 17. The protein can be a protein showing a homology of 80% or more, in another example 90% or more, in another example 95% or more, and in another example 98% or more, to the total amino acid sequence of SEQ ID NO: 17, so long as it increases the glycerol uptake ability in a microorganism belonging to the family Enterobacteriaceae, when it is introduced into the microorganism.
Moreover, the gene may be a DNA coding for a protein having an amino acid sequence of SEQ ID NO: 17 including substitution, deletion, insertion, addition or the like of one or several amino acid residues, so long as the glycerol uptake activity is not reduced. The activity can be increased by a method similar to the aforementioned methods for enhancing glycerol dehydrogenase and dihydroxyacetone kinase.
The glycerol uptake activity can be measured by using the transport assay method using a membrane protein (Voegele, R. T., Sweet, G. D., and Boos, W. J., Bacteriol., 175:1087-1094 (1993)).
The microorganism can be modified to increase activities of one or more enzymes including triosephosphate isomerase, fructose bisphosphate aldolase, fructose-1,6-bisphosphatase and fructose-6-phosphate aldolase, in addition to enhancing glycerol dehydrogenase and dihydroxyacetone kinase and the enhancement of glycerol uptake activity.
Triosephosphate isomerase is an enzyme which catalyzes a reaction which reversibly converts dihydroxyacetone phosphate into glyceraldehyde-3-phosphate (EC:5.3.1.1).
Dihydroxyacetone phosphate=D-glyceraldehyde-3-phosphate
The phrase “being modified to increase the triosephosphate isomerase activity” can mean that the number of the triosephosphate isomerase molecules per cell can be increased compared with that of a wild-type strain or non-modified strain, or when the activity of the triosephosphate isomerase per molecule can be improved compared with that of a wild-type strain or non-modified strain. The modification can be performed so that the triosephosphate isomerase activity per cell can be improved to 150% or more, in another example 200% or more, in another example 300% or more, of the activity of a wil-type strain or non-modified strain. Examples of wild-type strains of the microorganism belonging to the family Enterobacteriaceae which can serve as a reference for comparison include the Escherichia coli MG1655 strain (ATCC No. 47076) and W3110 strain (ATCC No. 27325), Pantoea ananatis AJ13335 strain (FERM BP-6615), and so forth.
Examples of the gene coding for triosephosphate isomerase include the tpiA gene derived from Escherichia coli (SEQ ID NO: 18, complementary strand of the nucleotide numbers 4108763.4109530 of GenBank Accession No. NC—000913).
The gene coding for triosephosphate isomerase may be a DNA which hybridizes with a complementary sequence of the nucleotide sequence of SEQ ID NO: 18 or a probe which can be prepared from the complementary sequence under stringent conditions, and codes for a protein having the triosephosphate isomerase activity. Examples also include a DNA coding for the protein of SEQ ID NO: 19. The protein can be a protein showing a homology of 80% or more, in another example 90% or more, in another example 95% or more, in another example 98% or more, to the total amino acid sequence of SEQ ID NO: 19, so long as it shows increased triosephosphate isomerase activity in a microorganism belonging to the family Enterobacteriaceae, when it is introduced into the microorganism.
Moreover, the gene may be a DNA coding for a protein having an amino acid sequence of SEQ ID NO: 19 including substitution, deletion, insertion, addition or the like of one or several amino acid residues, so long as the triosephosphate isomerase activity is not reduced.
The triosephosphate isomerase activity can be measured by using the method of Andersen and Cooper (FEBS Lett., 4, 19-20 (1969)). The activity can be increased by methods similar to the aforementioned methods for enhancing glycerol dehydrogenase and dihydroxyacetone kinase.
Fructose bisphosphate aldolase” is an enzyme which reversibly catalyzes the following reaction which converts dihydroxyacetone phosphate and glyceroaldehyde-3-phosphate into D-fructose-1,6-bisphosphate (EC:4.1.2.13).
Dihydroxyacetone phosphate (Glycerone phosphate)+D-Glyceraldehyde-3-phosphate=D-Fructose-1,6-bisphosphate
The phrase “being modified to increase the fructose bisphosphate aldolase activity” can mean that number of the fructose bisphosphate aldolase molecules per cell can be increased compared with that of a wild-type strain or non-modified strain, or when the activity of the fructose bisphosphate aldolase per molecule can be improved compared with that of a wild-type strain or non-modified strain. The modification can be performed so that the fructose bisphosphate aldolase activity per cell can be improved to 150% or more, in another example 200% or more, in another example 300% or more, of the activity of a wild-type strain or non-modified strain. Examples of wild-type strains of the microorganism belonging to the family Enterobacteriaceae which can serve as a reference for the comparison include the Escherichia coli MG1655 strain (ATCC No. 47076) and W3110 strain (ATCC No. 27325), Pantoea ananatis AJ13335 strain (FERM BP-6615), and so forth.
Examples of the gene coding for fructose bisphosphate aldolase include the fbaA gene derived from Escherichia coli (SEQ ID NO: 20, complementary strand of the nucleotide numbers 3068187.3069266 of GenBank Accession No. NC—000913) and the fbaB gene derived from Escherichia coli (SEQ ID NO: 72, complementary strand of the nucleotide numbers 2175534 . . . 2176586 of GenBank Accession No. NC—000913).
The gene coding for fructose bisphosphate aldolase can be a DNA which hybridizes with a complementary sequence of the nucleotide sequence of SEQ ID NO: 20 or 72 or a probe which can be prepared from the complementary sequence under a stringent condition, and codes for a protein having the fructose bisphosphate aldolase activity. Examples also include a DNA coding for the protein of SEQ ID NO: 21 or 73. The protein may be show a homology of 80% or more, in another example 90% or more, in another example 95% or more, in another example 98% or more, to the total amino acid sequence of SEQ ID NO: 21, so long as it shows increased fructose bisphosphate aldolase activity in a microorganism belonging to the family Enterobacteriaceae, when it is introduced into the microorganism.
Moreover, the gene can be a DNA coding for a protein having an amino acid sequence of SEQ ID NO: 21 or 73, but which can include substitution, deletion, insertion, addition or the like of one or several amino acid residues, so long as the fructose bisphosphate aldolase activity is not reduced.
The fructose bisphosphate aldolase activity can be measured by using the method of Richard & Rutter (J. Biol. Chem., 236, 3177-3184). The activity can be increased by methods similar to the aforementioned methods for enhancing glycerol dehydrogenase and dihydroxyacetone kinase.
The fructose-1,6-bisphosphatase is an enzyme which reversibly catalyzes the following reaction that converts D-fructose-1,6-bisphosphate into D-fructose-6-phosphate (EC:3.1.3.11).
D-Fructose-1,6-bisphosphate+H2O=D-Fructose-6-phosphate+Phosphate
The phrase “being modified to increase the fructose-1,6-bisphosphatase activity” can mean that the number of the fructose-1,6-bisphosphatase molecules per cell can be increased compared with that of a wild-type strain or non-modified strain, or when the activity of the fructose-1,6-bisphosphatase per molecule can be improved compared with that of a wild-type strain or non-modified strain. The modification can be performed so that the fructose-1,6-bisphosphatase activity per cell can be improved to 150% or more, in another example 200% or more, in another example 300% or more, of the activity of a wild-type strain or non-modified strain. Examples of wild-type strains of the microorganism belonging to the family Enterobacteriaceae which serve as a reference for the comparison include the Escherichia coli MG1655 strain (ATCC No. 47076) and W3110 strain (ATCC No. 27325), Pantoea ananatis AJ13335 strain (FERM BP-6615), and so forth.
Examples of the gene coding for fructose-1,6-bisphosphatase include the glpX gene (SEQ ID NO: 22, complementary strand of the nucleotide numbers 4112592.4113602 of GenBank Accession No. NC—000913), the fbp gene (SEQ ID NO: 82, the nucleotide numbers 4452634 . . . 4453632 of GenBank Accession No. NC—000913), and the ybhA gene (SEQ ID NO: 84, the nucleotide numbers 796836.7976554 of GenBank Accession No. NC—000913), which are derived from Escherichia coli. The gene coding for the fructose-1,6-bisphosphatase may be a DNA which hybridizes with a complementary sequence of the nucleotide sequence of SEQ ID NO: 22, 82 or 84 or a probe which can be prepared from the complementary sequence under a stringent condition, and codes for a protein having the fructose-1,6-bisphosphatase activity. Examples also include a DNA coding for the protein of SEQ ID NO: 23, 83 or 85. The protein may show a homology of 80% or more, in another example 90% or more, in another example 95% or more, in another example 98% or more, to the total amino acid sequence of SEQ ID NO: 23, 83 or 85, so long as it shows increased fructose-1,6-bisphosphatase activity in a microorganism belonging to the family Enterobacteriaceae, when it is introduced into the microorganism.
Moreover, the gene can be a DNA coding for a protein having an amino acid sequence of SEQ ID NO: 23, 83 or 85, but can include substitution, deletion, insertion, addition or the like of one or several amino acid residues, so long as the fructose-1,6-bisphosphatase activity is not reduced.
The fructose-1,6-bisphosphatase activity can be measured by using the method of Nakajima et al. (Protein Nucleic Enzyme, 22, 1585-1589). The activity can be increased by methods similar to the aforementioned methods for enhancing glycerol dehydrogenase and dihydroxyacetone kinase.
In the present invention, “fructose-6-phosphate aldolase” is an enzyme which reversibly catalyzes the following reaction that converts dihydroxyacetone into fructose-6-phosphate.
D-Fructose-6-phosphate=Dihydroxyacetone+D-Glyceraldehyde-3-phosphate
The phrase “being modified to increase the fructose-6-phosphate aldolase activity” can mean that the number of the fructose-6-phosphate aldolase molecules per cell can be increased compared with that of a wild-type strain or non-modified strain, or when the activity of the fructose-6-phosphate aldolase per molecule can be improved compared with that of a wild-type strain or non-modified strain. The modification can be performed so that the fructose-6-phosphate aldolase activity per cell can be improved to 150% or more, in another example 200% or more, and in another example 300% or more, of the activity observed in a wild-type strain or non-modified strain. Examples of wild-type strains of the microorganism belonging to the family Enterobacteriaceae which can serve as a reference for comparison include the Escherichia coli MG1655 strain (ATCC No. 47076) and W3110 strain (ATCC No. 27325), Pantoea ananatis AJ13335 strain (FERM BP-6615), and so forth.
Examples of the gene coding for fructose-6-phosphate aldolase include the fsaA gene coding for type I aldolase (SEQ ID NO: 68, the nucleotide numbers 862865.863527 of GenBank Accession No. NC—000913), and the fsaB gene (talC gene) (SEQ ID NO: 70, complementary strand of the nucleotide numbers 4137069.4137731 of GenBank Accession No. NC—000913) coding for type II aldolase, which are derived from Escherichia coli.
The gene coding for fructose-6-phosphate aldolase can be a DNA which hybridizes with a complementary sequence of the nucleotide sequence of SEQ ID NO: 68 or 70 or a probe which can be prepared from the complementary sequence under stringent conditions, and codes for a protein having the fructose-6-phosphate aldolase activity. Examples also include a DNA coding for the protein of SEQ ID NO: 69 or 71. The protein may be a protein showing a homology of 80% or more, in another example 90% or more, in another example 95% or more, and in another example 98% or more, to the total amino acid sequence of SEQ ID NO: 69 or 71, so long as it shows increased fructose-6-phosphate aldolase activity in a microorganism belonging to the family Enterobacteriaceae, when it is introduced into the microorganism.
Moreover, the gene may be a DNA coding for a protein having an amino acid sequence of SEQ ID NO: 69 or 71, but which can include substitution, deletion, insertion, addition or the like of one or several amino acid residues, so long as the fructose-6-phosphate aldolase activity is not reduced.
The fructose-6-phosphate aldolase activity can be measured by using the method of Schurmann M., Sprenger G. A. et al. (J. Biol. Chem., 2001 Apr. 6, 276 (14):11055-61). The activity can be increased by methods similar to the aforementioned methods for enhancing glycerol dehydrogenase and dihydroxyacetone kinase.
The microorganism can be modified to reduce glycerol kinase and/or membrane-binding type glycerol-3-phosphate dehydrogenase activity, in addition to the enhancement of glycerol dehydrogenase and dihydroxyacetone kinase, the enhancement of the glycerol uptake activity, and the enhancement of activities of one or more kinds of enzymes including triosephosphate isomerase, fructose bisphosphate aldolase, fructose-1,6-bisphosphatase and fructose-6-phosphate aldolase.
“Glycerol kinase” can mean an enzyme which reversibly catalyzes the following reaction that generates glycerol-3-phosphate and ADP from glycerol and ATP (EC2.7.1.30)
ATP+Glycerol=ADP+sn-Glycerol-3-phosphate
The phrase “being modified to reduce the glycerol kinase activity” can mean that the number of the glycerol kinase molecules per cell can be decreased compared with that of a wild-type strain or non-modified strain, or a state that the activity of the glycerol kinase per molecule can be reduced compared with that of a wild-type strain or non-modified strain. The modification can be performed so that the glycerol kinase activity per cell can be reduced to 70% or less, in another example 50% or less, in another example 30% or less, in another example 20% or less, of the activity of a wild-type strain or non-modified strain, and the enzymatic activity can be deleted. The enzymatic activity can be decreased by reducing the expression amount of the gene coding for the enzyme. Reduction of the expression amount of the gene includes reduction of the transcription amount of mRNA transcribed from the gene and reduction of translation amount of this mRNA.
Complete elimination of the production of the enzyme protein molecule or reduction or deletion of the activity per enzyme protein molecule is attained by disrupting the gene coding for the enzyme. Examples of wild-type strains of the microorganism belonging to the family Enterobacteriaceae which can serve as a reference for comparison include the Escherichia coli MG1655 strain (ATCC No. 47076) and W3110 strain (ATCC No. 27325), Pantoea ananatis AJ13335 strain (FERM BP-6615), and so forth.
Examples of the gene coding for glycerol kinase include the glpK gene (SEQ ID NO: 24, complementary strand of the nucleotide numbers 4113737.4115245 of GenBank Accession No. NC—000913) derived from Escherichia coli. The enzymatic activity of glycerol kinase can be measured by the method of Thorner & Paulus (The Enzymes, 3rd ed., 8, 487-508).
“Membrane-binding type glycerol-3-phosphate dehydrogenase” is an enzyme which catalyzes the oxidation reaction converting glycerol-3-phosphate to dihydroxyacetone phosphate, and is an enzyme which reversibly catalyzes the following reaction.
sn-Glycerol-3P+Ubiquinone=Dihydroxyacetone-P+Ubiquinol (EC:1.1.99.5)
The phrase “being modified to reduce the membrane-binding type glycerol-3-phosphate dehydrogenase activity” can mean that the number of the membrane-binding type glycerol-3-phosphate dehydrogenase molecules per cell is decreased compared with that of a wild-type strain or non-modified strain, or a state that the activity of the membrane-binding type glycerol-3-phosphate dehydrogenase per molecule is reduced compared with that of a wild-type strain or non-modified strain. The modification can be performed so that the membrane-binding type glycerol-3-phosphate dehydrogenase activity per cell is reduced to 70% or less, in another example 50% or less, in another example 30% or less, of the activity of a wild-type strain or non-modified strain, and the enzymatic activity may be deleted. The enzymatic activity can be decreased by reducing the expression amount of the gene coding for the enzyme. Examples of wild-type strains of the microorganism belonging to the family Enterobacteriaceae which can serve as a reference for comparison include the Escherichia coli MG1655 strain (ATCC No. 47076) and W3110 strain (ATCC No. 27325), Pantoea ananatis AJ13335 strain (FERM BP-6615), and so forth.
The membrane-binding type glycerol-3-phosphate dehydrogenase is encoded by the glpABC operon and the glpD gene, and examples of the glpA gene of Escherichia coli include the sequence of SEQ ID NO: 26 (the nucleotide numbers 2350669.2352297 of GenBank Accession No. NC—000913), examples of the glpB gene of Escherichia coli include the sequence of SEQ ID NO: 28 (the nucleotide numbers 2352287.2353546 of GenBank Accession No. NC—000913), examples of the glpC gene of Escherichia coli include the sequence of SEQ ID NO: 30 (the nucleotide numbers 2353543.2354733 of GenBank Accession No. NC—000913), and examples of the glpD gene of Escherichia coli include the sequence of SEQ ID NO: 32 (the nucleotide numbers 3560036.3561541 of GenBank Accession No. NC—000913).
Reduction of activity of an objective enzyme such as glycerol kinase and glycerol-3-phosphate dehydrogenase mentioned above can be attained by
(1) reduction or deletion of the enzymatic activity by introduction of a mutation into a coding region of a gene coding for the objective enzyme, or
(2) reduction or deletion of the enzymatic activity by modification of an expression control sequence of a gene coding for the objective enzyme.
(1) Reduction or deletion of enzymatic activity by introduction of mutation into coding region of gene coding for objective enzyme
Introduction of a mutation into a coding region of a gene coding for an objective enzyme can be attained by introducing a mutation for an amino acid substitution (missense mutation), a stop codon (nonsense mutation), or a frame shift mutation which adds or deletes one or two nucleotides into a region of the objective gene coding for the enzyme on a chromosome by genetic recombination (Journal of Biological Chemistry, 272:8611-8617 (1997); Proceedings of the National Academy of Sciences, USA, 95 5511-5515 (1998); Journal of Biological Chemistry, 266, 20833-20839 (1991)). It can also be attained by deleting a part or all of the gene in the coding region. Specifically, it can be attained by introducing a mutation into a part of DNA of SEQ ID NO: 24, 26, 28, 30 or 32, or deleting a part or all of such DNA.
As for the introduction of mutation, the enzymatic activity can also be reduced or deleted by constructing a gene coding for a mutant enzyme of which the coding region is deleted or introduced with a mutation, and substituting the constructed gene for the normal gene on a chromosome by homologous recombination or the like, or by introducing a transposon or IS factor into the gene.
For introduction of such mutations for reducing or deleting activity of an enzyme as described above into a gene by genetic recombination, for example, the following methods are used. By modifying a partial sequence of an objective gene to prepare a mutant gene designed so that it does not produce an enzyme that functions normally, and transforming a microorganism belonging to the family Enterobacteriaceae with a DNA containing the gene to cause recombination of the mutant gene and the corresponding gene on a chromosome, the objective gene on a chromosome can be replaced with the mutant gene. For such gene substitution utilizing homologous recombination, there can be utilized a method called Red-driven integration (Datsenko, K. A, and Wanner, B. L., Proc. Natl. Acad. Sci. USA, 97:6640-6645 (2000)), a method of using a linear DNA such as a method utilizing the Red driven integration in combination with an excisive system derived from λ phage (Cho, E. H., Gumport, R. I., Gardner, J. F., J. Bacteriol., 184:5200-5203 (2002)), a method of using a plasmid containing a temperature sensitive replication origin (Datsenko, K. A, and Wanner, B. L., Proc. Natl. Acad. Sci. USA, 97:6640-6645 (2000), U.S. Pat. No. 6,303,383, Japanese Patent Laid-open No. 05-007491), and so forth. Moreover, such site-specific mutagenesis based on gene substitution utilizing homologous recombination as described above can also be performed by using a plasmid which is not able to replicate in a host. Moreover, reduction or deletion of the enzymatic activity can also be attained by modification for introducing a mutation into a coding region of an objective gene caused by a usual mutation treatment based on X-ray or ultraviolet irradiation or use of a mutation agent such as N-methyl-N′-nitro-N-nitrosoguanidine.
(2) Reduction or deletion of enzymatic activity by modification of expression control sequence of gene coding for objective enzyme
Reduction or deletion of an enzymatic activity by modification of an expression control sequence of a gene coding for an objective enzyme can also be attained by reducing the expression amount by introducing a mutation into an expression control sequence such as a promoter and SD sequence on a chromosomal DNA, by amplifying a gene coding for a regulator which reduces expression of the gene, or by deleting or attenuating a gene coding for an activator which improves expression of the gene. Methods for evaluating potency of promoters and examples of potent promoters are described in the paper of Goldstein et al. (Prokaryotic promoters in biotechnology, Biotechnol. Annu. Rev., 1995, 1, 105-128), and so forth. Furthermore, it is known that by replacing several nucleotides in the spacer region between the ribosome binding site (RBS) and the start codon, in particular, in the region immediately upstream from the start codon, the translation efficiency of mRNA can be significantly affected, and such a region can also be modified. In particular, the glpA, B and C genes take an operon structure, and therefore the expression amount thereof can be reduced by introducing a mutation into an expression control region such as a promoter region locating upstream of glpA.
<2> Production Method
An exemplary production method of the present invention is a method for producing an L-amino acid, which includes culturing a microorganism belonging to the family Enterobacteriaceae, having an L-amino acid-producing ability and modified to increase glycerol dehydrogenase and dihydroxyacetone kinase activities in a medium containing glycerol as a carbon source to produce and accumulate an L-amino acid in the medium or cells, and collecting the L-amino acid from the medium or the cells. Any batch culture, fed-batch culture, or continuous culture may be used. Glycerol contained in the medium can be contained in the starting medium, feed medium, or both.
The aforementioned fed-batch culture refers to a culture method in which the medium is continuously or intermittently fed into the culture vessel, and the medium is not extracted until the end of the culture. The continuous culture can mean a method in which the medium is continuously or intermittently fed into the culture vessel, and the medium is extracted from the vessel (usually in a volume equal to the volume of the fed medium) at the same time. The starting medium can mean a medium used in batch culture before feeding the feed medium in the fed-batch culture or continuous culture (medium used at the start of the culture). The feed medium can mean a medium which is supplied to the fermentation tank in the fed-batch culture or continuous culture. The batch culture can mean a method in which fresh medium is prepared for every culture, a strain is inoculated into the fresh medium, and medium is not added thereafter until harvest.
The glycerol present in the medium can be the sole carbon source, or a mixed medium can be used which contains other carbon sources in addition to glycerol. Saccharides can be used such as glucose, fructose, sucrose, lactose, galactose, blackstrap molasses, and a sugar solution obtained by hydrolysis of starch hydrolysate or biomass, alcohols such as ethanol, and organic acids such as fumaric acid, citric acid, and succinic acid. When a mixed medium is used, glycerol can be present in the medium at a ratio of 50% or more, in another example 60% or more, in another example 70% or more, in another example 80% or more, in another example 90% or more. Glycerol obtained as a by-product of biodiesel fuel production can also be used (Mu Y, et al, Biotechnol Lett., 28, 1755-91759 (2006); Haas M. J., et al., Bioresour. Technol., 97, 4, 671-8678 (2006)).
As for other components which can be added to the medium, a typical medium can contain, besides the carbon source, a nitrogen source, inorganic ions, and other organic components as required can be used. As the nitrogen source, ammonia, ammonium salts such as ammonium sulfate, ammonium carbonate, ammonium chloride, ammonium phosphate, ammonium acetate and urea, nitrates, and so forth can be used. Ammonia gas and aqueous ammonia used to adjust the pH can also be utilized as the nitrogen source. Furthermore, peptone, yeast extract, meat extract, malt extract, corn steep liquor, soybean hydrolysate, and so forth can also be utilized. The medium can contain one or more of these nitrogen sources. These nitrogen sources can also be used for both the starting medium and the feed medium. Furthermore, the same nitrogen source can be used for both the starting medium and the feed medium, or the nitrogen source of the feed medium may be different from that of the starting medium.
The medium can contain a phosphoric acid source and a sulfur source in addition to the carbon source, the nitrogen source and sulfur. As the phosphoric acid source, potassium dihydrogenphosphate, dipotassium hydrogenphosphate, phosphate polymers such as pyrophosphoric acid and so forth can be utilized. The sulfur source may be any sulfur source so long as it contains a sulfur atom, and salts of sulfuric acid such as sulfates, thiosulfates and sulfites and sulfur-containing amino acids such as cysteine, cystine and glutathione are examples. Among these, ammonium sulfate is another example.
Furthermore, the medium can contain a growth promoting factor (nutrient having a growth promoting effect) in addition to the carbon source, the nitrogen source and sulfur. As the growth promoting factor, trace metals, amino acids, vitamins, nucleic acids as well as peptone, casamino acid, yeast extract, soybean protein degradation product and so forth containing the foregoing substances can be used. Examples of the trace metals include iron, manganese, magnesium, calcium and so forth. Examples of the vitamins include vitamin B1, vitamin B2, vitamin B6, nicotinic acid, nicotinic acid amide, vitamin B12 and so forth. These growth promoting factors may be contained in the starting medium or the feed medium.
When an auxotrophic mutant that requires an amino acid or the like for growth thereof is used, the required nutrient should be supplemented to the medium. In particular, since L-lysine biosynthetic pathway is enhanced and L-lysine degrading ability is attenuated in many of L-lysine-producing bacteria as described below, one or more types of substances, such as L-threonine, L-homoserine, L-isoleucine and L-methionine can be added.
The starting medium and the feed medium can have the same or different compositions. Furthermore, the starting medium and the feed medium may have the same or different sulfur concentrations. Furthermore, when the feed medium is fed at multiple stages, the compositions of the feed media may be the same or different.
The culture is preferably performed as an aeration culture at a fermentation temperature of 20 to 45° C., particularly preferably at 30 to 42° C. The oxygen concentration is adjusted to 5 to 50%, desirably about 10%. Furthermore, the aeration culture is preferably performed with pH adjusted to 5 to 9. If pH drops during the culture, for example, calcium carbonate or an alkali such as ammonia gas and aqueous ammonia can be added to neutralize the culture. When the culture is performed for about 10 to 120 hours, a marked amount of L-amino acid accumulates in the culture medium. Although the concentration of L-amino acid which accumulates is not limited so long as it is higher than that observed with wild-type strains, and the L-amino acid can be isolated and collected from the medium, it may be 50 g/L or higher, in another example 75 g/L or higher, and in another example 100 g/L or higher.
The L-amino acid can be collected by a known collection method from the culture medium after the culture. For example, by removing cells from the culture medium by centrifugation or the like, and then crystallizing the L-amino acid by concentration, the L-amino acid can be collected.
The culture of the microorganism can be performed as a seed culture and main culture in order to ensure accumulation of the L-amino acid higher than a certain level. The seed culture can be performed as a shaking culture using a flask or the like, or batch culture, and the main culture can be performed as fed-batch culture or continuous culture. Alternatively, both the seed culture and the main culture can be performed as batch culture.
When fed-batch culture or continuous culture is performed, the feed medium can be intermittently fed so that the supply of glycerol and other carbon sources is temporarily stopped. The supply of the feed medium can be stopped for, at maximum, 30% or less, in another example 20% or less, and in another example 10% or less, of the feeding time. When the feed medium is intermittently fed, the feed medium can be initially added over a predetermined time, and the second and following additions can be controlled so that they are started when an elevation of pH or dissolved oxygen concentration is detected by a computer upon depletion of the carbon source in the fermentation medium. This usually occurs during the period when no medium is being fed, and prior to when the medium is fed, and thus the substrate concentration in the culture tank is always automatically maintained at a low level (U.S. Pat. No. 5,912,113).
The feed medium used for the fed-batch culture can be a medium containing glycerol or another carbon source and a nutrient having a growth promoting effect (growth promoting factor), and the glycerol concentration and the other carbon source concentration in the fermentation medium can be controlled to be at predetermined concentrations or lower. As the other carbon source, glucose, sucrose and fructose are examples. As the growth promoting factor, nitrogen source, phosphoric acid, amino acids and so forth are examples. As the nitrogen source, ammonia, ammonium salts such as ammonium sulfate, ammonium carbonate, ammonium chloride, ammonium phosphate, ammonium acetate and urea, nitrates and so forth can be used. Further, as the phosphoric acid source, potassium dihydrogenphosphate and dipotassium hydrogenphosphate can be used. As for the amino acids, when an auxotrophic mutant strain is used, the required nutrients can be added. Further, the feed medium can include one type of medium, or a mixture of two or more types of media. When two or more types of feed media are used, the media may be mixed and fed by using one feed tin or fed by using two or more feed tins.
When the continuous culture method is used, the medium may be extracted and fed simultaneously, or a part of the medium may be extracted, and then the medium may be fed. Further, the method may also be a continuous culture method which includes extracting the culture medium containing the L-amino acid and bacterial cells and returning only the cells to the fermenter to reuse the cells (French Patent No. 2669935). As the method of continuously or intermittently feeding a nutrient source, the same method as used in the fed-batch culture can be used.
The continuous culture method of reusing bacterial cells is a method of intermittently or continuously extracting the fermentation medium when the amino acid concentration reaches a predetermined level, extracting only the L-amino acid and re-circulating filtration residues containing bacterial cells into the fermenter, and it can be performed by referring to, for example, French Patent No. 2669935.
When the culture medium is intermittently extracted, a portion of the amount of L-amino acid can be extracted when the L-amino acid concentration reaches a predetermined level, and fresh medium is fed to continue the culture. Further, as for the volume of the medium to be added, the culture can be performed so that the final volume of the medium after the addition of the medium is equal to the volume of the culture medium before the extraction. The term “equal” can mean that the volume corresponds to about 93 to 107% of the volume of the culture medium before the extraction.
When the culture medium is continuously extracted, the extraction can be started at the same time as or after the feeding of the nutrient medium. For example, the starting time of the extraction is, at maximum, 5 hours, in another example3 hours, and in another example 1 hour, after the start of the feeding. Further, the extraction volume of the culture medium is preferably equal to the volume of the medium fed.
<3> Microorganisms which can be Used as Parent Strains to Derive Exemplary Microorganisms of the Present Invention
A bacterium belonging to the family Enterobacteriaceae and having an L-amino acid-producing ability, which can metabolize glycerol as a carbon source, can be used as a parent strain, and the desired property can be imparted by the aforementioned methods.
The family Enterobacteriaceae encompasses bacteria belonging to the genera of Escherichia, Enterobacter, Erwinia, Klebsiella, Pantoea, Photorhabdus, Providencia, Salmonella, Serratia, Shigella, Morganella, Yersinia, and so forth. In particular, bacteria classified into the family Enterobacteriaceae according to the taxonomy used by the NCBI (National Center for Biotechnology Information) database (http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=91347) are examples.
The expression of “a bacterium belonging to the genus Escherichia” can mean that the bacterium is classified into the genus Escherichia according to classification known to a person skilled in the art of microbiology, although the bacterium is not particularly limited. Examples of the bacterium belonging to the genus Escherichia include, but are not limited to, Escherichia coli (E. coli).
The bacterium belonging to the genus Escherichia is not particularly limited. However, examples include, for example, the bacteria of the phyletic groups described in the work of Bachmann et al., Table 1 (Bachmann, B. J., 1996, pp. 2460-2488, In F. D. Neidhardt (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology/Second Edition, American Society for Microbiology Press, Washington, D.C.). Specific examples include the Escherichia coli W3110 (ATCC 27325), Escherichia coli MG1655 (ATCC 47076) and so forth derived from the prototype wild-type strain, K12 strain.
These strains are available from, for example, American Type Culture Collection (Address: 12301 Parklawn Drive, Rockville, Md. 20852, United States of America). That is, accession numbers are given to each of the strains, and the strains can be ordered by using these numbers. The accession numbers of the strains are listed in the catalogue of the American Type Culture Collection.
The expression “bacterium belonging to the genus Pantoea” can mean that the bacterium is classified into the genus Pantoea according to classification known to a person skilled in the art of microbiology. Some strains of Enterobacter agglomerans have been recently re-classified into Pantoea agglomerans, Pantoea ananatis, Pantoea stewartii or the like based on the nucleotide sequence analysis of 16S rRNA etc. (Int. J. Syst. Bacteriol., 43, 162-173 (1993)). Bacteria belonging to the genus Pantoea can encompass such bacteria re-classified into the genus Pantoea as described above.
A bacterium having an L-amino acid-producing ability (an ability to produce an L-amino acid) can mean a bacterium which can produce and secrete an L-amino acid in a medium when it is cultured in the medium. It can also mean a bacterium which can accumulate an objective L-amino acid in the medium in an amount not less than 0.5 g/L, and in another example not less than 1.0 g/L. The term “L-amino acid” encompasses L-alanine, L-arginine, L-asparagine, L-aspartic acid, L-cysteine, L-glutamic acid, L-glutamine, glycine, L-histidine, L-isoleucine, L-leucine, L-lysine, L-methionine, L-phenylalanine, L-proline, L-serine, L-threonine, L-tryptophan, L-tyrosine and L-valine.
As a parent strain which can be used, any of the L-amino acid-producing bacteria reported so far can be used, so long as a strain that can assimilate glycerol is chosen. Hereafter, L-amino acid-producing bacteria are described.
L-Threonine-Producing Bacteria
Examples of L-threonine-producing bacteria and parent strains which can be used to derive such bacteria include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli TDH-6/pVIC40 (VKPM B-3996) (U.S. Pat. No. 5,175,107, U.S. Pat. No. 5,705,371), E. coli 472T23/pYN7 (ATCC 98081) (U.S. Pat. No. 5,631,157), E. coli NRRL-21593 (U.S. Pat. No. 5,939,307), E. coli FERM BP-3756 (U.S. Pat. No. 5,474,918), E. coli FERM BP-3519 and FERM BP-3520 (U.S. Pat. No. 5,376,538), E. coli MG442 (Gusyatiner et al., Genetika (in Russian), 14, 947-956 (1978)), E. coli VL643 and VL2055 (EP 1149911 A) and so forth.
The strain TDH-6 is deficient in the thrC gene, as well as being sucrose-assimilative, and the ilvA gene has a leaky mutation. This strain also has a mutation in the rhtA gene, which imparts resistance to high concentration of threonine or homoserine. The B-3996 strain harbors the plasmid pVIC40 obtained by inserting a thrA*BC operon containing a mutant thrA gene into a RSF1010-derived vector. This mutant thrA gene encodes aspartokinase homoserine dehydrogenase I which is substantially desensitized to feedback inhibition by threonine. The B-3996 strain was deposited on Nov. 19, 1987 at the All-Union Scientific Center of Antibiotics (Nagatinskaya Street 3-A, 117105 Moscow, Russia) under the accession number RIA 1867. The strain was also deposited at the Russian National Collection of Industrial Microorganisms (VKPM) on Apr. 7, 1987 under the accession number VKPM B-3996.
E. coli VKPM B-5318 (EP 0593792 B) can also be used. The B-5318 strain is prototrophic with regard to isoleucine, and in this strain, a temperature-sensitive lambda-phage Cl repressor and PR promoter replace the regulatory region of the threonine operon in the plasmid pVIC40. The strain VKPM B-5318 was deposited at the Russian National Collection of Industrial Microorganisms (VKPM) (1 Dorozhny proezd., 1 Moscow 117545, Russia) on May 3, 1990 under the accession number of VKPM B-5318.
The bacterium can be additionally modified so that expression of one or more of the following genes is increased:
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- the mutant thrA gene which codes for aspartokinase-homoserine dehydrogenase I resistant to feed back inhibition by threonine;
- the thrB gene which codes for homoserine kinase;
- the thrC gene which codes for threonine synthase;
- the rhtA gene which codes for a putative transmembrane protein;
- the asd gene which codes for aspartate-β-semialdehyde dehydrogenase; and
- the aspC gene which codes for aspartate aminotransferase (aspartate transaminase).
The thrA gene which encodes aspartokinase-homoserine dehydrogenase I of Escherichia coli has been elucidated (nucleotide numbers 337 to 2799, GenBank accession NC—000913.2, gi: 49175990). The thrA gene is located between the thrL and thrB genes on the chromosome of E. coli K-12. The thrB gene which encodes homoserine kinase of Escherichia coli has been elucidated (nucleotide numbers 2801 to 3733, GenBank accession NC—000913.2, gi: 49175990). The thrB gene is located between the thrA and thrC genes on the chromosome of E. coli K-12. The thrC gene which encodes threonine synthase of Escherichia coli has been elucidated (nucleotide numbers 3734 to 5020, GenBank accession NC—000913.2, gi: 49175990). The thrC gene is located between the thrB gene and the yaaX open reading frame on the chromosome of E. coli K-12. All three of these genes function as a single threonine operon. To increase expression of the threonine operon, the attenuator region which affects the transcription is desirably removed from the operon (WO2005/049808, WO2003/097839).
The mutant thrA gene which codes for aspartokinase-homoserine dehydrogenase I resistant to feed back inhibition by threonine as well as the thrB and thrC genes can be obtained as one operon from the well-known plasmid pVIC40 which is present in the threonine-producing E. coli strain VKPM B-3996. The plasmid pVIC40 is described in detail in U.S. Pat. No. 5,705,371.
The rhtA gene is present at 18 min on the E. coli chromosome close to the glnHPQ operon, which encodes components of the glutamine transport system. The rhtA gene is identical to ORF1 (ybiF gene, nucleotide numbers 764 to 1651, GenBank accession number AAA218541, gi:440181) and is located between the pexB and ompX genes. The unit expressing a protein encoded by the ORF1 has been designated rhtA gene (rht: resistance to homoserine and threonine). It has also been revealed that the rhtA23 mutation is an A-for-G substitution at position −1 with respect to the ATG start codon (ABSTRACTS of the 17th International Congress of Biochemistry and Molecular Biology in conjugation with Annual Meeting of the American Society for Biochemistry and Molecular Biology, San Francisco, Calif. Aug. 24-29, 1997, abstract No. 457, EP 1013765 A).
The asd gene of E. coli has already been elucidated (nucleotide numbers 3572511 to 3571408, GenBank Accession NC—000913.1, gi:16131307), and can be obtained by PCR (refer to White, T. J., Arnheim, N., and Erlich, H. A., Trends Genet., 5, 185-189 (1989)) utilizing primers prepared based on the nucleotide sequence of the gene. The asd genes of other microorganisms can be obtained in a similar manner.
The aspC gene of E. coli has also already been elucidated (nucleotide numbers 983742 to 984932, GenBank Accession NC—000913.1, gi:16128895), and can be obtained by PCR. The aspC genes of other microorganisms can be obtained in a similar manner.
L-Lysine-Producing Bacteria
Examples of L-lysine-producing bacteria belonging to the genus Escherichia include mutants having resistance to an L-lysine analogue. L-Lysine analogues inhibit growth of bacteria belonging to the genus Escherichia, but this inhibition is fully or partially desensitized when L-lysine is present in a medium. Examples of the L-lysine analogue include, but are not limited to, oxalysine, lysine hydroxamate, S-(2-aminoethyl)-L-cysteine (AEC), γ-methyllysine, α-chlorocaprolactam and so forth. Mutants having resistance to these lysine analogues can be obtained by subjecting bacteria belonging to the genus Escherichia to a conventional artificial mutagenesis treatment. Specific examples of bacterial strains useful for producing L-lysine include Escherichia coli AJ11442 (FERM BP-1543, NRRL B-12185; see U.S. Pat. No. 4,346,170) and Escherichia coli VL611. In these microorganisms, feedback inhibition of aspartokinase by L-lysine is desensitized.
The WC196 strain can be used as an L-lysine-producing bacterium of Escherichia coli. This bacterial strain was bred by conferring AEC resistance to the W3110 strain, which was derived from Escherichia coli K-12. This strain was designated Escherichia coli AJ13069 and was deposited at the National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology (currently National Institute of Advanced Industrial Science and Technology, International Patent Organism Depositary, Central 6, 1-1, Higashi 1-Chome, Tsukuba-shi, Ibaraki-ken, 305-8566, Japan) on Dec. 6, 1994 and assigned an accession number of FERM P-14690. Then, it was converted to an international deposit under the provisions of the Budapest Treaty on Sep. 29, 1995, and assigned an accession number of FERM BP-5252 (U.S. Pat. No. 5,827,698).
Examples of L-lysine-producing bacteria and parent strains which can be used to derive such bacteria also include strains in which expression of one or more genes encoding an L-lysine biosynthetic enzyme can be increased. Examples of such genes include, but are not limited to, dihydrodipicolinate synthase gene (dapA), aspartokinase gene (lysC), dihydrodipicolinate reductase gene (dapB), diaminopimelate decarboxylase gene (lysA), diaminopimelate dehydrogenase gene (ddh) (U.S. Pat. No. 6,040,160), phosphoenolpyrvate carboxylase gene (ppc), aspartate semialdehyde dehydrogenease gene (asd), and aspartase gene (aspA) (EP 1253195 A). In addition, the parent strains can have an increased level of expression of the gene involved in energy efficiency (cyo) (EP 1170376 A), the gene encoding nicotinamide nucleotide transhydrogenase (pntAB) (U.S. Pat. No. 5,830,716), the ybjE gene (WO2005/073390), the gene coding for glutamate dehydrogenase (gdhA, Gene, 23:199-209 (1983)), or combinations thereof. Abbreviations of the genes are indicated in the parentheses.
It is known that wild-type dihydrodipicolinate synthetase derived from Escherichia coli suffers from feedback inhibition by L-lysine, while wild-type aspartokinase from Escherichia coli suffers from suppression and feedback inhibition by L-lysine. Therefore, when the dapA and lysC genes are used, these genes are preferably mutant genes coding the enzymes that do not suffer from the feedback inhibition by L-lysine.
Examples of DNA encoding a mutant dihydrodipicolinate synthetase desensitized to feedback inhibition by L-lysine include a DNA encoding a protein which has the amino acid sequence of the enzyme in which the histidine at position 118 is replaced by tyrosine. Examples of DNA encoding a mutant aspartokinase desensitized to feedback inhibition by L-lysine include a DNA encoding an AKIII having the amino acid sequence in which the threonine at position 352, the glycine at position 323, and the methionine at position 318 are replaced by isoleucine, asparagine and isoleucine, respectively (U.S. Pat. No. 5,661,012 and U.S. Pat. No. 6,040,160). Such mutant DNAs can be obtained by site-specific mutagenesis using PCR or the like.
Wide host-range plasmids RSFD80, pCAB1, and pCABD2 are known as plasmids containing a mutant dapA gene encoding a mutant dihydrodipicolinate synthetase and a mutant lysC gene encoding a mutant aspartokinase (U.S. Pat. No. 6,040,160). Escherichia coli JM109 strain transformed with RSFD80 was named AJ12396 (U.S. Pat. No. 6,040,160), and the strain was deposited at the National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology, Ministry of International Trade and Industry (currently, International Patent Organism Depositary, National Institute of Advanced Industrial Science and Technology) on Oct. 28, 1993 and assigned an accession number of FERM P-13936, and the deposit was then converted to an international deposit under the provisions of Budapest Treaty on Nov. 1, 1994 and assigned an accession number of FERM BP-4859. RSFD80 can be obtained from the AJ12396 strain by a known method.
Examples of L-lysine-producing bacteria and parent strains which can be used to derive such bacteria also include strains having decreased or eliminated activity of an enzyme that catalyzes a reaction for generating a compound other than L-lysine by branching off from the biosynthetic pathway of L-lysine. Examples of the enzymes that catalyze a reaction for generating a compound other than L-lysine by branching off from the biosynthetic pathway of L-lysine include homoserine dehydrogenase, lysine decarboxylase (U.S. Pat. No. 5,827,698), and the malic enzyme (WO2005/010175). In order to reduce or delete the lysine decarboxylase activity, it is preferable to reduce expression of both the cadA gene and ldcC gene coding for lysine decarboxylase (International Publication WO2006/038695).
L-Cysteine-Producing Bacteria
Examples of L-cysteine-producing bacteria and parent strains which can be used to derive such bacteria include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli JM15 which is transformed with different cysE alleles coding for feedback-resistant serine acetyltransferases (U.S. Pat. No. 6,218,168, Russian Patent Application No. 2003121601); E. coli W3110 having over-expressed genes which encode proteins suitable for secreting substances toxic for cells (U.S. Pat. No. 5,972,663); E. coli strains having lowered cysteine desulfohydrase activity (Japanese Patent Laid-open No. 11-155571); and E. coli W3110 with increased activity of a positive transcriptional regulator for cysteine regulon encoded by the cysB gene (WO01/27307).
L-Leucine-Producing Bacteria
Examples of L-leucine-producing bacteria and parent strains which can be used to derive such bacteria include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli strains resistant to leucine (for example, the strain 57 (VKPM B-7386, U.S. Pat. No. 6,124,121)) or leucine analogues including β-2-thienylalanine, 3-hydroxyleucine, 4-azaleucine and 5,5,5-trifluoroleucine (Japanese Patent Publication (Kokoku) No. 62-34397 and Japanese Patent Laid-open No. 8-70879); E. coli strains obtained by a gene engineering method described in WO96/06926; and E. coli H-9068 (Japanese Patent Laid-open No. 8-70879).
The bacterium can be improved by enhancing expression of one or more genes involved in L-leucine biosynthesis. Examples of such genes include genes of the leuABCD operon, of which typical example is a mutant leuA gene coding for isopropyl malate synthase desensitized to feedback inhibition by L-leucine (U.S. Pat. No. 6,403,342). In addition, the bacterium can be improved by increasing expression of one or more genes coding for proteins which excrete L-amino acid from bacterial cells. Examples of such genes include the b2682 and b2683 genes (ygaZH genes) (EP 1239041 A2).
L-Histidine-Producing Bacteria
Examples of L-histidine-producing bacteria and parent strains which can be used to derive such bacteria include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli strain 24 (VKPM B-5945, RU 2003677); E. coli strain 80 (VKPM B-7270, RU 2119536); E. coli NRRL B-12116 to B12121 (U.S. Pat. No. 4,388,405); E. coli H-9342 (FERM BP-6675) and H-9343 (FERM BP-6676) (U.S. Pat. No. 6,344,347); E. coli H-9341 (FERM BP-6674) (EP 1085087); and E. coli AI80/pFM201 (U.S. Pat. No. 6,258,554).
Examples of L-histidine-producing bacteria and parent strains which can be used to derive such bacteria also include strains in which expression of one or more genes encoding an L-histidine biosynthetic enzyme can be increased. Examples of such genes include ATP phosphoribosyl transferase gene (hisG), phosphoribosyl AMP cyclohydrolase gene (hisI), phosphoribosyl-ATP pyrophosphohydrolase gene (hisI), phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase gene (hisA), amidotransferase gene (hisH), histidinol phosphate aminotransferase gene (hisC), histidinol phosphatase gene (hisB), histidinol dehydrogenase gene (hisD), and so forth.
It is known that the L-histidine biosynthetic enzymes encoded by hisG and hisBHAFI are inhibited by L-histidine, and therefore L-histidine-producing ability can also be efficiently enhanced by introducing a mutation which confers resistance to the feedback inhibition into the ATP phosphoribosyl transferase gene (hisG) (Russian Patent Nos. 2003677 and 2119536).
Specific examples of strains having L-histidine-producing ability include E. coli FERM-P 5038 and 5048 which are introduced with a vector carrying a DNA encoding an L-histidine biosynthetic enzyme (Japanese Patent Laid-open No. 56-005099), E. coli strains introduced with a gene for amino acid-export (EP 1016710 A), E. coli 80 strain imparted with sulfaguanidine, DL-1,2,4-triazole-3-alanine, and streptomycin resistance (VKPM B-7270, Russian Patent No. 2119536), and so forth.
L-Glutamic Acid-Producing Bacteria
Examples of L-glutamic acid-producing bacteria and parent strains which can be used to derive such bacteria include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli VL334thrC+ (EP 1172433). E. coli VL334 (VKPM B-1641) is an L-isoleucine and L-threonine auxotrophic strain having mutations in thrC and ilvA genes (U.S. Pat. No. 4,278,765). A wild-type allele of the thrC gene was transferred by the method of general transduction using a bacteriophage P1 grown on the wild-type E. coli K12 strain (VKPM B-7) cells. As a result, an L-isoleucine auxotrophic L-glutamic acid-producing strain VL334thrC+ (VKPM B-8961) was obtained.
Examples of L-glutamic acid-producing bacteria and parent strains which can be used to derive such bacteria include, but are not limited to, strains in which expression of one or more genes encoding an L-glutamic acid biosynthetic enzyme can be increased. Examples of such genes include genes encoding glutamate dehydrogenase (gdhA), glutamine synthetase (glnA), glutamate synthetase (gitAB), isocitrate dehydrogenase (icdA), aconitate hydratase (acnA, acnB), citrate synthase (OA), phosphoenolpyruvate carboxylase (ppc), pyruvate dehydrogenase (aceEF, lpdA), pyruvate kinase (pykA, pykF), phosphoenolpyruvate synthase (ppsA), enolase (eno), phosphoglyceromutase (pgmA, pgmI), phosphoglycerate kinase (pgk), glyceraldehyde-3-phophate dehydrogenase (gapA), triose phosphate isomerase (tpiA), fructose bisphosphate aldolase (fbp), phosphofructokinase (pfkA, pfkB), glucose phosphate isomerase (pgi), and so forth.
Examples of strains modified to increase expression of the citrate synthetase gene, the phosphoenolpyruvate carboxylase gene, and/or the glutamate dehydrogenase gene include those disclosed in EP 1078989 A, EP 955368 A and EP 952221 A.
Examples of L-glutamic acid-producing bacteria and parent strains which can be used to derive such bacteria also include strains having decreased or eliminated activity of an enzyme that catalyzes synthesis of a compound other than L-glutamic acid by branching off from an L-glutamic acid biosynthesis pathway. Examples of such enzymes include isocitrate lyase (aceA), α-ketoglutarate dehydrogenase (sucA), phosphotransacetylase (pta), acetate kinase (ack), acetohydroxy acid synthase (ilvG), acetolactate synthase (ilvI), formate acetyltransferase (pfl), lactate dehydrogenase (ldh), glutamate decarboxylase (gadAB), and so forth. Bacteria belonging to the genus Escherichia deficient in α-ketoglutarate dehydrogenase activity or having reduced α-ketoglutarate dehydrogenase activity and methods for obtaining them are described in U.S. Pat. Nos. 5,378,616 and 5,573,945.
Specific examples of such strains include the following:
E. coli W3110sucA::Kmr
E. coli AJ12624 (FERM BP-3853)
E. coli AJ12628 (FERM BP-3854)
E. coli AJ12949 (FERM BP-4881)
E. coli W3110sucA::Kmr is a strain obtained by disrupting the α-ketoglutarate dehydrogenase gene (hereinafter also referred to as “sucA gene”) of E. coli W3110. This strain is completely deficient in α-ketoglutarate dehydrogenase.
Other examples of L-glutamic acid-producing bacteria include those which belong to the genus Escherichia and have resistance to an aspartic acid antimetabolite. These strains may also be deficient in α-ketoglutarate dehydrogenase, and examples include, for example, E. coli AJ13199 (FERM BP-5807) (U.S. Pat. No. 5,908,768), FFRM P-12379) which additionally has a lowered L-glutamic acid decomposing ability (U.S. Pat. No. 5,393,671); AJ13138 (FERM BP-5565) (U.S. Pat. No. 6,110,714), and so forth.
Examples of L-glutamic acid-producing bacteria include mutant strains belonging to the genus Pantoea which are deficient in α-ketoglutarate dehydrogenase activity or have a decreased α-ketoglutarate dehydrogenase activity, and they can be obtained as described above. Such strains include Pantoea ananatis AJ13356 (U.S. Pat. No. 6,331,419). Pantoea ananatis AJ13356 was deposited at the National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology (currently, National Institute of Advanced Industrial Science and Technology, International Patent Organism Depositary, Central 6, 1-1, Higashi 1-Chome, Tsukuba-shi, Ibaraki-ken, 305-8566, Japan) on Feb. 19, 1998 under an accession number of FERM P-16645. It was then converted to an international deposit under the provisions of Budapest Treaty on Jan. 11, 1999 and assigned an accession number of FERM BP-6616. Pantoea ananatis AJ13356 is deficient in α-ketoglutarate dehydrogenase activity as a result of disruption of the αKGDH-E1 subunit gene (sucA). This strain was identified as Enterobacter agglomerans when it was isolated and deposited as the Enterobacter agglomerans AJ13356. However, it was recently re-classified as Pantoea ananatis on the basis of nucleotide sequencing of 16S rRNA and so forth. Although AJ13356 was deposited at the aforementioned depository as Enterobacter agglomerans, it is described as Pantoea ananatis in this specification.
L-Phenylalanine-Producing Bacteria
Examples of L-phenylalanine-producing bacteria and parent strains which can be used to derive such bacteria include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli AJ12739 (tyrA::Tn10, tyrR) (VKPM B-8197); E. coli HW 1089 (ATCC 55371) harboring the mutant pheA34 gene (U.S. Pat. No. 5,354,672); E. coli MWEC101-b (KR
8903681); E. coli NRRL B-12141, NRRL B-12145, NRRL B-12146 and NRRL B-12147 (U.S. Pat. No. 4,407,952). As parent strains, E. coli K-12 [W3110 (tyrA)/pPHAB] (FERM BP-3566), E. coli K-12 [W3110 (tyrA)/pPHAD] (FERM BP-12659), E. coli K-12 [W3110 (tyrA)/pPHATerm] (FERM BP-12662) and E. coli K-12 [W3110 (tyrA)/pBR-aroG4, pACMAB] named as AJ12604 (FERM BP-3579) may also be used (EP 488424 B1). Furthermore, L-phenylalanine-producing bacteria belonging to the genus Escherichia with an enhanced activity of the protein encoded by the yedA gene or the yddG gene can also be used (U.S. Patent Published Application Nos. 2003/0148473 A1 and 2003/0157667 A1).
L-Tryptophan-Producing Bacteria
Examples of tryptophan-producing bacteria and parent strains which can be used to derive such bacteria, but are not limited to, strains belonging to the genus Escherichia, such as E. coli JP4735/pMU3028 (DSM10122) and JP6015/pMU91 (DSM10123) which are deficient in the tryptophanyl-tRNA synthetase encoded by mutant trpS gene (U.S. Pat. No. 5,756,345); E. coli SV164 (pGH5) having a serA allele encoding phosphoglycerate dehydrogenase free from feedback inhibition by serine and a trpE allele encoding anthranilate synthase free from feedback inhibition by tryptophan (U.S. Pat. No. 6,180,373); E. coli AGX17(pGX44) (NRRL B-12263) and AGX6(pGX50)aroP(NRRL B-12264) deficient in tryptophanase (U.S. Pat. No. 4,371,614); and E. coli AGX17/pGX50,pACKG4-pps in which phosphoenolpyruvate-producing ability is enhanced (WO97/08333, U.S. Pat. No. 6,319,696). L-Tryptophan-producing bacteria belonging to the genus Escherichia with an enhanced activity of the protein encoded by the yedA gene or the yddG gene may also be used (U.S. Patent Published Application Nos. 2003/0148473 A1 and 2003/0157667 A1).
Examples of L-tryptophan-producing bacteria and parent strains which can be used to derive such bacteria also include strains in which one or more activities of the enzymes anthranilate synthase (trpE), phosphoglycerate dehydrogenase (serA), and tryptophan synthase (trpAB) are increased. The anthranilate synthase and phosphoglycerate dehydrogenase both suffer from feedback inhibition by L-tryptophan and L-serine, and therefore a mutation desensitizing them to the feedback inhibition may be introduced into these enzymes. Specific examples of strains having such a mutation include E. coli SV164 which harbors desensitized anthranilate synthase and a transformant strain obtained by introducing the plasmid pGH5 (WO94/08031), which contains a mutant serA gene encoding feedback inhibition-desensitized phosphoglycerate dehydrogenase, into the E. coli SV164.
Examples of L-tryptophan-producing bacteria and parent strains which can be used to derive such bacteria also include strains into which the tryptophan operon containing a gene encoding inhibition-desensitized anthranilate synthase is introduced (Japanese Patent Laid-open Nos. 57-71397, 62-244382, U.S. Pat. No. 4,371,614). Moreover, L-tryptophan-producing ability may be imparted by increasing expression of a gene which encodes tryptophan synthase in the tryptophan operon (trpBA). The tryptophan synthase consists of α and β subunits which are encoded by the trpA and trpB genes, respectively. In addition, L-tryptophan-producing ability can also be improved by increasing expression of the isocitrate lyase-malate synthase operon (WO2005/103275).
L-Proline-Producing Bacteria
Examples of L-proline-producing bacteria and parent strains which can be used to derive such bacteria include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli 702ilvA (VKPM B-8012) which is deficient in the ilvA gene and is able to produce L-proline (EP 1172433).
The bacterium can be improved by increasing expression of one or more genes involved in L-proline biosynthesis. Examples of such genes include the proB gene coding for glutamate kinase desensitized to feedback inhibition by L-proline (DE 3127361). In addition, the bacterium can be improved by increasing expression of one or more genes coding for proteins excreting L-amino acid from bacterial cells. Examples of such genes include the b2682 and b2683 genes (ygaZH genes) (EP 1239041 A2).
Examples of bacteria belonging to the genus Escherichia and having L-proline-producing ability include the following E. coli strains: NRRL B-12403 and NRRL B-12404 (British Patent No. 2075056), VKPM B-8012 (Russian Patent Application No. 2000124295), plasmid mutants described in German Patent No. 3127361, plasmid mutants described by Bloom F. R. et al. (The 15th Miami winter symposium, 1983, p. 34), and so forth.
L-Arginine-Producing Bacteria
Examples of L-arginine-producing bacteria and parent strains which can be used to derive such bacteria include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli strain 237 (VKPM B-7925) (U.S. Patent Published Application 2002/058315A1) and its derivative strains harboring mutant N-acetylglutamate synthase (Russian Patent Application No. 2001112869), E. coli strain 382 (VKPM B-7926) (EP 1170358 A1), and an arginine-producing strain into which argA gene encoding N-acetylglutamate synthetase is introduced (EP 1170361 A1).
Examples of L-arginine-producing bacteria and parent strains which can be used to derive such bacteria also include strains in which expression of one or more genes encoding an L-arginine biosynthetic enzyme can be increased. Examples of such genes include N-acetylglutamyl phosphate reductase gene (argC), ornithine acetyl transferase gene (argJ), N-acetylglutamate kinase gene (argB), acetylornithine transaminase gene (argD), ornithine carbamoyl transferase gene (argF), argininosuccinic acid synthetase gene (argG), argininosuccinic acid lyase gene (argH), and carbamoyl phosphate synthetase gene (carAB).
L-Valine-Producing Bacteria
Example of L-valine-producing bacteria and parent strains which can be used to derive such bacteria include, but are not limited to, strains which have been modified to overexpress the ilvGMEDA operon (U.S. Pat. No. 5,998,178). It is desirable to remove the region of the ilvGMEDA operon which is required for attenuation so that expression of the operon is not attenuated by produced L-valine. Further, the ilvA gene in the operon is desirably disrupted so that threonine deaminase activity is decreased.
Examples of L-valine-producing bacteria and parent strains which can be used to derive such bacteria also include mutants having a mutation of amino-acyl t-RNA synthetase (U.S. Pat. No. 5,658,766). For example, E. coli VL1970, which has a mutation in the ileS gene encoding isoleucine tRNA synthetase, can be used. E. coli VL1970 was deposited at the Russian National Collection of Industrial Microorganisms (VKPM) (1 Dorozhny Proezd, 1 Moscow 117545, Russia) on Jun. 24, 1988 under the accession number of VKPM B-4411.
Furthermore, mutants requiring lipoic acid for growth and/or lacking H+-ATPase (WO96/06926) can also be used as the parent strains.
L-Isoleucine-Producing Bacteria
Examples of L-isoleucine-producing bacteria and parent strains include, but are not limited to, mutants having resistance to 6-dimethylaminopurine (Japanese Patent Laid-open No. 5-304969 A), mutants having resistance to an isoleucine analogue such as thiaisoleucine and isoleucine hydroxamate, and such mutants further having resistance to DL-ethionine and/or arginine hydroxamate (Japanese Patent Laid-open No. 5-130882). In addition, recombinant strains transformed with genes encoding proteins involved in L-isoleucine biosynthesis, such as threonine deaminase and acetohydroxate synthase, can also be used as the parent strains (Japanese Patent Laid-open No. 2-458, FR 0356739, and U.S. Pat. No. 5,998,178).
EXAMPLES Example 1 Construction of L-Lysine-Producing Bacterium with Enhanced Fructose-6-phosphate aldolase, glycerol dehydrogenase and dihydroxyacetone kinase activities<1-1> Construction of Plasmid for dak1 Gene Expression
The total nucleotide sequence of Saccharomyces cerevisiae chromosome has already been elucidated (Science, 25 (1996)). On the basis of the nucleotide sequence of the dak1 gene reported in this literature, the synthetic oligonucleotide of SEQ ID NO: 14 was prepared as a 5′ primer, and the synthetic oligonucleotide of SEQ ID NO: 15 was prepared as a 3′ primer. PCR was performed by using these synthetic oligonucleotides and the chromosomal DNA of the Saccharomyces cerevisiae JCM7255 strain as a template. The PCR product was purified and ligated with the vector pMW119 (Takara Bio) digested with HindIII and SalI to construct a dak1 expression plasmid pMW-dak1. The JCM7255 strain is stored in the independent administrative agency, RIKEN, “Japan Collection of Microorganisms”, 2-1, Hirosawa, Wako-shi, Saitama-ken.
<1-2> Construction of Glycerol Dehydrogenase Activity-Improved Strain
A WC196ΔcadAΔldcC strain modified to have the structure shown in SEQ ID NO: 11 was constructed. For the construction of the strain having this structure, the sequence of SEQ ID NO: 9 (PCR product) was used. In the sequence of SEQ ID NO: 9, the sequence of the nucleotide numbers 1 to 172 is the attR sequence of λ phage, the sequence of the nucleotide numbers 324 to 983 is a chloramphenicol resistance gene (cat), the sequence of the nucleotide numbers 1540 to 1653 is the attL sequence of λ phage, and the sequence of the nucleotide numbers 1654 to 1733 is the tacM promoter.
The tacM promoter (SEQ ID NO: 10) can be constructed by replacing the TTGACA sequence of the tac promoter (Gene, 25 (2-3), 167-178 (1983)) at the −35 region with TTCACA. The sequence of SEQ ID NO: 9 can be constructed by referring to the construction of pMW118-attL-Cm-attR (WO2005/010175).
The sequence of SEQ ID NO: 9 as a template was amplified by PCR using the primers of SEQ ID NOS: 12 and 13, and this amplification product was inserted into chromosome of the WC196ΔcadAΔldcC strain (refer to International Publication WO2006/038695) by the λ-RED method (WO2005/010175) to construct a strain in which the promoter sequence upstream of the gldA was replaced. In this way, a strain with improved glycerol dehydrogenase activity, WC196ΔcadAΔldcCPtacMgldA::Cm strain, was obtained.
<1-3> Construction of L-Lysine-Producing Bacterium with Enhanced Fructose-6-Phosphate Aldolase and Glycerol Dehydrogenase Activities
A WC196ΔcadAΔldcC strain modified to have the structure shown in SEQ ID NO: 92 was constructed. For construction of the strain having this structure, the sequence of SEQ ID NO: 9 (PCR product) was used. In the sequence of SEQ ID NO: 9, the sequence of the nucleotide numbers 1 to 172 is the attR sequence of λ phage, the sequence of the nucleotide numbers 324 to 983 is a chloramphenicol resistance gene (cat), the sequence of the nucleotide numbers 1540 to 1653 is the attL sequence of λ phage, and the sequence of the nucleotide numbers 1654 to 1733 is the tacM promoter.
The tacM promoter (SEQ ID NO: 10) can be constructed by replacing the TTGACA sequence of the tac promoter (Gene, 25 (2-3), 167-178 (1983)) at the −35 region with TTCACA. The sequence of SEQ ID NO: 9 can be constructed by referring to the construction of pMW118-attL-Cm-attR (WO2005/010175).
The sequence of SEQ ID NO: 9 as a template was amplified by PCR using the primers of SEQ ID NOS: 93 and 94, and this amplification product was inserted into chromosome of the WC196ΔcadAΔldcC strain (refer to International Publication WO2006/038695) by the λ-RED method (WO2005/010175) to construct a strain in which the promoter sequence upstream of the fsaB-gldA operon was replaced. In this way, a strain with improved fructose-6-phosphate aldolase and glycerol dehydrogenase activities, WC196ΔcadAΔldcCPtacM fsaB-gldA::Cm strain, was obtained.
<1-4> Construction of L-Lysine-Producing Bacteria with Enhanced Fructose-6-Phosphate Aldolase, Glycerol Dehydrogenase and Dihydroxyacetone Kinase Activities
The WC196ΔcadAΔldcC strain (refer to International Publication WO2006/038695), the WC196ΔcadAΔldcCPtacMgldA::Cm strain and the WC196ΔcadAΔldcCPtacM fsaB-gldA::Cm strain were transformed with the plasmid pCABD2 for Lys production carrying dapA, dapB and lysC genes (International Publication WO01/53459) in a conventional manner to obtain WC196ΔcadAΔldcC/pCABD2 strain, WC196ΔcadAΔldcCPtacMgldA::Cm/pCABD2 strain, and WC196ΔcadAΔldcCPtacM fsaB-gldA::Cm/pCABD2 strain. Furthermore, the WC196ΔcadAΔldcC/pCABD2 strain, the WC196ΔcadAΔldcCPtacMgldA::Cm/pCABD2 strain and the WC196ΔcadAΔldcCPtacM fsaB-gldA::Cm/pCABD2 strain were transformed with the dak1 expression plasmid pMW-dak1 in a conventional manner to obtain WC196ΔcadAΔldcC/pCABD2,pMW-dak1 strain, WC196ΔcadAΔldcCPtacMgldA::Cm/pCABD2,pMW-dak1 strain and WC196ΔcadAΔldcCPtacM fsaB-gldA::Cm/pCABD2,pMW-dak1 strain.
These strains were each cultured in L medium containing 20 mg/L of streptomycin or 20 mg/L of streptomycin and 50 mg/L of ampicillin at 37° C. until the final OD600 became about 0.6, then a 40% glycerol solution in a volume equal to the culture medium was added to each culture medium, and the mixture was stirred, then divided into appropriate volumes, and stored at −80° C. These are called glycerol stocks.
Example 2 Evaluation of L-Lysine-Producing Bacteria with Enhanced Fructose-6-Phosphate Aldolase, Glycerol Dehydrogenase and Dihydroxyacetone Kinase ActivitiesThe aforementioned glycerol stocks of the strains were thawed, 100 μL of each stock was uniformly applied to an L plate containing 20 mg/L of streptomycin or 20 mg/L of streptomycin and 50 mg/L of ampicillin, and culture was performed at 37° C. for 24 hours. The obtained cells on the plate were suspended in 1 ml of physiological saline, the suspension was inoculated in a volume V obtained by dividing a constant 50 with absorbance at 600 nm (n) of the suspension diluted 101 times (V=50/n) into 20 mL of a fermentation medium containing 20 mg/L of streptomycin or 20 mg/L of streptomycin and 50 mg/L of ampicillin contained in a 500-mL Sakaguchi flask, and culture was performed at 37° C. for 48 hours on a reciprocally shaking culture machine. After the culture, amount of lysine accumulated in the medium was measured by a known method (Biotec Analyzer AS210, SAKURA SEIKI).
The composition of the fermentation medium is shown below (unit: g/L).
The medium was adjusted to pH 7.0 with KOH, and autoclaved at 115° C. for 10 minutes, provided that glycerol and MgSO4.7H2O were separately sterilized, and 30 g/L of CaCO3 of Japanese Pharmacopoeia subjected to hot air sterilization at 180° C. for 2 hours was added.
As antibiotics, 20 mg/L of streptomycin or 20 mg/L of streptomycin and 50 mg/L of ampicillin were added. The culture was performed under the conditions of a temperature of 37° C. and stifling at 115 rpm for 48 hours.
The results are shown in Table 5 (OD means absorbance at 600 nm representing cell amount, Lys (g/L) means the amount of L-lysine accumulated in flask, and yield (%) means yield of L-lysine based on the substrate). Whereas the strain in which only glycerol dehydrogenase was enhanced, the strain in which only dihydroxyacetone kinase was enhanced, and the strain in which fructose-6-phosphate aldolase and glycerol dehydrogenase were enhanced did not show change of yield and productivity compared with the non-modified strain, the WC196ΔcadAΔldcCPtacMgldA::Cm/pCABD2,pMW-dak1 strain in which both glycerol dehydrogenase and dihydroxyacetone kinase using ATP as a phosphate donor were enhanced accumulated a larger amount of L-lysine compared with the other strains. Further, the WC196ΔcadAΔldcCPtacM fsaB-gldA::Cm/pCABD2,pMW-dak1 strain in which fructose-6-phosphate aldolase, glycerol dehydrogenase and dihydroxyacetone kinase using ATP as a phosphate donor were enhanced accumulated a further larger amount of L-lysine.
<3-1> Construction Of Glycerol Dehydrogenase Activity-Improved Strain
B5318 strains modified to have the structures shown in SEQ ID NOS: 90 and 91 were constructed. For construction of the strains having these structures, sequences of SEQ ID NOS: 88 and 89 (PCR products) were used. In the sequences of SEQ ID NOS: 88 and 89, the sequences of the nucleotide numbers 1 to 72 are the attR sequences of λ phage, the sequences of the nucleotide numbers 324 to 983 are chloramphenicol resistance genes (cat), the sequences of the nucleotide numbers 1540 to 1653 are the attL sequences of λ phage, and the sequences of the nucleotide numbers 1654 to 1733 are the tacM2 and tacM3 promoters.
The tacM2 and tacM3 promoters are constitutive promoters which can be constructed by replacing the TTGACA sequence of the tac promoter (Gene, 25 (2-3), 167-178 (1983)) at the −35 region with TGTACA and TTGGCA (Molecular Biology 39 (5) 719-726 (2005)). The sequences of SEQ ID NOS: 88 and 89 can be constructed by referring to the construction of pMW118-attL-Cm-attR (WO2005/010175).
The sequences of SEQ ID NOS: 88 and 89 as templates were amplified by PCR using the primers of SEQ ID NOS: 12 and 13, and these amplification products were each inserted into chromosome of the B5318 strain (VKPM B-5318) by the λ-RED method (WO2005/010175) to obtain strains in which the promoter sequence upstream of the gldA was replaced. In this way, strains with improved glycerol dehydrogenase activity, B5318PtacM2gldA::Cm strain and B5318PtacM3gldA::Cm strain, were obtained.
<1-3> Construction of L-Threonine-Producing Bacteria with Enhanced Glycerol Dehydrogenase and Dihydroxyacetone Kinase Activities
The B5318PtacM2gldA::Cm strain and the B5318PtacM3gldA::Cm strain were transformed with the dak1 expression plasmid pMW-dak1 in a conventional manner to obtain B5318PtacM2gldA::Cm/pMW-dak1 strain and B5318PtacM3gldA::Cm/pMW-dak1 strain.
These strains were each cultured in L medium containing 20 mg/L of streptomycin or 20 mg/L of streptomycin and 50 mg/L of ampicillin at 37° C. until the final OD600 became about 0.6, then a 40% glycerol solution in a volume equal to the culture medium was added to each culture medium, and the mixture was stirred, then divided into appropriate volumes, and stored at −80° C. These are called glycerol stocks.
Example 4 Evaluation of L-Threonine-Producing Bacteria with Enhanced Glycerol Dehydrogenase and Dihydroxyacetone Kinase ActivitiesThe aforementioned glycerol stocks of the strains were thawed, 100 μL of each stock was uniformly applied to an L plate containing 20 mg/L of streptomycin or 20 mg/L of streptomycin and 50 mg/L of ampicillin, and culture was performed at 37° C. for 24 hours. The obtained cells on the plate were suspended in 1 ml of physiological saline, the suspension was inoculated in a volume (V) obtained by dividing a constant 50 with absorbance at 600 nm (n) of the suspension diluted 101 times (V=50/n) into 20 mL of a fermentation medium containing 20 mg/L of streptomycin or 20 mg/L of streptomycin and 50 mg/L of ampicillin contained in a 500-mL conical flask with baffle, and culture was performed at 40° C. for 24 hours on a rotary culture machine. After the culture, amount of threonine accumulated in the medium was measured by a known method (Hitachi Liquid Chromatography ODS-2 Column).
The composition of the fermentation medium is shown below (unit: g/L).
The medium was adjusted to pH 7.0 with KOH, and autoclaved at 115° C. for 10 minutes, provided that glycerol and MgSO4. 7H2O were separately sterilized, and 30 g/L of CaCO3 of Japanese Pharmacopoeia subjected to hot air sterilization at 180° C. for 2 hours was added.
As antibiotics, 20 mg/L of streptomycin or 20 mg/L of streptomycin and 50 mg/L of ampicillin were added. The culture was performed under the conditions of a temperature of 40° C. and stifling at 144 rpm for 24 hours.
The results are shown in Table 6 (OD means absorbance at 600 nm representing cell amount, Thr (g/L) means amount of L-threonine accumulated in flask, and yield (%) means yield of L-threonine based on the substrate). Whereas the strain in which only glycerol dehydrogenase was enhanced did not show change of yield and productivity compared with the non-modified strain, the B5318PtacM2gldA::Cm/pMW-dak1 strain and the B5318PtacM3gldA::Cm/pMW-dak1 strain in which both glycerol dehydrogenase and dihydroxyacetone kinase using ATP as a phosphate donor were enhanced accumulated a larger amount of L-threonine compared with the other strains.
Explanation of Sequence Listing:
SEQ ID NO: 1: gldA gene sequence of Escherichia coli (1104 bp)
SEQ ID NO: 2: GldA amino acid sequence of Escherichia coli (367 AA)
SEQ ID NO: 3: dakA1 gene sequence of Saccharomyces cerevisiae (1755 bp)
SEQ ID NO: 4: DakA amino acid sequence of Saccharomyces cerevisiae (584 AA)
SEQ ID NO: 5: dhbK1 gene sequence of Agrobacterium tumefaciens (1695 bp)
SEQ ID NO: 6: Dhbk1 amino acid sequence of Agrobacterium tumefaciens (564 AA)
SEQ ID NO: 7: dhaK gene sequence of Citrobacter freundii (1659 bp)
SEQ ID NO: 8: DhaK amino acid sequence of Citrobacter freundii (552 AA)
SEQ ID NO: 9: attR-cat-attL-ptacM-SD-spacer sequence (1740 bp)
SEQ ID NO: 10: tacM promoter (80 bp)
SEQ ID NO: 11: PtacMgldA::Cm sequence
SEQ ID NO: 12: atL-Ptac-gldA (PCR primer for enhancing gldA on chromosome)
SEQ ID NO: 13: atR-Ptac-fsaB1 (PCR primer for enhancing gldA on chromosome)
SEQ ID NO: 14: pMW-dak1F (primer for dakA cloning)
SEQ ID NO: 15: pMW-dak1R (primer for dakA cloning)
SEQ ID NO: 16: glpF gene sequence of Escherichia coli (846 bp)
SEQ ID NO: 17: GlpF amino acid sequence of Escherichia coli (281 AA)
SEQ ID NO: 18: tpiA gene sequence of Escherichia coli (768 bp)
SEQ ID NO: 19: TpiA amino acid sequence of Escherichia coli (255 AA)
SEQ ID NO: 20: fbaA gene sequence of Escherichia coli (1080 bp)
SEQ ID NO: 21: FbaA amino acid sequence of Escherichia coli (359 AA)
SEQ ID NO: 22: glpX gene sequence of Escherichia coli (1011 bp)
SEQ ID NO: 23: GlpX amino acid sequence of Escherichia coli (336 AA)
SEQ ID NO: 24: glpK gene sequence of Escherichia coli (1509 bp)
SEQ ID NO: 25: GlpK amino acid sequence of Escherichia coli (502 AA)
SEQ ID NO: 26: glpA gene sequence of Escherichia coli (1629 bp)
SEQ ID NO: 27: GlpA amino acid sequence of Escherichia coli (542 AA)
SEQ ID NO: 28: glpB gene sequence of Escherichia coli (1260 bp)
SEQ ID NO: 29: GlpB amino acid sequence of Escherichia coli (419 AA)
SEQ ID NO: 30: glpC gene sequence of Escherichia coli (1191 bp)
SEQ ID NO: 31: GlpC amino acid sequence of Escherichia coli (396 AA)
SEQ ID NO: 32: glpD gene sequence of Escherichia coli (1506 bp)
SEQ ID NO: 33: GlpD amino acid sequence of Escherichia coli (501 AA)
SEQ ID NO: 34: dhaK gene sequence of Escherichia coli (1071 bp)
SEQ ID NO: 35: DhaK amino acid sequence of Escherichia coli (356 AA)
SEQ ID NO: 36: dhaL gene sequence of Escherichia coli (633 bp)
SEQ ID NO: 37: DhaL amino acid sequence of Escherichia coli (210 AA)
SEQ ID NO: 38: dhaM gene sequence of Escherichia coli (1419 bp)
SEQ ID NO: 39: DhaM amino acid sequence of Escherichia coli (472 AA)
SEQ ID NO: 40: Dihydroxyacetone kinase gene of Schizosaccharomyces pombe (1776 bp)
SEQ ID NO: 41: Dihydroxyacetone kinase of Schizosaccharomyces pombe (591 AA)
SEQ ID NO: 42: Dihydroxyacetone kinase gene of Pichia angusta (1830 bp)
SEQ ID NO: 43: Dihydroxyacetone kinase of Pichia angusta (609 AA)
SEQ ID NO: 44: Dihydroxyacetone kinase gene of Pichia pastoris (1827 bp)
SEQ ID NO: 45: Dihydroxyacetone kinase of Pichia pastoris (608 AA)
SEQ ID NO: 46: Dihydroxyacetone kinase gene of Debaryomyces hansenii (1824 bp)
SEQ ID NO: 47: Dihydroxyacetone kinase of Debaryomyces hansenii (607 AA)
SEQ ID NO: 48: Dihydroxyacetone kinase gene of Escherichia blattae (1752 bp)
SEQ ID NO: 49: Dihydroxyacetone kinase of Escherichia blattae (583 AA)
SEQ ID NO: 50: Dihydroxyacetone kinase gene of Enterobacter sp. 638 (1647 bp)
SEQ ID NO: 51: Dihydroxyacetone kinase of Enterobacter sp. 638 (548 AA)
SEQ ID NO: 52: Dihydroxyacetone kinase gene of Psychromonas sp. CNPT3 (1695 bp)
SEQ ID NO: 53: Dihydroxyacetone kinase of Psychromonas sp. CNPT3 (564 AA)
SEQ ID NO: 54: Dihydroxyacetone kinase gene of Stappia aggregata (1647 bp)
SEQ ID NO: 55: Dihydroxyacetone kinase of Stappia aggregata (548 AA)
SEQ ID NO: 56: Dihydroxyacetone kinase gene of Rhizobium leguminosarum bv. viciae 3841 (1641 bp)
SEQ ID NO: 57: Dihydroxyacetone kinase of Rhizobium leguminosarum bv. viciae 3841 (546 AA)
SEQ ID NO: 58: Dihydroxyacetone kinase gene of Myxococcus xanthus DK 1622 (1701 bp)
SEQ ID NO: 59: Dihydroxyacetone kinase of Myxococcus xanthus DK 1622 (566 AA)
SEQ ID NO: 60: Dihydroxyacetone kinase gene of Burkholderia sp. 383 (1701 bp)
SEQ ID NO: 61: Dihydroxyacetone kinase of Burkholderia sp. 383 (566 AA)
SEQ ID NO: 62: Dihydroxyacetone kinase gene of Burkholderia thailandensis E264 (1704 bp)
SEQ ID NO: 63: Dihydroxyacetone kinase of Burkholderia thailandensis E264 (567 AA)
SEQ ID NO: 64: Dihydroxyacetone kinase gene of Burkholderia multivorans ATCC 17616 (1851 bp)
SEQ ID NO: 65: Dihydroxyacetone kinase of Burkholderia multivorans ATCC 17616 (616 AA)
SEQ ID NO: 66: dhaR gene of Escherichia coli (1920 bp)
SEQ ID NO: 67: DhaR amino acid sequence of Escherichia coli (639 AA)
SEQ ID NO: 68: fsaA gene of Escherichia coli (663 bp)
SEQ ID NO: 69: FsaA amino acid sequence of Escherichia coli (220 AA)
SEQ ID NO: 70: fsaB gene of Escherichia coli (663 bp)
SEQ ID NO: 71: FsaB amino acid sequence of Escherichia coli (220 AA)
SEQ ID NO: 72: fbaB gene of Escherichia coli (1053 bp)
SEQ ID NO: 73: FbaB amino acid sequence of Escherichia coli (350 AA)
SEQ ID NO: 74: gldA gene of Shigella dysenteriae Sd197 (1143 bp)
SEQ ID NO: 75: GldA amino acid sequence of Shigella dysenteriae Sd197 (380 AA)
SEQ ID NO: 76: gldA gene of Salmonella typhimurium LT2 (1104 bp)
SEQ ID NO: 77: GldA amino acid sequence of Salmonella typhimurium LT2 (367 AA)
SEQ ID NO: 78: gldA gene of Pseudomonas putida (1098 bp)
SEQ ID NO: 79: GldA amino acid sequence of Pseudomonas putida (365 AA)
SEQ ID NO: 80: gldA gene of Bacillus coagulans 36D1 (1104 bp)
SEQ ID NO: 81: GldA amino acid sequence of Bacillus coagulans 36D1 (367 AA)
SEQ ID NO: 82: fbp gene of Escherichia coli (999 bp)
SEQ ID NO: 83: Fbp amino acid sequence of Escherichia coli (322 AA)
SEQ ID NO: 84: ybhA gene of Escherichia coli (819 bp)
SEQ ID NO: 85: YbhA amino acid sequence of Escherichia coli (272 AA)
SEQ ID NO: 86: ptsI gene of Escherichia coli (1782 bp)
SEQ ID NO: 87: PtsI amino acid sequence of Escherichia coli (575 AA)
SEQ ID NO: 88: attR-cat-attL-PtacM2-SD-spacer sequence
SEQ ID NO: 89: attR-cat-attL-PtacM3-SD-spacer sequence
SEQ ID NO: 90: PtacM2gldA::Cm sequence
SEQ ID NO: 91: PtacM3gldA::Cm sequence
SEQ ID NO: 92: PtacM fsaB-gldA::Cm sequence
SEQ ID NO: 93: atL-Ptac-fsaB (PCR primer for enhancing fsaB+gldA on chromosome)
SEQ ID NO: 94: atR-Ptac-fsaB (PCR primer for enhancing fsaB+gldA on chromosome)
INDUSTRIAL APPLICABILITYBy using the microorganism of the present invention, efficient production of an L-amino acid from glycerol by fermentation is enabled.
While the invention has been described in detail with reference to exemplary embodiments thereof, it will be apparent to one skilled in the art that various changes can be made, and equivalents employed, without departing from the scope of the invention. Each of the aforementioned documents is incorporated by reference herein in its entirety.
Claims
1. A method for producing an L-amino acid, the method comprising:
- (A) providing a microorganism belonging to the family Enterobacteriaceae having an L-amino acid-producing ability and modified to increase glycerol dehydrogenase and dihydroxyacetone kinase activities,
- (B) culturing said microorganism in a medium containing glycerol as a carbon source to produce and accumulate an L-amino acid in the medium or cells, and
- (C) collecting the L-amino acid from the medium or the cells.
2. The method according to claim 1, wherein the glycerol dehydrogenase and dihydroxyacetone kinase activities are increased by increasing copy numbers of genes coding for glycerol dehydrogenase and dihydroxyacetone kinase, or modifying expression control sequences of the genes.
3. The method according to claim 1, wherein the dihydroxyacetone kinase uses ATP as a phosphate donor.
4. The method according to claim 1, wherein the microorganism is further modified to increase glycerol uptake activity.
5. The method according to claim 1, wherein the microorganism is further modified to increase activity or activities of an enzyme selected from the group consisting of triosephosphate isomerase, fructose bisphosphate aldolase, fructose-1,6-bisphosphatase, fructose-6-phosphate aldolase, and combinations thereof.
6. The method according to claim 1, wherein the microorganism is further modified to reduce activity or activities of glycerol kinase and/or membrane-binding type glycerol-3-phosphate dehydrogenase.
7. The method according to claim 1, wherein the microorganism belonging to the family Enterobacteriaceae is an Escherichia bacterium, or a Pantoea bacterium.
8. The method according to claim 1, wherein the L-amino acid is selected from the group consisting of L-glutamic acid, L-lysine, L-leucine, L-isoleucine, L-valine, L-tryptophan, L-phenylalanine, L-tyrosine, L-threonine, L-methionine, L-cysteine, L-arginine, L-serine, L-proline, L-asparatic acid, L-asparagine, L-glutamine, L-histidine, and combinations thereof.
Type: Application
Filed: Jul 10, 2013
Publication Date: Oct 31, 2013
Inventors: Yuri Nagai (Kanagawa), Kazuyuki Hayashi (Kanagawa), Takuji Ueda (Kanagawa), Yoshihiro Usuda (Kanagawa), Kazuhiko Matsui (Kanagawa)
Application Number: 13/938,601
International Classification: C12P 13/08 (20060101);
