# Patent

## Title
Method for producing an organic acid

## Abstract

An organic acid is produced by allowing a bacterium belonging to the family Enterobacteriaceae, which has an ability to produce an organic acid and has been modified so that the phosphoenolpyruvate carboxykinase activity is enhanced, which is selected from Enterobacter, Pantoea, Erwinia, Klebsiella and Raoultella bacteria, or a product obtained by processing the bacterium, to act on an organic raw material in a reaction mixture containing carbonate ions, bicarbonate ions, or carbon dioxide gas to produce the organic acid, and collecting the organic acid.

## Background
This application is a continuation under 35 U.S.C. §120 of PCT Patent Application No. PCT/JP2008/072055, filed on Dec. 4, 2008, which claims priority under 35 U.S.C. §119 to Japanese Patent Application No. 2007-315764, filed on Dec. 6, 2007, both of which are incorporated in their entireties by reference. The Sequence Listing in electronic format filed herewith is also hereby incorporated by reference in its entirety (File Name: 2010-06-03T_US-429_Seq_List; File Size: 202 KB; Date Created: Jun. 3, 2010).


BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates to a method for producing an organic acid such as succinic acid using a bacterium.
2. Brief Description of the Related Art
For the production of non-amino organic acids, including succinic acid, by fermentation, anaerobic bacteria are typically used, including bacteria belonging to the genus Anaerobiospirillum or Actinobacillus (U.S. Pat. Nos. 5,142,834 and 5,504,004, International Journal of Systematic Bacteriology (1999), 49, 207-216). Although such anaerobic bacteria provide high product yields, many nutrients are required for their growth, 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 sources of organic nitrogen results in not only an increase in cost for the culture medium, but also an increase in the purification cost for isolating the product, and therefore it is not economical.
In addition, methods are known in which aerobic bacteria such as coryneform bacteria are cultured once under aerobic conditions to proliferate the bacterial cells, then the bacteria are harvested and washed. As a result, a non-amino organic acid is produced without having to supply oxygen (Japanese Patent Laid-open (KOKAI) Nos. 11-113588 and 11-196888). These methods are economical, since smaller amounts of organic nitrogen can be added, and sufficient growth of the bacteria can be obtained in a simple culture medium. However, there is still room for improvement in terms of production amounts, concentration, and production rate per cell of the target organic acids, and the like. Furthermore, the production process could be simplified.
Escherichia coli is a facultative anaerobic gram negative bacterium, and similar to when using coryneform bacteria, methods are known for producing a non-amino organic acid by culturing the bacteria once under aerobic conditions to allow for bacterial growth, and then culturing again in the absence of oxygen to anaerobically produce the non-amino organic acid (Journal of Industrial Microbiology and Biotechnology (2002), 28 (6), 325-332). Alternatively, the bacteria 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.
As for the breeding of such bacteria as described above and in regards to the anaplerotic pathway, the production of non-amino organic acids by fermentation utilizing strains of Escherichia coli, coryneform bacterium, or the like, has been reported. Specifically, in these bacteria, phosphoenolpyruvate carboxylase (PEPC) activity or pyruvate carboxylase (PYC) activity is enhanced, and the like (for example, Japanese Patent Laid-open Nos. 11-196888 and 11-196887, Applied and Environmental Microbiology (1996), 62, 1808-1810).
As for phosphoenolpyruvate carboxykinase (PEPCK), it is thought that this enzyme generates phosphoenolpyruvic acid from oxalacetic acid by decarboxylation, and it mainly advances the metabolic reactions toward glyconeogenesis (Applied and Environmental Microbiology (1996), 62, 1808-1810, Applied and Environmental Microbiology (1993), 59, 4261-4265). Another type of PEPCK enzyme has been reported that is in equilibrium with the reverse reaction of the reaction described above, that is, the reaction that generates oxalacetic acid from phosphoenolpyruvic acid by carbon dioxide fixation. The presence of this type of PEPCK has been confirmed in some bacteria which produce succinic acid in the presence of high concentrations of carbon dioxide, that is, Mannheimia succiniciproducens, Actinobacillus succinogenes, Anaerobiospirillum succiniciproducens, and Selenomonas ruminantium (Applied and Environmental Microbiology (2006), 72, 1939-1948, Applied and Environmental Microbiology (1997), 63, 2273-2280, Applied and Environmental Microbiology (2004), 70, 1238-1241, Microbiology (2001), 147, 681-690). It has also been reported that increasing the activity of PEPCK derived from Actinobacillus succinogenes in Escherichia coli is effective for increasing production of succinic acid (Applied and Environmental Microbiology (2004), 70, 1238-1241). However, this improvement was confirmed only in a PEPC-deficient strain, and the converse has also been reported, in that the increase in the production of succinic acid is NOT observed in a non-deficient strain (Applied and Environmental Microbiology (2004), 70, 1238-1241).
Furthermore, although efficient production of ethanol and hydrogen has been reported in strains of Enterobacter bacteria, it has not been reported whether any strain can efficiently produce a non-amino organic acid (Journal of Bioscience and Bioengineering (2005), 100, 260-265, Japanese Patent Laid-open No. 2006-180782).
SUMMARY OF THE INVENTION
An aspect of the present invention is to provide a method for producing an organic acid using a bacterium that shows higher production efficiency.
It has been found that the production yield of an organic acid can be increased by using a bacterium which belongs to the family Enterobacteriaceae, such as Enterobacter, Pantoea, Erwinia, Klebsiella, and Raoultella, and has been modified so that the phosphoenolpyruvate carboxykinase activity is enhanced. A product obtained by processing such a bacterium can also be used.
It is an aspect of the present invention to provide a method for producing an organic acid 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) a bacterium belonging to the family Enterobacteriaceae which has an ability to produce an organic acid and has been modified so that the phosphoenolpyruvate carboxykinase activity is enhanced,
        ii) a product obtained by processing the bacterium of i), and
        iii) combinations thereof; and
    
    


B) collecting the organic acid,
wherein the bacterium belongs to a genus selected from the group consisting of Enterobacter, Pantoea, Erwinia, Klebsiella, and Raoultella. 
It is a further aspect of the present invention to provide the method as described above, wherein the bacterium has been modified by a method selected from the group consisting of:
i) increasing the copy number of the pckA gene,
ii) modifying an expression control sequence of the pckA gene, and
iii) combinations thereof.
It is a further aspect of the present invention to provide the method as described above, wherein the pckA gene is selected from the group consisting of:
(a) a DNA comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 6, 8, 10, 12, 14, 16 and 64, and
(b) a DNA which hybridizes with a nucleotide sequence complementary to a nucleotide sequence selected from the group consisting of SEQ ID NO: 6, 8, 10, 12, 14, 16 and 64 under stringent conditions, and said DNA codes for a protein having phosphoenolpyruvate carboxykinase activity.
It is a further aspect of the present invention to provide the method as described above, wherein the pckA gene codes for a protein selected from the group consisting of:
A) a protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 7, 9, 11, 13, 15, 17, 65, and 24; and
B) a protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 7, 9, 11, 13, 15, 17, 65 and 24, but which includes one or more substitutions, deletions, insertions, or additions of one or several amino acid residues.
It is a further aspect of the present invention to provide the method as described above, wherein the bacterium has been further modified to decrease the activity of an enzyme selected from the group consisting of alcohol dehydrogenase, lactate dehydrogenase, phosphate acetyltransferase, α-acetolactate decarboxylase, pyruvate formate lyase, and combinations thereof.
It is a further aspect of the present invention to provide the method as described above, wherein the enzyme is alcohol dehydrogenase.
It is a further aspect of the present invention to provide the method as described above, wherein the enzymes are alcohol dehydrogenase and lactate dehydrogenase.
It is a further aspect of the present invention to provide the method as described above, wherein the enzymes are alcohol dehydrogenase, lactate dehydrogenase, and phosphate acetyltransferase.
It is a further aspect of the present invention to provide the method as described above, wherein the enzymes are alcohol dehydrogenase, lactate dehydrogenase, phosphate acetyltransferase, and α-acetolactate decarboxylase.
It is a further aspect of the present invention to provide the method as described above, wherein the enzymes are alcohol dehydrogenase, lactate dehydrogenase, phosphate acetyltransferase, α-acetolactate decarboxylase, and pyruvate formate lyase.
It is a further aspect of the present invention to provide the method as described above, wherein the bacterium has been further modified so that pyruvate carboxylase activity is enhanced.
It is a further aspect of the present invention to provide the method as described above, wherein the organic acid is succinic acid.
It is a further aspect of the present invention to provide a method for producing a succinic acid-containing polymer comprising:
A) producing succinic acid by the method as described above, and
B) polymerizing the succinic acid.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the structure of the helper plasmid RSF-Red-TER.
FIG. 2 shows the construction scheme of the helper plasmid RSF-Red-TER.
FIG. 3 shows the alignment and consensus sequence of the amino acid sequences of various types of PEPCK.
FIG. 4 shows the alignment and consensus sequence of amino acid sequences of various types of PEPCK (continuation).
FIG. 5 shows the alignment and consensus sequence of amino acid sequences of various types of PEPCK (continuation).
FIG. 6 shows the alignment and consensus sequence of amino acid sequences of various types of PEPCK (continuation).



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
Hereinafter, aspects of the presently disclosed subject matter will be explained in detail.
<1> Bacterium
The bacterium used in accordance with the presently disclosed subject matter can be a bacterium which has an ability to produce an organic acid and has been modified so that the phosphoenolpyruvate carboxykinase (henceforth abbreviated as “PEPCK”) activity is enhanced. The term “ability to produce an organic acid” can mean that the bacterium is able to produce and accumulate an organic acid in a medium to such a degree that the organic acid can be collected from the medium when the bacterium is cultured in the medium. The bacterium of the present invention can produce a target organic acid in a medium in an amount of, for example, 0.5 g/L or more, or 1.0 g/L or more in another example. Such a bacterium can be obtained by modifying a parent bacterial strain which already is able to produce an organic acid so that the PEPCK activity is enhanced. When the parent strain does not naturally produce an organic acid, the ability to produce an organic acid can be imparted to the parent strain, and then the bacterium can be modified so that the PEPCK activity is enhanced. Furthermore, the ability to produce an organic acid can be imparted to a strain which has already been modified to enhance the PEPCK activity. The ability to produce an organic acid can be native to the chosen bacterium, or can be obtained by modifying the bacterium using mutational techniques or recombinant DNA techniques.
The organic acid can be a metabolic intermediate of the TCA cycle, and examples include succinic acid, malic acid, fumaric acid, citric acid, isocitric acid, cis-aconitic acid, and the like.
The parent strain that can be used to derive the bacterium as described in the presently disclosed subject matter can be a bacterium belonging to the family Enterobacteriaceae, such as Enterobacter, Pantoea, Erwinia, Klebsiella, and Raoultella bacteria.
Pantoea bacteria, Erwinia bacteria, Enterobacter bacteria, Klebsiella bacteria and Raoultella 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 (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 strain (Biotechnol Bioeng., 2007, Mar. 27; 98(2):340-348), Enterobacter aerogenes AJ110637 (FERM ABP-10955), and the like.
These strains are available from, for example, the American Type Culture Collection (Address: 10801 University Boulevard, Manassas, Va. 20110, United States of America). That is, registration numbers are given to each of the strains, and the strains can be ordered using these numbers. The registration numbers of the strains are listed in the catalogue of the American Type Culture Collection. The Enterobacter aerogenes AJ110637 strain was deposited at the 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 BP-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 oxytoca and Klebsiella planticola, and examples of the Raoultella bacteria include Raoultella terrigena and 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 as Raoultella planticola (Int. J. Syst. Evol. Microbiol., 2001 May, 51(Pt 3):925-32).
<1-1> Impartation of the Ability to Produce an Organic Acid
Hereinafter, methods for imparting to bacteria the ability to produce an organic acid, or methods to enhance the ability of bacteria to produce an organic acid are described.
To impart the ability to produce an organic acid, methods conventionally used to breed bacteria for producing substances by fermentation can be used (see “Amino Acid Fermentation”, Japan Scientific Societies Press, 1st Edition, published May 30, 1986, pp. 77-100). Such methods include by acquiring an auxotrophic mutant, an analogue-resistant strain, or a metabolic regulation mutant, or by constructing a recombinant strain having enhanced expression of an enzyme involved in the biosynthesis of an organic acid. When breeding bacteria to produce an organic acid, one or more properties, such as an auxotrophic mutation, analogue resistance, or metabolic regulation mutation, can be imparted. The expression of one or more enzymes involved in biosynthesis of an organic acid can be enhanced. Furthermore, imparting properties such as auxotrophy, analogue resistance, or metabolic regulation can be combined with enhancing biosynthetic enzymes.
An auxotrophic mutant strain, a strain resistant to an organic acid analogue, or a metabolic regulation mutant strain which is able to produce an organic acid 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 the bacteria which exhibit an auxotrophy, analogue resistance, or metabolic regulation mutation and which also are able to produce an organic acid.
Methods for imparting to bacteria an ability to produce an organic acid, and organic acid-producing bacteria will be specifically exemplified below.
Succinic Acid-Producing Bacteria
Bacteria which can be used to produce succinic acid include strains that are unable to produce acetic acid, lactic acid, ethanol, 2,3-butanediol and formic acid.
Strains that are unable to produce acetic acid, lactic acid, ethanol, 2,3-butanediol and formic acid include strains that cannot assimilate acetic acid and lactic acid in a minimal medium, or strains in which the activities of the lactic acid biosynthesis genes and acetic acid biosynthesis enzymes mentioned below are decreased (International Patent Publication WO2005/052135).
Moreover, such strains as described above can also be obtained by imparting resistance to monofluoroacetic acid (U.S. Pat. No. 5,521,075).
Production of succinic acid can be improved by imparting the ability to assimilate glucose under anaerobic conditions to a strain that is unable to produce both formic acid and lactic acid (International Patent Publication WO97/16528).
The ability to produce succinic acid can also be imparted by amplifying a gene which encodes an enzyme which is involved in the succinic acid biosynthesis system, or by deleting a gene which encodes an enzyme which catalyzes a reaction which branches off from the succinic acid biosynthesis system to produce another compound.
The ability to produce succinic acid can also be imparted by modifying a bacterium 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 bacteria can have L-lactate dehydrogenase and D-lactate dehydrogenase, and such bacteria can be modified to decrease the activity of either one, or both, of these enzymes.
The ability to produce succinic acid can also be imparted by modifying a bacterium 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., Millard, C. S., Clark, D. P., Chen, M. J., Rathke, J. W., 1998, Appl. Biochem. Biotechnol., 70-72, 187-198.).
The ability to produce succinic acid can also be imparted by modifying a bacterium 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 all 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 bacterium to decrease the enzymatic activity of alcohol dehydrogenase (ADH), which is an ethanol biosynthesis system enzyme (refer to International Patent Publication WO2006/031424).
A strain with an enhanced ability to produce succinic acid can also be obtained by decreasing the activity of α-acetolactate decarboxylase, which is a 2,3-butanediol biosynthesis system enzyme (J. Biosci. Bioeng., 2004, 97(4):227-32).
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, No. 2007007933, Japanese Patent Laid-open No. 2005-168401). The gene abbreviations are 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 succinic acid production.
The ability to produce succinic acid can also be enhanced by enhancing enzymatic activities of pyruvate carboxylase, malic enzyme, phosphoenolpyruvate carboxylase, fumarase, fumarate reductase, and malate dehydrogenase (Japanese Patent Laid-open No. 11-196888, International Patent Publication WO99/53035, 2001. Biotechnol. Bioeng., 74:89-95, Millard, C. S., Chao, Y. P., Liao, J. C., Donnelly, M. I., 1996, Appl. Environ. Microbiol., 62:1808-1810, International Patent Publication WO2005/021770, Japanese Patent Laid-open No. 2006-320208, Pil Kim, Maris Laivenieks, Claire Vieille, and J. Gregory Zeikus, 2004, Appl. Environ. Microbiol., 70:1238-1241). The enzymatic activities of these target enzymes can be enhanced by referring to the methods for enhancing expression of the pckA gene described later.
Specific examples of succinic acid-producing bacteria belonging to the family Enterobacteriaceae include the following strains:
Enterobacter aerogenes AJ110637 strain (FERM ABP-10955)
Enterobacter aerogenes VP-1 strain (J. Biosci. Bioeng., 2004, 97(4):227-32)
<1-2> Enhancing the Phosphoenolpyruvate Carboxykinase Activity
The bacterium in accordance with the presently disclosed subject matter can be obtained by modifying a bacterium having an ability to produce an organic acid such as those described above so that the phosphoenolpyruvate carboxykinase (PEPCK) activity is enhanced. However, the modification to enhance the PEPCK activity can be performed first, and then the ability to produce an organic acid can be imparted.
Phosphoenolpyruvate carboxykinase (PEPCK) reversibly catalyzes the reaction which produces oxalacetic acid (OAA) from phosphoenolpyruvic acid (PEP) by carbon dioxide fixation. “PEPCK activity” can mean the activity of catalyzing the reaction to produce OAA from PEP. PEPCK enzymes which are able to achieve reaction equilibrium and advance the reaction which results in the production of OAA from PEP can be used. The enzyme activity can be determined, for example, by measuring the amount of ATP produced at 37° C. according to the method of Pil Kim et al. using Sigma Diagnostics ATP Kit (Pil, Kim., Maris, Laivenieks., Claire, Vieille., Gregory, Zeikus., Applied And Environmental Microbiology, February 2004, pp. 1238-1241).
The increase of the PEPCK activity as compared to that of, for example, a wild-type or unmodified strain can be confirmed by measuring the enzyme activity according to the aforementioned method, or by comparing the amount of mRNA of a gene coding for PEPCK with that of the wild-type or unmodified strain. To confirm expression, exemplary methods include Northern hybridization and reverse transcriptase PCR (RT-PCR, Sambrook, J., and Russell, D. W., Molecular Cloning A Laboratory Manual/Third Edition, New York: Cold Spring Harbor Laboratory Press (2001)). The enzyme activity can be increased to any level so long as the activity is increased as compared to that of a wild-type or unmodified strain, and for example, is increased not less than 1.5 times, not less than 2 times in another example, or not less than 3 times in another example, as compared to that of, for example, a wild-type or an unmodified strain. Moreover, the increase in the enzyme activity can also be confirmed on the basis of detection of an increase in the amount of the PEPCK protein as compared to that in an unmodified or a wild-type strain, and it can be detected by, for example, Western blotting using an antibody (Sambrook, J., and Russell, D. W., Molecular Cloning A Laboratory Manual/Third Edition, New York: Cold Spring Harbor Laboratory Press (2001)).
Examples of the gene coding for PEPCK can include the pckA gene derived from Actinobacillus succinogenes (GenBank Accession No. YP—001343536.1, SEQ ID NO: 6), and homologues of this pckA gene. A pckA gene homologue is a gene that can be derived from another microorganism, shows high homology to the aforementioned pckA gene of Actinobacillus succinogenes, and codes for a protein having the PEPCK activity. Examples include, for example, the pckA gene of Haemophilus influenzae (GenBank Accession No. YP—248516.1, SEQ ID NO: 8), the pckA gene of Pasteurella multocida (GenBank Accession No. NP—246481.1, SEQ ID NO: 10), the pckA gene of Mannheimia succiniciproducens (GenBank Accession No. YP—089485.1, SEQ ID NO: 12), the pckA gene of Yersinia pseudotuberculosis (GenBank Accession No. YP—072243, SEQ ID NO: 14), the pckA gene of Vibrio cholerae (GenBank Accession No. ZP—01981004.1, SEQ ID NO: 16), the pckA gene of Selenomonas ruminantium (GenBank Accession No. AB016600, SEQ ID NO: 64), and so forth.
Examples of pckA gene homologues include genes coding for a protein having a homology of, for example, 90% or more, 95% or more, 98% or more, or 99% or more in another example, to the amino acid sequence of SEQ ID NO: 7, 9, 11, 13, 15, 17 or 65, and coding for phosphoenolpyruvate carboxykinase. Homology of amino acid sequences and nucleotide sequences can be determined by using, for example, the algorithm BLAST of Karlin and Altschul (Pro. Natl. Acad. Sci. USA, 90, 5873 (1993)) or FASTA (Methods Enzymol., 183, 63 (1990)). The BLASTN and BLASTX programs were developed on the basis of this algorithm BLAST (refer to http://www.ncbi.nlm.nih.govbi.nlm.nih.gov). In this specification, the term “homology” can also refer to “identity”, at least when referring to DNA sequences.
Alignment of the amino acid sequences of SEQ ID NOS: 7, 9, 11, 13, 15, 17 and 65 is shown in FIGS. 3 to 6. A consensus of these sequences is shown as SEQ ID NO: 24. The aforementioned pckA gene homologues can include a gene coding for the amino acid sequence of SEQ ID NO: 24, and genes coding for a protein having a homology of, for example, 90% or more, 95% or more, 98% or more, or 99% or more in another example, to the amino acid sequence of SEQ ID NO: 24, and coding for phosphoenolpyruvate carboxykinase.
Since sequences of the pckA gene from several different sources have already been reported as described above, the gene can be obtained by PCR using primers prepared on the basis of those nucleotide sequences. For example, the coding region of the pckA gene of Actinobacillus succinogenes and a flanking region which includes a control region, can be obtained by PCR (polymerase chain reaction, see White, T. J. et al., Trends Genet., 5, 185 (1989)) using the primers shown in SEQ ID NOS: 4 and 5 and chromosomal DNA of Actinobacillus succinogenes can be used as the template. Specific examples of Actinobacillus succinogenes include the 130Z strain (ATCC 55618). This strain can be obtained from American Type Culture Collection (Address: 10801 University Boulevard, Manassas, Va. 20110, United States of America). Homologues of pckA from other microorganisms can also be obtained in a similar manner.
Since the nucleotide sequence of the pckA gene can differ depending on the species or strain of bacteria belonging to the family Enterobacteriaceae, the pckA gene is not limited to a gene coding for the amino acid sequence of SEQ ID NO: 7, 9, 11, 13, 15, 17, 65 or 24, and it can be a mutant or artificially modified gene that codes for a protein having a sequence of SEQ ID NO: 7, 9, 11, 13, 15, 17, 65 or 24, but which includes substitutions, deletions, insertions, additions, etc. of one or several amino acid residues at one or more positions so long as the ability is maintained to improve production of an organic acid by the bacterium with enhanced expression of the gene. Although the number meant by the term “several” can differ depending on positions in the three-dimensional structure of the protein or types of amino acid residues, it can be 1 to 20, 1 to 10 in another example, or 1 to 5 in another example. The substitutions, deletions, insertions, additions, inversions or the like of amino acid residues described above can also include those caused by a naturally occurring mutation based on individual differences, differences in species of microorganisms that contain the pckA gene (mutant or variant), or the like.
The aforementioned substitution can be a conservative substitution that is a neutral substitution, that is, one that does not result in a functional change. The conservative mutation is a mutation wherein substitution takes place mutually among Phe, Trp and Tyr, if the substitution site is an aromatic amino acid; among Leu, Ile and Val, if 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 substitutions considered to be conservative substitutions can 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.
Furthermore, the pckA gene can include a nucleotide sequence encoding a protein having a homology not less than 80% in one example, not less than 90% in another example, not less than 95% in another example, or not less than 97% in another example, to the entire amino acid sequence of SEQ ID NO: 7, 9, 11, 13, 15, 17, 65 or 24, and wherein the encoded protein improves the ability of the bacterium to produce an organic acid when expression of the gene is enhanced. Furthermore, the degree of degeneracy of the gene can vary depending on the host into which the pckA gene is introduced, and therefore codons can be replaced with those which are favorable for the chosen host. Moreover, the pckA gene can code for a protein with an elongated or deleted N- or C-terminal sequence, so long as the gene improves the ability of the bacterium to produce an organic acid when expression of the gene is enhanced in the bacterium. The length of the amino acid sequence to be elongated or deleted can be 50 amino acid residues or less, 20 or less in another example, 10 or less in another example, or 5 or less in another example. More specifically, the pckA gene can encode a protein having the amino acid sequence of SEQ ID NO: 7, 9, 11, 13, 15, 17, 65, or 24, but wherein the sequence is elongated by 5 to 50 amino acid residues on the N-terminal or C-terminal side, or 5 to 50 residues are deleted on either side.
Genes homologous to the pckA gene as described above can be obtained by modifying a gene coding for the amino acid sequence of SEQ ID NO: 7, 9, 11, 13, 15, 17, 65 or 24 so that the protein encoded by the gene includes substitutions, deletions, insertions, or additions of amino acid residues at a specific site(s), for example, by site-specific mutagenesis. Furthermore, homologous genes can also be obtained by conventionally known mutation treatments, such as those described below. For example, the pckA gene can be treated with hydroxylamine or the like in vitro, or the microorganism, for example, Actinobacillus succinogenes, containing the gene can be treated with ultraviolet ray irradiation or a mutagen typically used for mutation, such as N-methyl-N′-nitro-N-nitrosoguanidine (NTG) or ethyl methanesulfonate (EMS). Another method for introducing mutations is error-prone PCR (Cadwell, R. C., PCR Meth. Appl., 2, 28 (1992)), DNA shuffling (Stemmer, W. P., Nature, 370, 389 (1994)), or StEP-PCR (Zhao, H., Nature Biotechnol., 16, 258 (1998)). Regardless of the method used, a mutation can be artificially introduced into the pckA gene by gene recombination to obtain a gene coding for highly active PEPCK.
Whether such homologous pckA genes code for a protein which improves the ability of the bacterium to produce an organic acid when expression is enhanced can be confirmed, for example, by introducing these genes into a ΔadhE strain of the Enterobacter aerogenes AJ110637 strain (FERM BP-10955) or the like, and determining whether the organic acid-producing ability of the bacterium is improved or not. For example, by adding a reducing substance such as glucose, and an organic acid such as malic acid, to the medium and comparing the amount of succinic acid or fumaric acid which is converted from the malic acid utilizing the reducing power which occurs when glucose is assimilated, the effect can be more clearly verified.
Examples of the pckA gene also include a DNA that hybridizes with a nucleotide sequence complementary to the sequence of SEQ ID NO: 6, 8, 10, 12, 14, 16 or 64, or a probe that can be prepared from these sequences under stringent conditions and codes for a protein which has the PEPCK activity. The “stringent conditions” can be conditions under which a so-called specific hybrid is formed, and non-specific hybrid is not formed. Examples include, for example, conditions under which DNAs having high homology to each other, for example, DNAs having a homology of, for example, not less than 80%, not less than 90%, not less than 95%, or not less than 97% in another example, hybridize with each other, and DNAs having homology lower than the above levels do not hybridize with each other. “Stringent conditions” can also include washing conditions which are typical in Southern hybridization, for example, washing once, or twice or three times, at salt concentrations and a temperature of 1×SSC, 0.1% SDS at 60° C., 0.1×SSC, 0.1% SDS at 60° C. in another example, or 0.1×SSC, 0.1% SDS at 68° C. in another example.
A partial sequence of a nucleotide sequence complementary to the sequence of SEQ ID NO: 6, 8, 10, 12, 14, 16 or 64 can also be used as the probe. Such a probe can be prepared by PCR using oligonucleotides prepared on the basis of any one of these nucleotide sequences as primers and a DNA fragment containing any one of the sequences as the template. When a DNA fragment having a length of about 300 bp is used as the probe, the washing conditions after hybridization under the aforementioned conditions can be exemplified by 2×SSC, 0.1% SDS at 50° C.
The aforementioned descriptions concerning gene homologues and conservative mutations can be similarly applied to the other enzyme genes described in this specification.
By modifying a bacterium so that expression of a pckA gene as described above is enhanced, the PEPCK enzyme activity can be enhanced.
The expression “modified so that expression of the pckA gene is enhanced” or “modified to enhance express of the pckA gene” can mean that the number of PEPCK molecules per cell is increased, or that the activity per PEPCK molecule is increased, etc., as compared to a parent strain or a wild-type strain. Examples of the wild-type strain that can be used for comparison include the Enterobacter aerogenes ATCC 13048 strain and so forth.
Expression of the pckA gene can be enhanced by increasing the copy number of the pckA gene. For example, the copy number of the gene can be increased by ligating a fragment containing the pckA gene to a vector that functions in the chosen bacterium, for example, a multi copy vector, to prepare a recombinant DNA, and transforming the bacterium which is able to produce an organic acid as described above with the DNA. Alternatively, after the transformation of a wild-type strain of a bacterium, the ability to produce an organic acid can be imparted to the transformed bacterium. The copy number of the gene can also be increased by transferring a single copy or multiple copies of the pckA gene to the bacterial chromosome. Transfer of the pckA gene to the chromosome can be confirmed by Southern hybridization using a portion of the pckA gene as a probe.
Expression of the pckA gene can also be enhanced by modifying an expression control sequence of the pckA gene. For example, the promoter sequence of the pckA gene can be replaced with a stronger promoter, or by making a promoter sequence closer to a consensus sequence (WO00/18935).
Methods for constructing a bacterium which has an ability to produce an organic acid and has been modified so that the expression level of the pckA gene is increased are explained below. These methods can be performed as described in a manual such as Molecular Cloning (Cold Spring Harbor Laboratory Press, Cold Spring Harbor (USA), 2001).
Expression of the pckA gene can be enhanced by increasing the copy number by amplifying the pckA gene using a plasmid such as those described below. First, the pckA gene is cloned from the chromosome of Actinobacillus succinogenes or the like. Chromosomal DNA can be prepared from a bacterium, for example, by the method of Saito and Miura (see H. Saito and K. Miura, Biochem. Biophys. Acta, 72, 619 (1963); Text for Bioengineering Experiments, Edited by the Society for Bioscience and Bioengineering, Japan, p 97-98, Baifukan Co., Ltd., 1992), or the like. Oligonucleotides for use in PCR can be synthesized on the basis of the aforementioned known information, for example, the synthetic oligonucleotides shown in SEQ ID NOS: 4 and 5 can be used to amplify the pckA gene.
A gene fragment including the pckA gene amplified by PCR can itself be amplified by inserting the fragment into a vector having a replication origin that enables autonomous replication in the chosen bacterium, then transforming the bacterium with the vector. Examples of vectors which can be used to transform Enterobacteriaceae bacteria include pUC19, pUC18, pHSG299, pHSG399, pHSG398, RSF1010, pBR322, pACYC184, pMW219, and the like.
To prepare a recombinant DNA by ligating the pckA gene to a vector that functions in the chosen bacterium, the vector is digested with a restriction enzyme suitable for the ends of the pckA gene. Such a restriction enzyme site can be introduced in advance into the synthetic oligonucleotide which is used to amplify the pckA gene. Ligation is usually performed by a ligase such as T4 DNA ligase.
In order to introduce a recombinant plasmid prepared as described above into a bacterium, any known transformation method reported to date can be employed. For example, recipient cells can be treated with calcium chloride so as to increase permeability for the DNA, which has been reported for Escherichia coli K-12 (Mandel, M. and Higa, A., J. Mol. Biol., 53, 159 (1970)). Also, competent cells can be prepared from growing cells and DNA can be introduced into these cells, which has been reported for Bacillus subtilis (Duncan, C. H., Wilson, G. A. and Young, F. E., Gene, 1, 153 (1977)). Another method is to make DNA recipient cells into protoplasts or spheroplasts which easily take up a recombinant DNA, and a recombinant DNA can be introduced into these cells, which are known for Bacillus subtilis, actinomycetes, and yeasts (Chang, S. and Choen, S. N., Mol. Gen. Genet., 168, 111 (1979); Bibb, M. J., Ward, J. M. and Hopwood, O. A., Nature, 274, 398 (1978); Hinnen, A., Hicks, J. B. and Fink, G. R., Proc. Natl. Acad. Sci. USA, 75, 1929 (1978)). In addition, bacteria can also be transformed by the electric pulse method (Japanese Patent Laid-open No. 2-207791) or by the conjugal transfer method (Biotechnology (NY). 1991 January; 9(1):84-7).
The copy number of the pckA gene can also be increased by integrating multiple copies of the pckA gene into the chromosomal DNA of the bacterium, which can be accomplished by homologous recombination. This technique is performed by targeting a sequence which is present in multiple copies on the chromosomal DNA. Such sequences can include a repetitive DNA or inverted repeat present at the end of a transposable element. Alternatively, as disclosed in Japanese Patent Laid-open No. 2-109985, multiple copies of the pckA gene can be introduced into a chromosomal DNA by incorporating them into a transposon, and transferring the transposon (Japanese Patent Laid-open Nos. 2-109985, 7-107976, Mol. Gen. Genet., 245, 397-405 (1994); Plasmid, 2000 November; 44(3): 285-91).
Expression of the pckA gene can also be enhanced by replacing a native expression control sequence, such as a promoter of the pckA gene, on the chromosomal DNA or a plasmid with a stronger promoter. Other methods include modifying a factor involved in expression control of the pckA gene, such as operator or repressor, or ligating a strong terminator (Hamilton et al., Journal of Bacteriology 171:4617-4622; WO98/004715). For example, the lac promoter, trp promoter, trc promoter, tac promoter, PR promoter derived from λ-phage, lacUV promoter, and the like are known as strong promoters. Methods for evaluating the strength of promoters and examples of strong promoters are described in the paper of Goldstein et al. (Prokaryotic promoters in biotechnology, Biotechnol. Annu. Rev., 1955, 1, 105-128), and the like. Furthermore, as disclosed in WO00/18935, the strength of a promoter can be increased by making several nucleotide substitutions in the promoter region of a target gene so as to make the sequence closer to a consensus sequence. For example, the −35 region can be replaced with TTGACA or TTGCCA, and the −10 region can be replaced with TATAAT or TATAAC. In addition, it is known that the translation efficiency of mRNA is significantly affected by substituting several nucleotides in the spacer region between the ribosome-binding site (RBS) and the translation initiation codon, in particular, the sequence immediately upstream of the initiation codon.
Expression of a gene can also be enhanced by extending the survival time of the mRNA or by preventing degradation of the encoded protein in the cells. An expression control sequence such as a promoter which is upstream of the pckA gene can also be identified by using a promoter search vector or gene analysis software such as GENETYX. Expression of the pckA gene can be enhanced by substituting or modifying the promoter.
Modifying an expression control sequence can be combined with increasing the copy number of the pckA gene.
A bacterial strain which is modified to decrease the activity of one or more enzymes such as lactate dehydrogenase (LDH), α-acetolactate decarboxylase (α-ALDC), alcohol dehydrogenase (ADH), pyruvate formate lyase (PFL) and phosphate acetyltransferase (PTA), in addition to increasing the expression of the pckA gene, can be more effective. The expression “modified so that lactate dehydrogenase activity is decreased” can mean that the lactate dehydrogenase activity is decreased as compared to the activity in a strain in which lactate dehydrogenase is unmodified. The lactate dehydrogenase activity per cell can be decreased to 10% or lower as compared to that of a strain in which lactate dehydrogenase is unmodified. The lactate dehydrogenase activity can also be completely deleted. The 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 a method for producing a mutant strain of bacteria belonging to the family Enterobacteriaceae 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.
In order to decrease or delete the activity of LDH, a mutation can be introduced into the LDH gene on the chromosome by a typical 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/or the Shine-Dalgarno (SD) sequence can be modified by gene recombination. Furthermore, a mutation which results in 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 LDH coding on the chromosome can be introduced. Alternatively, a part of the gene, or the entire gene can be deleted (Journal of Biological Chemistry 272:8611-8617 (1997)). Furthermore, the LDH activity can also be decreased or deleted by gene disruption, for example, by mutating or deleting the coding region of the LDH gene, and replacing the normal or native LDH gene on the chromosome with the mutant LDH gene by homologous recombination or the like. Alternatively, a transposon or IS factor can be introduced into the gene.
In order to introduce a mutation that reduces or deletes the LDH activity by genetic recombination, for example, the following methods can be used. The LDH gene on the chromosome 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 a functional enzyme, and transforming a bacterium with a DNA containing the mutant gene to cause homologous recombination between the mutant gene and the gene on the chromosome. Such site-specific mutagenesis based on gene substitution utilizing homologous recombination has been already reported, and includes the method of Red driven integration developed by Datsenko and Wanner (Proc. Natl. Acad. Sci. USA, 2000, vol. 97, No. 12, pp. 6640-6645), which can use a linear DNA in the Red driven integration in combination with an excision system derived from λ phage (Cho, E. H., Gumport, R. I., Gardner, J. F., J. Bacteriol., 184: 5200-5203 (2002, and WO2005/010175), and/or 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. Site-specific mutagenesis based on gene substitution using homologous recombination as described above can also be performed with a plasmid that is unable to replicate in the chosen host.
The LDH gene of Enterobacter aerogenes, and specifically the nucleotide sequence of the D-LDH gene (ldhA) of the Enterobacter aerogenes AJ110637 strain (FERM BP-10955), is shown in SEQ ID NO: 20. The amino acid sequence encoded by this gene is shown in SEQ ID NO: 48.
The expression “modified so that alcohol dehydrogenase activity is decreased” or “modified to decrease alcohol dehydrogenase activity” can mean that the alcohol dehydrogenase activity is decreased as compared to that of a strain in which the alcohol dehydrogenase is unmodified. The alcohol dehydrogenase activity per cell can be decreased to 10% or lower as compared to that of a strain in which the alcohol dehydrogenase is unmodified. The alcohol dehydrogenase activity can also be completely deleted. The decrease of the alcohol dehydrogenase activity can be confirmed by measuring the alcohol dehydrogenase activity by a known method (Lutstorf, U. M., Schurch, P. M. & von Wartburg, J. P., Eur. J. Biochem., 17, 497-508 (1970)). Specific examples of the method for producing a mutant strain of bacterium belonging to the family Enterobacteriaceae 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. A bacterium in which the alcohol dehydrogenase activity is decreased and expression of the pckA gene is enhanced can be obtained, for example, by disrupting the gene coding for alcohol dehydrogenase (ADH), and transforming the bacterium with a recombinant vector containing the pckA gene. However, either the modification for decreasing the ADH activity or the modification for enhancing expression of the pckA gene can be performed first. The alcohol dehydrogenase activity can be decreased by a method similar to the method for decreasing the lactate dehydrogenase activity described above.
The nucleotide sequence of the ADH gene (adhE) from the Enterobacter aerogenes AJ110637 strain (FERM ABP-10955) is shown in SEQ ID NO: 21, and the amino acid sequence encoded by this gene is shown in SEQ ID NO: 49.
The bacterium in which the alcohol dehydrogenase activity is decreased and expression of the pckA gene is enhanced can be obtained, for example, by disrupting the ADH gene, and transforming the bacterium with a recombinant vector containing the pckA gene, as described in the examples section. A bacterium in which the ADH activity and the LDH activity are decreased and expression of the pckA gene is enhanced can be obtained by, for example, preparing a bacterium in which an LDH gene is disrupted from a bacterium in which an ADH gene is disrupted, and transforming this bacterium with a recombinant vector containing the pckA gene, as described in the examples section.
The expression “modified so that phosphate acetyltransferase activity is decreased” or “modified to decrease phosphate acetyltransferase activity” can mean that the phosphate acetyltransferase activity is decreased as compared to that of a strain in which the phosphate acetyltransferase is unmodified. The phosphate acetyltransferase activity per cell can be decreased to 10% or lower of that of an unmodified phosphate acetyltransferase. The phosphate acetyltransferase activity can also be completely deleted. The decrease of the phosphate acetyltransferase activity can be confirmed by measuring the phosphate acetyltransferase activity by a known method (Klotzsch, H. R., Meth. Enzymol., 12, 381-386 (1969)). The bacterium in which the phosphate acetyltransferase activity is decreased and expression of the pckA gene is enhanced can be obtained by, for example, preparing a bacterium in which the PTA gene is disrupted, and transforming this bacterium with a recombinant vector containing the pckA gene. However, either the modification for decreasing the PTA activity or the modification for enhancing expression of the pckA gene can be performed first. The phosphate acetyltransferase activity can be decreased by a method similar to the method for decreasing the lactate dehydrogenase activity described above.
The nucleotide sequence of the PTA gene (pta) of the Enterobacter aerogenes AJ110637 strain (FERM ABP-10955) is shown in SEQ ID NO: 50, and the amino acid sequence encoded by this gene is shown in SEQ ID NO: 51. Although the first amino acid residue is indicated as Val using the universal code in these sequences, gtg can be used as the start codon in bacteria, and it is very likely to be actually Met.
The bacterium in which the ADH activity, the LDH activity and the PTA activity are decreased, and expression of the pckA gene is enhanced can be obtained, for example, by disrupting the PTA gene in a bacterium in which the ADH gene and the LDH gene are already disrupted, and transforming the bacterium with a recombinant vector containing the pckA gene, as described in the examples section.
The expression “modified so that α-acetolactate decarboxylase activity is decreased” or “modified to decrease α-acetolactate decarboxylase activity” can mean that the α-acetolactate decarboxylase activity is decreased as compared to that of a strain in which α-acetolactate decarboxylase is unmodified. The α-acetolactate decarboxylase activity per cell can be decreased to 10% or lower as compared to that of a strain in which the α-acetolactate decarboxylase is unmodified. The α-acetolactate decarboxylase activity can be completely deleted. The decrease of the α-acetolactate decarboxylase activity can also be confirmed by measuring the α-acetolactate decarboxylase activity by a known method (Juni, E. J., Biol. Chem., 195, 715-726 (1952)). The bacterium in which the α-acetolactate decarboxylase is decreased and expression of the pckA gene is enhanced can be obtained, for example, by disrupting the α-ALDC gene (aldC), and transforming the bacterium with a recombinant vector containing the pckA gene. However, either the modification for decreasing the α-ALDC activity or the modification for enhancing expression of the pckA gene can be performed first. The α-ALDC activity can be decreased by a method similar to the method for decreasing the lactate dehydrogenase activity described above.
The nucleotide sequence of the α-ALDC gene (aldC) from the Enterobacter aerogenes AJ110637 strain (FERM ABP-10955) is shown in SEQ ID NO: 52, and the amino acid sequence encoded by this gene is shown in SEQ ID NO: 53.
The bacterium in which the ADH activity, the LDH activity, the PTA activity and the α-ALDC activity are decreased, and expression of the pckA gene is enhanced can be obtained, for example, by disrupting the α-ALDC gene in a bacterium in which the ADH gene, the LDH gene and the PTA gene are already disrupted, and transforming the bacterium with a recombinant vector containing the pckA gene, as described in the examples section.
The expression “modified so that pyruvate formate lyase activity is decreased” or “modified to decrease 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 per cell can be decreased to 10% or lower of that of a strain in which the pyruvate formate lyase is unmodified. The pyruvate formate lyase activity can also be completely deleted. The decrease of 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 bacterium in which pyruvate formate lyase activity is decreased and expression of the pckA gene is enhanced can be obtained, for example, by disrupting the PFL gene, and transforming the bacterium with a recombinant vector containing the pckA gene. However, either the modification for decreasing the PFL activity or the modification for enhancing expression of pckA 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.
The nucleotide sequence of the PFL gene (pflB) from the Enterobacter aerogenes AJ110637 strain (FERM ABP-10955) is shown in SEQ ID NO: 54, and the amino acid sequence encoded by this gene is shown in SEQ ID NO: 55.
The bacterium in which the ADH activity, the LDH activity, the PTA activity, the α-ALDC activity and the PFL activity are decreased, and expression of the pckA gene is enhanced can be obtained, for example, by disrupting the PFL gene in a bacterium in which the ADH gene, the LDH gene, the PTA gene and the α-ALDC gene are already disrupted, and transforming this bacterium with a recombinant vector containing the pckA gene, as described in the examples section.
A bacterium modified so that the pyruvate carboxylase (PC) activity is enhanced, in addition to the enhanced expression of the pckA gene, can also be used. Enhancing the pyruvate carboxylase activity can be combined with decreasing the activities of one or more enzymes, such as lactate dehydrogenase (LDH), the α-acetolactate decarboxylase (α-ALDC), the alcohol dehydrogenase (ADH), the pyruvate formate lyase (PFL), and the phosphate acetyltransferase (PTA). The expression “modified so that pyruvate carboxylase activity is enhanced” or “modified to enhance 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, by measuring decrease of NADH (Moss, J. & Lane, M. D., Adv. Enzymol., 35, 321-442 (1971)).
As the PC gene, a gene for which the nucleotide sequence is already determined, or a gene obtained by isolating a DNA fragment encoding a protein having the PC activity from a chromosome of a microorganism, animal, plant, or the like and determining the nucleotide sequence can be used. After the nucleotide sequence is determined, a gene synthesized on the basis of that sequence can also be used.
As the PC gene, for example, a PC gene derived from or native to a coryneform bacterium such as Corynebacterium glutamicum or Brevibacterium flavum (Peters-Wendisch, P. G. et al., 1998, Microbiology, vol. 144:915-927) (SEQ ID NO: 22) can be used. Furthermore, so long as the function of the encoded PC, that is, the characteristic concerning carbon dioxide fixation, is not substantially degraded, the PC gene can have the nucleotide sequence of SEQ ID NO: 22, but can include substitution or deletion of one or more nucleotides, insertion of one or more nucleotides, or dislocation of a portion of the nucleotide sequence, or other derivatives. A DNA that hybridizes with a DNA having the nucleotide sequence of SEQ ID NO: 22 under stringent conditions, or a DNA having a homology of, for example, 90% or more, 95% or more, or 99% or more in another example, to the nucleotide sequence of SEQ ID NO: 22 and coding for a protein having the PC activity can also be used. Examples of the stringent conditions can include conditions of washing in ordinary Southern hybridization, i.e., conditions for hybridization at salt concentrations and temperatures of 1×SSC, 0.1% SDS at 60° C., or 0.1×SSC, 0.1% SDS at 60° C. in another example.
PC genes from bacteria other than Corynebacterium glutamicum, as well as from other microorganisms, animals, and plants can also be used. In particular, the reported sequences of PC genes derived from microorganisms, animals and plants described below (citations are indicated in brackets), and they can be obtained by hybridization or amplification of the ORF regions by PCR 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 those used for enhancing expression of the pckA gene described above.
The activity of phosphoenolpyruvate carboxylase (PEPC) of the bacterium of the present invention may not be decreased or eliminated, and the gene encoding PEPC can be a wild-type gene.
<2> Method for Producing Organic Acid
An organic acid can be produced by using a bacterium that is able to produce an organic acid, and has been modified so that expression of the pckA gene is enhanced as described above. Specifically, an organic acid can be produced by allowing the bacterium, or a product obtained by processing the bacterium, to act on an organic raw material in a reaction mixture containing carbonate ions, bicarbonate ions, or carbon dioxide gas to produce the organic acid, and collecting the organic acid.
In one example of the method, by culturing the bacterium in a medium containing carbonate ions, bicarbonate ions, or carbon dioxide gas, and an organic raw material, proliferation of the bacterium and production of the organic acid occur simultaneously. In this example, the medium can be the reaction mixture. Proliferation of the bacterium and production of the organic acid can be simultaneously attained, or there can be a period during the culture when proliferation of the bacterium mainly occurs, and a period in which production of the organic acid mainly occurs.
In another example, by allowing cells to proliferate in a medium in the presence of carbonate ions, bicarbonate ions, or carbon dioxide gas, and an organic raw material, and thereby allowing the cells to act on the organic raw material in the medium or reaction mixture, an organic acid can be produced. In this example, a product obtained by processing the cells of the bacterium can also be used. Examples of the product obtained by processing cells include, for example, immobilized cells which can be obtained with acrylamide, carragheenan, or the like, disrupted cells, centrifugation supernatant of the disrupted product, fraction obtained by partial purification of the supernatant by ammonium sulfate treatment or the like.
Although the bacteria can be cultured on a solid medium such as agar medium by slant culture, bacteria previously cultured in a liquid medium (seed culture) are other examples.
As the medium used for the culture, a typical microorganism culture medium can be used. For example, a typical medium obtained by adding natural nutrients such as meat extract, yeast extract and peptone, to a composition including inorganic salts such as ammonium sulfate, potassium phosphate and magnesium sulfate can be used.
In the aforementioned first example, the carbon source that is added to the medium also serves as the organic raw material for the production of the organic acid.
In the aforementioned second example, after the culture, the cells 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 it includes a carbon source which the chosen bacterium can assimilate to produce succinic acid. However, fermentable carbohydrates including carbohydrates such as galactose, lactose, glucose, fructose, glycerol, sucrose, saccharose, starch and cellulose, polyalcohols such as mannitol, xylitol and ribitol, and the like are usually used. 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 fermentable carbohydrates can also be used. The fermentable carbohydrates can be used independently or in combination. Although the concentration of the aforementioned organic raw material is not particularly limited, it is more advantageous when the concentration is as high as possible within such a range that the production of the organic acid is not inhibited. In the aforementioned first example, 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, additional organic raw material can be added as its concentration decreases as the reaction progresses.
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 medium for culturing bacteria, 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 as it is a nitrogen source which the chosen bacterium can assimilate 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 at the time of the reaction, an appropriate amount of 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, the pH of the reaction mixture is adjusted to be within the aforementioned range with an alkaline substance, carbonate, urea, or the like even during the reaction, if needed.
The reaction mixture can include water, a buffer, a medium, or the like, but media is a particular example. The media 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. The carbonate or bicarbonate ions can be supplied from magnesium carbonate, sodium carbonate, sodium bicarbonate, potassium carbonate, or potassium bicarbonate, which 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 the 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 present 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 bacterium is generally in the range of 25 to 40° C. 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 can be, 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 bacterial culture can be performed under aerobic conditions. Alternatively, the organic acid production reaction can be performed under aerobic conditions, microaerobic conditions or anaerobic conditions. For the reaction under microaerobic conditions or anaerobic conditions, the reaction can be performed in a sealed reaction vessel without aeration, by supplying an inert gas such as nitrogen gas to the reaction mixture, by supplying an inert gas containing carbon dioxide gas to the reaction mixture, and the like.
The organic acid that accumulates in the reaction mixture (culture medium) 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, and then the resulting solution can be desalted with an ion exchange resin or the like. 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, after succinic acid is produced, a polymerization reaction can be carried out by using the 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. 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 obtainable by polymerizing a diol such as butanediol and ethylene glycol, and succinic acid, succinic acid polyamides obtainable by polymerizing a diamine such as hexamethylenediamine and succinic acid, and the like. In addition, succinic acid and succinic acid-containing polymers, and compositions containing these can be used as food additives, pharmaceutical agents, cosmetics, and the like.
EXAMPLES
Hereinafter, the present invention will be explained more specifically with reference to the following non-limiting examples.
Example 1
1-1> Acquisition of the Threonine Operon Promoter Fragment from the Escherichia coli MG1655 Strain
The entire genomic nucleotide 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, the promoter region of the threonine operon (thrLABC) was amplified by PCR using a synthetic oligonucleotide having a Sad site (SEQ ID NO: 1) as the 5′ primer, a synthetic oligonucleotide (SEQ ID NO: 2) as the 3′ primer, and genomic DNA from the Escherichia coli MG1655 strain (ATCC 47076, ATCC 700926) as the template. As a result, the threonine operon promoter fragment (A) (SEQ ID NO: 3) was obtained.
<1-2> Acquisition of a Phosphoenolpyruvate Carboxykinase Gene Fragment from the Actinobacillus succinogenes 130Z Strain (ATCC 55618)
The entire genomic nucleotide sequence of the Actinobacillus succinogenes 130Z strain has also already been elucidated (GenBank Accession No. CP000746). Primers were designed based on the nucleotide sequence of the gene coding for PEPCK (gene name: pckA), and used to perform PCR amplification. PCR was performed by using the synthetic oligonucleotide shown in SEQ ID NO: 4 as the 5′ primer, the synthetic oligonucleotide having an Sad site shown in SEQ ID NO: 5 as the 3′ primer, and the genomic DNA from the Actinobacillus succinogenes 130Z strain as the template to obtain a pckA gene fragment (B) (SEQ ID NO: 6).
<1-3> Construction of the Plasmid for pckA Gene Amplification
PCR was performed by using the fragments (A) and (B) as templates, and the primers of SEQ ID NOS: 1 and 5 having the SalI site to obtain a gene fragment (C) consisting of the fragments (A) and (B) ligated to each other. This gene fragment (C) was treated with the restriction enzyme Sad, purified, and the product was ligated with the plasmid vector pSTV28 (Takara Bio) which had been digested with the restriction enzyme Sad to construct a plasmid pSTV28::Pthr::pckA for pckA amplification.
<1-4> Preparation of a pckA-amplified Strain from the Enterobacter aerogenes AJ110637 Strain (FERM BP-10955)
The Enterobacter aerogenes AJ110637 strain (FERM BP-10955, see Reference Example 1) was transformed with pSTV28::Pthr::pckA obtained above, and pSTV28 by the electric pulse method, applied to an LB agar medium containing 40 μg/ml of chloramphenicol, and cultured at 37° C. for about 18 hours. The colonies that appeared were purified, and plasmids were extracted in a conventional manner to confirm that the target plasmids were present. The obtained strains were designated Enterobacter aerogenes AJ110637 pSTV28::Pthr::pckA and Enterobacter aerogenes AJ110637 pSTV28, respectively.
Example 2
Effect of pckA Amplification in a Succinic Acid-Producing Strain from Enterobacter Bacterium
The Enterobacter aerogenes AJ110637 pSTV28::Pthr::pckA and the Enterobacter aerogenes AJ110637 pSTV28 were each uniformly applied to an LB plate containing 40 μg/ml of chloramphenicol, and cultured at 37° C. for 16 hours. Then, each plate was put into Anaeropack (for compromised culture of anaerobes, Mitsubishi Gas Chemical, product number A-04), and incubated at 37° C. for 16 hours under anaerobic conditions. The cells which appeared on the plate were washed with 0.8% brine and suspended so that the resulting cell suspension has an OD=1.0 (600 nm) after 51-times dilution. This cell suspension in a volume of 100 μl, and a production medium in a volume of 1.3 ml in which dissolved gases in the medium were replaced with carbon dioxide beforehand, were put into a 1.5-ml volume microtube, and the cells were cultured at 31.5° C. for 10 hours with shaking. The composition of the production medium is shown below.
Composition of organic acid production medium for Enterobacter bacteria:












Mixture A:











Glucose
40
g/L









(final concentration)











Magnesium sulfate heptahydrate
1
g/L







Mixture B:











Ammonium sulfate
1
g/L



Potassium dihydrogenphosphate
1
g/L



Manganese sulfate pentahydrate
10
mg/L



Iron sulfate heptahydrate
10
mg/L



Yeast Extract
2
g/L



Biotin
1
mg/L










(adjusted to pH 5.5 with KOH)








C:











Calcium carbonate
50
g/L










(Japanese Pharmacopoeia)










The ingredients of the A and B mixtures were sterilized at 115° C. for 10 minutes by autoclaving, the calcium carbonate (C) was sterilized at 180° C. for 3 hours with dry heat, and then left to cool, and A, B, and C were mixed.
After the culture, the amount of the organic acid which had accumulated in the medium was analyzed by liquid chromatography. Two Shim-pack SCR-102H (Shimadzu) columns connected in series were used, and the 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 the organic acid was quantified by measuring electric conductivity with CDD-10AD (Shimadzu). The amount of consumed glucose, change in OD, and the accumulated organic acid and yield based on the consumed glucose determined after 24 hours are shown in Table 1.










TABLE 1







pSTV28
pSTV28::Pthr::pckA


















Consumed glucose
16.6 (±0.78)
13.6 (±0.13)


(g/L)


ΔOD
1.54 (±0.08)
2.27 (±0.07)


(600 nm)


Accumulated malic
0.04 (±0.01)
0.20 (±0.02)


acid (g/L)


Yield of malic acid based on
0.24 (±0.05)
1.45 (±0.15)


consumed glucose (%)


Accumulated succinic
0.63 (±0.01)
2.97 (±0.13)


acid (g/L)


Yield of succinic
3.80 (±0.12)
21.8 (±0.75)


acid based on


consumed glucose (%)









The pckA gene-amplified strain, Enterobacter aerogenes AJ110637 pSTV28::Pthr::pckA provided markedly improved accumulation of malic acid and succinic acid and yields thereof based on consumed glucose as compared to the control, Enterobacter aerogenes AJ110637 pSTV28.
Example 3
<3-1> Construction of adhE-deficient Strain of Enterobacter aerogenes AJ110637
When Enterobacter aerogenes AJ110637 is grown in a medium containing a sugar source, it produces a marked amount of ethanol. Therefore, adhE coding for alcohol dehydrogenase was deleted to suppress the production of ethanol.
A gene fragment for deletion of adhE was prepared by PCR using a plasmid pMW-attL-Tc-attR (WO2005/010175) as the template, and the oligonucleotides of SEQ ID NOS: 18 and 19 as primers. pMW118-attL-Tc-attR was obtained by inserting the attL and attR genes, which are the attachment sites of λ phage, and the Tc gene, which is an antibiotic resistance gene, into pMW118 (Takara Bio), in the following order: attL-Tc-attR (see Reference Example 3). By PCR described above, a gene fragment containing a tetracycline resistance gene, attL and attR sites of λ phage at the both ends of tetracycline gene, and 60 bp of the upstream sequence and 59 bp of the 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 (see FIG. 1, Reference Example 2) to obtain the Enterobacter aerogenes AJ110637/RSF-Red-TER strain. This strain was cultured overnight in LB medium containing 40 μg/mL of chloramphenicol. Then, the culture medium was inoculated in a 1/100 volume to 50 mL of LB medium containing 40 μg/mL of chloramphenicol and 0.4 mM isopropyl-β-D-thiogalactopyranoside, and a second 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 500 ng of the PCR fragment prepared in the above section was introduced into the cells by using GENE PULSER II (BioRad) under the following conditions: a field strength of 20 kV/cm, capacitor capacity of 25 μF, and resistance of 200 μl Ice-cooled SOC medium (20 g/L of Bacto tryptone, 5 g/L of yeast extract, 0.5 g/L of NaCl, 10 g/L of glucose) 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 on the same plate, and then it was confirmed by PCR that the adhE gene had been replaced with the tetracycline resistance gene.
Then, in order to eliminate the RSF-Red-TER plasmid from each recombinant strain obtained as described above, the strains were applied to an LB medium containing 10% sucrose and 1 mM IPTG, and cultured overnight at 37° C. A strain lacking chloramphenicol resistance was selected as AJ110637ΔadhE from the colonies that appeared.
<3-2> Construction of a pckA-amplified Strain from Enterobacter aerogenes AJ110637ΔadhE
The Enterobacter aerogenes AJ110637ΔadhE strain obtained above was transformed with the pSTV28::Pthr::pckA plasmid for amplification of pckA and pSTV28, applied to a LB agar medium containing 40 μg/ml of chloramphenicol and 25 μg/ml of tetracycline, and cultured at 37° C. for about 18 hours. The colonies that appeared were purified, and plasmids were extracted in a conventional manner to confirm that the target plasmids were present. The obtained strains were designated Enterobacter aerogenes AJ110637ΔadhE+pSTV28::Pthr::pckA and Enterobacter aerogenes AJ110637ΔadhE+pSTV28, respectively.
<3-3> Effect of pckA Amplification in a Succinic Acid-Producing Strain of Enterobacter Bacterium which is Deficient in Alcohol Dehydrogenase
Succinic acid-producing abilities of Enterobacter aerogenes AJ110637ΔadhE+pSTV28::Pthr::pckA and Enterobacter aerogenes AJ110637ΔadhE+pSTV28 were compared by using the same evaluation method as outlined above. The results obtained after 45 hours are shown in Table 2.










TABLE 2







ΔadhE+pSTV28
ΔadhE+pSTV28::Pthr::pckA


















Consumed glucose
3.29 (±0.43)
7.45 (±0.95)


(g/L)


ΔOD
0.30 (±0.10)
0.85 (±0.18)


(600 nm)


Accumulated succinic
0.40 (±0.10)
5.19 (±0.69)


acid (g/L)


Yield of succinic
11.95 (±1.48) 
69.61 (±0.39) 


acid based on


consumed glucose (%)









The pckA gene-amplified strain, Enterobacter aerogenes AJ110637ΔadhE+pSTV28::Pthr::pckA, showed markedly increased accumulation of succinic acid and yield thereof based on consumed glucose compared with Enterobacter aerogenes AJ110637ΔadhE+pSTV28 as compared to the control.
Example 4
<4-1> Construction of a Strain from Enterobacter aerogenes AJ110637ΔadhE which is Deficient in the Acetic Acid, Lactic Acid, 2,3-butanediol, and Formic Acid Synthesis Genes
If AJ110637ΔadhE is allowed to grow in a medium containing a sugar source, acetic acid, lactic acid, 2,3-butanediol, and formic acid are produced in the medium. Therefore, a strain with an improved ability to produce succinic acid was constructed by deleting the synthesis pathways of these substances.
<4-2> Deletion of an Antibiotic Resistance Gene from AJ110637ΔadhE
The RSF-int-xis plasmid was used to remove the tetracycline resistance gene from AJ110637ΔadhE (refer to Reference Example 4). RSF-int-xis was introduced into the gene-disrupted strain by the electric pulse method, and the transformant was added to an LB medium containing 40 μg/ml of chloramphenicol, and cultured at 30° C. to obtain a strain containing RSF-int-xis. This strain was purified on LB medium containing 40 μg/ml of chloramphenicol and 1 mM IPTG, and plural single colonies were obtained. The obtained strains were added to a medium containing 25 μg/ml of tetracycline, and cultured overnight at 37° C. It was confirmed that the strains did not grow. Thus, these strains were confirmed to be lacking the antibiotic resistance gene. Then, in order to eliminate the RSF-int-xis plasmid from the strains, they were added to LB medium containing 10% sucrose and 1 mM IPTG, and cultured overnight at 37° C. A strain without chloramphenicol resistance was selected from the colonies that appeared, and used to delete the biosynthetic pathways of acetic acid, lactic acid, 2,3-butanediol and formic acid.
<4-3> Construction of a D-lactate Dehydrogenase-Deficient Strain
Lactic acid production can be suppressed by deleting lactate dehydrogenase. The ldhA gene, which encodes D-lactate dehydrogenase, was disrupted as follows. By performing PCR using the oligonucleotide primers shown in SEQ ID NOS: 56 and 57, and the template pMW-attL-Km-attR, AJ110637ΔadhEΔldhA was constructed from AJ110637ΔadhE in which the antibiotic resistance gene was deleted in the same manner as that of Example 3 described above. This strain was designated ES02.
<4-4> Construction of a Strain Deficient in Phosphate Acetyltransferase
Production of acetic acid can be suppressed by deleting phosphate acetyltransferase. The pta gene coding for phosphate acetyltransferase was disrupted as follows. By performing PCR using the oligonucleotides shown in SEQ ID NOS: 58 and 59 and pMW-attL-Km-attR as a template, AJ110637ΔadhEΔldhAΔpta was constructed from AJ110637ΔadhEΔldhA, in which the antibiotic resistance gene was deleted in the same manner as that of Example 3 mentioned above. This strain was designated ES03.
<4-5> Construction of a Strain Deficient in α-acetolactate Decarboxylase
Production of 2,3-butanediol can be suppressed by deleting α-acetolactate decarboxylase. The aldC gene coding for α-acetolactate decarboxylase was disrupted as follows. By performing PCR using the oligonucleotides shown in SEQ ID NOS: 60 and 61 and pMW-attL-Km-attR as a template, AJ110637ΔadhEΔldhAΔptaΔaldC was constructed from AJ110637ΔadhEΔldhAΔpta, in which the antibiotic resistance gene was deleted in the same manner as that of Example 3 described above. This strain was designated ES04.
<4-6> Construction of a Strain Deficient in Pyruvate Formate Lyase
Production of formic acid can be suppressed by deleting pyruvate formate lyase. The pflB gene coding for pyruvate formate lyase was disrupted as follows. By performing PCR using the oligonucleotides shown in SEQ ID NOS: 62 and 63 and pMW-attL-Km-attR as a template, AJ110637ΔadhEΔldhAΔptaΔaldCΔpflB was constructed from AJ110637ΔadhEΔldhAΔptaΔaldC, in which the antibiotic resistance gene was deleted in the same manner as that of Example 3 mentioned above. This strain was designated ES05.
Example 5
The Effect of Amplifying pckA on Succinic Acid Fermentation in the Various Deficient Strains
Each of the ES02, ES03, ES04 and ES05 strains obtained above was transformed with pSTV28::Pthr::pckA and pSTV28 by the electric pulse method, applied to an LB agar medium containing 40 μg/ml of chloramphenicol, and cultured at 37° C. for about 18 hours. The colonies that appeared were purified, and plasmids were extracted in a conventional manner to confirm that the target plasmids were introduced. The obtained strains were designated ES02/pSTV28, ES02/pSTV28::Pthr::pckA, ES03/pSTV28, ES03/pSTV28::Pthr::pckA, ES04/pSTV28, ES04/pSTV28::Pthr::pckA, ES05/pSTV28, and ES05/pSTV28::Pthr::pckA, respectively.
The aforementioned strains were each inoculated into 4 ml of a seed medium containing 40 mg/L of chloramphenicol, and cultured at 31.5° C. for 16 hours in a test tube with shaking. Then, 4 ml of a glucose-containing production medium was added to the culture, the test tube was closed with a silicone stopper, and culture was performed at 31.5° C. for 24 hours with shaking. In this evaluation method, the inside of test tube was made to be under an anaerobic condition by the consumption of glucose. Therefore, the yield of succinic acid based on the consumed glucose is determined by combining the amount of consumed glucose used to form succinic acid with the amount of glucose necessary to establish the anaerobic conditions. The compositions of the seed medium and the glucose-containing production medium are shown below.
The composition of the organic acid production medium for Enterobacter bacteria, test tube evaluation










Seed medium:


















Bacto tryptone
20 g/L




(final concentration)



Yeast Extract
10 g/L



Sodium chloride
10 g/L










These were autoclaved at 120° C. for 10 minutes.










Glucose-containing production medium:


















Glucose
100 g/L




(final concentration)



Calcium carbonate
100 g/L



(Japanese Pharmacopoeia)










The glucose solution was autoclaved at 120° C. for 10 minutes, and the calcium carbonate was sterilized at 180° C. for 3 hours with dry heat. These were then left to cool and mixed.
After the culture, the amount of the organic acid which had accumulated in the medium was analyzed by liquid chromatography. Two Shim-pack SCR-102H (Shimadzu) were connected in series 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 the organic acid was quantified by measuring electric conductivity with CDD-10AD (Shimadzu). The amount of consumed glucose, OD, accumulated organic acid, and yield based on the consumed glucose determined after 24 hours are shown in Table 3.











TABLE 3








Accumulated
Yield of succinic acid




Consumed glucose
succinic acid
based on consumed


Strain
OD (600 nm)
(g/L)
(g/L)
glucose (%)





















ES02/pSTV28
7.03 (±0.47)
4.35
(±0.25)
0.03 (±0.06)
0.72
(±1.44)


ES02/pSTV28::Pthr::pckA
7.26 (±0.54)
6.50
(±1.05)
1.63 (±0.38)
25.04
(±2.61)


ES03/pSTV28
7.30 (±0.68)
8.93
(±0.30)
0.36 (±0.04)
4.03
(±0.44)


ES03/pSTV28::Pthr::pckA
9.64 (±0.72)
20.54
(±1.19)
5.80 (±0.11)
28.22
(±1.14)


ES04/pSTV28
7.65 (±0.37)
11.18
(±1.15)
0.46 (±0.03)
4.30
(±0.42)


ES04/pSTV28::Pthr::pckA
8.14 (±0.40)
18.76
(±0.86)
7.20 (±0.29)
38.44
(±2.46)


ES05/pSTV28
8.18 (±0.11)
11.12
(±0.71)
2.02 (±0.48)
18.23
(±4.65)


ES05/pSTV28::Pthr::pckA
8.97 (±0.27)
15.47
(±0.36)
8.23 (±0.33)
53.17
(±1.41)









Accumulation of succinic acid and yield based on consumed glucose were markedly increased by the pckA amplification in all the ES02, ES03, ES04 and ES05 strains.
Reference Example 1
Acquisition of Succinic Acid-Producing Bacterium Belonging to Genus Enterobacter 
The Enterobacter aerogenes AJ110637 strain was obtained from 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 a homology of 99.9% to that of the Enterobacter aerogenes NCTC 10006 strain was found. Moreover, also in a physiological test using an API kit, the strain showed results similar to the prototype species of Enterobacter aerogenes, and therefore the obtained isolated strain was identified as Enterobacter aerogenes. 
Reference Example 2
Construction of the Helper Plasmid RSF-Red-TER
The scheme for constructing the helper plasmid RSF-Red-TER shown in FIG. 2.
As the first step of 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: 25 and 26, and 27 and 28, respectively. These oligonucleotides contain BglII, Sad, XbaI and BamHI restriction enzyme sites, which are required and convenient for further cloning, in the 5′ end regions, respectively. 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 contains 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 Sad, and cloned into the RSF-PlaclacIsacB plasmid which had been obtained in the previous step at the BamHI-SacI site. pMW-PlaclacIsacBcat contains 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 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: 29 and 30 as primers and the pMW119-PlaclacI plasmid as the 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: 31 and 32 as primers, and the pKD46 plasmid (Datsenko, K. A., Wanner, B. L., 2000, Proc. Natl. Acad. Sci. USA, 97, 6640-6645) as the 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 from 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: 33 and 34 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 sand TrrnB was amplified by PCR using the oligonucleotides of SEQ ID NOS: 35 and 36 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 pMW118-(λattL-Kmr-λattR) plasmid
A pMW118-(λattL-Kmr-λattR) plasmid was constructed from the pMW118-attL-Tc-attR plasmid by substituting the kanamycin resistance gene of the pUC4K plasmid for the tetracycline resistance marker gene. For this purpose, the EcoRI-HindIII large fragment of the pMW118-attL-Tc-attR plasmid was ligated with two fragments of the pUC4K plasmid, HindIII-PstI (676 bp) and EcoRI-HindIII (585 bp) fragments. pMW118-attL-Tc-attR serving as the basic structure was obtained by ligating the following four fragments.
Construction of the pMW118-attL-Tc-attR Plasmid
1) The BglII-EcoRI fragment (114 bp) which includes attL (SEQ ID NO: 37) was obtained by PCR amplification of the region corresponding to attL from the Escherichia coli W3350 (containing λ prophage) chromosome using the primers P1 and P2 (SEQ ID NOS: 35 and 36) (these primers contained the subsidiary recognition sites for BglII and EcoRI).
2) The PstI-HindIII fragment (182 bp) which includes attR (SEQ ID NO: 40) was obtained by PCR amplification of the region corresponding to attR from the Escherichia coli W3350 (containing λ prophage) chromosome using the primers P3 and P4 (SEQ ID NOS: 38 and 39) (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) which includes the AatII-EcoRI fragment of pMW118 that was obtained by digesting pMW118 with EcoRI, treating with DNA polymerase I Klenow fragment, and then digesting with AatII;
        The small AatII-BglII fragment (1194 bp) of pUC19 which includes the bla gene for ampicillin resistance (ApR) was obtained by PCR amplification of the corresponding region of the pUC19 plasmid using the primers P5 and P6 (SEQ ID NOS: 41 and 42) (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: 43 and 44) (these primers contained the subsidiary recognition sites for PstI, BglII and PstI).
    
    


4) The small EcoRI-PstI fragment (1388 bp) (SEQ ID NO: 45) of pML-Tc-ter_thrL which includes the tetracycline resistance gene and the ter_thrL transcription terminator. The plasmid pML-Tc-ter_thrL 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: 46 and 47) (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 ligation with the small EcoRI-Van91I fragment (1317 bp) of pBR322 which includes the tetracycline resistance gene (pBR322 was digested with EcoRI and Van91I and then treated with DNA polymerase I Klenow fragment).
    
    


Reference Example 4
Construction of Plasmid RSF-int-xis for Eliminating an Antibiotic Resistance Gene
RSF-int-xis was constructed to eliminate the antibiotic resistance gene from the plasmid used to disrupt the gene from the gene-disrupted strain. pMW-intxis-ts was used for the construction. pMW-intxis-ts carries the gene coding for the integrase (Int) of λ phage, the gene coding for excisionase (Xis), and has a temperature-sensitive replication origin (WO2007/037460, Japanese Patent Laid-open No. 2005-058827).
A DNA fragment which includes the intxis region was amplified by PCR using primer intxis_f (SEQ ID NO: 66), primer intxis_R (SEQ ID NO: 67), and pMW-intxis-ts as the template. The obtained DNA fragment was digested with NotI and PvuI, and ligated with the large fragment of the RSF-Red-TER plasmid which had been digested with NotI and PvuI. The obtained plasmid was designated RSF-int-xis.
EXPLANATION OF SEQUENCE LISTING
SEQ ID NO: 1: Primer for amplification of threonine promoter
SEQ ID NO: 2: Primer for amplification of threonine promoter
SEQ ID NO: 3: Threonine promoter gene fragment
SEQ ID NO: 4: Primer for amplification of pckA gene of Actinobacillus succinogenes 
SEQ ID NO: 5: Primer for amplification of pckA gene of Actinobacillus succinogenes 
SEQ ID NO: 6: Gene sequence of pckA of Actinobacillus succinogenes ATCC 55618 strain
SEQ ID NO: 7: Amino acid sequence of pckA of Actinobacillus succinogenes ATCC 55618 strain
SEQ ID NO: 8: Gene sequence of pckA of Haemophilus influenzae 86-028NP strain
SEQ ID NO: 9: Amino acid sequence of pckA of Haemophilus influenzae 86-028NP strain
SEQ ID NO: 10: Gene sequence of pckA of Pasteurella multocida subsp. multocida str. PM70 strain
SEQ ID NO: 11: Amino acid sequence of pckA of Pasteurella multocida subsp. multocida str. PM70 strain
SEQ ID NO: 12: Gene sequence of pckA of Mannheimia succiniciproducens MBEL55E strain
SEQ ID NO: 13: Amino acid sequence of pckA of Mannheimia succiniciproducens MBEL55E strain
SEQ ID NO: 14: Gene sequence of pckA of Yersinia pseudotuberculosis IP 32953 strain
SEQ ID NO: 15: Amino acid sequence of pckA of Yersinia pseudotuberculosis IP 32953 strain
SEQ ID NO: 16: Gene sequence of pckA of Vibrio cholerae 623-39
SEQ ID NO: 17: Amino acid sequence of pckA of Vibrio cholerae 623-39
SEQ ID NO: 18: Primer for deletion of adhE
SEQ ID NO: 19: Primer for deletion of adhE
SEQ ID NO: 20: Gene sequence of ldhA of Enterobacter aerogenes AJ110637
SEQ ID NO: 21: Gene sequence of adhE of Enterobacter aerogenes AJ110637
SEQ ID NO: 22: Nucleotide sequence of PC gene coding for pyruvate carboxylase of Brevibacterium fluvum 
SEQ ID NO: 23: Amino acid sequence of pyruvate carboxylase of Brevibacterium fluvum 
SEQ ID NO: 24: Consensus sequence of PEPCK
SEQ ID NO: 25: Primer for amplification of cat gene
SEQ ID NO: 26: Primer for amplification of cat gene
SEQ ID NO: 27: Primer for amplification of sacB gene
SEQ ID NO: 28: Primer for amplification of sacB gene
SEQ ID NO: 29: Primer for amplification of DNA fragment containing PlacUV5 promoter
SEQ ID NO: 30: Primer for amplification of DNA fragment containing PlacUV5 promoter
SEQ ID NO: 31: Primer for amplification of DNA fragment containing λRedαβγ genes and tL3
SEQ ID NO: 32: Primer for amplification of DNA fragment containing λRedαβγ genes and tL3
SEQ ID NO: 33: Primer for amplification of DNA fragment containing PlacUV5 promoter and TrrnB
SEQ ID NO: 34: Primer for amplification of DNA fragment containing PlacUV5 promoter and TrrnB
SEQ ID NO: 35: Primer for amplification of attL
SEQ ID NO: 36: Primer for amplification of attL
SEQ ID NO: 37: Nucleotide sequence of attL
SEQ ID NO: 38: Primer for amplification of attR
SEQ ID NO: 39: Primer for amplification of attR
SEQ ID NO: 40: Nucleotide sequence of attR
SEQ ID NO: 41: Primer for amplification of DNA fragment containing bla gene
SEQ ID NO: 42: Primer for amplification of DNA fragment containing bla gene
SEQ ID NO: 43: Primer for amplification of DNA fragment containing ter_rrnB
SEQ ID NO: 44: Primer for amplification of DNA fragment containing ter_rrnB
SEQ ID NO: 45: Nucleotide sequence of DNA fragment containing ter_thrL terminator
SEQ ID NO: 46: Primer for amplification of DNA fragment containing ter_thrL terminator
SEQ ID NO: 47: Primer for amplification of DNA fragment containing ter_thrL terminator
SEQ ID NO: 48: Amino acid sequence of ldhA of Enterobacter aerogenes AJ110637
SEQ ID NO: 49: Amino acid sequence of adhE of Enterobacter aerogenes AJ110637
SEQ ID NO: 50: Gene sequence of pta of Enterobacter aerogenes AJ110637
SEQ ID NO: 51: Amino acid sequence of pta of Enterobacter aerogenes AJ110637
SEQ ID NO: 52: Gene sequence of aldC of Enterobacter aerogenes AJ110637
SEQ ID NO: 53: Amino acid sequence of aldC of Enterobacter aerogenes AJ110637
SEQ ID NO: 54: Gene sequence of pflB of Enterobacter aerogenes AJ110637
SEQ ID NO: 55: Amino acid sequence of pflB of Enterobacter aerogenes AJ110637
SEQ ID NO: 56: Primer for deletion of ldhA
SEQ ID NO: 57: Primer for deletion of ldhA
SEQ ID NO: 58: Primer for deletion of pta
SEQ ID NO: 59: Primer for deletion of pta
SEQ ID NO: 60: Primer for deletion of aldC
SEQ ID NO: 61: Primer for deletion of aldC
SEQ ID NO: 62: Primer for deletion of pflB
SEQ ID NO: 63: Primer for deletion of pflB
SEQ ID NO: 64: Gene sequence of pckA of Selenomonas ruminantium subsp. lactilytica TH1
SEQ ID NO: 65: Amino acid sequence of pckA of Selenomonas ruminantium subsp. lactilytica TH1
SEQ ID NO: 66: Nucleotide sequence of primer intxis_f for construction of RSF-int-xis
SEQ ID NO: 67: Nucleotide sequence of primer intxis_R for construction of RSF-int-xis
INDUSTRIAL APPLICABILITY
According to the method of the present invention, an organic acid can be quickly and highly efficiently produced. When the organic acid is succinic acid, the obtained succinic acid can be used for food additives, pharmaceuticals, cosmetics, and the like. Moreover, succinic acid-containing polymers can also be produced by performing a polymerization reaction using the obtained succinic acid as a raw material.
While the invention has been described in detail with reference to exemplary embodiments thereof, it will be apparent to one skilled in the art that various changes can be made, and equivalents employed, without departing from the scope of the invention. Each of the aforementioned documents is incorporated by reference herein in its entirety.

## Claims

1. A method for producing an organic acid 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) a bacterium belonging to the family Enterobacteriaceae which has an ability to produce an organic acid and has been modified so that the phosphoenolpyruvate carboxykinase activity is enhanced,
ii) a product obtained by processing the bacterium of i), and
iii) combinations thereof; and

B) collecting the organic acid,
wherein the bacterium belongs to a genus selected from the group consisting of Enterobacter, Pantoea, Erwinia, Klebsiella, and Raoultella; 
wherein the phosphoenolpyruvate carboxykinase is encoded by a pckA gene selected from the group consisting of:
(a) a DNA comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 6, 8, 10, 12, 14, 16, and 64, and
(b) a DNA which hybridizes with a nucleotide sequence complementary to a nucleotide sequence selected from the group consisting of SEQ ID NO: 6, 8, 10, 12, 14, 16, and 64 under stringent conditions comprising washing at 60° C. at a salt concentration of 0.1×SSC and 0.1% SDS, and said DNA codes for a protein having phosphoenolpyruvate carboxykinase activity;
and wherein the bacterium has been modified by a method selected from the group consisting of:
i) increasing the copy number of the pckA gene,
ii) modifying an expression control sequence of the pckA gene, and
iii) combinations thereof.

2. The method according to claim 1, wherein the the phosphoenolpyruvate carboxykinase is a protein selected from the group consisting of:
A) a protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 7, 9, 11, 13, 15, 17, 65, and 24, and
B) a protein comprising an amino acid sequence which is at least 95% homologous to an amino acid sequence selected from the group consisting of SEQ ID NO: 7, 9, 11, 13, 15, 17, 65 and 24.

3. The method according to claim 1, wherein the bacterium has been further modified to decrease the activity of an enzyme selected from the group consisting of alcohol dehydrogenase, lactate dehydrogenase, phosphate acetyltransferase, α-acetolactate decarboxylase, pyruvate formate lyase, and combinations thereof.

4. The method according to claim 3, wherein the enzyme is alcohol dehydrogenase.

5. The method according to claim 3, wherein the enzymes are alcohol dehydrogenase and lactate dehydrogenase.

6. The method according to claim 3, wherein the enzymes are alcohol dehydrogenase, lactate dehydrogenase, and phosphate acetyltransferase.

7. The method according to claim 3, wherein the enzymes are alcohol dehydrogenase, lactate dehydrogenase, phosphate acetyltransferase, and α-acetolactate decarboxylase.

8. The method according to claim 3, wherein the enzymes are alcohol dehydrogenase, lactate dehydrogenase, phosphate acetyltransferase, α-acetolactate decarboxylase, and pyruvate formate lyase.

9. The method according to claim 1, wherein the bacterium has been further modified so that pyruvate carboxylase activity is enhanced.

10. The method according to claim 1, wherein the organic acid is succinic acid.

11. A method for producing a succinic acid-containing polymer comprising:
A) producing succinic acid by the method according to claim 10, and
B) polymerizing the succinic acid.