Method for Producing an Acidic Substance Having a Carboxyl Group
An acidic substance having a carboxyl group is produced by culturing in a medium a microorganism which has been modified to enhance expression of the ybjL gene, and collecting the acidic substance having a carboxyl group from the medium.
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This application is a Divisional of, and claims priority under 35 U.S.C. §120 to, U.S. patent application Ser. No. 14/723,776, filed May 28, 2015, which was a Divisional under 35 U.S.C. §120 of U.S. patent application Ser. No. 12/579,577, filed Oct. 15, 2009, which was a Continuation under 35 U.S.C. §120 of PCT Patent Application No. PCT/JP2008/057478, filed Apr. 17, 2008, which claimed priority under 35 U.S.C. §119 to Japanese Patent Application No. 2007-108631, filed on Apr. 17, 2007, and Japanese Patent Application No. 2007-242859, filed on Sep. 19, 2007, which are incorporated in their entireties by reference herein. Also, the Sequence Listing filed electronically herewith is hereby incorporated by reference (File name: 2017-10-19T_US-408D2_Seq_List; File size: 240 KB; Date recorded: Oct. 19, 2017).
BACKGROUND OF THE INVENTION Field of the InventionThe present invention relates to a method for producing an acidic substance having a carboxyl group. L-Glutamic acid and L-aspartic acid are widely used as raw materials in making seasonings and so forth. Succinic acid is widely used as a raw material in making seasonings and biodegradable plastics.
Brief Description of the Related ArtL-Glutamic acid is mainly produced by fermentation utilizing L-glutamic acid-producing bacteria of the so-called coryneform bacteria belonging to the genus Brevibacterium, Corynebacterium or Microbacterium, or their mutant strains (see, for example, Kunihiko Akashi et al., Amino Acid Fermentation, Japan Scientific Societies Press (Gakkai Shuppan Center), pp. 195-215, 1986). Methods are known for producing L-glutamic acid by fermentation using other bacterial strains, including microorganisms belonging to the genera Bacillus, Streptomyces, Penicillium or the like (see, for example, U.S. Pat. No. 3,220,929), microorganisms belonging to the genera Pseudomonas, Arthrobacter, Serratia, Candida or the like (see, for example, U.S. Pat. No. 3,563,857), microorganisms belonging to the genera Bacillus, Pseudomonas, Serratia, Aerobacter aerogenes (currently referred to as Enterobacter aerogenes) or the like (see, for example, Japanese Patent Publication (KOKOKU) No. 32-9393), a mutant strain of Escherichia coli (see, for example, Japanese Patent Laid-open (KOKAI) No. 5-244970), and the like. In addition, methods for producing L-glutamic acid have also been disclosed using microorganisms belonging to the genera Klebsiella, Erwinia, Pantoea or Enterobacter (see, for example, Japanese Patent Laid-open No. 2000-106869 (U.S. Pat. No. 6,682,912), Japanese Patent Laid-open No. 2000-189169 (U.S. Patent Published Application No. 2001009836), Japanese Patent Laid-open No. 2000-189175 (U.S. Pat. No. 7,247,459)).
Furthermore, various techniques have been disclosed for increasing the L-glutamic acid-producing ability by enhancing the L-glutamic acid biosynthetic enzymes using recombinant DNA techniques. For example, it has been reported for Corynebacterium or Brevibacterium bacteria that introduction of a gene coding for citrate synthase derived from Escherichia coli or Corynebacterium glutamicum was effective to enhance the L-glutamic acid-producing ability of coryneform bacteria (see, for example, Japanese Patent Publication No. 7-121228). Furthermore, it has also been reported that introduction of a citrate synthase gene derived from a coryneform bacterium into enterobacteria belonging to the genera Enterobacter, Klebsiella, Serratia, Erwinia or Escherichia was effective to enhance the bacteria's L-glutamic acid-producing ability (see, for example, Japanese Patent Laid-open No. 2000-189175 (U.S. Pat. No. 7,247,459)).
Methods for improving the production of target substances such as amino acids are also known, including by modifying the uptake or secretion systems of target substances. Such methods include, for example, by deleting or attenuating the system for uptake of a target substance into cells. Specifically, known methods to improve production of L-glutamic acid include deleting the gluABCD operon, or a part thereof, to eliminate or attenuate uptake of L-glutamic acid into cells (see, for example, European Patent Application Laid-open No. 1038970), and enhancing production of purine nucleotides by attenuating uptake of purine nucleotides into cells (see, for example, European Patent Application Laid-open No. 1004663), and the like.
Furthermore, methods of enhancing the secretion system for a target substance, and methods of deleting or attenuating the secretion system for an intermediate or substrate in the biosynthetic system of a target substance are known. Known methods of enhancing the secretion system of a target substance include, for example, production of L-lysine by utilizing a Corynebacterium strain in which the L-lysine secretion gene (lysE) is enhanced (see, for example, WO2001/5959), and production of L-glutamic acid by using an enterobacterium in which the L-glutamic acid secretion system gene (yhfK) is enhanced (see, for example, Japanese Patent Laid-open No. 2005-278643 (U.S. Patent Published Application No. 2005196846)). Furthermore, methods for producing an L-amino acid using the rhtA, B, C genes, which have been suggested to be involved in the secretion of L-amino acids, have also been reported (see, for example, Japanese Patent Laid-open No. 2000-189177 (U.S. Patent Published Application No. 2005239177)). Known methods for, for example, deleting a secretion system for an intermediate or substrate in a biosynthesis system of a target substance include, for L-glutamic acid, mutating or disrupting the 2-oxoglutarate permease gene to attenuate secretion of 2-oxoglutarate, which is an intermediate of the target substance (see, for example, WO97/23597).
Furthermore, use of the gene coding for the ATP binding cassette superfamily (ABC transporter), which is involved in transportation of substances through cell membranes, in the breeding of microorganisms in which transmembrane transportation of amino acids is modified has been suggested (see, for example, WO00/37647).
Furthermore, it has also been reported that L-glutamic acid production efficiency can be improved in Escherichia bacteria by enhancing the expression of genes thought to participate in secretion of L-amino acids such as yfiK (see, for example, Japanese Patent Laid-open No. 2000-189180 (U.S. Pat. No. 6,979,560)). Moreover, it has also been reported that L-glutamic acid-producing ability can be improved by enhancing expression of the yhfK gene (see, for example, Japanese Patent Laid-open No. 2005-278643 (U.S. Patent Published Application No. 2005196846)).
Moreover, methods are known for producing L-glutamic acid by culturing a microorganism under acidic conditions to precipitate the L-glutamic acid (see, for example, Japanese Patent Laid-open No. 2001-333769 (U.S. Patent Published Application No. 2007134773)). When the pH is kept low, L-glutamic acid is precipitated, and the ratio of L-glutamic acid in free form with no electrical charge increases. As a result, the L-glutamic acid easily penetrates cell membranes. When L-glutamic acid is taken up into cells, it is converted into an intermediate of the TCA cycle, 2-oxoglutaric acid, in one step by glutamate dehydrogenase, and therefore it is generally thought that L-glutamic acid taken up into cells is easily metabolized. However, 2-oxoglutarate dehydrogenase activity can be deleted or attenuated, or the like, in the fermentative production of L-glutamic acid (for example, Japanese Patent Laid-open No. 2001-333769 (U.S. Patent Published Application No. 2007134773), Japanese Patent Laid-open No. 7-203980 (U.S. Pat. No. 5,573,945)), but then 2-oxoglutaric acid is not degraded, intracellular 2-oxoglutaric acid concentration increases which inhibits the growth of the microorganism. Thus, the culture fails. Therefore, as described in Japanese Patent Laid-open No. 2001-333769 (U.S. Patent Published Application No. 2007134773), a strain was bred using a mutation that is deficient in 2-oxoglutarate dehydrogenase activity and can produce L-glutamic acid accompanying precipitation, and this strain can be used for the production of L-glutamic acid.
For fermentative production of non-amino organic acids, including succinic acid, anaerobic bacteria including those belonging to the genus Anaerobiospirillum or Actinobacillus are usually used (U.S. Pat. Nos. 5,142,834 and 5,504,004, Guettler, M. V. et al., 1999, International Journal of Systematic Bacteriology, 49:207-216). Although the use of such anaerobic bacteria provides high product yields, many nutrients are required for sufficient proliferation, and therefore, it is necessary to add large amounts of organic nitrogen sources such as corn steep liquor (CSL) into the culture medium. The addition of large amounts of organic nitrogen sources can result in not only an increase in the cost of the culture, but also an increase in the cost for isolating or purifying the product, and therefore, their use is not economical.
In addition, methods are known in which aerobic bacteria such as coryneform bacteria are cultured once under aerobic conditions, then harvested, washed, and allowed to rest, producing a non-amino organic acid in the absence of supplied oxygen (Japanese Patent Laid-open Nos. 11-113588 and 11-196888). These methods are economical since a smaller amount of organic nitrogen can be added, and the bacteria will sufficiently grow in a simple culture medium. However, there is still a room for improvement in terms of production amount, concentration, and production rate per cell of the target organic acids, as well as simplification of the production process, and the like. Furthermore, the production of a non-amino organic acid by fermentation using a bacterium in which phosphoenolpyruvate carboxylase activity is enhanced (for example, Japanese Patent Laid-open No. 11-196887), and the like have also been reported.
Furthermore, as for Escherichia coli, which is a facultative anaerobic gram negative bacterium, methods for producing a non-amino organic acid by culturing it once under aerobic conditions, and then allowing the cells to rest in the absence of supplied oxygen, resulting in an anaerobically produced non-amino organic acid (Vemuri G. N. et al., 2002, Journal of Industrial Microbiology and Biotechnology, 28(6):325-332). This is similar to the methods using coryneform bacteria. Alternatively, E. coli can be aerobically cultured to aerobically produce the non-amino organic acid (U.S. Patent Published Application No. 20050170482). However, since Escherichia coli is a gram negative bacterium, it is vulnerable to osmotic pressure, and there remains room for improvement in productivity per cell etc.
The ybjL gene is located on the genome of Escherichia coli (see, for example, Blattner, F. R. et al., 1997, Science, 277(5331):1453-74), and it is also thought to code for a transporter on the basis of the motifs, topology etc. of the deduced amino acid sequence. However, cloning of the gene, as well as expression of the gene and analysis of the expression product have not been reported, and the actual functions of the gene remained unknown.
SUMMARY OF THE INVENTIONAn aspect of the present invention is to provide a bacterial strain that can efficiently produce an acidic substance having a carboxyl group, especially L-glutamic acid, L-aspartic acid, and succinic acid, and to provide a method for efficiently producing an acidic substance having a carboxyl group by using such a strain.
The ybjL gene was isolated and shown to be involved in L-glutamic acid resistance. Also, it has been found that when the expression of the ybjL gene is enhanced, L-glutamic acid fermentation yield is improved and the production rate or yield of succinic acid is improved.
It is an aspect of the present invention to provide a microorganism that has an ability to produce an acidic substance having a carboxyl group and has been modified to enhance expression of the ybjL gene.
It is a further aspect of the present invention to provide the aforementioned microorganism, wherein enhanced expression is obtained by a method selected from the group consisting of: A) increasing copy number of the ybjL gene, B) modifying an expression control sequence of the ybjL gene, and C) combinations thereof.
It is a further aspect of the present invention to provide the aforementioned microorganism, wherein the ybjL gene encodes a protein: (A) a protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 2, 4 and 87; (B) a protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 2, 4 and 87, but wherein one or several amino acid residues are substituted, deleted, inserted or added, and the protein improves the ability of the microorganism to produce an acidic substance having a carboxyl group when expression of the gene encoding the protein is enhanced in the microorganism.
It is a further aspect of the present invention to provide the aforementioned microorganism, wherein the ybjL gene encodes the protein selected from the group consisting of SEQ ID NO: 5 and 88.
It is a further aspect of the present invention to provide the aforementioned microorganism, wherein the microorganism is a bacterium belonging to the family Enterobacteriaceae.
It is a further aspect of the present invention to provide the aforementioned microorganism, wherein the bacterium belongs to a genus selected from the group consisting of Escherichia, Enterobacter, Raoultella, Pantoea, and Klebsiella.
It is a further aspect of the present invention to provide the aforementioned microorganism, wherein the microorganism is a rumen bacterium.
It is a further aspect of the present invention to provide the aforementioned microorganism, wherein the microorganism is Mannheimia succiniciproducens.
It is a further aspect of the present invention to provide the aforementioned microorganism, wherein the acidic substance is an organic acid selected from the group consisting of succinic acid, fumaric acid, malic acid, oxalacetic acid, citric acid, isocitric acid, α-ketoglutaric acid, and combinations thereof.
It is a further aspect of the present invention to provide the aforementioned microorganism, wherein the acidic substance is L-glutamic acid and/or L-aspartic acid.
It is a further aspect of the present invention to provide a method for producing an acidic substance having a carboxyl group comprising culturing the aforementioned microorganism in a medium to produce and accumulate the acidic substance having a carboxyl group in the medium, and collecting the acidic substance having a carboxyl group from the medium.
It is a further aspect of the present invention to provide the aforementioned method, wherein the acidic substance is an organic acid selected from the group consisting of succinic acid, fumaric acid, malic acid, oxalacetic acid, citric acid, isocitric acid, α-ketoglutaric acid, and combinations thereof.
It is a further aspect of the present invention to provide the aforementioned method, wherein the acidic substance is L-glutamic acid and/or L-aspartic acid.
It is a further aspect of the present invention to provide a method for producing an acidic substance having a carboxyl group comprising: A) allowing a substance to act on an organic raw material in a reaction mixture containing carbonate ions, bicarbonate ions, or carbon dioxide gas, wherein the substance is selected from the group consisting of i) the microorganism as described above, ii) a product obtained by processing the microorganism of i), and iii) combinations thereof, and collecting the acidic substance having a carboxyl group.
It is a further aspect of the present invention to provide the aforementioned method, wherein the acidic substance is an organic acid selected from the group consisting of succinic acid, fumaric acid, malic acid, oxalacetic acid, citric acid, isocitric acid, α-ketoglutaric acid, and combinations thereof.
It is a further aspect of the present invention to provide a method for producing a polymer comprising succinic acid comprising A) producing succinic acid by the aforementioned method, and B) polymerizing the succinic acid.
Hereinafter, the present invention will be explained in detail.
<1> Microorganism Having Ability to Produce Acidic Substance Having a Carboxyl Group
The microorganism in accordance with the presently disclosed subject matter has an ability to produce an acidic substance having a carboxyl group and has been modified so that expression of the ybjL gene is enhanced. The term “ability to produce an acidic substance having a carboxyl group” can mean the ability of a microorganism to produce and cause accumulation of an acidic substance having a carboxyl group in a medium or cells to such a degree that the acidic substance having a carboxyl group can be collected from the cells or medium when the microorganism of the present invention is cultured in the medium. The microorganism can originally have the ability to produce an acidic substance having a carboxyl group, or the ability to produce an acidic substance can be obtained by modifying a microorganism such as those described below using mutation or recombinant DNA techniques. Also, a microorganism can be imparted with the ability to produce an acidic substance having a carboxyl group, or the ability to produce an acidic substance having a carboxyl group can be enhanced by introducing the gene described herein.
In the present invention, the “acidic substance having a carboxyl group” can mean an organic compound having one or more carboxyl groups and which is acidic when the substance is in the free form, and not in the salt form. Specifically, examples include organic acids and L-amino acids having two carboxyl groups, for example, acidic amino acids. Examples of the L-amino acids include L-glutamic acid and L-aspartic acid, and examples of the organic acids include succinic acid, fumaric acid, malic acid, oxalacetic acid, citric acid, isocitric acid, α-ketoglutaric acid, and the like.
The parent strain which can be used to derive the microorganism in accordance with the presently disclosed subject matter is not particularly limited, and can include bacteria, for example, Enterobacteriaceae, rumen bacteria, and coryneform bacteria.
The Enterobacteriaceae family encompasses bacteria belonging to the genera Escherichia, Enterobacter, Erwinia, Klebsiella, Pantoea, Photorhabdus, Providencia, Raoultella, Salmonella, Serratia, Shigella, Morganella, Yersinia, and the like. In particular, bacteria classified into the family Enterobacteriaceae according to the taxonomy used by the NCBI (National Center for Biotechnology Information) database (www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=91347) are examples. Among these, bacteria belonging to the genus Escherichia, Enterobacter, Raoultella, Pantoea, Klebsiella, or Serratia are particular examples.
A “bacterium belonging to the genus Escherichia” means that the bacterium is classified into the genus Escherichia according to the 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). Other examples include, for example, the bacteria of the phyletic groups described in the work of Neidhardt et al. (Neidhardt F. C. Ed., 1996, Escherichia coli and Salmonella: Cellular and Molecular Biology/Second Edition, pp. 2477-2483, Table 1, American Society for Microbiology Press, Washington, D.C.). Specific examples include Escherichia coli W3110 (ATCC 27325), Escherichia coli MG1655 (ATCC 47076), and the like, and others derived from the prototype wild-type strain, the K12 strain.
These strains are available from, for example, the American Type Culture Collection (Address: 12301 10801 University Boulevard, Manassas, Va. 20108, United States of America). That is, registration numbers are given to each of the strains, and the strains can be ordered by using these numbers. The registration numbers of the strains are listed in the catalogue of the American Type Culture Collection.
Pantoea, Erwinia, and Enterobacter bacteria are classified as γ-proteobacteria, and they are taxonomically very close to one another (J. Gen. Appl. Microbiol., 1997, 43, 355-361; Int. J. Syst. Bacteriol., 1997, 43, 1061-1067). In recent years, some bacteria belonging to the genus Enterobacter were reclassified as Pantoea agglomerans, Pantoea dispersa, or the like, on the basis of DNA-DNA hybridization experiments etc. (Int. J. Syst. Bacteriol., 1989, 39:337-345). Furthermore, some bacteria belonging to the genus Erwinia were reclassified as Pantoea ananas or Pantoea stewartii (refer to Int. J. Syst. Bacteriol., 1993, 43:162-173).
Examples of the Enterobacter bacteria include Enterobacter agglomerans, Enterobacter aerogenes, and the like. Specifically, the strains exemplified in European Patent Application Laid-open No. 952221 can be used. Typical strains of the genus Enterobacter include Enterobacter agglomerans ATCC 12287, Enterobacter aerogenes ATCC 13048, Enterobacter aerogenes NBRC 12010 (Biotechnol Bioeng., 2007, Mar. 27; 98(2):340-348), and Enterobacter aerogenes AJ110637 (FERM ABP-10955), and the like. The AJ110637 strain was obtained from the soil at the seashore of Susuki Kaigan, Makinohara-shi, Shizuoka-ken on March, 2006 by cumulative liquid culture using glycerol as the carbon source. The full-length 16S rDNA sequence was then determined, and it was found to be 99.9% homologous to that from Enterobacter aerogenes NCTC 10006. Moreover, in a physiological test using an API kit, the strain gave results similar to the prototype species of Enterobacter aerogenes, and therefore it was identified as Enterobacter aerogenes. This strain was deposited at International Patent Organism Depository, Agency of Industrial Science and Technology (Central 6, 1-1, Higashi 1-Chome, Tsukuba-shi, Ibaraki-ken, 305-8566, Japan) on Aug. 22, 2007, and assigned an accession number of FERM P-21348. Then, the deposit was converted to an international deposit based on the Budapest Treaty on Mar. 13, 2008, and assigned an accession number of FERM ABP-10955.
Typical strains of the Pantoea bacteria include Pantoea ananatis, Pantoea stewartii, Pantoea agglomerans, and Pantoea citrea. Specific examples include the following strains:
Pantoea ananatis AJ13355 (FERM BP-6614, European Patent Laid-open No. 0952221)
Pantoea ananatis AJ13356 (FERM BP-6615, European Patent Laid-open No. 0952221)
Although these strains are described as Enterobacter agglomerans in European Patent Laid-open No. 0952221, they are currently classified as Pantoea ananatis on the basis of nucleotide sequence analysis of the 16S rRNA etc., as described above.
Examples of the Erwinia bacteria include Erwinia amylovora and Erwinia carotovora, examples of the Klebsiella bacteria include Klebsiella planticola, and examples of the Raoultella bacteria include Raoultella planticola. Specific examples include the following strains:
Erwinia amylovora ATCC 15580 strain
Erwinia carotovora ATCC 15713 strain
Klebsiella planticola AJ13399 strain (FERM BP-6600, European Patent Laid-open No. 955368)
Klebsiella planticola AJ13410 strain (FERM BP-6617, European Patent Laid-open No. 955368).
Raoultella planticola ATCC 33531 strain
Although the AJ13399 strain and the AJ13410 strain were classified as Klebsiella planticola at the time of the deposit, Klebsiella planticola is currently classified into Raoultella planticola (Drancourt, M., 2001, Int. J. Syst. Evol. Microbiol, 51:925-32).
Examples of rumen bacteria include Mannheimia, Actinobacillus, Anaerobiospirillum, Pyrobacterium, and Selenomonas. Bacteria including Mannheimia succiniciproducens, Actinobacillus succinogenes, Selenomonas ruminantium, Veillonella parvula, Wolnella succinogenes, Anaerobiospirillum succiniciproducens, and the like, can be used. Specific strains include Mannheimia sp. 55E (KCTC0769BP strain, U.S. Patent Published Application No. 20030113885, International Patent Publication WO2005/052135).
<1-1> Imparting an Ability to Produce an Acidic Substance Having a Carboxyl Group
Hereinafter, methods for imparting an ability to produce an acidic substance having a carboxyl group to bacteria, or methods for enhancing the ability to produce an acidic substance having a carboxyl group are described.
To impart an ability to produce an acidic substance having a carboxyl group, methods conventionally employed in the breeding of bacteria for producing substances by fermentation (see “Amino Acid Fermentation”, Japan Scientific Societies Press, 1st Edition, published May 30, 1986, pp. 77-100) can be applied. Such methods include the acquisition of an auxotrophic mutant, an analogue-resistant strain, or a metabolic regulation mutant, or construction of a recombinant strain having enhanced expression of an enzyme involved in biosynthesis of acidic substances having a carboxyl group. In the breeding of bacteria that produce an acidic substance having a carboxyl group, one or more properties, such as auxotrophic mutation, analogue resistance, or metabolic regulation mutation, can be imparted. The expression of one or two or more enzymes involved in the biosynthesis of an acidic substance having a carboxyl group can be enhanced. Furthermore, the impartation of properties such as auxotrophic mutation, analogue resistance, or metabolic regulation mutation can be combined with the enhancement of the biosynthetic enzymes.
A mutant strain auxotrophic for an acidic substance having a carboxyl group, a strain resistant to an analogue of an acidic substance having a carboxyl group, or a metabolic regulation mutant strain can be obtained by subjecting a parent or wild-type strain to a conventional mutagenesis, such as exposure to X-rays or UV irradiation, or a treatment with a mutagen such as N-methyl-N′-nitro-N-nitrosoguanidine, and then selecting bacteria which exhibit an autotrophy, analogue resistance, or metabolic regulation mutation and which also have the ability to produce an acidic substance having a carboxyl group.
Methods for imparting an amino acid- or organic acid-producing ability to microorganisms, and amino acid- or organic acid-producing bacteria will be specifically exemplified below.
<L-Glutamic Acid-Producing Bacteria>
Examples of the method of modifying a microorganism to impart L-glutamic acid-producing ability to the microorganism include, for example, enhancing expression of a gene coding for an enzyme involved in L-glutamic acid biosynthesis. Examples of an enzyme involved in L-glutamic acid biosynthesis include glutamate dehydrogenase (“GDH”)(gdh), glutamine synthetase (glnA), glutamate synthetase (gltAB), isocitrate dehydrogenase (icdA), aconitate hydratase (acnA, acnB), citrate synthase (“CS”)(gltA), methylcitrate synthase (hereinafter also referred to as “PRPC” (prpC), phosphoenolpyruvate carboxylase (“PEPC”) (ppc), pyruvate carboxylase (pyc), pyruvate dehydrogenase (aceEF, ipdA), 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), and glucose phosphate isomerase (pgi), and the like. The capital letter abbreviations in parentheses after the enzyme names are the enzyme abbreviation, while the lower case abbreviations indicate the name of the gene encoding the enzyme.
Methods for modifying a microorganism to increase expression of a target gene will be explained below.
The first method is to increase the copy number of the target gene by cloning the target gene on an appropriate plasmid and transforming the chosen host bacterium with the obtained plasmid. For example, when the target gene is the gene coding for CS (OA gene), the gene coding for PEPC (ppc gene) or the gene coding for GDH (gdhA gene), nucleotide sequences of these genes from Escherichia bacteria and Corynebacterium bacteria have already been reported (Ner, S. et al., 1983, Biochemistry, 22:5243-5249; Fujita, N. et al., 1984, J. Biochem., 95:909-916; Valle, F. et al., 1984, Gene, 27:193-199; Microbiology, 140:1817-1828, 1994; Eikmanns, B. J. et al., 1989, Mol. Gen. Genet., 218:330-339; Bormann, E. R. et al., 1992, Molecular Microbiology, 6:317-326), and therefore they can be obtained by synthesizing primers based on their respective nucleotide sequences, and performing PCR using chromosomal DNA as the template.
Examples of plasmids which can be used for transformation include a plasmid which autonomously replicates in the host bacterium belonging to the family Enterobacteriaceae, such as pUC19, pUC18, pBR322, RSF1010, pHSG299, pHSG298, pHSG399, pHSG398, pSTV28, pSTV29 (pHSG and pSTV are available from Takara Bio), pMW119, pMW118, pMW219, pMW218 (pMW vectors are available from Nippon Gene), and the like. Moreover, a phage DNA can also be used as the vector instead of a plasmid. Examples of plasmids for simultaneously enhancing the activities of CS or PRPC, PEPC, and GDH as described above include RSFCPG which includes the gltA gene, ppc gene, and gdhA gene (refer to European Patent Laid-open No. 0952221), and RSFPPG which is the same as RSFCPG, but the gltA gene is replaced with the prpC gene.
Examples of transformation methods include treating recipient cells with calcium chloride so to increase permeability for DNA, which has been reported for Escherichia coli K-12 (Mandel, M. and Higa, A., 1970, J. Mol. Biol., 53:159-162), and preparing competent cells from cells which are in the growth phase, followed by transformation with DNA, which has been reported for Bacillus subtilis (Duncan, C. H., et al., 1977, Gene, 1:153-167). Alternatively, a method of making potential host cells into protoplasts or spheroplasts, which can easily take up recombinant DNA, followed by introducing the recombinant DNA into the cells. This method is known to be applicable to Bacillus subtilis, actinomycetes and yeasts (Chang, S. and Choen, S. N., 1979, Molec. Gen. Genet., 168:111-115; Bibb, M. J. et al., 1978, Nature, 274:398-400; Hinnen, A., et al., 1978, Proc. Natl. Sci., USA, 75:1929-1933). In addition, microorganisms can also be transformed by the electric pulse method (Japanese Patent Laid-open No. 2-207791).
The copy number of a target gene can also be increased by introducing multiple copies of the gene into the chromosomal DNA of the microorganism. Multiple copies of a gene can be introduced into the chromosomal DNA by homologous recombination (Experiments in Molecular Genetics, 1972, Cold Spring Harbor Laboratory) using multiple copies of a sequence as targets in the chromosomal DNA. Sequences, which are present in multiple copies on the chromosomal DNA, repetitive DNAs, and inverted repeats present at the end of a transposable element, are exemplary. Also, as disclosed in Japanese Patent Laid-open No. 2-109985, it is possible to incorporate a target gene into a transposon, and allow it to be transferred to introduce multiple copies of the gene into the chromosomal DNA. The target gene can also be introduced into the bacterial chromosome by using Mu phage (Japanese Patent Laid-open No. 2-109985).
The second method is to increase expression of the target gene by replacing an expression regulatory sequence of the target gene, such as promoter, on the chromosomal DNA or plasmid with a stronger promoter. For example, the lac promoter, trp promoter, trc promoter, etc. are known as strong promoters. Moreover, it is also possible to substitute several nucleotides in the promoter region of a gene so that the promoter is stronger, or to modify the SD sequence as disclosed in International Patent Publication WO00/18935. Examples of methods for evaluating the strength of promoters and strong promoters are described in the article of Goldstein et al. (Goldstein, M. A., and Doi, R. H., 1995, Biotechnol. Annu. Rev., 1:105-128), etc.
Substitution of an expression regulatory sequence can be performed, for example, in the same manner as for gene substitution using a temperature-sensitive plasmid. Examples of vectors having a temperature-sensitive replication origin and are usable for Escherichia coli and Pantoea ananatis include, for example, the pMAN997 plasmid described in International Publication WO99/03988, and the like. Furthermore, an expression regulatory sequence can also be substituted by the method called “Red-driven integration” using Red recombinase of λ phage (Datsenko, K. A. and Wanner, B. L., 2000, Proc. Natl. Acad. Sci. USA. 97:6640-6645), or by combining the Red-driven integration method and the λ phage excisive system (Cho, E. H., et al., 2002, J. Bacteriol., 184:5200-5203) (WO2005/010175), and the like. Modification of an expression regulatory sequence can be combined with increasing the gene copy number.
As shown in Reference Example 1, a strain resistant to a λ Red gene product, for example, Pantoea ananatis SC17(0), can be used for the Red driven integration. The SC17(0) strain was deposited at the Russian National Collection of Industrial Microorganisms (VKPM), GNII Genetika (Russia, 117545 Moscow 1, Dorozhny proezd. 1) on Sep. 21, 2005 under an accession number of VKPM B-9246.
Examples of microorganisms modified by the method described above so that expression of citrate synthase gene, methylcitrate synthase gene, phosphoenolpyruvate carboxylase gene and/or glutamate dehydrogenase gene are enhanced include the microorganisms disclosed in Japanese Patent Laid-open Nos. 2001-333769, 2000-106869, 2000-189169, 2000-333769, 2006-129840, WO2006/051660, and the like.
Furthermore, L-glutamic acid-producing ability can also be imparted by enhancing the 6-phosphogluconate dehydratase activity, 2-keto-3-deoxy-6-phosphogluconate aldolase activity, or both. Examples of the microorganism in which 6-phosphogluconate dehydratase activity and 2-keto-3-deoxy-6-phosphogluconate aldolase activity are increased include the microorganism disclosed in Japanese Patent Laid-open No. 2003-274988.
L-glutamic acid-producing ability can also be imparted by decreasing or eliminating the activity of an enzyme that catalyzes a reaction that branches off from the L-glutamic acid biosynthesis pathway, producing a compound other than L-glutamic acid. Examples of these include 2-oxoglutarate dehydrogenase (sucA), isocitrate lyase (aceA), phosphate acetyltransferase (pta), acetate kinase (ack), acetohydroxy acid synthase (ilvG), acetolactate synthase (ilvI), formate acetyltransferase (pfl), lactate dehydrogenase (ldh), glutamate decarboxylase (gadAB), 1-pyrroline-5-carboxylate dehydrogenase (putA), and the like. Gene names are indicated in the parentheses after the enzyme names. The activity of 2-oxoglutarate dehydrogenase can be decreased or completely eliminated.
In order to decrease or eliminate the activities of the aforementioned enzymes, methods similar to the method for decreasing or eliminating the activity of lactate dehydrogenase (LDH) described later can be used.
A decrease in the intracellular activity of the target enzyme and the degree by which the activity is decreased, including if it is completely eliminated, can be confirmed by measuring the enzyme activity of a cell extract or a purified fraction thereof obtained from a candidate strain and comparing it with that of a wild-type strain. For example, 2-oxoglutarate dehydrogenase activity can be measured by the method of Reed et al. (Reed L. J. and Mukherjee B. B., 1969, Methods in Enzymology, 13, pp. 55-61).
Methods of eliminating or decreasing the 2-oxoglutarate dehydrogenase activity in Escherichia bacteria are disclosed in Japanese Patent Laid-open Nos. 5-244970, 7-203980 and the like. A method of eliminating or decreasing 2-oxoglutarate dehydrogenase activity in coryneform bacteria is disclosed in International Patent Publication WO95/34672. Furthermore, such a method for Enterobacter bacteria is disclosed in Japanese Patent Laid-open No. 2001-333769.
Specific examples of Escherichia bacteria which are deficient in 2-oxoglutarate dehydrogenase activity or in which the 2-oxoglutarate dehydrogenase activity is decreased include the following strains (U.S. Pat. Nos. 5,378,616 and 5,573,945).
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 obtained by disrupting the 2-oxoglutarate dehydrogenase gene (sucA gene) of Escherichia coli W3110. This strain is completely deficient in 2-oxoglutarate dehydrogenase.
Other specific examples of bacteria wherein the activity of 2-oxoglutarate dehydrogenase is deleted or decreased include the following strains:
Pantoea ananatis AJ13601 (FERM BP-7207, European Patent Laid-open No. 1078989)
Pantoea ananatis AJ13356 (FERM BP-6615, U.S. Pat. No. 6,331,419)
Pantoea ananatis SC17sucA (FERM BP-8646, WO2005/085419)
Klebsiella planticola AJ13410 strain (FERM BP-6617, U.S. Pat. No. 6,197,559)
Brevibacterium lactofermentum ΔS strain (refer to International Patent Publication WO95/34672)
The SC17sucA strain is obtained by obtaining a low phlegm production mutant strain (SC17) from the AJ13355 strain, which was isolated from nature as a strain that could proliferate in a medium containing L-glutamic acid and a carbon source at low pH, and disrupting the 2-oxoglutarate dehydrogenase gene (sucA) in the mutant strain. The AJ13601 strain is obtained by introducing the plasmid RSFCPG containing the gltA, ppc and gdhA genes derived from Escherichia coli and the plasmid pSTVCB containing the gltA gene derived from Brevibacterium lactofermentum into the SC17sucA strain to obtain the SC17sucA/RSFCPG+pSTVCB strain, and selecting a high concentration L-glutamic acid-resistant strain at a low pH and a strain showing a high proliferation degree and a high L-glutamic acid-producing ability (European Patent Laid-open No. 0952221). The AJ13356 strain was obtained by deleting the αKGDH-E1 subunit gene (sucA) from the AJ13355 strain.
The SC17sucA strain was assigned a private number of AJ417, deposited in the International Patent Organism Depositary, National Institute of Advanced Industrial Science and Technology (Central 6, 1-1, Higashi 1-Chome, Tsukuba-shi, Ibaraki-ken, Japan, postal code: 305-8566) on Feb. 26, 2004, and assigned an accession number of FERM BP-08646.
The AJ13410 strain was deposited in the International Patent Organism Depositary, National Institute of Advanced Industrial Science and Technology (Central 6, 1-1, Higashi 1-Chome, Tsukuba-shi, Ibaraki-ken, Japan, postal code: 305-8566) on Feb. 19, 1998, and assigned an accession number of FERM P-16647. The deposit was then converted to an international deposition under the provisions of Budapest Treaty on Jan. 11, 1999 and assigned an accession number of FERM BP-6617.
The aforementioned Pantoea ananatis AJ13355, AJ13356, and AJ13601 strains and the Klebsiella planticola AJ13399 strain have an ability to accumulate L-glutamic acid in a concentration which exceeds the saturation concentration of L-glutamic acid in a liquid medium when it is cultured under acid conditions.
Furthermore, in order to improve the L-glutamic acid-producing ability of Enterobacteriaceae bacteria, the method of deleting the arcA gene (U.S. Pat. No. 7,090,998), and the method of amplifying the yhfK gene, which is a glutamic acid secretion gene (WO2005/085419) can also be used.
Other than the above, examples of coryneform bacteria having L-glutamic acid-producing ability include the following strains:
Brevibacterium flavum AJ11573 (FERM P-5492, refer to Japanese Patent Laid-open No. 56-151495)
Brevibacterium flavum AJ12210 (FERM P-8123, refer to Japanese Patent Laid-open No. 61-202694)
Brevibacterium flavum AJ12212 (FERM P-8123, refer to Japanese Patent Laid-open No. 61-202694)
Brevibacterium flavum AJ12418 (FERM-BP2205, refer to Japanese Patent Laid-open No. 2-186994)
Brevibacterium flavum DH18 (FERM P-11116, refer to Japanese Patent Laid-open No. 3-232497)
Corynebacterium melassecola DH344 (FERM P-11117, refer to Japanese Patent Laid-open No. 3-232497)
Corynebacterium glutamicum AJ11574 (FERM P-5493, refer to Japanese Patent Laid-open No. 56-151495)
Microorganisms having L-glutamic acid-producing ability include the Brevibacterium lactofermentum AJ13029 strain (FERM BP-5189, refer to WO96/06180), which was made to be able to produce L-glutamic acid in a medium containing an excessive amount of biotin in the absence of biotin action inhibitor, such as surfactant, by introducing a mutation which imparts temperature sensitivity to the biotin action inhibitor. Examples further include microorganisms that belong to the genus Alicyclobacillus and are resistant to a L-glutamic acid antimetabolite (Japanese Patent Laid-open No. 11-262398).
Furthermore, the microorganism having a L-glutamic acid producing ability can also be unable to degrade L-glutamic acid, or express the maleate synthase (aceB)•isocitrate lyase (aceA)•isocitrate dehydrogenase kinase/phosphatase (aceK) operon (henceforth abbreviated as “ace operon”) constitutively. Examples of such microorganisms include, for example, the following:
Escherichia coli AJ12628 (FERM BP-3854)
Escherichia coli AJ12624 (FERM BP-3853)
The former is a mutant strain in which 2-oxoglutarate dehydrogenase activity is decreased and expression of the ace operon has become constitutive. The latter is a mutant strain in which 2-oxoglutarate dehydrogenase activity is decreased and the ability to degrade L-glutamic acid is decreased (refer to French Patent No. 2680178).
When a Pantoea bacterium is used, a mutation can be imparted that results in production of less extracellular phlegm as compared to a wild-type strain when it is cultured in a medium containing a saccharide. In order to introduce such a mutation, bacterial strains can be screened for their ability to produce viscous materials on the solid medium (Japanese Patent Laid-open No. 2001-333769), and the ams operon that is involved in polysaccharide synthesis can be disrupted. The nucleotide sequence of the ams operon is shown in SEQ ID NO: 66, and the amino acid sequences of AmsH, I, A, C and B encoded by this operon are shown in SEQ ID NOS: 67, 68, 69, 70 and 71, respectively.
<Succinic Acid-Producing Bacteria>
As succinic acid-producing bacteria, strains which are unable to form acetic acid, lactic acid, ethanol, and formic acid can be used, and specific examples include the Escherichia coli SS373 strain (International Patent Publication WO99/06532).
Strains deficient in their abilities to form acetic acid, lactic acid, ethanol and formic acid can be obtained by using a strain that cannot assimilate acetic acid and lactic acid in a minimal medium, or by decreasing the activities of the lactic acid or acetic acid biosynthetic enzymes described below (International Patent Publication WO2005/052135).
Moreover, such strains as described above can also be obtained by imparting monofluoroacetic acid resistance (U.S. Pat. No. 5,521,075).
Other examples of methods for obtaining a strain with improved succinic acid-producing ability include culturing a strain which is deficient in both formate lyase and lactate dehydrogenase and cannot assimilate pyruvic acid in a glucose-enriched medium under anaerobic conditions, and isolating a mutant strain having the ability to assimilate pyruvic acid (International Patent Publication WO97/16528).
The ability to produce succinic acid can also be imparted by amplifying a gene encoding an enzyme which is involved in the succinic acid biosynthesis system described below, or deleting a gene encoding an enzyme which catalyzes a reaction which branches away from the succinic acid biosynthesis system to produce another compound.
The ability to produce succinic acid can also be imparted by modifying a microorganism to decrease the enzymatic activity of lactate dehydrogenase (LDH), which is a lactic acid biosynthesis system enzyme (International Patent Publications WO2005/052135, WO2005/116227, U.S. Pat. No. 5,770,435, U.S. Patent Published Application No. 20070054387, International Patent Publication WO99/53035, Alam, K. Y. and Clark, D. P., 1989, J. Bacteriol., 171:6213-6217). Some microorganisms can have both L-lactate dehydrogenase and D-lactate dehydrogenase, and can be modified to decrease the activity of either one of the enzymes, or the activities of both the enzymes, in another example.
The ability to produce succinic acid can also be imparted by modifying a microorganism to decrease the enzymatic activity of the formic acid biosynthesis system enzyme, pyruvate-formate lyase (PFL) (U.S. Patent Published Application No. 20070054387, International Patent Publications WO2005/116227, WO2005/52135, Donnelly, M. I. et al., 1998, Appl. Biochem. Biotechnol., 70-72:187-198).
The ability to produce succinic acid can also be imparted by modifying a microorganism to decrease the enzymatic activities of phosphate acetyltransferase (PTA), acetate kinase (ACK), pyruvate oxidase (PDXB), acetyl-CoA synthetase (ACS) and acetyl-CoA hydrolase (ACH), which are acetic acid biosynthesis system enzymes (U.S. Patent Published Application No. 20070054387, International Patent Publications WO2005/052135, WO99/53035, WO2006/031424, WO2005/113745, and WO2005/113744).
The ability to produce succinic acid can also be enhanced by modifying a microorganism to decrease the enzymatic activity of alcohol dehydrogenase (ADH), which is an ethanol biosynthesis system enzyme (refer to International Patent Publication WO2006/031424).
The ability to produce succinic acid can also be enhanced by decreasing the activities of pyruvate kinase, glucose PTS (ptsG), ArcA protein, IclR protein (iclR), glutamate dehydrogenase (gdh) and/or glutamine synthetase (glnA), and glutamate synthase (gltBD) (International Patent Publication WO2006/107127, WO2007007933, Japanese Patent Laid-open No. 2005-168401). The gene names are indicated in the parentheses following the enzyme names.
The ability to produce succinic acid can also be imparted by enhancing a biosynthesis system enzyme involved in the succinic acid production.
The ability to produce succinic acid can also be enhanced by increasing the enzymatic activities of pyruvate carboxylase, malic enzyme, phosphoenolpyruvate carboxylase, fumarase, fumarate reductase, malate dehydrogenase and phosphoenolpyruvate carboxykinase (Japanese Patent Laid-open No. 11-196888, International Patent Publication WO99/53035, Hong, S. H., and S. Y. Lee, 2001, Biotechnol. Bioeng., 74:89-95, Millard, C. S. et al., 1996, Appl. Environ. Microbiol., 62:1808-1810, International Patent Publication WO2005/021770, Japanese Patent Laid-open No. 2006-320208, Kim, P. et al., 2004, Appl. Environ. Microbiol., 70:1238-1241). Increasing the enzymatic activities of these target enzymes can be performed by referring to the methods for enhancing expression of a target gene described herein, and the methods for enhancing expression of ybjL gene described later.
Specific examples of succinic acid-producing bacteria belonging to the family Enterobacteriaceae include the following strains:
Escherichia coli SS373 strain (International Patent Publication WO99/06532)
Escherichia coli AFP111 strain (International Patent Publication WO97/16528)
Escherichia coli NZN111 strain (U.S. Pat. No. 6,159,738)
Escherichia coli AFP184 strain (International Patent Publication WO2005/116227)
Escherichia coli SBS100MG strain, SBS110MG strain, SB S440MG strain, SBS550MG strain, and SBS660MG strain (International Patent Publication WO2006/031424)
Examples of succinic acid-producing bacteria belonging to coryneform bacteria include the following strains.
Brevibacterium flavum AB-41 strain (Japanese Patent Laid-open No. 11-113588)
Brevibacterium flavum AB-41 strain (PC-amplified strain, Japanese Patent Laid-open No. 11-196888)
Corynebacterium glutamicum AJ110655 strain (FERM BP-10951)
Brevibacterium flavum MJ233Δldh strain (International Patent Publication WO2005/021770)
Brevibacterium lactofermentum (Corynebacterium glutamicum) 2256Δ(ldh, ach, pta, ack) (International Patent Publication WO2005/113744)
Brevibacterium lactofermentum 2256Δ(ldh, pta, ack, poxB) (International Patent Publication WO2005/113745)
Corynebacterium glutamicum Rldh-/pCRB-1 PC strain (International Patent Publication WO2005/010182)
Examples of succinic acid-producing rumen bacteria include the following strains.
Mannheimia succiniciproducens LPK, LPK7 and LPK4 (International Patent Publication WO2005/052135)
Actinobacillus succinogenes 130Z (U.S. Pat. No. 5,504,004)
Anaerobiospirillum succiniciproducens FZ10 (U.S. Pat. No. 5,521,075)
Anaerobiospirillum succiniciproducens FZ53 (U.S. Pat. No. 5,573,931)
<1-2> Enhancement of Expression of ybjL Gene
A microorganism that has an ability to produce an acidic substance having a carboxyl group can be modified such as those described above so that expression of the ybjL gene is enhanced. However, the modification to enhance expression of the ybjL gene is performed first, and then the ability to produce an acidic substance having a carboxyl group can be imparted. Furthermore, the microorganism can already have the ability to produce an acidic substance having a carboxyl group, or the ability to produce an acidic substance having a carboxyl group can be enhanced by amplification of the ybjL gene.
The “ybjL gene” refers to the ybjL gene of Escherichia coli or a homologue thereof, the ybjL gene of Pantoea ananatis or a homologue thereof, or the ybjL gene of Enterobacter aerogenes or a homologue thereof. Examples of the ybjL gene of Escherichia coli include a gene coding for a protein having the amino acid sequence of SEQ ID NO: 4, for example, a gene having the nucleotide sequence of the nucleotides 101 to 1783 in SEQ ID NO: 3. Furthermore, examples of the ybjL gene derived from Pantoea ananatis include a gene coding for a protein having the amino acid sequence of SEQ ID NO: 2, for example, a gene having the nucleotide sequence of the nucleotides 298 to 1986 in SEQ ID NO: 1. Furthermore, examples of the ybjL gene derived from the Enterobacter aerogenes AJ110673 strain include a gene coding for a protein having the amino acid sequence of SEQ ID NO: 87, for example, a gene having the nucleotide sequence of the nucleotides 19 to 1704 in SEQ ID NO: 86. Furthermore, examples of the ybjL gene derived from Salmonella typhimurium include a gene coding for a protein having the amino acid sequence of SEQ ID NO: 25 (SEQ ID NO: 24). Examples of the ybjL gene derived from Yersinia pestis include a gene coding for a protein having the amino acid sequence of SEQ ID NO: 27 (SEQ ID NO: 26). Examples of the ybjL gene derived from Erwinia carotovora include a gene coding for a protein having the amino acid sequence of SEQ ID NO: 29 (SEQ ID NO: 28). Examples of the ybjL gene derived from Vibrio cholerae include a gene coding for a protein having the amino acid sequence of SEQ ID NO: 31 (SEQ ID NO: 30). Examples of the ybjL gene derived from Aeromonas hydrophila include a gene coding for a protein having the amino acid sequence of SEQ ID NO: 33 (SEQ ID NO: 32). Examples of the ybjL gene derived from Photobacterium profundum include a gene coding for a protein having the amino acid sequence of SEQ ID NO: 35 (SEQ ID NO: 34). Furthermore, the ybjL gene can be cloned from a coryneform bacterium such as Corynebacterium glutamicum and Brevibacterium lactofermentum, Pseudomonas bacterium such as Pseudomonas aeruginosa, Mycobacterium bacterium such as Mycobacterium tuberculosis or the like, on the basis of homology to the genes exemplified above. The amino acid sequences of the proteins encoded by the ybjL genes of Salmonella typhimurium, Yersinia pestis, Erwinia carotovora, Vibrio cholerae, Aeromonas hydrophila and Photobacterium profundum described above are 96%, 90%, 88%, 64%, 60% and 68% homologous to the amino acid sequence of SEQ ID NO: 4, respectively, and 86%, 90%, 84%, 63%, 60% and 67% homologous to the amino acid sequence of SEQ ID NO: 2, respectively. The amino acid sequences of SEQ ID NOS: 2 and 4 are 86% homologous. The consensus sequence of SEQ ID NOS: 2 and 4 is shown in SEQ ID NO: 5. The amino acid sequences of SEQ ID NOS: 4 and 87 re 92% homologous, and the amino acid sequences of SEQ ID NOS: 2 and 87 are 83% homologous. The sequence of the ybjL gene from the Enterobacter aerogenes AJ110637 strain (SEQ ID NO: 86) and the encoded amino acid sequence (SEQ ID NO: 87) have not been previously reported. The consensus sequence for the amino acid sequences of SEQ ID NOS: 2, 4 and 87 is shown in SEQ ID NO: 88.
The term “ybjL gene homologue” refers to a gene derived from a microorganism other than Escherichia coli, Pantoea ananatis, and Enterobacter aerogenes, which exhibits high structural similarity to the ybjL gene of Escherichia coli, Pantoea ananatis, or Enterobacter aerogenes and codes for a protein that improves an ability of a microorganism to produce an acidic substance having a carboxyl group when expression of the gene is enhanced in the microorganism. Examples of ybjL gene homologues include genes coding for a protein having a homology of 70% or more, 80% or more in another example, 90% or more in another example, 95% or more in another example, 97% or more in another example, to the entire amino acid sequence of SEQ ID NO: 2, 4 or 87 or the amino acid sequence of SEQ ID NO: 2, 4 or 87, and which improves an ability to produce an acidic substance having a carboxyl group of a microorganism when expression of the gene is enhanced in the microorganism. The ybjL gene homologue can code for a protein having a homology of 70% or more, 80% or more in another example, 90% or more in another example, 95% or more in another example, or 97% or more in another example, to any of the aforementioned amino acid sequences, and the consensus sequences of the SEQ ID NOS: 5 or 88. Homology of the 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 (Methods Enzymol., 183, 63 (1990)). Programs called BLASTN and BLASTX were developed on the basis of the algorithm BLAST (refer to www.ncbi.nlm.nih.gov). The term “homology” can also be used to mean “identity”.
The ybjL gene can have one or more conservative mutations, and can be artificially modified, so long as enhancement of the tbjL gene's expression results in an improved ability to produce a target substance by a microorganism. That is, the ybjL gene can encode for an amino acid sequence of a known protein, for example, a protein having an amino acid sequence of SEQ ID NO: 2, 4, 25, 27, 29, 31, 33, 35 or 87, but which includes a conservative mutation, specifically, substitution, deletion, insertion or addition, of one or several amino acid residues at one or several positions. Although the number meant by the term “several” can differ depending on the position in the three-dimensional structure of the protein, or the type of amino acid residue. For example, it can be 1 to 20, 1 to 10 in another example, 1 to 5 in another example. Furthermore, the ybjL gene can encode for a protein having a homology of 70% or more, 80% or more in another example, 90% or more in another example, 95% or more in another example, or 97% or more in another example, to the entire amino acid sequence of SEQ ID NO: 2, 4, 25, 27, 29, 31, 33, 35 or 87, and which improves an ability to produce a target substance by a microorganism when expression of the gene is enhanced in the microorganism.
The aforementioned conservative substitution can be neutral, in that the function of the protein is not changed. The conservative mutation can take place mutually among Phe, Trp and Tyr, if the substitution site is an aromatic amino acid; among Leu, Ile and Val, if the substitution site 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 hydroxyl group. Specific examples of substitution considered 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 Ile; substitution of Ile, Met, Val or Phe for Leu; substitution of Asn, Glu, Gln, His or Arg for Lys; substitution of Ile, 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.
Such a gene can be obtained by modifying the nucleotide sequence of the nucleotides 298 to 1986 in SEQ ID NO: 1, the nucleotide sequence of the nucleotides 101 to 1783 in SEQ ID NO: 3, the nucleotide sequence of the nucleotides 19 to 1704 in SEQ ID NO: 86, or the nucleotide sequence of SEQ ID NO: 24, 26, 28, 30, 32 or 34 by, for example, site-specific mutagenesis, so that substitution, deletion, insertion or addition of an amino acid residue or residues occurs at a specific site in the encoded protein. Furthermore, such a gene can also be obtained by a known mutation treatment, examples of which include treating a gene having any of the nucleotide sequences described above with hydroxylamine or the like in vitro, and treating a microorganism, for example, an Escherichia bacterium, containing the gene with ultraviolet ray irradiation or a mutagen used in a usual mutation treatment such as N-methyl-N′-nitro-N-nitrosoguanidine (NTG) or EMS (ethyl methanesulfonate). The mutation for the substitutions, deletions, insertions, additions, inversions or the like of amino acid residues described above also includes a naturally occurring mutation based on individual difference, difference in species of microorganisms that contain the ybjL gene (mutant or variant), and the like.
The ybjL gene can also be a DNA hybridizable with a complementary strand of DNA having the nucleotide sequence of the nucleotides 298 to 1986 in SEQ ID NO: 1, a DNA having the nucleotide sequence of the nucleotides 101 to 1783 in SEQ ID NO: 3, a DNA having the nucleotide sequence of the nucleotides 19 to 1704 in SEQ ID NO: 86, or a DNA having the nucleotide sequence of SEQ ID NO: 1, 3, 24, 26, 28, 30, 32, 34 or 86, or a probe that can be prepared from the DNAs having these sequences under stringent conditions and which codes for a protein which improves an ability to produce a substance of a microorganism when expression of the gene is enhanced in the microorganism.
The “stringent conditions” can be conditions under which a so-called specific hybrid is formed, and non-specific hybrid is not formed. It is difficult to clearly express this condition by using any numerical value. However, the stringent conditions include, for example, when DNAs having high homology to each other, for example, DNAs having a homology of, for example, not less than 80%, not less than 90% in another example, not less than 95% in another example, or not less than 97% in another example, hybridize with each other, and DNAs having homology lower than the above level do not hybridize with each other, and when washing in ordinary Southern hybridization, i.e., washing once, twice or three times in another example, at salt concentrations and temperature of 1×SSC, 0.1% SDS at 60° C., 0.1×SSC, 0.1% SDS at 60° C. in another example, 0.1×SSC, 0.1% SDS at 65° C., 0.1×SSC in another example, or 0.1% SDS at 68° C. in another example.
The probe can have a partial sequence of the ybjL gene. Such a probe can be produced by PCR using oligonucleotides prepared on the basis of the nucleotide sequence of the gene and a DNA fragment including the gene as the template and performed in a manner well known to those skilled in the art. When a DNA fragment having a length of about 300 bp is used as the probe, the washing conditions after hybridization can be exemplified by 2×SSC, 0.1% SDS at 50° C.
The aforementioned descriptions concerning the gene homologue and conservative mutations can be similarly applied to the other enzyme genes described herein.
The expression of the ybjL gene can be enhanced by increasing the copy number of the ybjL gene, modifying an expression control sequence of the ybjL gene, amplifying a regulator that increases expression of the ybjL gene, or deleting or attenuating a regulator that decreases expression of the ybjL gene. Expression can be enhanced or increased using transformation or homologous recombination performed in the same manner as the methods for enhancing expression of a target gene described above for L-glutamic acid-producing bacteria.
In the microorganism, an activity for secreting an acidic substance having a carboxyl group can be improved by enhancing the expression of the ybjL gene. Whether “the activity for secreting an acidic substance having a carboxyl group is improved” can be confirmed by comparing the amount of the acidic substance having a carboxyl group which has been secreted into the medium in which the microorganism is cultured with the amount obtained by culturing a control microorganism into which the ybjL gene is not introduced. That is, the “improvement in the activity for secreting the acidic substance having a carboxyl group” is observed as an increase in the concentration of the acidic substance having a carboxyl group in the medium in which the microorganism is cultured as compared to the concentration obtained with a control microorganism. Furthermore, the “improvement in the activity for secreting an acidic substance having a carboxyl group” is also observed as a decrease in intracellular concentration of the acidic substance having a carboxyl group in the microorganism. As for the improvement of the “activity for secreting an acidic substance having a carboxyl group”, the intracellular concentration of the acidic substance having a carboxyl group can be decreased by 10% or more, 20% or more in another example, 30% or more in another example, as compared to the concentration in a strain in which expression of the ybjL gene is not enhanced. The absolute “activity for secreting an acidic substance having a carboxyl group” of a microorganism can be detected by measuring the difference between the intracellular and extracellular concentrations of the acidic substance having a carboxyl group. Furthermore, the “activity for secreting an acidic substance having a carboxyl group” can also be detected by measuring the activity for taking up amino acids into the cells using reverted membrane vesicles with a radioisotope (J. Biol. Chem., 2002, vol. 277, No. 51, pp. 49841-49849). For example, the activity can be measured by preparing reverted membrane vesicles from cells in which the ybjL gene is expressed, adding a substrate which can act as a driving force such as ATP, and measuring the uptake activity for RI-labeled glutamic acid. Moreover, the activity can also be measured by detecting an exchange reaction rate of a labeled acidic substance having a carboxyl group and unlabeled acidic substance having a carboxyl group in live bacteria.
The microorganism can have an ability to accumulate L-glutamic acid in the liquid medium in an amount which is more than the amount at the saturation concentration of L-glutamic acid when it is cultured under acidic conditions (this ability is also referred to as the “L-glutamic acid accumulation ability under acidic conditions”). Such a microorganism can have the L-glutamic acid accumulation ability under acidic conditions by enhancing the expression of the ybjL gene. Alternatively, the microorganism can have a native ability to accumulate L-glutamic acid under acidic conditions.
Specific examples of microorganisms having L-glutamic acid accumulation ability under acidic conditions include the aforementioned Pantoea ananatis AJ13355 strain (FERM BP-6614), AJ13356 strain (FERM BP-6615), AJ13601 strain (FERM BP-7207) (for these, refer to Japanese Patent Laid-open No. 2001-333769), and the like. The Pantoea ananatis AJ13355 and AJ13356 strains were deposited at the National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology, Ministry of International Trade and Industry (currently, National Institute of Bioscience and Human-Technology, National Institute of Advanced Industrial Science and Technology, Address: Central 6, 1-1, Higashi 1-Chome, Tsukuba-shi, Ibaraki-ken, 305-8566, Japan) on Feb. 19, 1998 and given accession numbers of FERM P-16644 and FERM P-16645. The deposits were then converted to international deposits under the provisions of Budapest Treaty on Jan. 11, 1999 and given accession numbers of FERM BP-6614 and FERM BP-6615. The AJ13601 strain was deposited at the National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology (currently, International Patent Organism Depository, National Institute of Advanced Industrial Science and Technology) on Aug. 18, 1999 and given an accession number of FERM P-17516. The deposit was converted to an international deposit under the provisions of the Budapest Treaty on Jul. 6, 2000 and given an accession number of FERM BP-7207. These strains were identified as Enterobacter agglomerans when they were isolated and deposited as Enterobacter agglomerans AJ13355, AJ13356, and AJ13601 strains. However, they were recently re-classified as Pantoea ananatis on the basis of nucleotide sequencing of 16S rRNA and the like.
When an organic acid, especially succinic acid, is produced, using a microorganism which is modified to decrease the activities of one or more enzymes among lactate dehydrogenase (LDH), alcohol dehydrogenase (ADH), and pyruvate formate lyase (PFL), in addition to increasing the expression of the ybjL gene, is more effective.
The expression “modified so that lactate dehydrogenase activity is decreased” can mean that the lactate dehydrogenase activity is decreased as compared to that of a strain in which lactate dehydrogenase is unmodified. The lactate dehydrogenase activity can be decreased to 10% per cell or lower as compared to that of a lactate dehydrogenase-unmodified strain. The lactate dehydrogenase activity can also be completely deleted. Decrease of the lactate dehydrogenase activity can be confirmed by measuring the lactate dehydrogenase activity by a known method (Kanarek, L. and Hill, R. L., 1964, J. Biol. Chem., 239:4202). Specific examples of the method for producing a mutant strain of Escherichia coli in which the lactate dehydrogenase activity is decreased include the method described in Alam, K. Y., and Clark, D. P., 1989, J. Bacteriol., 171:6213-6217, and the like. The microorganism with decreased lactate dehydrogenase activity and enhanced expression of the ybjL gene can be obtained by, for example, preparing a microorganism in which the LDH gene is disrupted, and transforming this microorganism with a recombinant vector containing the ybjL gene, as described in Example 1. However, either the modification for decreasing the LDH activity or the modification for enhancing expression of the ybjL gene can be performed first. In Escherichia coli, LDH is encoded by the ldhA and lldD genes. The DNA sequence of the ldhA gene is shown in SEQ ID NO: 36, the amino acid sequence encoded thereby is shown in SEQ ID NO: 37, the DNA sequence of the lldD gene is shown in SEQ ID NO: 38, and the amino acid sequence encoded thereby is shown in SEQ ID NO: 39.
In order to decrease or delete activity of LDH, a mutation that decreases or deletes the intracellular activity of LDH can be introduced into the LDH gene on the chromosome by a known mutagenesis method. For example, the gene coding for LDH on the chromosome can be deleted, or an expression control sequence such as a promoter and the Shine-Dalgarno (SD) sequence can be modified by gene recombination. Furthermore, a mutation can also be introduced to cause an amino acid substitution (missense mutation), a stop codon (nonsense mutation), or a frame shift mutation that adds or deletes one or two nucleotides into the coding region of the LDH on the chromosome, or a part of, or the entire gene can be deleted (Qiu Z. and Goodman M. F., 1997, J. Biol. Chem., 272:8611-8617). Furthermore, the LDH activity can also be decreased or deleted by gene disruption, for example, by deleting the coding region of the LDH gene in a DNA construct, and replacing the normal LDH gene with the DNA construct on the chromosome by homologous recombination or the like, or by introducing a transposon or IS factor into the gene.
In order to introduce a mutation which results in decreasing or deleting the LDH activity by genetic recombination, for example, the following methods are used. The chromosomal LDH gene can be replaced with a mutant gene by preparing a mutant LDH gene in which a partial sequence of the LDH gene is modified so that it does not produce an enzyme that can function normally, and transforming a bacterium with a DNA containing the mutant gene to cause homologous recombination between the mutant gene and the gene on a chromosome. Such site-specific mutagenesis based on gene substitution utilizing homologous recombination has been already reported, and include a method called Red driven integration developed by Datsenko and Wanner (Datsenko, K. A, and Wanner, B. L., 2000, Proc. Natl. Acad. Sci. USA, 97:6640-6645), a method of using a linear DNA such as by utilizing Red driven integration in combination with an excision system derived from λ phage (Cho, E. H., et al., 2002, J. Bacteriol., 184:5200-5203), a method of using a plasmid containing a temperature sensitive replication origin (U.S. Pat. No. 6,303,383, Japanese Patent Laid-open No. 05-007491, WO2005/010175), and the like. Such site-specific mutagenesis based on gene substitution using homologous recombination as described above can also be performed by using a plasmid that is unable to replicate in a host.
The expression “modified so that alcohol dehydrogenase activity is decreased” can mean that the alcohol dehydrogenase activity is decreased as compared to that of a strain in which alcohol dehydrogenase is unmodified. The alcohol dehydrogenase activity can be decreased to 10% per cell or lower as compared to an alcohol dehydrogenase-unmodified strain. The alcohol dehydrogenase activity can also be completely deleted. Decrease in the alcohol dehydrogenase activity can be confirmed by measuring the alcohol dehydrogenase activity by a known method (Lutstorf, U. M. et al., 1970, Eur. J. Biochem., 17:497-508). Specific examples of the method for producing a mutant strain of Escherichia coli in which the alcohol dehydrogenase activity is decreased include the method described in Sanchez A. M. et al., 2005, Biotechnol. Prog., 21:358-365, and the like. The microorganism in which alcohol dehydrogenase activity is decreased and expression of the ybjL gene is enhanced can be obtained by, for example, preparing a microorganism in which the gene coding for alcohol dehydrogenase (ADH) is disrupted, and transforming this microorganism with a recombinant vector containing the ybjL gene. However, either the modification for decreasing the ADH activity or the modification for enhancing expression of the ybjL gene can be performed first. The alcohol dehydrogenase activity can be decreased by a method similar to that for decreasing the lactate dehydrogenase activity described above. The nucleotide sequence (partial sequence) of the ADH gene from the Enterobacter aerogenes AJ110637 strain (FERM ABP-10955) is shown in SEQ ID NO: 74. The entire nucleotide sequence of this gene can be determined by, for example, isolating the ADH gene (adhE) from the chromosomal DNA of Enterobacter aerogenes on the basis of this partial sequence.
The expression “modified so that pyruvate formate lyase activity is decreased” can mean that the pyruvate formate lyase activity is decreased as compared to that of a strain in which the pyruvate formate lyase is unmodified. The pyruvate formate lyase activity can be decreased to 10% per cell or lower as compared to a pyruvate formate lyase-unmodified strain. The pyruvate formate lyase activity can also be completely deleted. A decrease in the pyruvate formate lyase activity can be confirmed by measuring the pyruvate formate lyase activity by a known method (Knappe, J. and Blaschkowski, H. P., 1975, Meth. Enzymol., 41:508-518). The microorganism in which pyruvate formate lyase activity is decreased and expression of the ybjL gene is enhanced can be obtained by, for example, preparing a microorganism in which the PFL gene is disrupted, and transforming this microorganism with a recombinant vector containing the ybjL gene. However, either the modification for decreasing the PFL activity or the modification for enhancing expression of ybjL can be performed first. The pyruvate formate lyase activity can be decreased by a method similar to the method for decreasing the lactate dehydrogenase activity described above.
A bacterium modified so that the pyruvate carboxylase (PC) activity is enhanced, in addition to the enhanced the expression of the ybjL gene, can also be used to produce an organic acid, especially succinic acid. Enhancing the pyruvate carboxylase activity can be combined with decreasing the lactate dehydrogenase activity, alcohol dehydrogenase activity, and/or pyruvate formate lyase activity. The expression “modified so that pyruvate carboxylase activity is enhanced” can mean that the pyruvate carboxylase activity is increased as compared to that of an unmodified strain such as a wild-type strain or parent strain. The pyruvate carboxylase activity can be measured by, for example, a method of measuring a decrease of NADH as described later.
The nucleotide sequence of the PC gene can be a reported sequence or can be obtained by isolating a DNA fragment encoding a protein having the PC activity from the chromosome of a microorganism, animal, plant, or the like, and then the nucleotide sequence can be determined. After the nucleotide sequence is determined, a gene synthesized on the basis of that sequence can also be used.
The PC gene can be derived from a coryneform bacterium, such as Corynebacterium glutamicum (Peters-Wendisch, P. G. et al., 1998, Microbiology, vol. 144:915-927). Furthermore, so long as the functions of the encoded PC protein, such as its involvement in carbon dioxide fixation, are not substantially degraded, nucleotides in the PC gene can be replaced with other nucleotides or deleted, or other nucleotides can be inserted into the sequence. Alternatively, a part of the nucleotide sequence can be transferred.
PC genes obtained from bacteria other than Corynebacterium glutamicum, including from other microorganisms, animals, and plants, can also be used. In particular, the sequences of PC genes derived from other microorganisms, animals and plants described below are known (references are indicated below), and they can be obtained by hybridization or amplification by PCR of the ORF portions in the same manner as described above.
Human [Biochem. Biophys. Res. Comm., 202, 1009-1014, (1994)]
Mouse [Proc. Natl. Acad. Sci. USA., 90, 1766-1779, (1993)]
Rat [GENE, 165, 331-332, (1995)]
Yeast: Saccharomyces cerevisiae [Mol. Gen. Genet., 229, 307-315, (1991)], Schizosaccharomyces pombe [DDBJ Accession No.; D78170]
Bacillus stearothermophilus [GENE, 191, 47-50, (1997)]
Rhizobium etli [J. Bacteriol., 178, 5960-5970, (1996)]
The PC gene can be enhanced in the same manner as when enhancing expression of a target gene described above for L-glutamic acid-producing bacteria and enhancing expression of the ybjL gene.
<2> Method for Producing an Acidic Substance Having a Carboxyl Group
An acidic substance having a carboxyl group can be produced by culturing the microorganism in a medium to produce and cause accumulation of an acidic substance having a carboxyl group in the medium and collecting the substance from the medium. Furthermore, the acidic substance having a carboxyl group can also be produced by allowing the microorganism, or a product obtained by processing the microorganism, to act on an organic raw material in a reaction mixture containing carbonate ions, bicarbonate ions, or carbon dioxide gas to produce the acidic substance having a carboxyl group, and collecting the substance. The former method is exemplary for producing an acidic amino acid. The latter method is exemplary for producing an organic acid. Hereinafter, further examples methods for producing an acidic amino acid and an organic acid will be exemplified.
<2-1> Production of Acidic Amino Acid
An acidic amino acid can be produced by culturing the microorganism in a medium to produce and cause accumulation of an acidic amino acid in the medium and collecting the acidic amino acid from the medium.
As the medium used for the culture, a known medium containing a carbon source, nitrogen source, and inorganic salts, as well as trace amounts of organic nutrients such as amino acids and vitamins as required can be used. Either a synthetic medium or natural medium can be used. The carbon source and nitrogen source used in the medium can be of any type so long as substances that can be utilized by the chosen strain to be cultured.
As the carbon source, saccharides such as glucose, glycerol, fructose, sucrose, maltose, mannose, galactose, starch hydrolysate and molasses can be used. In addition, alcohols such as ethanol can be used independently or in combination with another carbon source. Furthermore, organic acids such as acetic acid and citric acid other than the target substance can also be used as the carbon source. As the nitrogen source, ammonia, ammonium salts such as ammonium sulfate, ammonium carbonate, ammonium chloride, ammonium phosphate and ammonium acetate, nitrates and the like can be used. As the trace amount organic nutrients, amino acids, vitamins, fatty acids, nucleic acids, those containing these substances such as peptone, casamino acid, yeast extract and soybean protein decomposition products can be used. When an auxotrophic mutant strain that requires an amino acid or the like for growth is used, the required nutrient can be supplemented. As mineral salts, phosphates, magnesium salts, calcium salts, iron salts, manganese salts and the like can be used.
The culture can be performed as an aeration culture, while the fermentation temperature can be controlled to be 20 to 45° C., and pH to be 3 to 9. When pH drops during the culture, the medium can be neutralized by addition of, for example, calcium carbonate, or with an alkali such as ammonia gas. An acidic amino acid can accumulate in the culture broth, for example, after 10 to 120 hours of culture under such conditions as described above.
When the acidic amino acid is L-glutamic acid, L-glutamic acid can precipitate into the medium by using a liquid medium, the pH of which is adjusted so that L-glutamic acid precipitates. L-glutamic acid precipitates around, for example, pH 5.0 to 4.0, pH 4.5 to 4.0 in another example, pH 4.3 to 4.0 in another example, or pH 4.0 in another example.
After completion of the culture, L-glutamic acid can be collected from the culture medium by any known collection method. For example, after cells are removed from the culture medium, L-glutamic acid can be collected by concentrating the culture medium so it crystallizes, or by ion exchange chromatography, or the like. When the culture is performed so that L-glutamic acid precipitates, the L-glutamic acid that has precipitated in the medium can be collected by centrifugation, filtration, or the like. In this case, it is also possible to crystallize L-glutamic acid that has dissolved in the medium, and then collect the precipitated L-glutamic acid in the culture broth together with the crystallized L-glutamic acid.
<2-2> Production of Organic Acid
An organic acid can be produced by allowing the microorganism, or a product obtained by processing the microorganism, to act on an organic raw material in a reaction mixture containing carbonate ions, bicarbonate ions, or carbon dioxide gas, and collecting the organic acid.
In a first example, by culturing the microorganism in a medium containing carbonate ions, bicarbonate ions, or carbon dioxide gas, and an organic raw material, proliferation of the microorganism and production of the organic acid simultaneously occur. In this example, the medium can be the reaction mixture. Proliferation of the microorganism and production of the organic acid can simultaneously occur, or there can be a period during the culture in which proliferation of the microorganism mainly occurs, and a period in which production of the organic acid mainly occurs.
In a second example, by allowing cells that have proliferated in the medium to coexist with a reaction mixture containing carbonate ions, bicarbonate ions, or carbon dioxide gas, and an organic raw material, and thereby allowing the microorganism to act on the organic raw material in the reaction mixture, an organic acid can be produced. In this example, a product obtained by processing the cells of the microorganism can also be used. Examples of the product obtained by processing cells include, for example, immobilized cells obtained with acrylamide, carragheenan, or the like, a disrupted cellular product, a centrifugation supernatant of the disrupted product, a fraction obtained by partial purification of the supernatant by ammonium sulfate treatment or the like, and the like.
Although the bacteria can be obtained on a solid medium such as an agar medium by slant culture, bacteria previously cultured in a liquid medium (seed culture) are examples.
A medium usually used for culture of microorganisms can be used. For example, a typical medium obtained by adding natural nutrients such as meat extract, yeast extract and peptone, to a composition comprising inorganic salts such as ammonium sulfate, potassium phosphate and magnesium sulfate can be used.
In the aforementioned first example, the carbon source added to the medium also serves as the organic raw material for the production of the organic acid.
In the aforementioned second example, the cells after the culture are collected by centrifugation, membrane separation, or the like, and used for the organic acid production reaction.
The organic raw material is not particularly limited so long as the chosen microorganism can assimilate it to produce succinic acid. However, fermentable carbohydrates including carbohydrates such as galactose, lactose, glucose, fructose, glycerol, sucrose, saccharose, starch and cellulose, polyalcohols such as glycerin, mannitol, xylitol and ribitol, and the like are typically used. Glucose, fructose and glycerol are examples, and glucose is a particular example. When the organic acid is succinic acid, fumaric acid or the like can be added in order to efficiently produce succinic acid as described in Japanese Patent Laid-open No. 5-68576, and malic acid can be added instead of fumaric acid.
Furthermore, a saccharified starch solution, molasses, or the like containing the aforementioned fermentable carbohydrates can also be used. The fermentable carbohydrates can be used independently or in combination. Although concentration of the aforementioned organic raw material is not particularly limited, it is more advantageous that the concentration is as high as possible and within such a range that the culture of the microorganism and production of the organic acid are not inhibited. In the aforementioned first example, the concentration of the organic raw material in the medium is generally in the range of 5 to 30% (w/v), or 10 to 20% (w/v) in another example. Furthermore, in the aforementioned second example, the concentration of the organic raw material in the reaction mixture is generally in the range of 5 to 30% (w/v), or 10 to 20% (w/v) in another example. Furthermore, it may be necessary to add additional organic raw material as the concentration of the organic raw material decreases with the progress of the culture or reaction.
The aforementioned reaction mixture containing carbonate ions, bicarbonate ions, or carbon dioxide gas and the organic raw material is not particularly limited, and it can be, for example, a typical medium for culturing microorganisms, or it can be a buffer such as phosphate buffer. The reaction mixture can be an aqueous solution containing a nitrogen source, inorganic salts, and the like. The nitrogen source is not particularly limited so long the chosen microorganism can assimilate it to produce an organic acid, and specific examples include various organic or inorganic nitrogen compounds such as ammonium salts, nitrates, urea, soybean hydrolysate, casein degradation products, peptone, yeast extract, meat extract, and corn steep liquor. Examples of the inorganic salts include various phosphates, sulfates, and metallic salts such as those of magnesium, potassium, manganese, iron, and zinc. If necessary, growth-promoting factors including vitamins such as biotin, pantothenic acid, inositol, and nicotinic acid, nucleotides, amino acids and the like can be added. In order to suppress foaming during the reaction, an appropriate amount of a commercially available antifoam can be added to the medium.
The pH of the reaction mixture can be adjusted by adding sodium carbonate, sodium bicarbonate, potassium carbonate, potassium bicarbonate, magnesium carbonate, sodium hydroxide, calcium hydroxide, magnesium hydroxide, or the like. Since the pH for the reaction is usually 5 to 10, or 6 to 9.5 in another example, the pH of the reaction mixture can be adjusted to be within the aforementioned range with an alkaline substance, carbonate, urea, or the like, even during the reaction, if needed.
Water, buffer, medium or the like can be used as the reaction mixture, but a medium is a particular example. The medium can contain, for example, the aforementioned organic raw material, and carbonate ions, bicarbonate ions, or carbon dioxide gas, and the reaction can be performed under anaerobic conditions. Magnesium carbonate, sodium carbonate, sodium bicarbonate, potassium carbonate, or potassium bicarbonate can be the source of the carbonate or bicarbonate ions, and these can also be used as a neutralizing agent. However, if necessary, carbonate or bicarbonate ions can also be supplied from carbonic acid or bicarbonic acid or salts thereof or carbon dioxide gas. Specific examples of salts of carbonic acid or bicarbonic acid include, for example, magnesium carbonate, ammonium carbonate, sodium carbonate, potassium carbonate, ammonium bicarbonate, sodium bicarbonate, potassium bicarbonate, and the like. Carbonate ions or bicarbonate ions can be added at a concentration of 0.001 to 5 M, 0.1 to 3 M in another example, or 1 to 2 M in another example. When carbon dioxide gas is present, it can be in an amount of 50 mg to 25 g, 100 mg to 15 g in another example, or 150 mg to 10 g in another example, per liter of the solution.
The optimal growth temperature of the chosen microorganism is generally in the range of 25 to 40° C. Therefore, the reaction temperature is generally in the range of 25 to 40° C., or in the range of 30 to 37° C. in another example. The amount of bacterial cells in the reaction mixture is, although it is not particularly limited, 1 to 700 g/L, 10 to 500 g/L in another example, or 20 to 400 g/L in another example. The reaction time can be 1 to 168 hours, or 3 to 72 hours in another example. The reaction can be performed batchwise or on a column.
The culture of the bacteria can be performed under aerobic conditions. On the other hand, the organic acid production reaction can be performed under aerobic conditions, microaerobic conditions, or anaerobic conditions. When performed under microaerobic conditions or anaerobic conditions, the reaction can be performed in a sealed reaction vessel without aeration, with a supplied inert gas such as nitrogen gas, or with a supplied inert gas containing carbon dioxide gas, and the like.
The organic acid can accumulate in the reaction mixture (culture medium) and can be separated and purified from the reaction mixture in a conventional manner. Specifically, solids such as bacterial cells can be removed by centrifugation, filtration, or the like, then the resulting solution can be desalted with an ion exchange resin or the like, and the organic acid can be separated and purified from the solution by crystallization or column chromatography.
Furthermore, when the target organic acid is succinic acid, and after the production, a polymerization reaction can be carried out by using the produced succinic acid as a raw material to produce a polymer containing succinic acid. In recent years, with the increase of environmentally friendly industrial products, polymers prepared from raw materials of plant origin have been attracting attention. The produced succinic acid can be converted into polymers such as polyesters and polyamides and used (Japanese Patent Laid-open No. 4-189822). Specific examples of succinic acid-containing polymers include succinic acid polyesters obtained by polymerizing a diol such as butanediol and ethylene glycol and succinic acid, succinic acid polyamides obtained by polymerizing a diamine such as hexamethylenediamine and succinic acid, and the like. In addition, succinic acid and succinic acid-containing polymers obtained by the production method described herein, and compositions containing these can be used for food additives, pharmaceutical agents, cosmetics, and the like.
EXAMPLESHereinafter, the present invention will be explained more specifically with reference to the following non-limiting examples.
Reference Example 1: Construction of Pantoea ananatis Strain Resistant to λ Red Gene ProductIn order to disrupt the sdhA gene in Pantoea ananatis, a recipient strain for efficiently carrying out the method called “Red-driven integration” or “Red-mediated integration” (Datsenko, K A. and Wanner, B. L., 2000, Proc. Natl. Acad. Sci. USA., 97, 6640-6645) was constructed.
First, the novel helper plasmid RSF-Red-TER which expresses the gam, bet and exo genes of λ (“λ Red genes”) was constructed (
This plasmid can be used in a wide range of hosts having different genetic backgrounds. This is because 1) this plasmid has the replicon of the RSF1010 wide host spectrum plasmid (Scholz, et al., 1989, Gene, 75:271-288; Buchanan-Wollaston et al., 1987, Nature, 328:172-175), which is stably maintained by many types of gram negative and gram positive bacteria, and even plant cells, 2) the λ Red genes, gam, bet and exo, are under the control of the PlacUV5 promoter, which is recognized by the RNA polymerases of many types of bacteria (for example, Brunschwig, E. and Darzins, A., 1992, Gene, 111, 1, 35-41; Dehio, M. et al, 1998, Gene, 215, 2, 223-229), and 3) the autoregulation factor PlacUV5-lacI and the p-non-dependent transcription terminator (TrrnB) of the rrnB operon of Escherichia coli lower the basal expression level of the λ Red genes (Skorokhodova, A. Y. et al, 2004, Biotekhnologiya (Rus), 5, 3-21). Furthermore, the RSF-Red-TER plasmid contains the levansucrase gene (sacB), and by the expression of this gene, the plasmid can be collected from cells in a medium containing sucrose.
In Escherichia coli, the frequency of integration of a PCR-generated DNA fragment along with the short flanking region provided by the RSF-Red-TER plasmid is as high as the frequency obtained when using the pKD46 helper plasmid (Datsenko, K. A., Wanner, B. L., 2000, Proc. Natl. Acad. Sci. USA, 97, 6640-6645). However, expression of the λ Red genes is toxic to Pantoea ananatis. Cells transformed with the RSF-Red-TER helper plasmid grow extremely slowly in LB medium containing IPTG (isopropyl-β-D-thiogalactopyranoside, 1 mM) and an appropriate antibiotic (25 μg/ml of chloramphenicol or 40 μg/ml of kanamycin), and the efficiency of λ Red-mediated recombination is extremely low (10−8), if observed at all.
A variant strain of Pantoea ananatis which is resistant to expression of all three of the λ Red genes was selected. For this purpose, the RSF-Red-TER plasmid was introduced into the Pantoea ananatis SC17 strain (U.S. Pat. No. 6,596,517) by electroporation. After an 18-hour culture, about 106 transformants were obtained, and among these, 10 clones formed colonies of a large size, and the remainder formed extremely small colonies. After an 18 hour culture, the large colonies were about 2 mm, and the small colonies were about 0.2 mm. While the small colonies did not grow any more even when the culture was extended up to 24 hours, the large colonies continued to grow. One of the large colony Pantoea ananatis mutant strains which was resistant to expression of all three of the λ Red genes (gam, bet, and exo) was used for further analysis.
The RSF-Red-TER plasmid DNA was isolated from one clone of the large colony clones, and from several clones of the small colony clones, and transformed again into Escherichia coli MG1655 to examine the ability of the plasmid to synthesize an active Red gene product. A control experiment for Red-dependent integration in the obtained transformants was used to demonstrate that only the plasmid isolated from the large colony clone induced expression of the λ Red genes required for the Red-dependent integration. In order to investigate whether the Red-mediated integration occurs in the selected large colony clone, electroporation was performed using a linear DNA fragment produced by PCR. This fragment was designed so that it contains a KmR marker and a flanking region of 40 bp homologous to the hisD gene, and is integrated into the hisD gene of Pantoea ananatis at the SmaI recognition site. Two small colony clones were used as control. The nucleotide sequence of the hisD gene of Pantoea ananatis is shown in SEQ ID NO: 40. For PCR, the oligonucleotides of SEQ ID NOS: 41 and 42 were used as primers, and the pMW118-(λatt-Kmr-λatt) plasmid was used as the template. The two small colony clones which were not resistant to the λ Red genes were used as the control. Construction of the pMW118-(λattL-Kmr-λattR) plasmid will be explained in detail in Reference Example 3.
The RSF-Red-TER plasmid can induce expression of the Red genes by the lacI gene carried on the plasmid. Two kinds of induction conditions were investigated. In the first group, IPTG (1 mM) was added 1 hour before the electroporation, and in the second group, IPTG was added at the start of the culture to prepare cells in which electroporation is possible. The growth rate of the progeny of the SC17 strain harboring RSF-Red-TER derived from the large colony clone was not significantly lower than that of a strain not having the RSF-Red-TER plasmid. The addition of IPTG only slightly decreased the growth rate of these cultures. On the other hand, the RSF-Red-TER-introduced SC17 strain derived from the progeny of the small colony clones grew extremely slowly even without the addition of IPTG, and after induction, growth was substantially arrested. After electroporation of RSF-Red-TER isolated from the cells of the progeny of the large colony clone, many KmR clones grew (18 clones after a short induction time, and about 100 clones after an extended induction time). All of the 100 clones that were investigated had a His− phenotype, and about 20 clones were confirmed by PCR to have the expected structure of the chromosome in the cells. On the other hand, even when electroporation was performed with RSF-Red-TER isolated from cells of the progeny of the small colony clones, an integrated strain was not obtained.
The large colony clone was grown on a plate containing 7% sucrose to eliminate the plasmid, and transformed again with RSF-Red-TER. The strain without the plasmid was designated SC17(0). This strain was deposited at the Russian National Collection of Industrial Microorganisms (VKPM), GNII Genetica (Address: 1 Dorozhny proezd., 1 Moscow 117545, Russia) on Sep. 21, 2005, and assigned an accession number of VKPM B-9246.
All the clones which grew after the aforementioned re-transformation were large like the parent strain clone SC17(0). The Red-mediated integration experiment was performed in the SC17(0) strain which had been re-transformed with the RSF-Red-TER plasmid. Three of the independent transformants obtained were investigated using the same DNA fragment as that used for the previous experiment. A short induction time (1 hour before electroporation) was employed. KmR clones exceeding ten clones grew in each experiment. All the examined clones had the His− phenotype. In this way, a mutant strain designated SC17(0) which is resistant to the expression of the λ Red genes was selected. This strain can be used as a recipient strain suitable for the Red-dependent integration into the Pantoea ananatis chromosome.
Reference Example 2: Construction of Helper Plasmid RSF-Red-TERThe scheme for constructing the helper plasmid RSF-Red-TER is shown in
As the first step in the construction, an RSFsacBPlacMCS vector was designed. For this purpose, DNA fragments containing the cat gene of the pACYC184 plasmid and the structural region of the sacB gene of Bacillus subtilis were amplified by PCR using the oligonucleotides of SEQ ID NOS: 43 and 44, and 45 and 46, respectively. These oligonucleotides contained the BglII, SacI, XbaI and BamHI restriction enzyme sites in the 5′ end regions. These sites are required and convenient for further cloning. The obtained sacB fragment of 1.5 kb was cloned into the previously obtained pMW119-PlaclacI vector at the XbaI-BamHI site. This vector was constructed in the same manner as that described for the pMW118-PlaclacI vector (Skorokhodova, A. Y. et al, 2004, Biotekhnologiya (Rus), 5:3-21). However, this vector contained a polylinker moiety derived from pMW219 instead of the pMW218 plasmid.
Then, the aforementioned cat fragment of 1.0 kb was treated with BglII and SacI, and cloned into the RSF-PlaclacIsacB plasmid obtained in the previous step at the BamHI-SacI site. The obtained plasmid pMW-PlaclacIsacBcat contained the PlacUV5-lacI-sacB-cat fragment. In order to subclone this fragment into the RSF1010 vector, pMW-PlaclacIsacBcat was digested with BglII, blunt-ended with DNA polymerase I Klenow fragment, and successively digested with SacI. A 3.8 kb BglII-SacI fragment of the pMWPlaclacIsacBcat plasmid was eluted from a 1% agarose gel, and ligated with the RSF1010 vector which had been treated with PstI and SacI. Escherichia coli TG1 was transformed with the ligation mixture, and plated on the LB medium containing chloramphenicol (50 mg/L). The plasmids isolated from the grown clones were analyzed with restriction enzymes to obtain an RSFsacB plasmid. In order to construct an RSFsacBPlacMCS vector, a DNA fragment containing the PlacUV5 promoter was amplified by PCR using the oligonucleotides of SEQ ID NOS: 47 and 48 as primers and the pMW119-PlaclacI plasmid as a template. The obtained fragment of 146 bp was digested with SacI and NotI, and ligated with the SacI-NotI large fragment of the RSFsacB plasmid. Then, by PCR using the oligonucleotides of SEQ ID NOS: 49 and 50 as primers, and the pKD46 plasmid (Datsenko, K. A., Wanner, B. L., 2000, Proc. Natl. Acad. Sci. USA, 97, 6640-6645) as a template, a DNA fragment of 2.3 kb containing the λRedαβγ genes and the transcription terminator tL3 was amplified. The obtained fragment was cloned into the RSFsacBPlacMCS vector at the PvuI-NotI site. In this way, the RSFRed plasmid was designed.
In order to eliminate read through transcription of the Red genes, a ρ-dependent transcription terminator of the rrnB operon of Escherichia coli was inserted at a position between the cat gene and the PlacUV5 promoter. For this purpose, a DNA fragment containing the PlacUV5 promoter and the TrrnB terminator was amplified by PCR using the oligonucleotides of SEQ ID NOS: 51 and 48 as primers and the chromosome of Escherichia coli BW3350 as the template. These obtained fragments were treated with KpnI and ligated. Then, the 0.5 kb fragment containing both PlacUV5 and TrrnB was amplified by PCR using the oligonucleotides of SEQ ID NOS: 48 and 52 as primers. The obtained DNA fragment was digested with EcoRI, blunt-ended by a treatment with DNA polymerase I Klenow fragment, digested with BamHI, and ligated with the Ecl136II-BamHI large fragment of the RSFsacBPlacMCS vector. The obtained plasmid was designated RSF-Red-TER.
Reference Example 3: Construction of the pMW118-(λattL-Kmr-λattR) plasmidThe pMW118-(λattL-Kmr-λattR) plasmid was constructed from the pMW118-attL-Tc-attR (WO2005/010175) plasmid by replacing the tetracycline resistance marker gene with the kanamycin resistance gene of the pUC4K plasmid. For that purpose, the EcoRI-HindIII large fragment from pMW118-attL-Tc-attR was ligated to two fragments from the pUC4K plasmid: the HindIII-PstI fragment (676 bp) and EcoRI-HindIII fragment (585 bp). Basic pMW118-attL-Tc-attR was obtained by ligation of the following four fragments.
1) The BglII-EcoRI fragment (114 bp) including attL (SEQ ID NO: 55) which was obtained by PCR amplification of the region corresponding to attL of the Escherichia coli W3350 (containing λ prophage) chromosome using the primers P1 and P2 (SEQ ID NOS: 53 and 54) (these primers contained the subsidiary recognition sites for B gill and EcoRI).
2) The PstI-HindIII fragment (182 bp) including attR (SEQ ID NO: 58) which was obtained by PCR amplification of the region corresponding to attR of the Escherichia coli W3350 (containing λ prophage) chromosome using the primers P3 and P4 (SEQ ID NOS: 56 and 57) (these primers contained the subsidiary recognition sites for PstI and HindIII).
3) The BglII-HindIII large fragment (3916 bp) of pMW118-ter_rrnB. The plasmid pMW118-ter_rrnB was obtained by ligation of the following three DNA fragments:
The large DNA fragment (2359 bp) including the AatII-EcoRI fragment of pMW118 that was obtained by digesting pMW118 with EcoRI, treated with DNA polymerase I Klenow fragment, and then digested with AatII;
The small AatII-BglII fragment (1194 bp) of pUC19 including the bla gene for ampicillin resistance (ApR), which was obtained by PCR amplification of the corresponding region of the pUC19 plasmid using the primers P5 and P6 (SEQ ID NOS: 59 and 60) (these primers contained the subsidiary recognition sites for PstI, AatII and BglII);
The small BglII-PstI fragment (363 bp) of the transcription terminator ter_rrnB, which was obtained by PCR amplification of the corresponding region of the Escherichia coli MG1655 chromosome using the primers P7 and P8 (SEQ ID NOS: 61 and 62) (these primers contained the subsidiary recognition sites for PstI, BglII and PstI).
4) The small EcoRI-PstI fragment (1388 bp) (SEQ ID NO: 63) of pML-Tc-ter_thrL including the tetracycline resistance gene and the ter_thrL transcription terminator; the pML-Tc-ter_thrL plasmid was obtained by the following two steps:
the pML-ter_thrL plasmid was obtained by digesting the pML-MCS plasmid (Mashko, S. V. et al., 2001, Biotekhnologiya (in Russian), no. 5, 3-20) with XbaI and BamHI, followed by ligation of the large fragment (3342 bp) with the XbaI-BamHI fragment (68 bp) carrying ter_thrL terminator obtained by PCR amplification of the corresponding region of the Escherichia coli MG1655 chromosome using the primers P9 and P10 (SEQ ID NOS: 64 and 65) (these primers contained the subsidiary recognition sites for PstI, XbaI and BamHI);
the pML-Tc-ter_thrL plasmid was obtained by digesting the pML-ter_thrL plasmid with KpnI and XbaI followed by treatment with Klenow fragment of DNA polymerase I and ligated with the small EcoRI-Van91I fragment (1317 bp) of pBR322 including the tetracycline resistance gene (pBR322 was digested with EcoRI and Van91I and then treated with DNA polymerase I Klenow fragment).
Example 1: Search of L-Glutamic Acid Secretion GeneA search for an L-glutamic acid secretion gene was performed as follows. Since L-glutamic acid is converted into an intermediate of the tricarboxylic acid cycle, 2-oxoglutarate, in one step by glutamate dehydrogenase, L-glutamic acid is thought to be easily metabolized in many microorganisms having glutamate dehydrogenase or the tricarboxylic acid cycle. However, since a strain in which 2-oxoglutarate dehydrogenase is deleted cannot degrade L-glutamic acid, growth of the cells is inhibited in the presence of a high concentration glutamic acid. In this example, the SC17sucAams strain derived from the Pantoea ananatis SC17sucA strain (refer to Japanese Patent Laid-open No. 2001-333769) is deficient in the extracellular polysaccharide biosynthesis system, and is also deficient in 2-oxoglutarate dehydrogenase. Therefore, this strain was used to try to obtain an L-glutamic acid excretion gene utilizing resistance to a high concentration of L-glutamic acid as a marker.
Since the SC17sucA strain produced a marked amount of extracellular polysaccharides when grown on an agar medium containing a sugar source, the handling of this strain is extremely difficult. Therefore, by deleting the ams operon coding for the extracellular polysaccharide biosynthesis system genes, production of extracellular polysaccharides was suppressed. PCR was performed by using pMW118-λattL-Kmr-λattR as the template and the primers of SEQ ID NOS: 6 and 7 to amplify a gene fragment containing a kanamycin resistance gene, attL and attR sequences of λ phage at the both ends of the resistance gene, and 50 bp upstream sequence of amsI and 50 bp downstream sequence of the amsC gene added to the outer ends of the λ phage sequences. This fragment was purified by using Wizard PCR Prep DNA Purification System (Promega).
Then, the SC17(0) strain was transformed with RSF-Red-TER to obtain an SC17(0)/RSF-Red-TER strain. This strain was cultured overnight in L medium (10 g of Bacto tryptone, 5 g of yeast extract and 5 g of NaCl in 1 L of pure water, pH 7.0) containing 25 mg/L of chloramphenicol, and then the culture medium after the overnight culture was inoculated in 1/100 volume into 100 mL of the L medium containing 25 mg/L of chloramphenicol and 1 mM isopropyl-β-D-thiogalactopyranoside, and culture was performed at 34° C. for 3 hours. The cells prepared as described above were collected, washed three times with ice-cooled 10% glycerol, and finally suspended in 0.5 mL of 10% glycerol. The suspended cells were used as competent cells, and 100 ng of the PCR fragment prepared in the above section was introduced into the cells by using GENE PULSER II (BioRad) with a field strength of 18 kV/cm, capacitor capacity of 25 and resistance of 200Ω. Ice-cooled SOC medium (20 g/L of Bacto tryptone, 5 g/L of yeast extract, 0.5 g/L of NaCl, and 10 g/L of glucose) was added to the cell suspension, and culture was performed at 34° C. for 2 hours with shaking. The culture was applied to a medium prepared by adding ingredients of minimal medium (5 g of glucose, 2 mM magnesium sulfate, 3 g of monopotassium phosphate, 0.5 g of sodium chloride, 1 g of ammonium chloride and 6 g of disodium phosphate in 1 L) and 40 mg/L of kanamycin to the L medium (10 g of Bacto tryptone, 5 g of yeast extract, 5 g of NaCl and 15 g of agar in 1 L of pure water, pH 7.0). The colonies that appeared were purified with the same medium, and then it was confirmed by PCR that the ams gene had been replaced with the kanamycin resistance gene.
The chromosome was extracted from the ams gene-deficient strain using a Bacterial Genomic DNA Purification Kit (Edge Biosystems). Separately, the SC17sucA strain was cultured overnight on an agar medium obtained by adding the ingredients of the minimal medium described above to the L medium. The cells were scraped with a loop, washed three times with ice-cooled 10% glycerol, and finally suspended in 10% glycerol to a final volume of 500 μL. The suspended cells were used as competent cells, and 600 ng of the aforementioned chromosome DNA was introduced into the competent cells using GENE PULSER II (BioRad) with a field strength of 17.5 kV/cm, capacitor capacity of 25 μF and resistance of 200Ω. Ice-cooled SOC medium was added to the cell suspension, and culture was performed at 34° C. for 2 hours with shaking. Then, the culture was applied on an agar medium prepared by adding ingredients of the minimal medium described above and 40 mg/L of kanamycin to the L medium. The colonies that appeared were purified with the same medium, and then it was confirmed by PCR that the ams gene had been replaced with the kanamycin resistance gene. This strain was designated as SC17sucAams.
Chromosomal DNA extracted from the Pantoea ananatis AJ13355 strain was partially digested with the restriction enzyme Sau3AI. Then, fragments of about 10 kb were collected and introduced into the BamHI site of pSTV28 (Takara Bio) to prepare a plasmid library. This plasmid library was introduced into competent cells of the SC17sucAams strain prepared in a conventional manner by electroporation.
Selection was performed for the SC17sucAams strain which had been introduced with a plasmid library on a plate of the L medium (10 g of Bacto tryptone, 5 g of yeast extract, 5 g of NaCl and 15 g of agar in 1 L of pure water, pH 7.0) added with ingredients of minimal medium (5 g of glucose, 2 mM magnesium sulfate, 3 g of monopotassium phosphate, 0.5 g of sodium chloride, 1 g of ammonium chloride and 6 g of disodium phosphate in 1 L of pure water) using chloramphenicol resistance as a marker to obtain transformants. These transformants were plated on a glucose minimal medium containing a high concentration L-glutamic acid (the glucose minimal medium mixed with 0.2 M L-glutamic acid, 100 mg/L each of lysine, methionine and diaminopimelic acid as final concentrations), in which SC17sucAams cannot form colonies.
The transformants were cultured at 34° C. for 3 days, and 64 clones among the colonies that appeared were allowed to again form single colonies on the same plate. As a result, 11 clones were found to form colonies after 48 hours, and the remaining colonies formed colonies after 72 hours.
Then, the genes inserted into the vectors harbored by the transformants were analyzed. Plasmids were extracted from the transformants, and nucleotide sequences were determined. It was found that among the 11 clones that formed colonies within 48 hours, 10 clones had the same loci, and all contained genes showing homology to ybjL, which was an Escherichia coli gene of unknown function. In addition, this ybjL gene could not be obtained under the same conditions that the glutamic acid secretion system gene described in WO2005/085419, yhfK, was obtained, and conversely, the yhfK gene could not be obtained under the selection conditions used in this example.
In order to confirm that the factor which imparts glutamic acid resistance is ybjL, the ybjL gene was cloned. PCR was performed using the chromosomal DNA of AJ13355 strain as the template and oligonucleotides ybjL-F1 and ybjL-R2 shown in SEQ ID NOS: 8 and 9 to amplify the fragment of about 1.8 kb containing the ybjL gene of P. ananatis. This fragment was purified using Wizard PCR Prep DNA Purification System (Promega), and then treated with the restriction enzymes KpnI and SphI, and the product was ligated with pSTV28 (Takara Bio) which had been treated with the same enzymes to obtain pSTV-PanybjL. The SC17sucA strain was transformed with this pSTV-PanybjL plasmid, and using pSTV28 as a control for comparison (Takara Bio) to construct the SC17sucA/pSTV-PanybjL and SC17sucA/pSTV28 strains.
The SC17sucA/pSTV-ybjL strain was plated on minimal medium (5 g of glucose or sucrose, 2 mM magnesium sulfate, 3 g of monopotassium phosphate, 0.5 g of sodium chloride, 1 g of ammonium chloride, 6 g of disodium phosphate, 0.2 M sodium L-glutamate, 100 mg/L each of lysine, methionine and diaminopimelic acid and 15 g of agar in 1 L of pure water) containing glutamic acid. Culture was performed at 34° C. for 2 days. As a result, it was confirmed that whereas the control vector-introduced strain, SC17sucA/pSTV28, could not form colonies, SC17sucA/pSTV-ybjL could form colonies on the minimal medium.
Then, the SC17sucA/pSTV-PanybjL strain was cultured in liquid minimal medium (5 g of glucose, 2 mM magnesium sulfate, 3 g of monopotassium phosphate, 0.5 g of sodium chloride, 1 g of ammonium chloride, 6 g of disodium phosphate, 0.2 M sodium L-glutamate, 100 mg/L each of lysine, methionine and diaminopimelic acid in 1 L of pure water) containing glutamic acid to examine growth of the strain in the presence of a high concentration of L-glutamic acid.
The results are shown in
Then, in order to examine the effect of this gene on L-glutamic acid production, the plasmid for ybjL amplification, pSTV-PanybjL, was introduced into the L-glutamic acid producing bacterium SC17sucA/RSFCPG having the plasmid for L-glutamic acid production, RSFCPG, shown in SEQ ID NO: 10 (refer to Japanese Patent Laid-open No. 2001-333769), and L-glutamic acid productivity thereof was examined.
pSTV-PanybjL and the control plasmid, pSTV28 (Takara Bio), were each introduced into SC17sucA/RSFCPG by electroporation, and transformants were obtained using chloramphenicol resistance as a marker. After confirmation of the presence of the plasmids, the strain with the plasmid for ybjL amplification was designated SC17sucA/RSFCPG+pSTV-PanybjL, and the strain with pSTV29 was designated SC17sucA/RSFCPG+pSTV28.
Then, SC17sucA/RSFCPG+pSTV-PanybjL and the control strain SC17sucA/RSFCPG+pSTV28 were cultured to examine the L-glutamic acid producing ability of the strains. The medium had the following composition:
Composition of Culture Medium:
Section A:
Group B:
(adjusted to pH 7.0 with KOH)
Group C:
The ingredients of groups A and B were sterilized at 115° C. for 10 minutes by autoclaving, and the ingredient of group C was sterilized at 180° C. for 3 hours with dry heat. Then, the ingredients of the three groups were mixed, and 12.5 mg/L of tetracycline hydrochloride and 25 mg/L of chloramphenicol were added to the mixture.
SC17sucA/RSFCPG+pSTV29 and SC17sucA/RSFCPG+pSTV-PanybjL were each precultured on a medium obtained by adding ingredients of the minimal medium (medium containing 5 g of glucose, 2 mM magnesium sulfate, 3 g of monopotassium phosphate, 0.5 g of sodium chloride, 1 g of ammonium chloride and 6 g of disodium phosphate in 1 L of pure water), 25 mg/L of chloramphenicol and 12.5 mg/L tetracycline to the L medium (medium containing 10 g of Bacto tryptone, 5 g of yeast extract, 5 g of NaCl and 15 g of agar in 1 L of pure water, pH 7.0), and inoculated into an appropriate amount to 5 ml of the aforementioned medium in a test tube.
The cells were cultured for 17.5 hours, and then cell density, L-glutamic acid concentration, and the amount of residual saccharide in the culture medium were measured. The cell density was examined by measuring turbidity at 620 nm of the medium diluted 51 times using a spectrophotometer (U-2000A, Hitachi). The L-glutamic acid concentration was measured in culture supernatant appropriately diluted with water by using Biotech Analyzer (AS-210, Sakera SI). The results are shown in Table 1. L-Glutamic acid accumulation was increased by about 3 g/L, and the yield based on saccharide increased by about 9% in the ybjL-amplified strain, SC17sucA/RSFCPG+pSTV-PanybjL, as compared to the control strain, SC17sucA/RSFCPG+pSTV28.
Then, the ybjL gene from Escherichia coli was introduced into the Pantoea ananatis SC17sucA/RSFCPG strain, and the effect of this amplification on glutamic acid production was examined.
PCR was performed using the oligonucleotides shown in SEQ ID NOS: 11 and 12 prepared on the basis of the sequence of the ybjL of Escherichia coli registered at GeneBank as AP009048 (SEQ ID NO: 3) and the chromosome from the Escherichia coli W3110 strain (ATCC 27325) as the template to obtain a fragment of about 1.7 kb containing the ybjL gene. This fragment was treated with SphI and KpnI, and ligated with pSTV28 (Takara Bio) at the corresponding site. The plasmid for amplification of ybjL of Escherichia coli was designated as pSTV-EcoybjL.
The plasmid pSTV-EcoybjL for ybjL amplification was introduced into the aforementioned SC17sucA/RSFCPG strain by electroporation, and a transformant was obtained using chloramphenicol resistance as a marker. The obtained Escherichia coli ybjL gene-amplified strain was designated as SC17sucA/RSFCPG+pSTV-EcoybjL.
Then, SC17sucA/RSFCPG+pSTV-EcoybjL and the control strain, SC17sucA/RSFCPG+pSTV28, were cultured to examine their L-glutamic acid producing ability. The medium had the following composition.
Composition of Culture Medium:
Group A:
Group B:
(adjusted to pH 7.0 with KOH)
Group C:
The ingredients of groups A and B were sterilized at 115° C. for 10 minutes by autoclaving, and the ingredient of group C was sterilized at 180° C. for 3 hours with dry heat. Then, the ingredients of the three groups were mixed, and 12.5 mg/L of tetracycline hydrochloride and 25 mg/L of chloramphenicol were added to the mixture.
SC17sucA/RSFCPG+pSTV28 and SC17sucA/RSFCPG+pSTV-EcoybjL were each precultured on a medium obtained by adding ingredients of the minimal medium (5 g of glucose, 2 mM magnesium sulfate, 3 g of monopotassium phosphate, 0.5 g of sodium chloride, 1 g of ammonium chloride and 6 g of disodium phosphate in 1 L of pure water), 25 mg/L of chloramphenicol, and 12.5 mg/L tetracycline to the L medium (10 g of Bacto tryptone, 5 g of yeast extract, 5 g of NaCl and 15 g of agar in 1 L of pure water, pH 7.0), and inoculated in an appropriate amount to 5 ml of the aforementioned medium in a test tube.
The cells were cultured for 17.5 hours, and then cell density and L-glutamic acid concentration in the culture medium were measured in the same manner as shown in Example 2. The results are shown in Table 2. L-Glutamic acid accumulation was increased by about 2 g/L, and the yield based on saccharide increased by about 7% in the ybjL-amplified strain, SC17sucA/RSFCPG+pSTV-EcoybjL, as compared to the control strain, SC17sucA/RSFCPG+pSTV28.
Then, the ybjL gene derived from Pantoea ananatis and the ybjL gene derived from Escherichia coli were each introduced into Escherichia coli, and the effect of the amplification was examined.
The aforementioned vector for amplification of the ybjL gene derived from Pantoea ananatis, pSTV-PanybjL, vector for amplification of ybjL gene derived from Escherichia coli, pSTV-EcoybjL, and the control plasmid pSTV28 were each introduced into an Escherichia coli wild-type strain, W3110, by electroporation to obtain transformants resistant to chloramphenicol. The strain in which ybjL derived from Pantoea ananatis had been amplified was designated W3110/pSTV-PanybjL, the strain in which ybjL derived from Escherichia coli had been amplified was designated W3110/pSTV-EcoybjL, and the control strain with pSTV28 was designated W3110/pSTV28.
Then, the ability to produce L-glutamic acid of the ybjL-amplified strains, W3110/pSTV-PanybjL and W3110/pSTV-EcoybjL, and the control strain W3110/pSTV28 were examined. W3110/pSTV-PanybjL, W3110/pSTV-EcoybjL, and W3110/pSTV28 were each precultured on L medium (10 g of Bacto tryptone, 5 g of yeast extract, 5 g of NaCl and 15 g of agar in 1 L of pure water, pH 7.0) containing chloramphenicol, and one loop of cells were inoculated by using a 1-mL volume loop (Nunc) to 5 mL of a medium having the following composition in a test tube, and cultured at 37° C. for 11.5 hours with shaking. Cell density and L-glutamic acid concentration in the culture medium were measured in the same manners as those in Example 2. The results are shown in Table 3.
Composition of Culture Medium:
Group A:
Group B:
(adjusted to pH 7.0 with KOH)
Group C:
The ingredients of groups A and B were sterilized at 115° C. for 10 minutes by autoclaving, and the ingredient of group C was sterilized at 180° C. for 3 hours with dry heat. Then, the ingredients of the three groups were mixed, and 25 mg/L of chloramphenicol was added to the mixture.
The L-glutamic acid producing ability was markedly improved in the Escherichia coli W3110/pSTV-PanybjL strain, which is a Pantoea ananatis in which the ybjL gene has been amplified, and the Escherichia coli W3110/pSTV-EcoybjL strain, which is an Escherichia coli in which the ybjL gene has been amplified, as compared to the the control strain W3110/pSTV28 strain.
Then, the ability of the ybjL-amplified strain to produce other amino acids was examined. W3110/pSTV-PanybjL, and the control strain W3110/pSTV28 were precultured in L medium (10 g of Bacto tryptone, 5 g of yeast extract, 5 g of NaCl and 15 g of agar in 1 L of pure water, pH 7.0) containing chloramphenicol, and one loop of cells were inoculated by using a 5-mL volume loop (Nunc) to 5 mL of a medium having the following composition in a test tube, and cultured at 37° C. for 7 hours with shaking. Cell densities and L-amino acid concentrations in the culture medium were measured in the same manner as in Example 2. The results are shown in Table 4.
Composition of Culture Medium:
Group A:
Group B:
(adjusted to pH 7.0 with KOH)
Group C:
The ingredients of groups A and B were sterilized at 115° C. for 10 minutes by autoclaving, and the ingredient of group C was sterilized at 180° C. for 3 hours with dry heat. Then, the ingredients of the three groups were mixed, and 25 mg/L of chloramphenicol was added to the mixture.
Not only did the amount of L-glutamic acid increase, but the L-aspartic acid amount also increased in the Escherichia coli W3110/pSTV-PanybjL, which is a ybjL gene-amplified strain, as compared to the vector-introduced control strain, W3110/pSTV28 strain.
Example 5: Effect of Amplification of the ybjL Gene on L-Glutamic Acid Production in Klebsiella planticolaThe ybjL gene derived from Pantoea ananatis was introduced into Klebsiella planticola, and the effect of the amplification of the gene was examined.
The aforementioned vector for amplification of ybjL gene derived from Pantoea ananatis, pSTV-PanybjL, and the control plasmid pSTV28 were each introduced into a Klebsiella planticola L-glutamic acid-producing strain, AJ13410 (Japanese Patent Application No. 11-68324), by electroporation to obtain transformants which are resistant to chloramphenicol. The strain in which ybjL derived from Pantoea ananatis had been amplified was designated as AJ13410/pSTV-PanybjL, and the control strain with pSTV28 was designated as AJ13410/pSTV28.
Then, the ability to produce L-glutamic acid of the ybjL-amplified strain, AJ13410/pSTV-PanybjL, and the control strain AJ13410/pSTV28 were examined. AJ13410/pSTV-PanybjL and AJ13410/pSTV28 were precultured on L medium (10 g of Bacto tryptone, 5 g of yeast extract, 5 g of NaCl and 15 g of agar in 1 L of pure water, pH 7.0) containing chloramphenicol, and one loop of cells were inoculated by using a 1-mL volume loop (Nunc) to 5 mL of a medium having the following composition in a test tube, and cultured at 37° C. for 17 hours with shaking. Cell density and L-glutamic acid concentration in the culture medium were measured in the same manner as in Example 2. The results are shown in Table 5.
Composition of Culture Medium:
Group A:
Group B:
(adjusted to pH 7.0 with KOH)
Group C:
The ingredients of groups A and B were sterilized at 115° C. for 10 minutes by autoclaving, and the ingredient of group C was sterilized at 180° C. for 3 hours with dry heat. Then, the ingredients of the three groups were mixed, and 25 mg/L of chloramphenicol was added to the mixture.
L-glutamic acid-producing ability was markedly improved in the Klebsiella planticola AJ13410/pSTV-PanybjL, which is a Pantoea ananatis ybjL gene-amplified strain, as compared to the control strain, AJ13410/pSTV28.
Reference Example 4: Construction of an Escherichia coli Strain Deficient in the L,D-Lactate Dehydrogenase GeneThis gene was deleted by using the method called “Red-driven integration” developed by Datsenko and Wanner (Datsenko, K. A. and Wanner, B. L., 2000, Proc. Natl. Acad. Sci. USA, vol. 97, No. 12, pp. 6640-6645), and the λ phage excision system (Cho, E. H., Gumport, R. I., and Gardner, J. F., 2002, J. Bacteriol., 184 (18):5200-5203). According to this method, it is possible to construct a gene-disrupted strain in a single step by using a PCR product obtained with synthetic oligonucleotide primers in which a part of the target gene is designed in the 5′ end and a part of an antibiotic resistance gene is designed in the 3′ end. Furthermore, by using the λ phage excision system in combination, the antibiotic resistance gene which is integrated into the gene-disrupted strain can be removed.
<1-1> Construction of a Strain Deficient in the ldhA Gene Coding for D-Lactate Dehydrogenase
According to the description of WO2005/00175, PCR was performed by using synthetic oligonucleotides having sequences corresponding to parts of the ldhA gene in the 5′ end and sequences corresponding to both ends of att, and altR of λ phage at the 3′ end as primers and plasmid pMW118-attL-Cm-attR as the template. pMW118-attL-Cm-attR is a plasmid obtained by inserting attL and attR genes, which are the attachment sites for λ phage, and the cat gene, which is an antibiotic resistance gene, into pMW118 (Takara Bio), and the genes are inserted in the order of attL-cat-attR. The sequences of the synthetic oligonucleotides used as the primers are shown in SEQ ID Nos. 13 and 14. The amplified PCR product was purified on an agarose gel and introduced into Escherichia coli MG1655 strain containing the plasmid pKD46, which is capable of temperature-sensitive replication by electroporation. Then, an ampicillin-sensitive strain not harboring pKD46 was obtained, and the deletion of the ldhA gene was confirmed by PCR. PCR was performed by using the synthetic oligonucleotides shown in SEQ ID NOS: 15 and 16 as primers. Whereas the PCR product obtained for the parent strain was about 1.2 kb, the deficient strain was about 1.9 kb.
To eliminate the att-cat gene introduced into the ldhA gene, the strain was transformed with helper plasmid pMW-intxis-ts, and an ampicillin resistant strain was selected. The pMW-intxis-ts contains the λ phage integrase (Int) gene and excisionase (Xis) gene and shows temperature-sensitive replication. Then, the strain in which att-cat and pMW-intxis-ts had been eliminated was confirmed by PCR on the basis of ampicillin sensitivity and chloramphenicol sensitivity. PCR was performed by using the synthetic oligonucleotides shown in SEQ ID NOS: 15 and 16 as primers. Whereas the PCR product obtained for the strain in which att-cal remained was about 1.9 kb, a band of about 0.3 kb was observed for the strain in which alt-cal was eliminated. The ldhA deficient strain obtained as described above was designated as MG1655ΔldhA strain.
<1-2> Construction of a Strain Deficient in the lldD Gene Coding for L-Lactate Dehydrogenase
A strain was constructed in the same manner as that of the construction of the ldhA gene-deficient strain. PCR was performed using synthetic oligonucleotides having sequences corresponding to parts of the lldD gene in the 5′ end and sequences corresponding to both ends of attL and attR of λ phage in the 3′ end as primers and plasmid pMW118-attL-Cm-attR as the template. The sequences of the synthetic oligonucleotides used as the primers are shown in SEQ ID Nos. 17 and 18. The amplified PCR product was purified on an agarose gel and introduced into the Escherichia coli MG1655ΔldhA strain containing plasmid pKD46 capable of temperature-sensitive replication by electroporation. Then, an ampicillin-sensitive strain not harboring pKD46 was obtained, and the deletion of the lldD gene was confirmed by PCR. PCR was performed by using the synthetic oligonucleotides shown in SEQ ID NOS: 19 and 20 as primers. Whereas the PCR product obtained for the parent strain was about 1.4 kb, a band of about 1.9 kb was observed for the deficient strain.
To eliminate the att-cat gene introduced into the lldD gene, the strain was transformed with helper plasmid pMW-intxis-ts, and an ampicillin resistant strain was selected. Then, the strain from which att-cat and pMW-intxis-ts had been eliminated was obtained and confirmed by PCR on the basis of ampicillin sensitivity and chloramphenicol sensitivity. PCR was performed by using the synthetic oligonucleotides shown in SEQ ID NOS: 19 and 20 as primers. Whereas the PCR product obtained for the strain in which alt-cat remained was about 1.9 kb, a band of about 0.3 kb was observed for the strain in which all-cat was eliminated. The lldD deficient strain obtained as described above was designated as MG1655ΔldhAΔlldD strain.
Example 6: Construction of ybjL Gene-Enhanced Strain of Succinic Acid-Producing Bacterium<6-1> Construction of Plasmid for Gene Amplification
In order to amplify the ybjL gene, plasmid pMW219::Pthr was used. This plasmid corresponds to the vector pMW219 (Nippon Gene) having the promoter region of the threonine operon (thrLABC) in the genome of the Escherichia coli shown in SEQ ID NO: 21 at the HindIII site and BamHI site, and enables amplification of a gene by cloning the gene at a position in the plasmid downstream from that promoter.
<6-2> Construction of Plasmid for Enhancing ybjL
PCR was performed by using the synthetic oligonucleotide having a BamHI site shown in SEQ ID NO: 22 as a 5′ primer, and the synthetic oligonucleotide having a BamHI site shown in SEQ ID NO; 23 as a 3′ primer, which were prepared on the basis of the nucleotide sequence of the ybjL gene in the genome sequence of Escherichia coli (GenBank Accession No. U00096), and the genomic DNA of Escherichia coli MG1655 strain as the template. The product was treated with the restriction enzyme BamHI to obtain a gene fragment containing the ybjL gene.
The PCR product was purified and ligated with the vector pMW219::Pthr which had been treated with BamHI to construct plasmid pMW219::Pthr::ybjL for ybjL amplification.
<6-3> Production of ybjL-Amplified Strain
pMW219::Pthr::ybjL obtained in <6-2> described above and pMW219 were used to transform the Escherichia coli MG1655ΔldhAΔlldD strain by the electric pulse method, and the transformants were applied to the LB agar medium containing 25 μg/ml of kanamycin, and cultured at 37° C. for about 18 hours. The colonies which appeared were purified, and plasmids were extracted from them in a conventional manner to confirm introduction of the target plasmid. The obtained strains were designated as MG1655ΔldhAΔlldD/pMW219::Pthr::ybjL and MG1655ΔldhAΔlldD/pMW219, respectively. The Enterobacter aerogenes AJ110637 strain was also transformed with pMW219::Pthr::ybjL and pMW219 by the electric pulse method, and the transformants were applied to the LB agar medium containing 50 μg/ml of kanamycin, and cultured at 37° C. for about 18 hours. The colonies which appeared were purified, and plasmids were extracted from them in a conventional manner to confirm introduction of the target plasmid. The obtained strains were designated as AJ110637/pMW219::Pthr::ybjL and AJ110637/pMW219, respectively.
Example 7: Effect of ybjL Amplification in Succinic Acid-Producing Strain of Escherichia BacteriumMG1655ΔldhAΔlldD/pMW219::Pthr::ybjL and MG1655ΔldhAΔlldD/pMW219 were each uniformly applied to an LB plate containing 25 μg/ml of kanamycin, and cultured at 37° C. for 16 hours. Then, each plate was incubated at 37° C. for 16 hours under an anaerobic condition by using Anaeropack (Mitsubishi Gas Chemical). The cells on the plate were washed with 0.8% brine, and then diluted 51 times, and thereby a cell suspension having OD=1.0 (600 nm) was prepared. This cell suspension in a volume of 100 μl and a production medium (10 g/l of glucose, 10 g/l 2Na malate, 45.88 g/l of TES, 6 g/l of Na2HPO4, 3 g/l of KH2PO4, 1 g/l of NH4Cl, adjusted to pH 7.3 with KOH and filtered) in a volume of 1.3 ml in which the dissolved gases in the medium were replaced with nitrogen gas by bubbling nitrogen gas beforehand were put into 1.5-ml volume micro tubes, and the cells were cultured at 31.5° C. for 10 hours by using a stirrer for micro tubes. After the culture, the amount of succinic acid which had accumulated in the medium was analyzed by liquid chromatography. Two Shim-pack SCR-102H (Shimadzu) connected in series were used as the column, and a sample was eluted at 50° C. with 5 mM p-toluenesulfonic acid. The eluate was neutralized with 20 mM Bis-Tris aqueous solution containing 5 mM p-toluenesulfonic acid and 100 μM EDTA, and succinic acid was quantified by measuring electric conductivity with CDD-10AD (Shimadzu).
The amounts of succinic acid which had accumulated after 10 hours are shown in Table 6, and the change in succinic acid accumulation is shown in
Succinic acid accumulation was markedly increased in the ybjL gene-amplified strain MG1655ΔldhAΔlldD/pMW219::Pthr::ybjL as compared to the control strain MG1655ΔldhAΔlldD/pMW219.
AJ110637/pMW219::Pthr::ybjL and AJ110637/pMW219 were each uniformly applied to an LB plate containing 50 μg/ml of kanamycin, and cultured at 37° C. for 16 hours. Then, each plate was incubated at 37° C. for 16 hours under an anaerobic condition by using Anaeropack (Mitsubishi Gas Chemical). The cells on the plate were washed with 0.8% brine, and then diluted 51 times, and thereby a cell suspension having OD=1.0 (600 nm) was prepared. This cell suspension in a volume of 100 μl and a production medium (10 g/l of glucose, 10 g/l 2Na malate, 45.88 g/l of TES, 6 g/l of Na2HPO4, 3 g/l of KH2PO4, 1 g/l of NH4Cl, adjusted to pH 7.3 with KOH and filtered) in a volume of 1.3 ml in which the dissolved gases in the medium were replaced with nitrogen gas by bubbling nitrogen gas beforehand were put into 1.5-ml volume micro tubes, and the cells were cultured at 31.5° C. for 6 hours by using a stirrer for micro tubes. After the culture, the amount of succinic acid which had accumulated in the medium was analyzed by liquid chromatography. Two Shim-pack SCR-102H Shimadzu) connected in series were used as the column, and a sample was eluted at 50° C. with 5 mM p-toluenesulfonic acid. The eluate was neutralized with 20 mM Bis-Tris aqueous solution containing 5 mM p-toluenesulfonic acid and 100 μM EDTA, and succinic acid was quantified by measuring electric conductivity with CDD-10AD (Shimadzu).
The amounts of succinic acid which had accumulated after 6 hours are shown in Table 7, and change of succinic acid accumulation is shown in
Succinic acid accumulation was markedly increased in the ybjL gene-amplified strain AJ110637/pMW219::Pthr::ybjL as compared to the control strain AJ110637/pMW219.
<9-1> Construction of an adhE-Deficient Strain of Enterobacter aerogenes AJ110637
When Enterobacter aerogenes AJ110637 is grown in a medium containing a sugar source under anaerobic conditions, it produces a marked amount of ethanol. Therefore, adhE coding for alcohol dehydrogenase was deleted to suppress the generation of ethanol.
A gene fragment for deleting adhE was prepared by PCR using the plasmid pMW-attL-Tc-attR described in WO2005/010175 as the template and oligonucleotides of SEQ ID NOS: 72 and 73 as primers. pMW118-attL-Tc-attR is a plasmid obtained by inserting attL and attR genes, which are the attachment sites of λ phage, and the Tc gene, which is a tetracycline resistance gene, into pMW118 (Takara Bio), and the genes are inserted in the order of attL-Tc-attR. By PCR described above, a gene fragment containing a tetracycline resistance gene, attL and attR sites of λ phage at the both ends of the resistance gene, and 60 bp upstream sequence and 59 bp downstream sequence of the adhE gene added to the outer ends of the λ phage sequences was amplified. This fragment was purified by using Wizard PCR Prep DNA Purification System (Promega).
Then, the Enterobacter aerogenes AJ110637 strain was transformed with RSF-Red-TER to obtain the Enterobacter aerogenes AJ110637/RSF-Red-TER strain. This strain was cultured overnight in LB medium containing 40 μg/mL of chloramphenicol, the culture medium was inoculated in a 1/100 volume to 50 mL of the LB medium containing 40 μg/mL of chloramphenicol and 0.4 mM isopropyl-β-D-thiogalactopyranoside, and culture was performed at 31° C. for 4 hours. The cells were collected, washed three times with ice-cooled 10% glycerol, and finally suspended in 0.5 mL of 10% glycerol. The suspended cells were used as competent cells, and the PCR fragment prepared in the above section was introduced into the cells by using GENE PULSER II (BioRad) under the conditions of a field strength of 20 kV/cm, capacitor capacity of 25 ρF and resistance of 200Ω. Ice-cooled LB medium was added to the cell suspension, and culture was performed at 31° C. for 2 hours with shaking. Then, the culture was applied to a LB plate containing 25 μg/mL of tetracycline. The colonies that appeared were purified with the same plate, and then it was confirmed by PCR that the adhE gene had been replaced with the tetracycline resistance gene.
<9-2> Construction of Pyruvate Carboxylase Gene-Enhanced Strain of AJ110637ΔadhE Strain
The ability to produce succinic acid was imparted to the Enterobacter aerogenes AJ110637ΔadhE strain by amplifying pyc coding for pyruvate carboxylase derived from Corynebacterium glutamicum.
In order to express pyc derived from Corynebacterium glutamicum in the AJ110637ΔadhE strain, it was attempted to obtain a threonine operon promoter fragment of the Escherichia coli MG1655 strain. The total genomic sequence of Escherichia coli (Escherichia coli K-12 strain) has already been elucidated (Genbank Accession No. U00096, Science, 277, 1453-1474 (1997)). On the basis of this sequence, PCR amplification of the promoter region of the threonine operon (thrLABC) was performed. PCR was performed by using the synthetic oligonucleotide having an SacI site shown in SEQ ID NO: 75 as a 5′ primer, the synthetic oligonucleotide shown in SEQ ID NO: 76 as a 3′ primer, and the genomic DNA of Escherichia coli MG1655 strain (ATCC 47076, ATCC 700926) as the template to obtain a threonine operon promoter fragment (A) (SEQ ID NO: 77).
Furthermore, a pyc gene fragment derived from the Corynebacterium glutamicum 2256 strain (ATCC 13869) was obtained. PCR was performed by using the synthetic oligonucleotide shown in SEQ ID NO: 78 as a 5′ primer, the synthetic oligonucleotide having an SacI site shown in SEQ ID NO; 79 as a 3′ primer, and the genomic DNA of the Corynebacterium glutamicum 2256 strain (ATCC 13869) as a template to obtain a pyc gene fragment (B) (SEQ ID NO; 80).
PCR was performed by using the fragments (A) and (B) as templates, the primers of SEQ ID NOS: 75 and 79 to obtain a gene fragment (C) including the fragments (A) and (B) ligated to each other. This gene fragment (C) was treated with the restriction enzyme SacI, and purified, and the product was ligated with the plasmid vector pSTV28 (Takara Bio) which had been digested with the restriction enzyme SacI to construct a plasmid pSTV28::Pthr::pyc for pyc amplification.
The plasmid pSTV28::Pthr::pyc for pyc amplification was introduced into the aforementioned Enterobacter aerogenes AJ110637ΔadhE strain by electroporation to obtain a transformant which are resistant to tetracycline and chloramphenicol. This pyc-amplified strain of Enterobacter aerogenes AJ110637ΔadhE was designated as AJ110637ΔadhE/pSTV28::Pthr::pyc.
<9-3> Construction of Enterobacter Aerogenes ybjL Gene-Enhanced Strain of AJ110637ΔadhE/pSTV28::Pthr::pyc
In the same manner as that described above, PCR amplification of the promoter region of the threonine operon (thrLABC) of Escherichia coli (Escherichia coli K-12 strain) was performed. PCR was performed by using the synthetic oligonucleotide shown in SEQ ID NO: 81 as a 5′ primer, the synthetic oligonucleotide shown in SEQ ID NO: 82 as a 3′ primer, and the genomic DNA of Escherichia coli MG1655 strain (ATCC 47076, ATCC 700926) as a template to obtain a threonine operon promoter fragment (A) (SEQ ID NO: 83).
Furthermore, in order to clone the ybjL gene of the Enterobacter aerogenes AJ110637 strain, PCR was performed by using the synthetic oligonucleotide shown in SEQ ID NO: 84 as a 5′ primer, the synthetic oligonucleotide shown in SEQ ID NO: 85 as a 3′ primer, and the genomic DNA of the Enterobacter aerogenes AJ110637 strain as the template to obtain a ybjL gene fragment (B) (SEQ ID NO: 86).
PCR was performed by using the fragments (A) and (B) as templates, and the primers of SEQ ID NOS: 81 and 85 to obtain a gene fragment (C) with the fragments (A) and (B) ligated to each other. This gene fragment (C) was blunt-ended by using TaKaRa BKL Kit (Takara Bio), and the 5′ end was phosphorylated. Then, the fragment was digested with the restriction enzyme SmaI, and the product was ligated with the plasmid vector pMW218 dephosphorylated with alkaline phosphatase to construct a plasmid pMW218::Pthr::Ent-ybjL for ybjL amplification.
The aforementioned vector pMW218::Pthr::Ent-ybjL for amplification of the ybjL gene derived from the Enterobacter aerogenes AJ110637 strain, and the control plasmid pMW218 were each introduced into the Enterobacter aerogenes AJ110637ΔadhE/pSTV28::Pthr::pyc strain by electroporation to obtain transformants which are resistant to tetracycline, chloramphenicol and kanamycin. The ybjL-amplified strain derived from the Enterobacter aerogenes AJ110637ΔadhE/pSTV28::Pthr::pyc strain was designated as AJ110637ΔadhE/pSTV28::Pthr::pyc/pMW218::Pthr::Ent-ybjL, and the control strain as with pMW218 was designated as AJ110637ΔadhE/pSTV28::Pthr::pyc/pMW218.
<9-4> Effect of Amplification of ybjL Derived from Enterobacter aerogenes in Enterobacter Bacterium
AJ110637ΔadhE/pSTV28::Pthr::pyc/pMW218::Pthr::Ent-ybjL, and AJ110637ΔadhE/pSTV28::Pthr::pyc/pMW218 were each uniformly applied to an LB plate containing 50 μg/ml of kanamycin, 25 μg/ml of tetracycline, and 40 μg/ml of chloramphenicol, and cultured at 31.5° C. for 16 hours. Then, the cells were inoculated into 3 ml of a seed medium (20 g/l of Bacto tryptone, 10 g/l of yeast extract, 20 g/L of NaCl) in a test tube, and cultured at 31.5° C. for 16 hours with shaking. A succinic acid production medium (100 g/l of glucose, 50 g/L of calcium carbonate subjected to hot air sterilization for 3 hours or more) in a volume of 3 ml was added to the medium obtained above, then the tube was sealed with a silicone stopper, and culture was performed at 31.5° C. for 24 hours with shaking. After the culture, the amount of succinic acid which had accumulated in the medium was analyzed by liquid chromatography. Two Shim-pack SCR-102H (Shimadzu) connected in series were used as the column, and a sample was eluted at 50° C. with 5 mM p-toluenesulfonic acid. The eluate was neutralized with 20 mM Bis-Tris aqueous solution containing 5 mM p-toluenesulfonic acid and 100 μM EDTA, and succinic acid was quantified by measuring electric conductivity with CDD-10AD (Shimadzu).
The amounts of succinic acid which had accumulated after 24 hours are shown in Table 8.
Succinic acid accumulation and succinic acid yield based on consumed glucose were markedly increased in the ybjL gene-amplified strain
110637ΔadhE/pSTV28::Pthr::pyc/pMW218::Pthr::Ent-ybjL as compared to control AJ110637ΔadhE/pSTV28::Pthr::pyc/pMW218.
Explanation of Sequence Listing
SEQ ID NO: 1: ybjL gene of Pantoea anantis
SEQ ID NO: 2: YbjL of Pantoea ananatis
SEQ ID NO: 3: ybjL gene of Escherichia coli
SEQ ID NO: 4: YbjL of Escherichia coli
SEQ ID NO: 5: Consensus sequence of YbjL of Pantoea ananatis and Escherichia coli
SEQ ID NO: 6: Primer for ams gene disruption
SEQ ID NO: 7: Primer for ams gene disruption
SEQ ID NO: 8: Primer for amplification of ybjL of P. ananatis
SEQ ID NO: 9: Primer for amplification of ybjL of P. ananatis
SEQ ID NO: 10: Sequence of RSFCPG plasmid
SEQ ID NO: 11: Primer for amplification of ybjL of E. coli W3110
SEQ ID NO: 12: Primer for amplification of ybjL of E. coli W3110
SEQ ID NO: 13: Primer for deletion of ldhA
SEQ ID NO: 14: Primer for deletion of ldhA
SEQ ID NO: 15: Primer for confirming deletion of ldhA
SEQ ID NO: 16: Primer for confirming deletion of ldhA
SEQ ID NO: 17: Primer for deletion of lldD
SEQ ID NO: 18: Primer for deletion of lldD
SEQ ID NO: 19: Primer for confirming deletion of lldD
SEQ ID NO: 20: Primer for confirming deletion of lldD
SEQ ID NO: 21: Threonine promoter sequence
SEQ ID NO: 22: Primer for amplification of ybjL of E. coli MG1655
SEQ ID NO: 23: Primer for amplification of ybjL of E. coli MG1655
SEQ ID NO: 24: ybjL gene of Salmonella typhimurium
SEQ ID NO: 25: YbjL of Salmonella typhimurium
SEQ ID NO: 26: ybjL gene of Yersinia pestis
SEQ ID NO: 27: YbjL of Yersinia pestis
SEQ ID NO: 28: ybjL gene of Erwinia carotovora
SEQ ID NO: 29: YbjL of Erwinia carotovora
SEQ ID NO: 30: ybjL gene of Vibrio cholerae
SEQ ID NO: 31: YbjL of Vibrio cholerae
SEQ ID NO: 32: ybjL gene of Aeromonas hydrophia
SEQ ID NO: 33: YbjL of Aeromonas hydrophia
SEQ ID NO: 34: ybjL gene of Photobacterium profundum
SEQ ID NO: 35: YbjL of Photobacterium profundum
SEQ ID NO: 36: ldhA gene of Escherichia coli
SEQ ID NO: 37: LdhA of Escherichia coli
SEQ ID NO: 38: lldD) gene of Escherichia coli
SEQ ID NO: 39: LldD of Escherichia coli
SEQ ID NO: 40: Nucleotide sequence of his) gene of Pantoea ananatis
SEQ ID NO: 41: Primer for amplification of fragment for incorporation of Kmr gene nto hisD gene
SEQ ID NO: 42: Primer for amplification of fragment for incorporation of Kmr gene into hisD gene
SEQ ID NO: 43: Primer for amplification of cat gene
SEQ ID NO: 44: Primer for amplification of cat gene
SEQ ID NO: 45: Primer for amplification of sacB gene
SEQ ID NO: 46: Primer for amplification of sacB gene
SEQ ID NO: 47: Primer for amplification of DNA fragment containing PlacUV5 promoter
SEQ ID NO: 48: Primer for amplification of DNA fragment containing PlacUV5 promoter
SEQ ID NO: 49: Primer for amplification of DNA fragment containing λRedαβγ gene and tL3
SEQ ID NO: 50: Primer for amplification of DNA fragment containing λRedαβγ gene and tL3
SEQ ID NO: 51: Primer for amplification of DNA fragment containing PlacUV5 promoter and TrrnB
SEQ ID NO: 52: Primer for amplification of DNA fragment containing PlacUV5 promoter and TrrnB
SEQ ID NO: 53: Primer for amplification of attL
SEQ ID NO: 54: Primer for amplification of attL
SEQ ID NO: 55: Nucleotide sequence of attL
SEQ ID NO: 56: Primer for amplification of attR
SEQ ID NO: 57: Primer for amplification of attR
SEQ ID NO: 58: Nucleotide sequence of attR
SEQ ID NO: 59: Primer for amplification of DNA fragment containing bla gene
SEQ ID NO: 60: Primer for amplification of DNA fragment containing bla gene
SEQ ID NO: 61: Primer for amplification of DNA fragment containing ter_rrnB
SEQ ID NO: 62: Primer for amplification of DNA fragment containing ter_rrnB
SEQ ID NO: 63: Nucleotide sequence of the DNA fragment containing ter_thrL terminator
SEQ ID NO: 64: Primer for amplification of DNA fragment containing ter_thrL terminator
SEQ ID NO: 65: Primer for amplification of DNA fragment containing ter_thrL terminator
SEQ ID NO: 66: ams operon of Pantoea ananatis
SEQ ID NO: 67: AmsH of Pantoea ananatis
SEQ ID NO: 68: AmsI of Pantoea ananatis
SEQ ID NO: 69: AmsA of Pantoea ananatis
SEQ ID NO: 70: AmsC of Pantoea ananatis
SEQ ID NO: 71: AmsB of Pantoea ananatis
SEQ ID NO: 72: Nucleotide sequence of primer for deletion of adhE
SEQ ID NO: 73: Nucleotide sequence of primer for deletion of adhE
SEQ ID NO: 74: Nucleotide sequence of adhE of Enterobacter aerogenes AJ110637 partial sequence)
SEQ ID NO: 75: Primer for amplification of threonine promoter
SEQ ID NO: 76: Primer for amplification of threonine promoter
SEQ ID NO: 77: Threonine promoter gene fragment
SEQ ID NO: 78: Primer for amplification of pyruvate carboxylase gene
SEQ ID NO: 79: Primer for amplification of pyruvate carboxylase gene
SEQ ID NO: 80: Pyruvate carboxylase gene fragment
SEQ ID NO: 81: Primer for amplification of threonine promoter
SEQ ID NO: 82: Primer for amplification of threonine promoter
SEQ ID NO: 83: Threonine promoter gene fragment
SEQ ID NO: 84: Nucleotide sequence of primer for amplification of ybjL of Enterobacter aerogenes AJ110637
SEQ ID NO: 85: Nucleotide sequence of primer for amplification of ybjL of Enterobacter aerogenes AJ110637
SEQ ID NO: 86: Nucleotide sequence of ybjL of Enterobacter aerogenes AJ110637
SEQ ID NO: 87: Amino acid sequence of YbjL of Enterobacter aerogenes AJ110637
SEQ ID NO: 88: Consensus sequence of YbjL of Escherichia, Pantoea and Enterobacter
INDUSTRIAL APPLICABILITYProduction efficiency of an acidic substance having a carboxyl group can be improved by using the microorganism of the present invention.
While the invention has been described in detail with reference to preferred embodiments thereof, it will be apparent to one skilled in the art that various changes can be made, and equivalents employed, without departing from the scope of the invention. Each of the aforementioned documents is incorporated by reference herein in its entirety.
Claims
1. A method for producing an acidic substance having a carboxyl group comprising culturing in a medium a microorganism, having an ability to produce the acidic substance having a carboxyl group, to produce and accumulate the acidic substance having a carboxyl group in the medium, and
- collecting the acidic substance having a carboxyl group from the medium,
- wherein the acidic substance is succinic acid,
- wherein the microorganism has been modified to enhance expression of an ybjL gene, and
- wherein the ybjL gene encodes a protein selected from the group consisting of:
- (A) a protein comprising the amino acid sequence of SEQ ID NO: 2; and
- (B) a protein comprising a variant of the amino acid sequence of SEQ ID NO: 2, wherein one to 5 amino acid residues are substituted, deleted, inserted or added, and wherein, upon expression, said variant improves the ability of the microorganism to produce the acidic substance having a carboxyl group.
2. The method according to claim 1, wherein said enhanced expression is obtained by a method selected from the group consisting of: A) increasing copy number of the ybjL gene, B) modifying an expression control sequence of the ybjL gene, and C) combinations thereof.
3. The method according to claim 1, wherein the microorganism is a bacterium belonging to the family Enterobacteriaceae.
4. The method according to claim 3, wherein the bacterium belongs to a genus selected from the group consisting of Escherichia, Enterobacter, Raoultella, Pantoea, and Klebsiella.
5. The method according to claim 1, wherein the microorganism is a rumen bacterium.
6. The method according to claim 5, wherein the microorganism is a bacterium belonging to the genus Mannheimia.
7. A method for producing an acidic substance having a carboxyl group comprising
- A) allowing a substance to act on an organic raw material in a reaction mixture containing carbonate ions, bicarbonate ions, or carbon dioxide gas, wherein said substance is selected from the group consisting of:
- i) a microorganism having an ability to produce the acidic substance having a carboxyl group,
- ii) a product obtained by processing the microorganism of i), and
- iii) combinations thereof, and
- B) collecting the acidic substance having a carboxyl group,
- wherein the acidic substance is succinic acid,
- wherein the microorganism has been modified to enhance expression of an ybjL gene, and
- wherein the ybjL gene encodes a protein selected from the group consisting of:
- (a) a protein comprising the amino acid sequence of SEQ ID NO: 2; and
- (b) a protein comprising a variant of the amino acid sequence of SEQ ID NO: 2, wherein one to 5 amino acid residues are substituted, deleted, inserted or added, and wherein, upon expression, said variant improves the ability of the microorganism to produce the acidic substance having a carboxyl group.
8. The method according to claim 7, wherein said enhanced expression is obtained by a method selected from the group consisting of: A) increasing copy number of the ybjL gene, B) modifying an expression control sequence of the ybjL gene, and C) combinations thereof.
9. The method according to claim 7, wherein the microorganism is a bacterium belonging to the family Enterobacteriaceae.
10. The method according to claim 9, wherein the bacterium belongs to a genus selected from the group consisting of Escherichia, Enterobacter, Raoultella, Pantoea, and Klebsiella.
11. The method according to claim 7, wherein the microorganism is a rumen bacterium.
12. The method according to claim 11, wherein the microorganism is a bacterium belonging to the genus Mannheimia.
13. A method for producing a polymer comprising succinic acid, comprising:
- A) producing succinic acid by the method according to claim 1, and
- B) polymerizing the obtained succinic acid.
14. A method for producing a polymer comprising succinic acid, comprising:
- A) producing succinic acid by the method according to claim 7, and
- B) polymerizing the obtained succinic acid.
Type: Application
Filed: Oct 19, 2017
Publication Date: Feb 15, 2018
Applicant: AJINOMOTO CO., INC. (Tokyo)
Inventors: Yoshihiko Hara (Kanagawa), Keita Fukui (Kanagawa), Yoshinori Tajima (Kanagawa), Kazue Kawamura (Kanagawa), Yoshihiro Usuda (Kanagawa), Kazuhiko Matsui (Kanagawa)
Application Number: 15/787,861
