Patent Grant
10155952
The present invention relates to a method for producing target substances such as L-amino acids using a coryneform bacterium. L-Amino acids are industrially useful as additives for animal feeds, ingredients of seasonings, foods and drinks, amino acid infusion solutions, and so forth.
L-Amino acids are industrially produced by, for example, fermentation using various microorganisms having an L-amino acid-producing ability. Examples of methods for producing an L-amino acid by fermentation include, for example, using a wild-type microorganism (wild-type strain), using an auxotrophic strain derived from a wild-type strain, using a metabolic regulation mutant strain derived as a mutant strain resistant to any of various drugs from a wild-type strain, and using a strain having characteristics of both an auxotrophic strain and metabolic regulation mutant strain.
Further, in recent years, microorganisms of which an L-amino acid-producing ability is improved by recombinant DNA techniques are used for the L-amino acid production. Examples of methods for improving an L-amino acid-producing ability of a microorganism include, for example, enhancing the expression of a gene encoding an L-amino acid biosynthetic enzyme (U.S. Pat. No. 5,168,056 and U.S. Pat. No. 5,776,736), and enhancing inflow of a carbon source into an L-amino acid biosynthesis system (U.S. Pat. No. 5,906,925).
In the conventional industrial production of target substances such as L-amino acids by fermentation, glucose, fructose, sucrose, blackstrap molasses, starch hydrolysates and so forth have been used as the carbon source. However, they are relatively expensive, and use of biomass raw materials derived from plants has also been advanced in recent years.
Although raw materials consisting of edible portions such as starch and fats and oils are mainly used as such biomass raw materials at present, it is desired to use biomass raw materials consisting of non-edible portions such as cellulose, hemicellulose, and lignin in future. Cellulose and hemicellulose are converted into pentoses and hexoses through a pretreatment using heat or acid, and a saccharification treatment using an enzyme such as cellulase, and they can be used as a raw material for fermentation (Japanese Patent Laid-open (Kohyo) No. 9-507386 and Japanese Patent Laid-open (Kohyo) No. 11-506934). It is known that if mixed saccharides of such pentoses and hexoses are used as the raw material for amino acid fermentation etc., Escherichia coli preferentially assimilates glucose, and as a result, phenomena of two-step proliferation (diauxy), and delayed growth have been confirmed (Nichols N. N. et al., Appl. Microbiol. Biotechnol., 2001 July, 56(1-2):120-1251 and Gonzalez, R., Biotechnol. Prog., 2002 January-February, 18(1):6-20)
In Escherichia coli, a xylose assimilation pathway including xylose isomerase encoded by the xylA gene and xylulokinase encoded by the xylB gene is known, and it is also known that an L-amino acid can be produced from xylose by using Escherichia coli or Corynebacterium glutamicum into which this pathway has been introduced (Tao H., et al., J. Bacteriol., 2001 May, 183(10):2979-2988 and Gopinath, V et al., Appl. Microbiol. Biotechnol., 2011 December, 92(5):985-96, European Patent No. 1577396 and WO2013/105802). As xylose assimilation pathway, there is also known another pathway in which xylose is converted into α-ketoglutaric acid via xylonic acid, and it is known that a target substance such as L-glutamic acid can be produced from xylose by using a bacterium into which this pathway has been introduced (WO2013/069634).
The NCgl2954 gene of Corynebacterium glutamicum is a gene encoding a transcription factor. However, a connection between the NCgl2954 gene and xylose assimilability has not been previously reported.
Aspects of the present invention include development of a novel technique for improving xylose assimilability of coryneform bacteria, and thereby provide a method for efficiently producing target substances such as L-amino acids and nucleic acids from a raw material containing xylose.
Coryneform bacteria into which a mutation was introduced into the NCgl2954 gene and coryneform bacteria deficient in the NCgl2954 gene were found to be able to efficiently assimilate xylose.
It is an aspect of the present invention to provide a method for producing a target substance comprising:
culturing a coryneform bacterium having an ability to produce a target substance in a medium containing xylose to produce and accumulate the target substance in the medium; and
collecting the target substance from the medium,
wherein the ability of the bacterium to assimilate xylose has been improved by introduction of a mutation into a coding region and/or an expression control region of the NCgl2954 gene on the chromosome of the bacterium.
It is a further aspect of the present invention to provide a method as described above, wherein the ability of the bacterium to assimilate xylose has been improved by improving the ability of the bacterium to take up xylose.
It is a further aspect of the present invention to provide a method as described above, wherein the ability of the bacterium to assimilate xylose has been improved by attenuation of expression of the NCgl2954 gene, or disruption of the gene.
It is a further aspect of the present invention to provide a method as described above, wherein the NCgl2954 gene is a DNA encoding a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence of SEQ ID NO: 14;
(B) a protein comprising the amino acid sequence of SEQ ID NO: 14, but which includes substitution, deletion, insertion, or addition of one or several amino acid residues, and wherein when said protein is deleted from the coryneform bacterium, the bacterium has an improved ability to assimilate xylose; and
(C) a protein comprising an amino acid sequence having an identity of 90% or higher to the amino acid sequence of SEQ ID NO: 14, and wherein when said protein is deleted from the coryneform bacterium, the bacterium has an improved ability to assimilate xylose.
It is a further aspect of the present invention to provide a method as described above, wherein the mutation is selected from the group consisting of:
(1) replacement of an amino acid residue corresponding to the leucine residue at position 438 of SEQ ID NO: 14 with an amino acid residue other than leucine residue;
(2) replacement of an amino acid residue corresponding to the tryptophan residue at position 274 of SEQ ID NO: 14 with an amino acid residue other than tryptophan residue;
(3) replacement of an amino acid residue corresponding to the tyrosine residue at position 377 of SEQ ID NO: 14 with an amino acid residue other than tyrosine residue;
(4) replacement of an amino acid residue corresponding to the leucine residue at position 365 of SEQ ID NO: 14 with an amino acid residue other than leucine residue;
(5) replacement of an amino acid residue corresponding to the leucine residue at position 366 of SEQ ID NO: 14 with an amino acid residue other than leucine residue;
(6) replacement of an amino acid residue corresponding to the alanine residue at position 367 of SEQ ID NO: 14 with an amino acid residue other than alanine residue;
(7) truncation of the N-terminus amino acid residues beginning with the amino acid residue at position 368 of SEQ ID NO: 14; and
(8) combinations thereof.
It is a further aspect of the present invention to provide a method as described above, wherein
said amino acid residue other than leucine residue at position 438 of SEQ ID NO: 14 is proline;
said amino acid residue other than tryptophan residue is arginine;
said amino acid residue other than tyrosine residue is asparagine;
said amino acid residue other than leucine residue at position 365 of SEQ ID NO: 14 is serine;
said amino acid residue other than leucine residue at position 366 of SEQ ID NO: 14 is arginine; and
said amino acid residue other than alanine residue is phenylalanine.
It is a further aspect of the present invention to provide a method as described above, wherein the bacterium has been further modified so that activities or activity of xylose isomerase and/or xylulokinase is increased.
It is a further aspect of the present invention to provide a method as described above, wherein the xylose isomerase is a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence of SEQ ID NO: 11;
(B) a protein comprising the amino acid sequence of SEQ ID NO: 11, but which includes substitution, deletion, insertion, or addition of one or several amino acid residues, and wherein said protein has xylose isomerase activity; and
(C) a protein comprising an amino acid sequence having an identity of 90% or higher to the amino acid sequence of SEQ ID NO: 11, and wherein said protein has xylose isomerase activity.
It is a further aspect of the present invention to provide a method as described above, wherein the xylulokinase is a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence of SEQ ID NO: 12;
(B) a protein comprising the amino acid sequence of SEQ ID NO: 12, but which includes substitution, deletion, insertion, or addition of one or several amino acid residues, and wherein said protein has xylulokinase activity; and
(C) a protein comprising an amino acid sequence having an identity of 90% or higher to the amino acid sequence of SEQ ID NO: 12, and wherein said protein has xylulokinase activity.
It is a further aspect of the present invention to provide a method as described above, wherein the bacterium has been further modified so that activity or activities of an enzyme selected from the group consisting of xylose dehydrogenase, xylonolactonase, xylonate dehydratase, 2-keto-3-deoxyxylonate dehydratase, α-ketoglutaric semialdehyde dehydrogenase, and combinations thereof is/are increased.
It is a further aspect of the present invention to provide a method as described above, wherein the xylonate dehydratase, 2-keto-3-deoxyxylonate dehydratase, and α-ketoglutaric semialdehyde dehydrogenase are derived from an Escherichia bacterium, Sphingomonas bacterium, and Bacillus bacterium, respectively.
It is a further aspect of the present invention to provide a method as described above, wherein the xylose dehydrogenase is a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence of SEQ ID NO: 16 or 42;
(B) a protein comprising the amino acid sequence of SEQ ID NO: 16 or 42, but which includes substitution, deletion, insertion, or addition of one or several amino acid residues, and wherein said protein has xylose dehydrogenase activity; and
(C) a protein comprising an amino acid sequence having an identity of 90% or higher to the amino acid sequence of SEQ ID NO: 16 or 42, and wherein said protein has xylose dehydrogenase activity.
It is a further aspect of the present invention to provide a method as described above, wherein the xylonolactonase is a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence of SEQ ID NO: 18 or 44;
(B) a protein comprising the amino acid sequence of SEQ ID NO: 18 or 44, but which includes substitution, deletion, insertion, or addition of one or several amino acid residues, and wherein said protein has xylonolactonase activity; and
(C) a protein comprising an amino acid sequence having an identity of 90% or higher to the amino acid sequence of SEQ ID NO: 18 or 44, and wherein said protein has xylonolactonase activity.
It is a further aspect of the present invention to provide a method as described above, wherein the xylonate dehydratase is a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence of SEQ ID NO: 20 or 46;
(B) a protein comprising the amino acid sequence of SEQ ID NO: 20 or 46, but which includes substitution, deletion, insertion, or addition of one or several amino acid residues, and wherein said protein has xylonate dehydratase activity; and
(C) a protein comprising an amino acid sequence having an identity of 90% or higher to the amino acid sequence of SEQ ID NO: 20 or 46, and wherein said protein has xylonate dehydratase activity.
It is a further aspect of the present invention to provide a method as described above, wherein the 2-keto-3-deoxyxylonate dehydratase is a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence of SEQ ID NO: 22 or 38;
(B) a protein comprising the amino acid sequence of SEQ ID NO: 22 or 38, but which includes substitution, deletion, insertion, or addition of one or several amino acid residues, and wherein said protein has 2-keto-3-deoxyxylonate dehydratase activity; and
(C) a protein comprising an amino acid sequence having an identity of 90% or higher to the amino acid sequence of SEQ ID NO: 22 or 38, and wherein said protein has 2-keto-3-deoxyxylonate dehydratase activity.
It is a further aspect of the present invention to provide a method as described above, wherein the α-ketoglutaric semialdehyde dehydrogenase is a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence of SEQ ID NO: 24 or 40;
(B) a protein comprising the amino acid sequence of SEQ ID NO: 24 or 40, but which includes substitution, deletion, insertion, or addition of one or several amino acid residues, and wherein said protein has α-ketoglutaric semialdehyde dehydrogenase activity; and
(C) a protein comprising an amino acid sequence having an identity of 90% or higher to the amino acid sequence of SEQ ID NO: 24 or 40, and wherein said protein has α-ketoglutaric semialdehyde dehydrogenase activity.
It is a further aspect of the present invention to provide a method as described above, wherein the target substance is selected from the group consisting of an amino acid, nucleic acid, and peptide.
It is a further aspect of the present invention to provide a method as described above, wherein the target substance is an amino acid selected from the group consisting of L-glutamic acid, L-glutamine, L-arginine, and L-lysine.
It is a further aspect of the present invention to provide a method as described above, wherein the target substance is a purine nucleoside selected from the group consisting of inosine, xanthosine, guanosine, and adenosine.
It is a further aspect of the present invention to provide a method as described above, wherein the target substance is a purine nucleotide selected from the group consisting of inosinic acid, xanthylic acid, and guanylic acid.
It is a further aspect of the present invention to provide a method as described above, wherein the bacterium is a Corynebacterium bacterium.
It is a further aspect of the present invention to provide a method as described above, wherein the bacterium is Corynebacterium glutamicum.
The method of the present invention is a method for producing a target substance which includes the steps of culturing a coryneform bacterium having an ability to produce the target substance in a medium containing xylose to produce and accumulate the target substance in the medium or cells of the bacterium, and collecting the target substance from the medium or cells, wherein a mutation of the NCgl2954 gene has been introduced into the bacterium that results in an increased ability of the bacterium to assimilate xylose. The bacterium can be referred to as “bacterium of the present invention”.
<1> Bacterium of the Present Invention
The bacterium of the present invention is a coryneform bacterium having an ability to produce a target substance, and the bacterium also has an improved ability to assimilate xylose due to the introduction of a mutation into the NCgl2954 gene.
<1-1> Coryneform bacterium having an ability to produce a target substance
The phrase “bacterium having an ability to produce a target substance” or “bacterium having a target substance-producing ability” can refer to a bacterium having an ability to produce and accumulate a target substance in a medium or cells of the bacterium in such a degree that the target substance can be collected, when the bacterium is cultured in the medium. The bacterium having a target substance-producing ability may be a bacterium that is able to accumulate a target substance in a medium in an amount larger than that obtained with a non-modified strain. Examples of the non-modified strain include wild-type strains and the parent strain of the bacterium. The bacterium having a target substance-producing ability may be a bacterium that is able to accumulate a target substance in a medium in an amount of 0.5 g/L or more, or 1.0 g/L or more.
The target substance is not particularly limited, so long as it can be produced by fermentation using a coryneform bacterium. Examples of the target substance include, for example, L-amino acids, nucleic acids, and proteins. Examples of the target substance further include, for example, α-ketoglutaric acid and derivatives thereof. The bacterium of the present invention may have an ability to produce one kind of target substance, or may have an ability to produce two or more kinds of target substances.
Examples of the L-amino acid include basic amino acids such as L-lysine, L-ornithine, L-arginine, L-histidine, and L-citrulline; aliphatic amino acids such as L-isoleucine, L-alanine, L-valine, L-leucine, and glycine; amino acids which are hydroxy-monoaminocarboxylic acids such as L-threonine and L-serine; cyclic amino acids such as L-proline; aromatic amino acids such as L-phenylalanine, L-tyrosine, and L-tryptophan; sulfur-containing amino acids such as L-cysteine, L-cystine, and L-methionine; acidic amino acids such as L-glutamic acid and L-aspartic acid; and amino acids having an amide group in the side chain such as L-glutamine and L-asparagine. The bacterium of the present invention may have an ability to produce one kind of L-amino acid, or may have an ability to produce two or more kinds of L-amino acids. The term “amino acid” may refer to L-amino acid, unless otherwise stated.
Examples of α-ketoglutaric acid and derivatives thereof include α-ketoglutaric acid, L-glutamic acid, L-glutamine, L-arginine, L-citrulline, L-ornithine, L-proline, γ-aminobutyric acid (GABA), and putrescine.
Examples of nucleic acids include purine substances. Examples of purine substances include purine nucleosides and purine nucleotides. Examples of the purine nucleosides include inosine, guanosine, xanthosine, and adenosine. Examples of the purine nucleotides include 5′-phosphate esters of the purine nucleosides. Examples of the 5′-phosphate esters of the purine nucleosides include inosinic acid (inosine-5′-monophosphate, IMP), guanylic acid (guanosine-5′-monophosphate, GMP), xanthylic acid (xanthosine-5′-monophosphate, XMP), and adenylic acid (adenosine-5′-monophosphate, AMP). The bacterium of the present invention may have an ability to produce one kind of purine substance, or may have an ability to produce two or more kinds of purine substances. For example, the bacterium of the present invention may have an ability to produce one or more kinds of purine nucleosides. For example, the bacterium of the present invention may have an ability to produce one or more kinds of purine nucleotides.
The protein is not particularly limited, so long as it can be expressed in a host coryneform bacterium. The protein may be a protein derived from the bacterium of the present invention or a heterogenous protein. The heterologous protein may be, for example, a protein derived from a microorganism, a protein derived from a plant, a protein derived from an animal, or a protein derived from a virus, or a an artificially designed protein. The proteins may be a monomeric protein or a multimeric protein. The proteins may be a naturally secretory protein or a naturally non-secretory protein. The term “protein” also includes peptides, oligopeptides, or polypeptides.
The target substance to be produced may be a free compound, salt thereof, or mixture thereof. That is, the term “target substance” may mean the target substance in the form of a free compound, salt thereof, or mixture thereof, unless otherwise stated. Examples of salt will be mentioned later.
Examples of the coryneform bacterium include bacteria belonging to the genus Corynebacterium, Brevibacterium, Microbacterium, or the like.
Specific examples of the coryneform bacteria include the following species.
Corynebacterium acetoacidophilum
Corynebacterium acetoglutamicum
Corynebacterium alkanolyticum
Corynebacterium callunae
Corynebacterium glutamicum
Corynebacterium lilium
Corynebacterium melassecola
Corynebacterium thermoaminogenes (Corynebacterium efficiens)
Corynebacterium herculis
Brevibacterium divaricatum (Corynebacterium glutamicum)
Brevibacterium flavum (Corynebacterium glutamicum)
Brevibacterium immariophilum
Brevibacterium lactofermentum (Corynebacterium glutamicum)
Brevibacterium roseum
Brevibacterium saccharolyticum
Brevibacterium thiogenitalis
Corynebacterium ammoniagenes (Corynebacterium stationis)
Brevibacterium album
Brevibacterium cerinum
Microbacterium ammoniaphilum
Specific examples of the coryneform bacteria include the following strains.
Corynebacterium acetoacidophilum ATCC 13870
Corynebacterium acetoglutamicum ATCC 15806
Corynebacterium alkanolyticum ATCC 21511
Corynebacterium callunae ATCC 15991
Corynebacterium glutamicum ATCC 13020, ATCC 13032, ATCC 13060, ATCC 13869, FERM BP-734
Corynebacterium lilium ATCC 15990
Corynebacterium melassecola ATCC 17965
Corynebacterium efficiens (Corynebacterium thermoaminogenes) AJ12340 (FERM BP-1539)
Corynebacterium herculis ATCC 13868
Corynebacterium glutamicum (Brevibacterium divaricatum) ATCC 14020
Corynebacterium glutamicum (Brevibacterium flavum) ATCC 13826, ATCC 14067, AJ12418 (FERM BP-2205)
Brevibacterium immariophilum ATCC 14068
Corynebacterium glutamicum (Brevibacterium lactofermentum) ATCC 13869
Brevibacterium roseum ATCC 13825
Brevibacterium saccharolyticum ATCC 14066
Brevibacterium thiogenitalis ATCC 19240
Corynebacterium ammoniagenes (Corynebacterium stationis) ATCC 6871, ATCC 6872
Brevibacterium album ATCC 15111
Brevibacterium cerinum ATCC 15112
Microbacterium ammoniaphilum ATCC 15354
The Corynebacterium bacteria include bacteria which have previously been classified into the genus Brevibacterium, but are presently united into the genus Corynebacterium (Int. J. Syst. Bacteriol., 41, 255 (1991)). Moreover,
Corynebacterium stationis includes such a bacterium that has previously been classified into Corynebacterium ammoniagenes, but is presently re-classified into Corynebacterium stationis on the basis of nucleotide sequence analysis of 16S rRNA etc. (Int. J. Syst. Evol. Microbiol., 60, 874-879 (2010)).
These strains are available from, for example, the American Type Culture Collection (Address: 12301 Parklawn Drive, Rockville, Md. 20852, P.O. Box 1549, Manassas, Va. 20108, United States of America). That is, registration numbers are assigned to the respective strains, and the strains can be ordered by using these registration numbers (refer to atcc.org/). The registration numbers of the strains are listed in the catalogue of the American Type Culture Collection.
The bacterium of the present invention may be a bacterium inherently having a target substance-producing ability, or may be a bacterium modified so that it has a target substance-producing ability. The bacterium having a target substance-producing ability can be obtained by, for example, imparting a target substance-producing ability to such a bacterium as mentioned above, or enhancing a target substance-producing ability of such a bacterium as mentioned above.
<1-1-1> L-Amino Acid-Producing Bacteria
To impart or enhance an L-amino acid-producing ability, methods conventionally employed in the breeding of amino acid-producing strains of coryneform bacteria, Escherichia bacteria, and so forth (see “Amino Acid Fermentation”, Gakkai Shuppan Center (Ltd.), 1st Edition, published May 30, 1986, pp. 77-100) can be used. Examples of such methods include, for example, acquiring an auxotrophic mutant strain, acquiring an L-amino acid analogue-resistant strain, acquiring a metabolic regulation mutant strain, and constructing a recombinant strain in which the activity of an L-amino acid biosynthetic enzyme is enhanced. In the breeding of L-amino acid-producing bacteria, one of the above-described properties such as auxotrophy, analogue resistance, and metabolic regulation mutation may be imparted alone, or two or three or more of such properties may be imparted in combination. The activity of one of L-amino acid biosynthetic enzymes may be enhanced alone, or the activities of two or three or more of such enzymes may be enhanced in combination. Furthermore, imparting property(s) such as auxotrophy, analogue resistance, and metabolic regulation mutation can be combined with enhancing the activity(s) of biosynthetic enzyme(s).
An auxotrophic mutant strain, analogue-resistant strain, or metabolic regulation mutant strain having an L-amino acid-producing ability can be obtained by subjecting a parent strain or wild-type strain to a usual mutagenesis treatment, and then selecting a strain exhibiting autotrophy, analogue resistance, or a metabolic regulation mutation, and having an L-amino acid-producing ability from the obtained mutant strains. Examples of the usual mutagenesis treatment include irradiation of X-ray or ultraviolet and a treatment with a mutation agent such as N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), ethyl methanesulfonate (EMS), and methyl methanesulfonate (MMS).
An L-amino acid-producing ability can also be imparted or enhanced by enhancing the activity of an enzyme involved in biosynthesis of an objective L-amino acid. An enzyme activity can be enhanced by, for example, modifying a bacterium so that the expression of a gene encoding the enzyme is enhanced. Methods for enhancing gene expression are described in WO00/18935, EP 1010755 A, and so forth. The detailed procedures for enhancing enzyme activity will be described later.
Further, an L-amino acid-producing ability can also be imparted or enhanced by reducing the activity of an enzyme that catalyzes a reaction branching away from the biosynthetic pathway of an objective L-amino acid to generate a compound other than the objective L-amino acid. The “enzyme that catalyzes a reaction branching away from the biosynthetic pathway of an objective L-amino acid to generate a compound other than the objective L-amino acid” referred to here includes an enzyme involved in decomposition of the objective amino acid. The method for reducing an enzyme activity will be described later.
Hereafter, L-amino acid-producing bacteria and methods for imparting or enhancing an L-amino acid-producing ability will be specifically exemplified. All of the properties of the L-amino acid-producing bacteria and modifications for imparting or enhancing an L-amino acid-producing ability may be used independently or in any appropriate combination.
<L-Glutamic Acid-Producing Bacteria>
Examples of methods for imparting or enhancing L-glutamic acid-producing ability include, for example, a method of modifying a bacterium so that the bacterium has an increased activity or activities of one or more kinds of enzymes selected from the L-glutamic acid biosynthesis enzymes. Examples of such enzymes include, but are not particularly limited to, glutamate dehydrogenase (gdhA), glutamine synthetase (glnA), glutamate synthase (gltBD), isocitrate dehydrogenase (icdA), aconitate hydratase (acnA, acnB), citrate synthase (OA), methylcitrate synthase (prpC), phosphoenolpyruvate carboxylase (ppc), pyruvate carboxylase (pyc), pyruvate dehydrogenase (aceEF, lpdA), pyruvate kinase (pykA, pykF), phosphoenolpyruvate synthase (ppsA), enolase (eno), phosphoglyceromutase (pgmA, pgml), phosphoglycerate kinase (pgk), glyceraldehyde-3-phophate dehydrogenase (gapA), triose phosphate isomerase (tpiA), fructose bisphosphate aldolase (fbp), phosphofructokinase (pfkA, pfkB), glucose phosphate isomerase (pgi), 6-phosphogluconate dehydratase (edd), 2-keto-3-deoxy-6-phosphogluconate aldolase (eda), and transhydrogenase. Shown in the parentheses after the names of the enzymes are examples of the names of the genes encoding the enzymes (the same shall apply to the same occasions hereafter). It is preferable to enhance the activity or activities of one or more kinds of enzymes selected from, for example, glutamate dehydrogenase, citrate synthase, phosphoenol pyruvate carboxylase, and methylcitrate synthase, among these enzymes.
Examples of coryneform bacteria modified so that expression of the glutamate synthetase gene (gltBD) is increased include those disclosed in WO99/07853.
Examples of methods for imparting or enhancing L-glutamic acid-producing ability also include, for example, a method of modifying a bacterium so that the bacterium has a reduced activity or activities of one or more kinds of enzymes selected from the enzymes that catalyze a reaction branching away from the biosynthesis pathway of L-glutamic acid to generate a compound other than L-glutamic acid. Examples of such enzymes include, but are not particularly limited to, isocitrate lyase (aceA), α-ketoglutarate dehydrogenase (sucA, odhA), phosphotransacetylase (pta), acetate kinase (ack), acetohydroxy acid synthase (ilvG), acetolactate synthase (ilvI), formate acetyltransferase (pfl), lactate dehydrogenase (ldh), alcohol dehydrogenase (adh), glutamate decarboxylase (gadAB), succinate dehydrogenase (sdhABCD), and 1-pyroline-5-carboxylate dehydrogenase (putA). It is preferable to reduce or delete, for example, the α-ketoglutarate dehydrogenase activity, among these enzymes.
Coryneform bacteria in which the α-ketoglutarate dehydrogenase activity is reduced or eliminated, and methods for obtaining those are disclosed in WO2008/075483. Specific examples of coryneform bacteria in which the α-ketoglutarate dehydrogenase activity is reduced or eliminated include, for example, the following strains.
Corynebacterium glutamicum (Brevibacterium lactofermentum) L30-2 strain (Japanese Patent Laid-open (Kokai) No. 2006-340603)
Corynebacterium glutamicum (Brevibacterium lactofermentum) ΔS strain (WO95/34672)
Corynebacterium glutamicum (Brevibacterium lactofermentum) AJ12821 (FERM BP-4172, French Patent No. 9401748)
Corynebacterium glutamicum (Brevibacterium flavum) AJ12822 (FERM BP-4173, French Patent No. 9401748)
Corynebacterium glutamicum AJ12823 (FERM BP-4174, French Patent No. 9401748)
Corynebacterium glutamicum L30-2 strain (Japanese Patent Laid-open (Kokai) No. 2006-340603)
Examples of L-glutamic acid-producing bacteria and parent strains for deriving them also include strains in which both the α-ketoglutarate dehydrogenase (sucA) activity and the succinate dehydrogenase (sdh) activity are reduced or eliminated (Japanese Patent Laid-open (Kokai) No. 2010-041920). Specific examples of such strains include, for example, Corynebacterium glutamicum 8L3GΔSDH strain, which is the odhAsdhA double-deficient strain of Corynebacterium glutamicum ATCC 14067 (Japanese Patent Laid-open (Kokai) No. 2010-041920).
Examples of methods for imparting or enhancing L-glutamic acid-producing ability also include a method of modifying a bacterium so that the D-xylulose-5-phosphate phosphoketolase activity and/or the fructose-6-phosphate phosphoketolase activity are/is enhanced (Japanese Patent Laid-open (Kohyo) No. 2008-509661). Either one of the D-xylulose-5-phosphate phosphoketolase activity and the fructose-6-phosphate phosphoketolase activity may be enhanced, or both may be enhanced. In this specification, D-xylulose-5-phosphate phosphoketolase and fructose-6-phosphate phosphoketolase may be collectively referred to as phosphoketolase.
The D-xylulose-5-phosphate phosphoketolase activity means an activity for converting xylulose-5-phosphate into glycelaldehyde-3-phosphate and acetyl phosphate with consuming phosphoric acid to release one molecule of H2O. This activity can be measured by the method described by Goldberg, M. et al. (Methods Enzymol., 9, 515-520, 1996) or the method described by L. Meile (J. Bacteriol., 183:2929-2936, 2001).
The fructose-6-phosphate phosphoketolase activity means an activity for converting fructose-6-phosphate into erythrose-4-phosphate and acetyl phosphate with consuming phosphoric acid to release one molecule of H2O. This activity can be measured by the method described by Racker, E. (Methods Enzymol., 5, 276-280, 1962) or the method described by L. Meile (J. Bacteriol., 183:2929-2936, 2001).
Examples of methods for imparting or enhancing L-glutamic acid-producing ability also include, for example, a method of enhancing the expression of the yhfK gene (WO2005/085419) or the ybjL gene (WO2008/133161), which is an L-glutamic acid secretion gene.
Furthermore, examples of methods for imparting or enhancing L-glutamic acid-producing ability to or in coryneform bacteria also include methods of imparting resistance to an organic acid analogue, respiratory inhibitor, or the like, and methods of imparting sensitivity to a cell wall synthesis inhibitor. Specific examples of such methods include, for example, the method of imparting monofluoroacetic acid resistance (Japanese Patent Laid-open (Kokai) No. 50-113209), the method of imparting adenine resistance or thymine resistance (Japanese Patent Laid-open (Kokai) No. 57-065198), the method of attenuating urease (Japanese Patent Laid-open (Kokai) No. 52-038088), the method of imparting malonic acid resistance (Japanese Patent Laid-open (Kokai) No. 52-038088), the method of imparting resistance to benzopyrones or naphthoquinones (Japanese Patent Laid-open (Kokai) No. 56-1889), the method of imparting HOQNO resistance (Japanese Patent Laid-open (Kokai) No. 56-140895), the method of imparting α-ketomalonic acid resistance (Japanese Patent Laid-open (Kokai) No. 57-2689), the method of imparting guanidine resistance (Japanese Patent Laid-open (Kokai) No. 56-35981), the method of imparting sensitivity to penicillin (Japanese Patent Laid-open (Kokai) No. 4-88994), and so forth.
Specific examples of such resistant or sensitive bacteria include the following strains.
Corynebacterium glutamicum (Brevibacterium flavum) AJ3949 (FERM BP-2632, refer to Japanese Patent Laid-open (Kokai) No. 50-113209)
Corynebacterium glutamicum AJ11628 (FERM P-5736, refer to Japanese Patent Laid-open (Kokai) No. 57-065198)
Corynebacterium glutamicum (Brevibacterium flavum) AJ11355 (FERM P-5007, refer to Japanese Patent Laid-open (Kokai) No. 56-1889)
Corynebacterium glutamicum AJ11368 (FERM P-5020, refer to Japanese Patent Laid-open (Kokai) No. 56-1889)
Corynebacterium glutamicum (Brevibacterium flavum) AJ11217 (FERM P-4318, refer to Japanese Patent Laid-open (Kokai) No. 57-2869)
Corynebacterium glutamicum AJ11218 (FERM P-4319, refer to Japanese Patent Laid-open (Kokai) No. 57-2869)
Corynebacterium glutamicum (Brevibacterium flavum) AJ11564 (FERM BP-5472, refer to Japanese Patent Laid-open (Kokai) No. 56-140895)
Corynebacterium glutamicum (Brevibacterium flavum) AJ11439 (FERM BP-5136, refer to Japanese Patent Laid-open (Kokai) No. 56-35981)
Corynebacterium glutamicum H7684 (FERM BP-3004, refer to Japanese Patent Laid-open (Kokai) No. 04-88994)
Corynebacterium glutamicum (Brevibacterium lactofermentum) AJ11426 (FERM P-5123, refer to Japanese Patent Laid-open (Kokai) No. 56-048890)
Corynebacterium glutamicum AJ11440 (FERM P-5137, refer to Japanese Patent Laid-open (Kokai) No. 56-048890)
Corynebacterium glutamicum (Brevibacterium lactofermentum) AJ11796 (FERM P-6402, refer to Japanese Patent Laid-open (Kokai) No. 58-158192)
Furthermore, examples of methods for imparting or enhancing L-glutamic acid-producing ability to or in coryneform bacteria also include a method of enhancing expression of the yggB gene and a method of introducing a mutant yggB gene having a mutation in the coding region (WO2006/070944). The yggB gene is a gene encoding a mechanosensitive channel. The yggB gene of the Corynebacterium glutamicum ATCC 13032 strain corresponds to the sequence complementary to the sequence of the nucleotide numbers 1,336,091 to 1,337,692 in the genome sequence registered as Genbank Accession No. NC_003450 in the NCBI database, and is also called NCgl1221. The YggB protein is registered as GenBank accession No. NP_600492. The nucleotide sequence of the yggB gene of Corynebacterium glutamicum 2256 (ATCC 13869) and the amino acid sequence of the YggB protein encoded by the gene are shown in SEQ ID NOS: 25 and 26, respectively.
Examples of the mutant yggB gene usable in the aforementioned methods include yggB genes having the following mutation(s). The YggB protein encoded by a mutant yggB gene is also referred to as a mutant YggB protein. A yggB gene not having such mutation(s) and the YggB protein encoded by the gene are also referred to as a wild-type yggB gene and wild-type YggB protein, respectively. Examples of the wild-type YggB protein include, for example, a protein having the amino acid sequence shown in SEQ ID NO: 26.
(1) Mutation on C-Terminal Side
The mutation on the C-terminal side is a mutation introduced into a part of the nucleotide sequence of the region encoding the sequence of the amino acid numbers 419 to 533 in SEQ ID NO: 26. Although the mutation on the C-terminal side is not particularly limited so long as a mutation is introduced into at least a part of the nucleotide sequence of the aforementioned region, the mutation on the C-terminal side is preferably a mutation for inserting an insertion sequence (henceforth also referred to as “IS”) or inserting transposon. The mutation on the C-terminal side may be any of a mutation for introducing amino acid substitution (missense mutation), a mutation for introducing frame shift mutation induced by insertion of the aforementioned IS or the like, and a mutation for introducing nonsense mutation.
Examples of the mutation on the C-terminus side include, for example, a mutation for inserting a nucleotide sequence at the site encoding the valine residue at the position 419 of the wild-type YggB protein (2A-1 type mutation). The 2A-1 type mutation may be, for example, a mutation that causes deletion or replacement of a part or all of the amino acid residues of the positions 419 to 533 of the wild-type YggB protein. Specific examples of a mutant yggB gene having the 2A-1 type mutation include, for example, a yggB gene having the nucleotide sequence of SEQ ID NO: 25, but which includes insertion of IS at the position next to “G” of the position 1255, and encoding a mutant YggB protein having a full length of 423 amino acid residues, which is shorter than the original wild-type YggB protein (SEQ ID NO: 26) (Japanese Patent Laid-open (Kokai) No. 2007-222163).
Examples of the mutation on C-terminus side also include, for example, a mutation for replacing a proline residue existing at any of the positions 419 to 533 of the wild-type YggB protein with an amino acid residue other than proline residue. Examples of such a proline residue include the proline residues at the positions 424, 437, 453, 457, 462, 469, 484, 489, 497, 515, 529, and 533 of the wild-type YggB protein.
(2) Mutation in Transmembrane Region
It is estimated that the YggB protein encoded by the yggB gene has five transmembrane regions. In the amino acid sequence of the wild-type YggB protein of SEQ ID NO: 26, the transmembrane regions correspond to the regions of the amino acid numbers 1 to 23 (first transmembrane region), 25 to 47 (second transmembrane region), 62 to 84 (third transmembrane region), 86 to 108 (fourth transmembrane region), and 110 to 132 (fifth transmembrane region). The yggB gene may have a mutation in a region encoding any of these transmembrane regions. The mutation in the transmembrane region is desirably a mutation including substitution, deletion, addition, insertion, or inversion of one or several amino acid residues while not accompanied by frame shift mutation or nonsense mutation. Examples of the mutation in the transmembrane region include a mutation for inserting one or several amino acid residues (for example, Cys-Ser-Leu) between the leucine residue at position 14 and the tryptophan residue at position 15, a mutation for replacing the alanine residue at position 100 with another amino acid residue (for example, an amino acid residue having hydroxyl group on the side chain (Thr, Ser, or Tyr), preferably Thr), and a mutation for replacing the alanine residue at position 111 with another amino acid residue (for example, an amino acid residue having hydroxyl group on the side chain (Thr, Ser, or Tyr), preferably Thr), in the amino acid sequence shown in SEQ ID NO: 26, and so forth. Specific examples of a mutant yggB gene having such a mutation in a transmembrane region include, for example, a yggB gene having the sequence of SEQ ID NO: 25, but which includes insertion of TTCATTGTG at the position next to “G” of the position 44 (A1 type mutation), a yggB gene having the sequence of SEQ ID NO: 25, but which includes substitution of “A” for “G” of the position 298 (19 type mutation), and a yggB gene having the sequence of SEQ ID NO: 25, but which includes substitution of “T” for “C” of the position 332 (L30 type mutation).
When the wild-type YggB protein has an amino acid sequence other than the amino acid sequence shown in SEQ ID NO: 26, the mutant yggB gene may have a mutation in a region encoding the amino acid residue corresponding to the amino acid residue at the aforementioned position in SEQ ID NO: 26. In an arbitrary wild-type YggB protein, which amino acid residue is “the amino acid residue corresponding to the amino acid residue at the aforementioned position in SEQ ID NO: 26” can be determined on the basis of an alignment between the amino acid sequence of the wild-type YggB protein and the amino acid sequence of SEQ ID NO: 26. The “amino acid number X in SEQ ID NO: 26” may be read as the “position X in SEQ ID NO: 26”.
<L-Glutamine-Producing Bacteria>
Examples of the method for imparting or enhancing L-glutamine-producing ability include, for example, a method of modifying a bacterium so that the activity or activities of one or more kinds of enzymes selected from the L-glutamine biosynthesis enzymes are enhanced. Examples of such enzymes include, but not particularly limited to, glutamate dehydrogenase (gdhA) and glutamine synthetase (glnA). The glutamine synthetase activity can also be enhanced by disruption of the glutamine adenylyltransferase gene (glnE) or disruption of the PII control protein gene (ginB) (EP 1229121).
Examples of the method for imparting or enhancing L-glutamine-producing ability also include, for example, a method of modifying a bacterium so that the activity or activities of one or more kinds of enzymes that catalyze a reaction branching away from the biosynthesis pathway of L-glutamine to generate a compound other than L-glutamine are reduced. Examples of such enzymes include, but not particularly limited to, glutaminase.
Specific examples of L-glutamine-producing bacteria and parent strains for deriving them include, for example, coryneform bacteria in which the activity or activities of glutamate dehydrogenase (gdhA) and/or glutamine synthetase (glnA) (EP 1229121, EP 1424398) are enhanced, and coryneform bacteria in which the glutaminase activity (Japanese Patent Laid-open (Kokai) No. 2004-187684) is reduced.
Examples of the methods for imparting or enhancing L-glutamine-producing ability to or in coryneform bacteria also include the method of imparting 6-diazo-5-oxo-norleucine resistance (Japanese Patent Laid-open (Kokai) No. 3-232497), the method of imparting purine analogue resistance and methionine sulfoxide resistance (Japanese Patent Laid-open (Kokai) No. 61-202694), and the method of imparting α-ketomalonic acid resistance (Japanese Patent Laid-open (Kokai) No. 56-151495). Specific examples of coryneform bacteria having L-glutamine-producing ability include, for example, the following strains.
Corynebacterium glutamicum (Brevibacterium flavum) AJ11573 (FERM P-5492, Japanese Patent Laid-open (Kokai) No. 56-151495)
Corynebacterium glutamicum (Brevibacterium flavum) AJ11576 (FERM BP-10381, Japanese Patent Laid-open (Kokai) No. 56-151495)
Corynebacterium glutamicum (Brevibacterium flavum) AJ12212 (FERM P-8123, Japanese Patent Laid-open (Kokai) No. 61-202694)
<L-Proline-Producing Bacteria>
Examples of methods for imparting or enhancing L-proline-producing ability include, for example, a method of modifying a bacterium so that the bacterium has an increased activity or activities of one or more kinds of enzymes selected from the L-proline biosynthesis enzymes. Examples of such enzymes include glutamate-5-kinase (proB), γ-glutamylphosphate reductase, and pyroline-5-carboxylate reductase (putA). For enhancing the activity of such an enzyme, for example, the proB gene encoding a glutamate kinase desensitized to feedback inhibition by L-proline (German Patent No. 3127361) can be preferably used.
Examples of methods for imparting or enhancing L-proline-producing ability also include, for example, a method of modifying a bacterium so that the bacterium has a reduced activity of an enzyme involved in decomposition of L-proline. Examples of such an enzyme include proline dehydrogenase and ornithine aminotransferase.
<L-Threonine-Producing Bacteria>
Examples of methods for imparting or enhancing L-threonine-producing ability include, for example, a method of modifying a bacterium so that the bacterium has an increased activity or activities of one or more kinds of enzymes selected from the L-threonine biosynthesis enzymes. Examples of such enzymes include, but not particularly limited to, aspartokinase III (lysC), aspartate semialdehyde dehydrogenase (asd), aspartokinase I (thrA), homoserine kinase (thrB), threonine synthase (thrC), and aspartate aminotransferase (aspartate transaminase) (aspC). Among these enzymes, it is preferable to enhance activity or activities of one or more kinds of enzymes selected from aspartokinase III, aspartate semialdehyde dehydrogenase, aspartokinase I, homoserine kinase, aspartate aminotransferase, and threonine synthase. Any of the genes encoding the L-threonine biosynthesis enzymes can be introduced into a bacterium having a reduced ability to decompose threonine.
The activities of the L-threonine biosynthesis enzymes are inhibited by the endproduct, L-threonine. Therefore, for constructing L-threonine-producing strains, it is preferred that the genes of the L-threonine biosynthesis enzymes are modified so that the enzymes are desensitized to feedback inhibition by L-threonine. The aforementioned thrA, thrB, and thrC genes constitute the threonine operon, which forms an attenuator structure. The expression of the threonine operon is inhibited by isoleucine and threonine in the culture medium and also suppressed by attenuation. Therefore, expression of the threonine operon can be enhanced by removing the leader sequence or the attenuator in the attenuation region (refer to Lynn, S. P., Burton, W. S., Donohue, T. J., Gould, R. M., Gumport, R. L, and Gardner, J. F., J. Mol. Biol. 194:59-69 (1987); WO02/26993; WO2005/049808; and WO2003/097839).
The native promoter of the threonine operon is present upstream of the threonine operon, and can be replaced with a non-native promoter (refer to WO98/04715). Also, the threonine operon may be constructed so that the threonine biosynthesis genes are expressed under control of the repressor and promoter of λ-phage (European Patent No. 0593792). Furthermore, a bacterium modified so that it is desensitized to feedback inhibition by L-threonine can also be obtained by selecting a strain resistant to α-amino-β-hydroxyisovaleric acid (AHV), which is an L-threonine analogue.
It is preferred that the expression amount of the threonine operon that is modified so as to be desensitized to feedback inhibition by L-threonine as described above is increased in a host by increasing the copy number thereof or by ligating it to a potent promoter. The copy number can be increased by introducing a plasmid containing the threonine operon into a host. The copy number can also be increased by transferring the threonine operon to the genome of a host using a transposon, Mu-phage, or the like.
Examples of methods for imparting or enhancing L-threonine-producing ability also include, for example, a method of imparting L-threonine resistance to a host, and a method of imparting L-homoserine resistance to a host. Such resistance can be imparted by, for example, enhancing the expression of a gene that imparts L-threonine resistance or a gene that imparts L-homoserine resistance. Examples of the genes that impart the above-mentioned resistance include the rhtA gene (Res. Microbiol. 154:123-135 (2003)), rhtB gene (European Patent Laid-open No. 0994190), rhtC gene (European Patent Laid-open No. 1013765), yfiK gene, and yeaS gene (European Patent Laid-open No. 1016710). As for methods for imparting L-threonine resistance to a host, those described in European Patent Laid-open No. 0994190 and WO90/04636 can be referred to.
The thrA gene encoding aspartokinase homoserine dehydrogenase I of E. coli has been elucidated (nucleotide numbers 337 to 2799, GenBank accession NC_000913.2, gi: 49175990). The thrA gene locates between the thrL and thrB genes on the chromosome of E. coli K-12. The thrB gene encoding homoserine kinase of Escherichia coli has been elucidated (nucleotide numbers 2801 to 3733, GenBank accession NC 000913.2, gi: 49175990). The thrB gene locates between the thrA and thrC genes on the chromosome of E. coli K-12. The thrC gene encoding threonine synthase of E. coli has been elucidated (nucleotide numbers 3734 to 5020, GenBank accession NC 000913.2, gi: 49175990). The thrC gene locates between the thrB gene and the yaaX open reading frame on the chromosome of E. coli K-12. The thrA*BC operon containing a mutant thrA gene encoding aspartokinase homoserine dehydrogenase I resistant to feedback inhibition by threonine and wild-type thrBC genes can be obtained from the well-known pVIC40 plasmid, which is present in the threonine-producing E. coli strain VKPM B-3996 (U.S. Pat. No. 5,705,371).
The rhtA gene of E. coli is present at 18 min on the E. coli chromosome close to the glnHPQ operon, which encodes components of the glutamine transport system. The rhtA gene is identical to ORF1 (ybiF gene, nucleotide numbers 764 to 1651, GenBank accession number AAA218541, gi:440181), and is located between the pexB and ompX genes. The unit that expresses the protein encoded by the ORP1 is referred to as rhtA gene (rht: resistant to homoserine and threonine). It was also revealed that the rhtA23 mutation, which imparts resistance against a high concentration of threonine or homoserine, is an A-for-G substitution at position −1 with respect to the ATG start codon (ABSTRACTS of the 17th International Congress of Biochemistry and Molecular Biology in conjugation with Annual Meeting of the American Society for Biochemistry and Molecular Biology, San Francisco, Calif. Aug. 24-29, 1997, Abstract No. 457, EP 1013765 A).
The asd gene of E. coli has already been elucidated (nucleotide numbers 3572511 to 3571408, GenBank accession NC 000913.1, gi:16131307), and can be obtained by PCR (refer to White, T. J. et al., Trends Genet, 5, 185 (1989)) utilizing primers prepared on the basis of the nucleotide sequence of the gene. The asd genes of other microorganisms can also be obtained in a similar manner.
The aspC gene of E. coli has also already been elucidated (nucleotide numbers 983742 to 984932, GenBank accession NC 000913.1, gi:16128895), and can be obtained by PCR utilizing primers prepared on the basis of the nucleotide sequence of the gene. The aspC genes of other microorganisms can also be obtained in a similar manner.
Further, examples of coryneform bacteria having L-threonine-producing ability include, for example, Corynebacterium acetoacidophilum AJ12318 (FERM BP-1172, refer to U.S. Pat. No. 5,188,949).
<L-Lysine-Producing Bacteria>
Examples of methods for imparting or enhancing L-lysine-producing ability include, for example, a method of modifying a bacterium so that the bacterium has an increased activity or activities of one or more kinds of enzymes selected from the L-lysine biosynthesis enzymes. Examples of such enzymes include, but not particularly limited to, dihydrodipicolinate synthase (dapA), aspartokinase III (lysC), dihydrodipicolinate reductase (dapB), diaminopimelate decarboxylase (lysA), diaminopimelate dehydrogenase (ddh) (U.S. Pat. No. 6,040,160), phosphoenolpyruvate carboxylase (ppc), aspartate semialdehyde dehydrogenase (asd), aspartate aminotransferase (aspartate transaminase) (aspC), diaminopimelate epimerase (dapF), tetrahydrodipicolinate succinylase (dapD), succinyl diaminopimelate deacylase (dapE), and aspartase (aspA) (EP 1253195 A). It is preferable to enhance the activity or activities of one or more kinds of enzymes selected from, for example, dihydrodipicolinate reductase, diaminopimelate decarboxylase, diaminopimelate dehydrogenase, phosphoenolpyruvate carboxylase, aspartate aminotransferase, diaminopimelate epimerase, aspartate semialdehyde dehydrogenase, tetrahydrodipicolinate succinylase, and succinyl diaminopimelate deacylase, among these enzymes. In addition, L-lysine-producing bacteria and parent strains for deriving them can express an increased level of the gene involved in energy efficiency (cyo) (EP 1170376 A), the gene encoding nicotinamide nucleotide transhydrogenase (pntAB) (U.S. Pat. No. 5,830,716), the ybjE gene (WO2005/073390), or combinations of these. Since aspartokinase III (lysC) is subject to feedback inhibition by L-lysine, a mutant lysC gene encoding an aspartokinase III desensitized to feedback inhibition by L-lysine (U.S. Pat. No. 5,932,453) may be used for enhancing the activity of this enzyme. Further, since dihydrodipicolinate synthase (dapA) is subject to feedback inhibition by L-lysine, a mutant dapA gene encoding a dihydrodipicolinate synthase desensitized to feedback inhibition by L-lysine may be used for enhancing the activity of this enzyme.
Examples of methods for imparting or enhancing L-lysine-producing ability also include, for example, a method of modifying a bacterium so that the bacterium has a reduced activity or activities of one or more kinds of enzymes selected from the enzymes that catalyze a reaction branching away from the biosynthetic pathway of L-lysine to generate a compound other than L-lysine. Examples of such enzymes include, but not particularly limited to, homoserine dehydrogenase, lysine decarboxylase (U.S. Pat. No. 5,827,698), and malic enzyme (WO2005/010175).
Examples of methods for imparting or enhancing L-lysine-producing ability to or in coryneform bacteria include, for example, the method of modifying bacteria so that the activity of the lysine secretory system (lysE) is increased (WO97/23597). The lysE gene of Corynebacterium glutamicum ATCC 13032 corresponds to the complementary sequence of the sequence of the positions 1329712 to 1330413 in the genome sequence registered at the NCBI database as GenBank accession NC_006958 (VERSION NC_006958.1 GI:62388892). The LysE protein of Corynebacterium glutamicum ATCC 13032 is registered as GenBank accession YP_225551 (YP_225551.1 GI:62390149).
Examples of L-lysine-producing bacteria and parent strains for deriving them also include mutant strains having resistance to an L-lysine analogue. L-Lysine analogues inhibit the growth of bacteria such as bacteria of the family Enterobacteriaceae and coryneform bacteria, but this inhibition is fully or partially released when L-lysine is present in the medium. Examples of these L-lysine analogues include, but not particularly limited to, oxalysine, lysine hydroxamate, S-(2-aminoethyl)-L-cysteine (AEC), γ-methyllysine, and α-chlorocaprolactam. Mutant strains having resistance to these lysine analogues can be obtained by subjecting a bacterium to a conventional artificial mutagenesis treatment.
Examples of coryneform bacteria having L-lysine-producing ability include, for example, the AEC-resistant mutant strains (Corynebacterium glutamicum (Brevibacterium lactofermentum AJ11082) (NRRL B-11470) strain etc., refer to Japanese Patent Publication (Kokoku) Nos. 56-1914, 56-1915, 57-14157, 57-14158, 57-30474, 58-10075, 59-4993, 61-35840, 62-24074, 62-36673, 5-11958, 7-112437 and 7-112438); mutant strains requiring an amino acid such as L-homoserine for their growth (refer to Japanese Patent Publication Nos. 48-28078 and 56-6499); mutant strains showing resistance to AEC and further requiring an amino acid such as L-leucine, L-homoserine, L-proline, L-serine, L-arginine, L-alanine, and L-valine (refer to U.S. Pat. Nos. 3,708,395 and 3,825,472); mutant strains showing resistance to DL-α-amino-ε-caprolactam, α-amino-lauryllactam, aspartic acid analogue, sulfa drug, quinoid, and N-lauroylleucine; mutant strains showing resistance to an oxaloacetate decarboxylase inhibitor or a respiratory chain enzyme inhibitor (Japanese Patent Laid-open (Kokai) Nos. 50-53588, 50-31093, 52-102498, 53-9394, 53-86089, 55-9783, 55-9759, 56-32995, 56-39778, Japanese Patent Publication Nos. 53-43591 and 53-1833); mutant strains requiring inositol or acetic acid (Japanese Patent Laid-open (Kokai) Nos. 55-9784 and 56-8692); mutant strains that are susceptible to fluoropyruvic acid or a temperature of 34° C. or higher (Japanese Patent Laid-open (Kokai) Nos. 55-9783 and 53-86090); and mutant strains showing resistance to ethylene glycol (U.S. Pat. No. 4,411,997).
<L-Arginine-Producing Bacteria>
Examples of methods for imparting or enhancing L-arginine-producing ability include, for example, a method of modifying a bacterium so that the bacterium has an increased activity or activities of one or more kinds of enzymes selected from the L-arginine biosynthesis enzymes. Examples of such enzymes include, but not particularly limited to, N-acetylglutamate synthase (argA), N-acetylglutamyl phosphate reductase (argC), ornithine acetyl transferase (argJ), N-acetylglutamate kinase (argB), acetylornithine transaminase (argD), acetylornithine deacetylase (argE), ornithine carbamoyl transferase (argF), argininosuccinate synthetase (argG), argininosuccinate lyase (argH), and carbamoyl phosphate synthetase (carAB). As the N-acetylglutamate synthase gene (argA), for example, a gene encoding a mutant N-acetylglutamate synthase desensitized to feedback inhibition by L-arginine by substitution for the amino acid residues corresponding to the positions 15 to 19 of the wild type enzyme (European Patent Laid-open No. 1170361) can preferably be used.
Examples of L-arginine-producing bacteria and parent strains for deriving them include such coryneform bacteria as a strain deficient in ArgR, which is an arginine repressor (U.S. Published Patent Application No. 20020045223), and a strain in which glutamine synthetase activity is increased (U.S. Published Patent Application No. 20050014236).
Examples of L-arginine-producing bacteria and parent strains for deriving them also include mutant strains of coryneform bacteria, the mutant strains having resistance to an amino acid analogue or the like. Examples of such strains include, for example, strains having resistance to 2-thiazolealanine and further exhibiting auxotrophy for L-histidine, L-proline, L-threonine, L-isoleucine, L-methionine, or L-tryptophan (Japanese Patent Laid-open (Kokai) No. 54-44096); strains resistant to ketomalonic acid, fluoromalonic acid, or monofluoroacetic acid (Japanese Patent Laid-open (Kokai) No. 57-18989); strains resistant to argininol (Japanese Patent Publication No. 62-24075); strains resistant to X-guanidine (X represents an aliphatic chain or a derivative thereof, Japanese Patent Laid-open (Kokai) No. 2-186995); and strains resistant to arginine hydroxamate and 6-azauracil (Japanese Patent Laid-open (Kokai) No. 57-150381). Specific examples of coryneform bacteria having L-arginine-producing ability include the following strains.
Corynebacterium glutamicum (Brevibacterium flavum) AJ11169 (FERM BP-6892)
Corynebacterium glutamicum (Brevibacterium lactofermentum) AJ12092 (FERM BP-6906)
Corynebacterium glutamicum (Brevibacterium flavum) AJ11336 (FERM BP-6893)
Corynebacterium glutamicum (Brevibacterium flavum) AJ11345 (FERM BP-6894)
Corynebacterium glutamicum (Brevibacterium lactofermentum) AJ12430 (FERM BP-2228)
<L-Citrulline-Producing Bacteria and L-Ornithine-Producing Bacteria>
The biosynthetic pathways of L-citrulline and L-ornithine are common to that of L-arginine. Therefore, an ability to produce L-citrulline and/or L-ornithine can be imparted or enhanced by increasing the activity or activities of N-acetylglutamate synthase (argA), N-acetylglutamyl phosphate reductase (argC), ornithine acetyltransferase (argJ), N-acetylglutamate kinase (argB), acetylornithine transaminase (argD), and/or acetylornithine deacetylase (argE) (WO2006/35831).
<L-Histidine-Producing Bacteria>
Examples of methods for imparting or enhancing L-histidine-producing ability include, for example, a method of modifying a bacterium so that the bacterium has an increased activity or activities of one or more kinds of enzymes selected from the L-histidine biosynthesis enzymes. Examples of such enzymes include, but not particularly limited to, ATP phosphoribosyltransferase (hisG), phosphoribosyl AMP cyclohydrolase (hisI), phosphoribosyl-ATP pyrophosphohydrolase (hisI), phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA), amidotransferase (hisH), histidinol phosphate aminotransferase (hisC), histidinol phosphatase (hisB), and histidinol dehydrogenase (hisD).
Among these enzymes, the L-histidine biosynthesis enzymes encoded by hisG and hisBHAFI are known to be inhibited by L-histidine. Therefore, the ability to produce L-histidine can be imparted or enhanced by, for example, introducing a mutation for conferring resistance to feedback inhibition into the gene encoding ATP phosphoribosyltransferase (hisG) (Russian Patent Nos. 2003677 and 2119536).
<L-Cysteine-Producing Bacteria>
Examples of methods for imparting or enhancing L-cysteine-producing ability include, for example, a method of modifying a bacterium so that the bacterium has an increased activity or activities of one or more kinds of enzymes selected from the L-cysteine biosynthesis enzymes. Examples of such enzymes include, but are not particularly limited to, serine acetyltransferase (cysE) and 3-phosphoglycerate dehydrogenase (serA). The serine acetyltransferase activity can be enhanced by, for example, introducing a mutant cysE gene encoding a mutant serine acetyltransferase resistant to feedback inhibition by cysteine into a bacterium. Such a mutant serine acetyltransferase is disclosed in, for example, Japanese Patent Laid-open (Kokai) No. 11-155571 and U.S. Patent Published Application No. 20050112731. Further, the 3-phosphoglycerate dehydrogenase activity can be enhanced by, for example, introducing a mutant serA gene encoding a mutant 3-phosphoglycerate dehydrogenase resistant to feedback inhibition by serine into a bacterium. Such a mutant 3-phosphoglycerate dehydrogenase is disclosed in, for example, U.S. Pat. No. 6,180,373.
Further, examples of methods for imparting or enhancing L-cysteine-producing ability also include, for example, a method of modifying a bacterium so that the bacterium has a reduced activity or activities of one or more kinds of enzymes selected form the enzymes that catalyze a reaction branching away from the biosynthesis pathway of L-cysteine to generate a compound other than L-cysteine. Examples of such enzymes include, for example, enzymes involved in decomposition of L-cysteine. Examples of the enzymes involved in decomposition of L-cysteine include, but are not particularly limited to, cysteine desulfhydrase (aecD) (Japanese Patent Laid-open (Kokai) No. 2002-233384).
Further, examples of methods for imparting or enhancing L-cysteine-producing ability also include, for example, a method of enhancing the L-cysteine excretory system, and a method of enhancing the sulfate/thiosulfate transport system. Examples of proteins of the L-cysteine excretory system include the protein encoded by the ydeD gene (Japanese Patent Laid-open (Kokai) No. 2002-233384), the protein encoded by the yfiK gene (Japanese Patent Laid-open (Kokai) No. 2004-49237), the proteins encoded by the emrAB, emrKY, yojIH, acrEF, bcr, and cusA genes (Japanese Patent Laid-open (Kokai) No. 2005-287333), and the protein encoded by the yeaS gene (Japanese Patent Laid-open (Kokai) No. 2010-187552). Examples of the proteins of the sulfate/thiosulfate transport system include the proteins encoded by the cysPTWAM gene cluster.
Further, examples of coryneform bacteria having L-cysteine-producing ability include coryneform bacteria having serine acetyltransferase desensitized to feedback inhibition by L-cysteine thereby to show enhanced intracellular serine acetyltransferase activity (Japanese Patent Laid-open (Kokai) No. 2002-233384).
<L-Serine-Producing Bacteria>
Examples of methods for imparting or enhancing L-serine-producing ability include, for example, a method of modifying a bacterium so that the bacterium has an increased activity or activities of one or more kinds of enzymes selected from L-serine biosynthesis enzymes (Japanese Patent Laid-open (Kokai) No. 11-253187). Examples of such enzymes include, but are not particularly limited to, 3-phosphoglycerate dehydrogenase (serA), phosphoserine transaminase (serf), and phosphoserine phosphatase (serB) (Japanese Patent Laid-open (Kokai) No. 11-253187). The 3-phosphoglycerate dehydrogenase activity can be enhanced by, for example, introducing a mutant serA gene encoding a mutant 3-phosphoglycerate dehydrogenase resistant to the feedback inhibition by serine into a bacterium. A mutant 3-phosphoglycerate dehydrogenase is disclosed in, for example, U.S. Pat. No. 6,180,373.
Examples of L-serine-producing bacteria and parent strains for deriving them include, for example, coryneform bacteria resistant to azaserine or β-(2-thienyl)-DL-alanine, and deficient in L-serine decomposition ability (Japanese Patent Laid-open (Kokai) No. 10-248588). Specific examples of such coryneform bacteria include, for example, Corynebacterium glutamicum (Brevibacterium flavum) AJ13324 (FERM P-16128), which is resistant to azaserine and deficient in serine decomposition ability, and Corynebacterium glutamicum (Brevibacterium flavum) AJ13325 (FERM P-16129), which is resistant to β-(2-thienyl)-DL-alanine and deficient in serine decomposition ability (Japanese Patent Laid-open (Kokai) No. 10-248588).
<L-Methionine-Producing Bacteria>
Examples of L-methionine-producing bacteria and parent strains for deriving them include L-threonine auxotrophic strains and mutant strains resistant to norleucine (Japanese Patent Laid-open (Kokai) No. 2000-139471). Examples of L-methionine-producing bacteria and parent strains for deriving them also include a strain containing a mutant homoserine transsuccinylase resistant to feedback inhibition by L-methionine (Japanese Patent Laid-open (Kokai) No. 2000-139471, U.S. Patent Published Application No. 20090029424). Since L-methionine is biosynthesized via L-cysteine as an intermediate, L-methionine-producing ability can also be improved by improving L-cysteine-producing ability (Japanese Patent Laid-open (Kokai) No. 2000-139471, U.S. Patent Published Application No. 20080311632).
<L-Leucine-Producing Bacteria>
Examples of methods for imparting or enhancing L-leucine-producing ability include, for example, a method of modifying a bacterium so that the bacterium has an increased activity or activities of one or more kinds of enzymes selected from the L-leucine biosynthesis enzymes. Examples of such enzymes include, but are not particularly limited to, the enzymes encoded by the genes of the leuABCD operon. Further, for enhancing the activity of such an enzyme, for example, the mutant leuA gene encoding an isopropyl maleate synthase desensitized to feedback inhibition by L-leucine (U.S. Pat. No. 6,403,342) can be preferably used.
Examples of coryneform bacteria having L-leucine-producing ability include, for example, Corynebacterium glutamicum (Brevibacterium lactofermentum) AJ3718 (FERM P-2516), which is resistant to 2-thiazole alanine and β-hydroxyleucine and auxotrophic for isoleucine and methionine.
<L-Isoleucine-Producing Bacteria>
Examples of the method for imparting or enhancing L-isoleucine-producing ability include, for example, a method of modifying a bacterium so that activity or activities of one or more kinds of enzymes selected from the L-isoleucine biosynthetic enzymes are increased. Examples of such enzymes include, but are not particularly limited to, threonine deaminase and acetohydroxy acid synthase (Japanese Patent Laid-open (Kokai) No. 2-458, FR 0356739, U.S. Pat. No. 5,998,178).
Examples of coryneform bacteria having L-isoleucine-producing ability include the coryneform bacterium in which brnE gene encoding a branched chain amino acid excretion protein is amplified (Japanese Patent Laid-open (Kokai) No. 2001-169788), the coryneform bacterium to which L-isoleucine-producing ability is imparted by protoplast fusion with an L-lysine-producing bacterium (Japanese Patent Laid-open (Kokai) No. 62-74293), the coryneform bacterium in which homoserine dehydrogenase is enhanced (Japanese Patent Laid-open (Kokai) No. 62-91193), the threonine hydroxamate resistant strain (Japanese Patent Laid-open (Kokai) No 62-195293), the α-ketomalonic acid resistant strain (Japanese Patent Laid-open (Kokai) No. 61-15695), the methyllysine resistant strain (Japanese Patent Laid-open (Kokai) No. 61-15696), and Corynebacterium glutamicum (Brevibacterium flavum) AJ12149 (FERM BP-759, U.S. Pat. No. 4,656,135).
<L-Valine-Producing Bacteria>
Examples of methods for imparting or enhancing L-valine-producing ability include, for example, a method of modifying a bacterium so that the bacterium has an increased activity or activities of one or more kinds of enzymes selected from the L-valine biosynthesis enzymes. Examples of such enzymes include, but are not particularly limited to, the enzymes encoded by the genes of the ilvGMEDA operon and the enzymes encoded by the ilvBNC operon. The ilvBN gene encodes acetohydroxy acid synthase, and the ilvC gene encodes isomeroreductase (WO00/50624). Expressions of the ilvGMEDA operon and the ilvBNC operon are suppressed (attenuated) by L-valine, L-isoleucine, and/or L-leucine. Therefore, for enhancing the activity of such an enzyme, it is preferred that the suppression of expression by the produced L-valine is released by removing or modifying a region required for the attenuation. Further, the threonine deaminase encoded by the ilvA gene is an enzyme that catalyzes the deamination reaction of L-threonine resulting 2-ketobutyric acid, which is the rate-limiting step of the L-isoleucine biosynthesis system. Therefore, for L-valine production, it is preferred that the ilvA gene is, for example, disrupted, and thereby the threonine deaminase activity is decreased.
Examples of methods for imparting or enhancing L-valine-producing ability also include, for example, a method of modifying a bacterium so that the bacterium has a reduced activity or activities of one or more kinds of enzymes selected from the enzymes that catalyze a reaction branching away from the biosynthesis pathway of L-valine to generate a compound other than L-valine. Examples of such enzymes include, but not particularly limited to, threonine dehydratase involved in the L-leucine synthesis, and the enzymes involved in the D-pantothenic acid synthesis (WO00/50624).
Examples of L-valine-producing bacteria and parent strains for deriving them also include strains resistant to an amino acid analogue or the like. Examples of such strains include, for example, the coryneform bacterium strains which are auxotrophic for L-isoleucine and L-methionine, and resistant to D-ribose, purine ribonucleoside, or pyrimidine ribonucleoside, and have an ability to produce L-valine (FERM P-1841, FERM P-29) (Japanese Patent Publication No. 53-025034), coryneform bacterium strains resistant to polyketides (FERM P-1763, FERM P-1764) (Japanese Patent Publication No. 06-065314), and coryneform bacterium strains resistant to L-valine in a medium containing acetic acid as the sole carbon source and sensitive to pyruvic acid analogues (fluoropyruvic acid etc.) in a medium containing glucose as the sole carbon source (FERM BP-3006, BP-3007) (Japanese Patent No. 3006929).
<L-Alanine-Producing Bacteria>
Examples of L-alanine-producing bacteria and parent strains for deriving them include the coryneform bacteria deficient in the H+-ATPase (Appl. Microbiol. Biotechnol., 2001 November, 57(4):534-40) and coryneform bacteria in which the aspartate β-decarboxylase activity is enhanced (Japanese Patent Laid-open (Kokai) No. 07-163383).
<L-Tryptophan-Producing Bacteria, L-Phenylalanine-Producing Bacteria, and L-Tyrosine-Producing Bacteria>
Examples of the method for imparting or enhancing L-tryptophan-producing ability, L-phenylalanine-producing ability, and/or L-tyrosine-producing ability include, for example, a method of modifying a bacterium so that the activity or activities of one or more kinds of enzymes selected from the L-tryptophan, L-phenylalanine, and/or L-tyrosine biosynthetic enzymes are enhanced.
Examples of enzymes common to the biosynthesis systems of these aromatic amino acids include, but are not particularly limited to, 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (aroG), 3-dehydroquinate synthase (aroB), shikimate dehydrogenase (aroE), shikimate kinase (aroL), 5-enolpyruvylshikimate-3-phosphate synthase (aroA), and chorismate synthase (aroC) (EP 763127 B). The expressions of the genes encoding these enzymes are controlled by the tyrosine repressor (tyrR), and the activities of these enzymes may be enhanced by deleting the tyrR gene (EP 763127 B).
Examples of the L-tryptophan biosynthetic enzymes include, but not particularly limited to, anthranilate synthase (trpE), tryptophan synthase (trpAB), and phosphoglycerate dehydrogenase (serA). For example, by introducing a DNA containing the tryptophan operon, L-tryptophan-producing ability can be imparted or enhanced. Tryptophan synthase consists of α and β subunits encoded by the trpA and trpB genes, respectively. Since the anthranilate synthase is subject to feedback inhibition by L-tryptophan, a gene encoding this enzyme introduced with a mutation for desensitization to feedback inhibition may be used for enhancing the activity of that enzyme. Since the phosphoglycerate dehydrogenase is subject to feedback inhibition by L-serine, a gene encoding this enzyme introduced with a mutation for desensitization to feedback inhibition may be used for enhancing the activity of that enzyme. Further, by enhancing expression of the operon (ace operon) consisting of the maleate synthase gene (aceB), isocitrate lyase gene (aceA), and isocitrate dehydrogenase kinase/phosphatase gene (aceK), L-tryptophan-producing ability may be imparted or enhanced (WO2005/103275).
Examples of the L-phenylalanine biosynthetic enzymes include, but are not particularly limited to, chorismate mutase and prephenate dehydratase. The chorismate mutase and prephenate dehydratase are encoded by the pheA gene as a bifunctional enzyme. Since the chorismate mutase and prephenate dehydratase are subject to feedback inhibition by L-phenylalanine, a gene encoding these enzymes introduced with a mutation for desensitization to feedback inhibition may be used for enhancing the activities of these enzymes.
Examples of the L-tyrosine biosynthetic enzymes include, but are not particularly limited to, chorismate mutase and prephenate dehydrogenase. The chorismate mutase and prephenate dehydrogenase are encoded by the tyrA gene as a bifunctional enzyme. Since the chorismate mutase and prephenate dehydrogenase are subject to feedback inhibition by L-tyrosine, a gene encoding these enzymes introduced with a mutation for desensitization to feedback inhibition may be used for enhancing the activities of these enzymes.
The L-tryptophan, L-phenylalanine, and/or L-tyrosine-producing bacteria may be modified so that biosynthesis of an aromatic amino acid other than the objective aromatic amino acid is reduced. Further, the L-tryptophan, L-phenylalanine, and/or L-tyrosine-producing bacteria may be modified so that a by-product uptake system is enhanced. Examples of the by-product include aromatic amino acids other than the objective aromatic amino acid. Examples of the gene encoding such a by-product uptake system include tnaB and mtr, which are genes encoding the L-tryptophan uptake system, pheP, which is a gene encoding the L-phenylalanine uptake system, and tyrP, which is a gene encoding the L-tyrosine uptake system (EP 1484410).
Examples of coryneform bacteria having L-tryptophan-producing ability include Corynebacterium glutamicum AJ12118 (FERM BP-478) (Japanese Patent No. 01681002), which is resistant to sulfaguanidine, the strain introduced with the tryptophan operon (Japanese Patent Laid-open (Kokai) No. 63-240794), and the strain introduced with a gene encoding shikimate kinase derived from a coryneform bacterium (Japanese Patent Laid-open (Kokai) No. 01-994749).
Examples of coryneform bacteria having L-phenylalanine-producing ability include, for example, the Corynebacterium glutamicum strains BPS-13 (FERM BP-1777), K77 (FERM BP-2062), and K78 (FERM BP-2063) (EP 331145 A, Japanese Patent Laid-open (Kokai) No. 02-303495), of which phosphoenolpyruvate carboxylase or pyruvate kinase activity is reduced, and the tyrosine-auxotrophic strain (Japanese Patent Laid-open (Kokai) No. 05-049489).
Examples of coryneform bacteria having L-tyrosine-producing ability include, for example, Corynebacterium glutamicum AJ11655 (FERM P-5836, Japanese Patent Publication No. 2-6517), and Corynebacterium glutamicum (Brevibacterium lactofermentum) AJ12081 (FERM P-7249, Japanese Patent Laid-open (Kokai) No. 60-70093).
Further, examples of methods for imparting or enhancing an L-amino acid-producing ability include, for example, a method of modifying a bacterium so that the activity for secreting an L-amino acid from the bacterial cell is increased. The activity for secreting an L-amino acid can be increased by, for example, increasing the expression of a gene encoding a protein responsible for secretion of the L-amino acid. Examples of genes encoding proteins responsible for secretion of various amino acids include, for example, b2682 gene (ygaZ), b2683 gene (ygaH), b1242 gene (ychE), and b3434 gene (yhgN) (Japanese Patent Laid-open (Kokai) No. 2002-300874).
Further, examples of methods for imparting or enhancing an L-amino acid-producing ability also include, for example, a method of modifying a bacterium so that the activity or activities of one or more of proteins involved in the glycometabolism and proteins involved in the energy metabolism are increased.
Examples of the proteins involved in the glycometabolism include proteins involved in uptake of saccharides and the glycolysis system enzymes. Examples of genes encoding the proteins involved in the glycometabolism include the glucose-6-phosphate isomerase gene (pgi, WO01/02542), phosphoenolpyruvate synthase gene (pps, EP 877090 A), phosphoenolpyruvate carboxylase gene (ppc, WO95/06114), pyruvate carboxylase gene (pyc, WO99/18228, EP 1092776 A), phosphoglucomutase gene (pgm, WO03/04598), fructose bisphosphate aldolase gene (pfkB, fbp, WO03/04664), pyruvate kinase gene (pykF, WO03/008609), transaldolase gene (talB, WO03/008611), fumarase gene (fum, WO01/02545), non-PTS sucrose uptake gene (csc, EP 149911 A), and sucrose utilization gene (scrAB operon, WO90/04636).
Examples of genes encoding the proteins involved in the energy metabolism include the transhydrogenase gene (pntAB, U.S. Pat. No. 5,830,716) and cytochrome bo-type oxidase gene (cyoB, EP 1070376 A).
<1-1-2> Nucleic Acid-Producing Bacteria
A purine substance-producing ability can be imparted or enhanced by the methods conventionally employed in the breeding of purine substance-producing bacteria such as those of Bacillus bacteria and Escherichia bacteria.
A purine substance-producing ability can be imparted or enhanced by, for example, imparting auxotrophy such as adenine auxotrophy, or further imparting resistance to purine analogues and a drug such as sulfaguanidine (refer to Japanese Patent Publication (Kokoku) Nos. 38-23099, 54-17033, 55-45199, 57-14160, 57-41915 and 59-42895, Published U.S. Patent Application No. 20040166575). A mutant strain having a purine substance-producing ability, such as an auxotrophic strain and a drug-resistant strain, can be obtained by subjecting a parent strain or wild-type strain to a mutagenesis treatment and selecting a mutant strain showing a desired phenotype using an appropriate selection medium. Examples of the mutagenesis treatment include, for example, X-ray irradiation, ultraviolet irradiation, and treatment with a mutagenesis agent such as N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), ethyl methanesulfonate (EMS), and methyl methanesulfonate (MMS).
A purine substance-producing ability can also be imparted or enhanced by enhancing the intracellular activity of an enzyme involved in biosynthesis of a purine substance. Activity of one kind of enzyme may be enhanced, or activities of two or more kinds of enzymes may be enhanced. Methods for enhancing an enzyme activity will be explained later. An enzyme activity can be enhanced by, for example, modifying a bacterium so that expression of a gene encoding the enzyme is enhanced. Methods for enhancing gene expression are described in WO18935, EP 1010755 A, and so forth.
Purine nucleotides are biosynthesized via phosphoribosylpyrophosphate (PRPP) as an intermediate. Purine nucleosides are biosynthesized by dephosphorylation of purine nucleotides. Examples of enzymes involved in the biosynthesis of these purine substances include, for example, PRPP synthetase (prs) and the proteins encoded by the purine operon.
Examples of the purine operon include, for example, the purEKBCSQLFMNHD operon of Bacillus subtilis (Bacillus subtilis and Its Closest Relatives, Editor in Chief: A. L. Sonenshein, ASM Press, Washington D.C., 2002) and the pur regulon of Escherichia coli (Escherichia and Salmonella, Second Edition, Editor in Chief: F. C. Neidhardt, ASM Press, Washington D.C., 1996). For example, expression of the total purine operon may be enhanced, or expression of one or more genes selected from the genes contained in the purine operon may be enhanced.
Among these, for example, activity or activities of one or more kinds of enzymes selected from PRPP synthetase (prs) and PRPP amidotransferase (purF) are preferably enhanced.
When an enzyme involved in biosynthesis of a purine substance is negatively regulated by feedback inhibition, expression inhibition, or the like, the enzymatic activity can be enhanced by, for example, reducing or eliminating such regulation, and the purine substance-producing ability can be thereby improved (WO99/003988).
Expression of the purine operon is suppressed by the purine repressor encoded by the purR gene. Therefore, expression of the purine operon can be enhanced by, for example, reducing the activity of the purine repressor (U.S. Pat. No. 6,284,495). The activity of the purine repressor can be reduced by, for example, disrupting the purR gene encoding the purine repressor (U.S. Pat. No. 6,284,495). Further, expression of the purine operon is regulated by the terminator-antiterminator sequence (it is also called attenuator sequence) locating downstream from the promoter (Ebbole, D. J. and Zalkin, H., J. Biol. Chem., 1987, 262, 8274-8287; Ebbole, D. J. and Zalkin, H., J. Biol. Chem., 1988, 263, 10894-10902; Ebbole, D. J. and Zalkin, H., J. Bacteriol., 1989, 171, 2136-2141). Therefore, expression of the purine operon can be enhanced by, for example, deleting the attenuator sequence. Deletion of the attenuator sequence can be attained by the same method as that used for disruption of a gene explained later.
The PRPP synthetase is subject to feedback inhibition by ADP. Therefore, for example, by making a bacterium harbor a mutant PRPP synthetase gene encoding a desensitized-type PRPP synthetase for which the feedback inhibition by ADP is reduced or eliminated, the PRPP synthetase activity can be enhanced, and the purine substance-producing ability can be thereby improved (WO99/003988). Examples of the desensitized-type PRPP synthetase include PRPP synthetase having a mutation that substitutes Ala (A) for Asp (D) of the position 128 of the wild-type PRPP synthetase (S. G. Bower et al., J. Biol. Chem., 264, 10287 (1989)).
The PRPP amidotransferase is subject to feedback inhibition by AMP and GMP. Therefore, for example, by making a bacterium harbor a mutant PRPP amidotransferase gene encoding a desensitized-type PRPP amidotransferase for which the feedback inhibition by AMP and/or GMP is reduced or eliminated, the PRPP amidotransferase activity can be enhanced, and the purine substance-producing ability can be thereby improved (WO99/003988). Examples of the desensitized-type PRPP amidotransferase include PRPP amidotransferase in which Gln (Q) substitutes for Lys (K) of the position 326 of the wild-type PRPP amidotransferase, and PRPP amidotransferase in which Gln (Q) substitutes for Lys (K) of the position 326, and Trp (W) substitutes for Pro (P) of the position 410 of the wild-type PRPP amidotransferase (G. Zhou et al., J. Biol. Chem., 269, 6784 (1994)).
A purine substance-producing ability can also be imparted or enhanced by reducing activity of an enzyme that catalyzes a reaction branching away from biosynthetic pathway of a purine substance to generate another compound (WO99/003988). Activity of one kind of enzyme may be reduced, or activities of two or more kinds of enzymes may be reduced. The “enzyme that catalyzes a reaction branching away from biosynthetic pathway of a purine substance to generate another compound” referred to here also includes an enzyme involved in decomposition of a purine substance. Methods for reducing enzymatic activity will be explained later.
Examples of the enzyme that catalyzes a reaction branching away from biosynthetic pathway of a purine substance to generate another compound include, for example, purine nucleoside phosphorylase (deoD, pupG), succinyl-AMP synthase (purA), adenosine deaminase (add), inosine-guanosine kinase (gsk), GMP reductase (guaC), 6-phosphogluconate dehydrase (edd), phophoglucose isomerase (pgi), adenine deaminase (yicP), xanthosine phosphorylase (xapA), and IMP dehydrogenase (guaB). The enzyme of which activity is to be reduced may be chosen according to kind of the target purine substance, and so forth.
A purine substance-producing ability can also be imparted or enhanced by reducing the activity of fructose bisphosphatase (fructose 1,6-bisphosphatase) (fbp) (WO2007/125782).
A purine substance-producing ability can also be imparted or enhanced by reducing the activity of a protein involved in uptake of a purine substance (WO99/003988). Examples of such a protein involved in uptake of a purine substance include, for example, nucleoside permease (nupG) (WO99/003988).
A purine substance-producing ability can also be imparted or enhanced by enhancing the activity of a protein involved in excretion of a purine substance. Examples of such a protein involved in excretion of a purine substance include, for example, proteins encoded by the rhtA (ybiF) gene (Russian Patent No. 2239656), yijE gene (Russian Patent No. 2244003), ydeD gene (Russian Patent No. 2244004), yicM gene (Russian Patent No. 2271391), ydhL gene (Japanese Patent Laid-open (Kohyo) No. 2007-530011), and nepI gene (FEMS Microbiology Letters, Volume 250, Issue 1, pages 39-47, September 2005).
Further, inosinic acid-producing ability can be imparted or enhanced by imparting resistance to an L-glutamine analogue and resistance to a proline analogue to a bacterium (Japanese Patent Laid-open (Kokai) No. 2004-516833). Examples of the L-glutamine analogue include azaserine and 6-diazo-5-oxo-L-norleucine (DON). Examples of the proline analogue include 3,4-dehydroproline, L-azetidine-2-carboxylic acid, L-thiazolidine-4-carboxylic acid, (S)-2,2-dimethyl-4-oxazolide-carboxylic acid, (S)-5,5-dimethyl-4-thiazolide-carboxylic acid, (4S,2RS)-2-ethyl-4-thiazolidine-carboxylic acid, (2S,4S)-4-hydroxy-2-pyrroline-carboxylic acid, 2-piperidine-carboxylic acid, and 2,5-pyrrolidinedione. Examples of inosinic acid-producing bacteria include, for example, Corynebacterium ammoniagenes CJIP009 (KCCM-10226, Japanese Patent Laid-open (Kokai) No. 2004-516833).
Further, xanthylic acid-producing ability can be imparted or enhanced by the methods used for breeding of xanthylic acid-producing bacteria of coryneform bacteria, of which typical example is Corynebacterium ammoniagenes. Examples of such methods include, for example, enhancing the PRPP amidotransferase activity (Japanese Patent Laid-open (Kokai) No. 8-168383), imparting resistance to an aliphatic amino acid (Japanese Patent Laid-open (Kokai) No. 4-262790), and imparting resistance to dehydroproline (South Korean Patent Laid-open No. 2003-56490).
Such methods for imparting or enhancing purine substance-producing ability as mentioned above may be used independently, or used as an arbitrary combination of them.
<1-1-3> Protein-Producing Bacteria
Secretory production of proteins can be enabled with coryneform bacteria using a signal peptide that functions in coryneform bacteria. Specifically, secretory production of a target protein can be enabled by making a coryneform bacterium harbor a gene construct comprising a promoter sequence that functions in the coryneform bacterium, a nucleic acid sequence encoding a signal peptide that functions in the coryneform bacterium and ligated downstream of the promoter sequence, and a nucleic acid sequence encoding a target protein and ligated downstream of the nucleic acid sequence encoding a signal peptide, and allowing expression of the target protein. It is sufficient that the nucleic acid sequence encoding the target protein is ligated downstream of the nucleic acid sequence encoding a signal peptide so that a heterogenous protein is expressed as a fused protein with this signal peptide. Examples of coryneform bacteria used for secretory production of proteins include, for example, strains of which the activity of cell surface protein is reduced. Examples of such strains include the C. glutamicum YDK010 strain (WO2004/029254), which is a cell surface protein PS2-deficient strain of the C. glutamicum AJ12036 strain (FERM BP-734). Further, examples of methods for imparting or enhancing ability of secretory production of protein include, for example, modifying a coryneform bacterium so that the activity of penicillin-binding protein is reduced (WO2013/065869), modifying a coryneform bacterium so that the expression of the gene encoding a metallopeptidase is increased (WO2013/065772), modifying a coryneform bacterium so that the coryneform bacterium harbors a mutant ribosomal protein S1 gene (WO2013/118544), and expressing a target protein with inserting an amino acid sequence containing Gln-Glu-Thr between a signal peptide and the target protein (WO2013/062029). Such methods for imparting or enhancing protein-producing ability as mentioned above may be used independently, or may be used in an arbitrary combination.
<1-2> Xylose Assimilability
The bacterium of the present invention is able to assimilate xylose. The bacterium of the present invention may be a bacterium inherently able to assimilate xylose, or may be a bacterium modified so that it is able to assimilate xylose. A bacterium able to assimilate xylose can be obtained by, for example, imparting the ability to assimilate xylose to such bacteria as mentioned above, or by enhancing the ability to assimilate xylose of such bacteria as mentioned above.
Xylose assimilability can be imparted or enhanced by modifying a bacterium so that activity or activities of one or more kinds of proteins constituting a xylose assimilation pathway are increased. The protein of which activity is to be increased can be appropriately chosen according to type of coryneform bacterium to be used, and so forth.
The following two kinds of pathways can be mentioned as the xylose assimilation pathway. The bacterium of the present invention may have the both pathways, or only one of the pathways.
Pathway 1: Xylose→xylulose→xylulose-5-phosphate
Pathway 2: Xylose→xylonolactone→xylonate→2-keto-3-deoxyxylonate→α-ketoglutaric semialdehyde→α-ketoglutarate
The pathway 1 is constituted by xylose isomerase and xylulokinase.
“Xylose isomerase” refers to a protein having an activity of catalyzing the following reaction of isomerizing D-xylose into D-xylulose (EC 5.3.1.5). This activity is also referred to as “xylose isomerase activity”.
D-Xylose→D-xylulose
“Xylulokinase” refers to a protein having an activity of catalyzing the following reaction of phosphorylating D-xylulose (EC 2.7.1.17). This activity is also referred to as “xylulokinase activity”.
ATP+D-xylulose→ADP+D-xylulose-5-phosphate
Examples of a gene encoding xylose isomerase include the xylA gene. Examples of a gene encoding xylulokinase include the xylB gene. Examples of the xylA gene and xylB gene include the xylA gene and xylB gene of Escherichia coli. The nucleotide sequence of the xylAB operon of the Escherichia coli K-12 MG1655 strain is shown as SEQ ID NO: 10. In the nucleotide sequence shown as SEQ ID NO: 10, the xylA gene and xylB gene correspond to the sequence of the positions 1 to 1323 and the sequence of the positions 1395 to 2849, respectively. The amino acid sequences of the XylA protein and XylB protein of the Escherichia coli K-12 MG1655 strain are shown as SEQ ID NOS: 11 and 12, respectively. Examples of the xylB gene also include the xylB gene of Corynebacterium glutamicum. The nucleotide sequence of the xylB gene and the amino acid sequence of XylB protein of C. glutamicum ATCC 13869 are shown as SEQ ID NOS: 35 and 36, respectively.
The pathway 2 is constituted by xylose dehydrogenase, xylonolactonase, xylonate dehydratase, 2-keto-3-deoxyxylonate dehydratase, and α-ketoglutaric semialdehyde dehydrogenase. The second half of the pathway 2, i.e., the pathway from xylonate to α-ketoglutarate constituted by xylonate dehydratase, 2-keto-3-deoxyxylonate dehydratase, and α-ketoglutaric semialdehyde dehydrogenase is also called “Weimberg pathway” (J. Biol. Chem., 236:629-636). The whole pathway 2 or Weimberg pathway is also called “NXA (Novel Xylose Assimilation) pathway”.
“Xylose dehydrogenase” refers to a protein having an activity of catalyzing the following reaction of oxidizing D-xylose into D-xylonolactone (EC 1.1.1.175 or 1.1.1.179). This activity is also referred to as “xylose dehydrogenase activity”.
D-Xylose+NAD(P)+→D-xylonolactone+NAD(P)H+H+
“Xylonolactonase” refers to a protein having an activity of catalyzing the following ring cleavage reaction of D-xylonolactone (EC 3.1.1.68). This activity is also referred to as “xylonolactonase activity”.
D-Xylono-1,4-lactone+H2O→D-xylonate
“Xylonate dehydratase” refers to a protein having an activity of catalyzing the following reaction of dehydrating D-xylonate (EC 4.2.1.82). This activity is also referred to as “xylonate dehydratase activity”.
D-Xylonate→2-dehydro-3-deoxy-D-xylonate+H2O
“2-Keto-3-deoxyxylonate dehydratase” refers to a protein having an activity of catalyzing the following reaction of dehydrating 2-keto-3-deoxyxylonate (EC 4.2.1.-). This activity is also referred to as “2-keto-3-deoxyxylonate dehydratase activity”.
2-Dehydro-3-deoxy-D-xylonate→
i. α-ketoglutaric semialdehyde+H2O
“α-Ketoglutaric semialdehyde dehydrogenase” refers to a protein having an activity of catalyzing the following reaction of oxidizing α-ketoglutaric semialdehyde (EC 1.2.1.26). This activity is also referred to as “α-ketoglutaric semialdehyde dehydrogenase activity”.
α-Ketoglutaric semialdehyde+NADP++H2O→
ii. 2-ketoglutarate+NADPH+2H+
Examples of genes encoding the enzymes constituting the pathway 2 include the genes of the xylXABCD operon. The xylB gene encodes xylose dehydrogenase. The xylC gene encodes xylonolactonase. The xylD gene encodes xylonate dehydratase. The xylX gene encodes 2-keto-3-deoxyxylonate dehydratase. The xylA gene encodes α-ketoglutaric semialdehyde dehydrogenase.
Although the same gene names are used, the xylA gene and xylB gene encoding xylose isomerase and xylulokinase of the pathway 1 are genes different from the xylA gene and xylB gene encoding α-ketoglutaric semialdehyde dehydrogenase and xylose dehydrogenase of the pathway 2, respectively.
Examples of the xylXABCD operon include the xylXABCD operon of the Caulobacter crescentus. Examples of Caulobacter crescentus include the CB15 strain, NA1000 strain, and K31 strain. The genome sequences of the Caulobacter crescentus CB15 strain, NA1000 strain, and K31 strain are registered at the NCBI database as GenBank Accession Nos. AE005673, CP001340, and CP000927, respectively. The xylXABCD genes of the Caulobacter crescentus CB15 strain are registered with the gene symbols of CC_0822, CC_0821, CC_0820, CC_0819, and CC_0823, respectively. The xylXABCD genes of the Caulobacter crescentus NA1000 strain are registered with the gene symbols of CCNA_00865, CCNA_00864, CCNA_00863, CCNA_00862, and CCNA_00866, respectively. The xylABCD genes (xylX is not identified yet) of the Caulobacter crescentus K31 strain are registered with the gene symbols of Caul_4001, Caul_4002, Caul_4003, and Caul_4000, respectively. The nucleotide sequences of the xylXABCD genes of the Caulobacter crescentus CB15 strain are shown as SEQ ID NOS: 37, 39, 41, 43, and 45, respectively. The amino acid sequences of the XylXABCD proteins of the Caulobacter crescentus CB15 strain are shown as SEQ ID NOS: 38, 40, 42, 44, and 46, respectively.
Examples of xylose dehydrogenase gene also include the xylB gene of Sphingomonas or Pseudomonas bacteria such as Sphingomonas elodea (formerly Pseudomonas elodea). The nucleotide sequence of the xylB gene and the amino acid sequence of XylB protein of Sphingomonas elodea are shown as SEQ ID NOS: 15 and 16, respectively.
Examples of xylonolactonase gene also include the xylC gene of Sphingomonas or Pseudomonas bacteria such as Sphingomonas elodea (Pseudomonas elodea). The nucleotide sequence of the xylC gene and the amino acid sequence of XylC protein of Sphingomonas elodea are shown as SEQ ID NOS: 17 and 18, respectively.
Examples of xylonate dehydratase gene also include the yjhG gene and yagF gene of Escherichia bacteria such as Escherichia coli, as well as xylD gene homologues of Agrobacterium bacteria such as Agrobacterium tumefaciens, Herbaspirillum bacteria such as Herbaspirillum seropedicae, Actinoplanes bacteria such as Actinoplanes missouriensis, and Aspergillus microorganisms such as Aspergillus oryzae. The nucleotide sequence of the yagF gene and the amino acid sequence of YagF protein of the Escherichia coli K-12 MG1655 strain are shown as SEQ ID NOS: 19 and 20, respectively.
Examples of the 2-keto-3-deoxyxylonate dehydratase gene include the xylX gene homologues of Agrobacterium bacteria such as Agrobacterium tumefaciens, Sphingomonas or Pseudomonas bacteria such as Sphingomonas elodea (Pseudomonas elodea), Zobellia bacteria such as Zobellia galactanivorans, Thermobacillus bacteria such as Thermobacillus composti, and Arthrobacter bacteria such as Arthrobacter globiformis. The nucleotide sequence of the xylX gene and the amino acid sequence of XylX protein of Sphingomonas elodea are shown as SEQ ID NOS: 21 and 22, respectively.
Examples of the α-ketoglutaric semialdehyde dehydrogenase gene include the xylA gene homologues of Azospirillum bacteria such as Azospirillum brasilense, and Halomonas bacteria such as Halomonas boliviensis, as well as the ycbD gene of Bacillus bacteria such as Bacillus subtilis. The nucleotide sequence of the ycbD gene and the amino acid sequence of YcbD protein of Bacillus subtilis are shown as SEQ ID NOS: 23 and 24, respectively.
The activity of each of the proteins constituting the xylose assimilation pathways can be measured according to the descriptions of published references (Non-patent document 3 and Patent document 8).
Further, some of glucose dehydrogenases (EC 1.1.1.47, EC 1.1.1.118, EC 1.1.1.119, EC 1.1.5.2 etc.) catalyze the reaction of oxidizing D-xylose into D-xylonolactone. Therefore, in order to impart or enhance xylose assimilability, the activity of such glucose dehydrogenase may be enhanced in addition to, or instead of the activity of xylose dehydrogenase mentioned above. Examples of such glucose dehydrogenase include the glucose dehydrogenase of Pseudomonas putida S12 (Jean-Paul Meijnen et al., Appl. Environ. Microbiol., 2009 May, 75(9):2784-2791). The glucose dehydrogenase of Pseudomonas putida S12 catalyzes the reaction of oxidizing D-xylose into D-xylonolactone by using pyrroloquinoline quinone as an electron acceptor.
The genes used for the aforementioned modifications of bacteria, such as the impartation or enhancement of a target substance-producing ability, and impartation or enhancement of xylose assimilability, are not limited to the genes exemplified above or genes having a known nucleotide sequence, but may be a variant thereof, so long as a protein that maintains the original function is encoded. For example, the genes used for the modifications of bacteria may be a gene encoding a protein having an amino acid sequence of known protein, but which includes substitution, deletion, insertion, or addition of one or several amino acid residues at one or several positions. To such variants of genes or proteins, the descriptions concerning variants of the NCgl2954 gene and the proteins encoded thereby mentioned later can be applied, mutatis mutandis.
<1-3> Improvement of Xylose Assimilability by Introduction of Mutation into NCgl2954 Gene
In the bacterium of the present invention, xylose assimilability has been improved by introduction of a mutation into the NCgl2954 gene. The bacterium of the present invention can be obtained by introducing a mutation into the NCgl2954 gene of a coryneform bacterium having a target substance-producing ability to improve xylose assimilability of the bacterium. The bacterium of the present invention can also be obtained by introducing a mutation into the NCgl2954 gene of a coryneform bacterium to improve xylose assimilability of the bacterium, and then imparting a target substance-producing ability to the bacterium. The bacterium of the present invention may be a bacterium that acquired a target substance-producing ability as a result of improvement of xylose assimilability provided by introduction of a mutation into the NCgl2954 gene. In the present invention, modifications for constructing the bacterium of the present invention can be performed in an arbitrary order.
Specifically, the xylose assimilability may be improved by improvement of xylose uptake ability. That is, the bacterium of the present invention may be a bacterium in which xylose uptake ability has been improved by introduction of a mutation into the NCgl2954 gene.
Improvement of xylose assimilability (for example, improvement of xylose uptake ability) can be confirmed by, for example, confirming improvement of growth or improvement of xylose consumption in culture of a coryneform bacterium performed in a medium containing xylose as a sole carbon source.
<1-3-1> NCgl2954 Gene and NCgl2954 Protein
The NCgl2954 gene is a gene encoding a transcription factor. The protein encoded by the NCgl2954 gene can also be referred to as NCgl2954 protein. The NCgl2954 gene of Corynebacterium glutamicum ATCC 13032 corresponds to the sequence of the positions 3261130 to 3261993 in the genome sequence registered at the NCBI database as GenBank accession NC 003450 (VERSION NC 003450.3 GI: 58036263). The NCgl2954 gene of Corynebacterium glutamicum ATCC 13032 is synonymous with Cgl3059. The NCgl2954 protein of Corynebacterium glutamicum ATCC 13032 is registered as GenBank accession NP_602251 (version NP_602251.2 GI:23309012). Further, the nucleotide sequence of the NCgl2954 gene and the amino acid sequence of the NCgl2954 protein of Corynebacterium glutamicum ATCC 13869 are shown as SEQ ID NOS: 13 and 14, respectively.
The NCgl2954 gene may be a variant of the genes exemplified above, so long as the variant maintains the original function. Similarly, the NCgl2954 protein may be a variant of the proteins exemplified above, so long as the variant maintains the original function. Such a variant that maintains the original function may be referred to as “conservative variant”. In the present invention, the term “NCgl2954 gene” includes not only the NCgl2954 genes exemplified above, but also conservative variants thereof. Similarly, the term “NCgl2954 protein” includes not only the NCgl2954 proteins exemplified above, but also conservative variants thereof. Examples of the conservative variants include, for example, homologues and artificially modified genes and proteins of the NCgl2954 genes and NCgl2954 proteins exemplified above.
The expression “variant maintains the original function” means that the variant has a function (such as activity and property) corresponding to the function (such as activity and property) of the original gene or protein. That is, the expression “variant maintains the original function” means that, in the case of the NCgl2954 gene, a variant of the gene has a property that deletion thereof in a coryneform bacterium improves xylose assimilability of the bacterium. Further, the expression “variant maintains the original function” may also mean that, in the case of the NCgl2954 gene, a variant of the gene encodes a protein that maintains the original function. Similarly, the expression “variant maintains the original function” means that, in the case of the NCgl2954 protein, a variant of the protein has a property that deletion thereof in a coryneform bacterium improves xylose assimilability of the bacterium. Specifically, the xylose assimilability may be improved by improvement of xylose uptake ability. That is, “to improve xylose assimilability” may mean to improve xylose uptake ability.
Whether a variant of the gene or protein has the property that deletion thereof in a coryneform bacterium improves xylose assimilability of the bacterium can be confirmed by deleting the gene or a gene encoding the protein in a coryneform bacterium having xylose assimilability, and confirming whether the xylose assimilability is improved or not.
Homologues of the aforementioned NCgl2954 genes can be easily obtained from public databases by, for example, BLAST search or FASTA search using a nucleotide sequence of the NCgl2954 gene mentioned above as a query sequence. Further, homologues of the aforementioned NCgl2954 genes can also be obtained by, for example, PCR using a chromosome of a coryneform bacterium as the template, and oligonucleotides prepared on the basis of a known gene sequence as the primers.
The NCgl2954 gene may encode a protein having any of the aforementioned amino acid sequences, but which includes substitution, deletion, insertion, or addition of one or several amino acid residues at one or several positions, so long as the protein maintains the original function. Although the number of “one or several” mentioned above may differ depending on the positions of amino acid residues in the three-dimensional structure of the protein or types of amino acid residues, specifically, it is, for example, 1 to 50, 1 to 40, or 1 to 30, 1 to 20, 1 to 10, 1 to 5, or 1 to 3.
The aforementioned substitution, deletion, insertion, or addition of one or several amino acid residues is a conservative mutation that maintains normal function of the protein. Typical examples of the conservative mutation are conservative substitutions. The conservative substitution is a mutation wherein substitution takes place mutually among Phe, Trp, and Tyr, if the substitution site is an aromatic amino acid; among Leu, Ile, and Val, if it is a hydrophobic amino acid; between Gln and Asn, if it is a polar amino acid; among Lys, Arg, and His, if it is a basic amino acid; between Asp and Glu, if it is an acidic amino acid; and between Ser and Thr, if it is an amino acid having a hydroxyl group. Examples of substitutions considered as conservative substitutions include, specifically, 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. Further, such substitution, deletion, insertion, addition, inversion, or the like of amino acid residues as mentioned above includes a naturally occurring mutation due to an individual difference, or a difference of species of the organism from which the gene is derived (mutant or variant).
The NCgl2954 gene may be a gene encoding a protein showing a homology of, for example, 80% or more, 90% or more, 95% or more, 97% or more, 99% or more, to the total amino acid sequence of any of the amino acid sequences mentioned above, so long as the protein maintains the original function. In this description, “homology” means “identity”.
The NCgl2954 gene may also be a DNA that is able to hybridize under stringent conditions with a probe that can be prepared from a known gene sequence, such as a sequence complementary to a partial or entire sequence of any of the aforementioned nucleotide sequences. The “stringent conditions” refer to conditions under which a so-called specific hybrid is formed, and a non-specific hybrid is not formed. Examples of the stringent conditions include those under which highly homologous DNAs hybridize to each other, for example, DNAs not less than 80% homologous, not less than 90% homologous, not less than 95% homologous, not less than 97% homologous, or not less than 99% homologous, hybridize to each other, and DNAs less homologous than the above do not hybridize to each other, or conditions of washing of typical Southern hybridization, i.e., conditions of washing once, or 2 or 3 times, at a salt concentration and temperature corresponding to 1×SSC, 0.1% SDS at 60° C., 0.1×SSC, 0.1% SDS at 60° C., or 0.1×SSC, 0.1% SDS at 68° C.
The probe used for the aforementioned hybridization may be a part of a sequence that is complementary to the gene as described above. Such a probe can be prepared by PCR using oligonucleotides prepared on the basis of a known gene sequence as primers and a DNA fragment containing any of the aforementioned nucleotide sequences as a template. As the probe, for example, a DNA fragment having a length of about 300 bp can be used. When a DNA fragment having a length of about 300 bp is used as the probe, the washing conditions of the hybridization may be, for example, 50° C., 2×SSC and 0.1% SDS.
Further, since the degeneracy of codons differs depending on the host, arbitrary codons in the NCgl2954 gene may be replaced with equivalent codons, so long as the original function is maintained.
The aforementioned descriptions concerning conservative variants of the genes and proteins can be applied mutatis mutandis to variants of arbitrary proteins such as L-amino acid biosynthesis system enzymes and genes encoding them.
<1-3-2> Mutation to be Introduced into NCgl2954 Gene
The expression “a mutation is introduced into the NCgl2954 gene” specifically means that a mutation is introduced into a coding region and/or an expression control region of the NCgl2954 gene on a chromosome. The “expression control region” is a generic term for referring to a site that affects gene expression. Examples of expression control region include promoter, Shine-Dalgarno (SD) sequence (also referred to as ribosome binding site (RBS)), and spacer region between RBS and start codon. Expression control regions can be determined by, for example, using a promoter search vector, or gene analysis software such as GENETYX.
The mutation to be introduced into the NCgl2954 gene is not particularly limited, so long as introduction of the mutation improves xylose assimilability of a coryneform bacterium. Examples of the mutation that improves xylose assimilability of a coryneform bacterium include a mutation that attenuates expression of the NCgl2954 gene and a mutation that disrupts the NCgl2954 gene. That is, the bacterium of the present invention may be, for example, a bacterium of which xylose assimilability has been improved by attenuation of the NCgl2954 gene expression or disruption of the gene.
The phrase “expression of a gene is attenuated” can also mean “expression of a gene is reduced”. The phrase “expression of a gene is reduced” can mean that the expression amount of the gene per cell is reduced compared with that observed in a non-modified strain such as wild-type strains and parent strain of the bacterium. The phrase “expression of a gene is reduced” can include when the gene is not expressed at all. Expression of a gene may be reduced to, for example, 50% or less, 20% or less, 10% or less, 5% or less, or 0% of that observed in a non-modifying strain.
A reduction in the expression of a gene may be provided by, for example, a reduction in the transcription efficiency, a reduction in the translation efficiency, or a combination of them. A reduction in the expression of a gene can be attained by, for example, modifying an expression control region of the gene such as promoter, SD sequence (RBS), and spacer region between RBS and the start codon of the gene. When an expression control region is modified, preferably one or more nucleotides, more preferably two or more nucleotides, particularly preferably three or more nucleotides, of the expression control region are modified. Further, a part or the whole of the expression control region may be deleted. A reduction in the expression of a gene can also be attained by, for example, introducing a mutation that reduces the expression of the gene into the coding region of the gene. For example, the expression of a gene can be reduced by replacing a codon in a coding region of a gene with a synonymous codon less frequently used in a host. Further, for example, gene expression itself may be reduced by disruption of a gene as described later.
The expression that “a gene is disrupted” can mean that the gene is modified so that it does not produce a protein that normally functions. The phrase “a protein that normally functions is not produced” can include when the protein is not produced at all from the gene, and when the protein of which function (such as activity and property) per molecule is reduced or eliminated is produced from the gene.
Disruption of a gene can be attained by, for example, deleting a part or the whole of the coding region of the gene on a chromosome. Furthermore, the whole of a gene including sequences upstream and downstream from the gene on a chromosome may be deleted. The sequences upstream and downstream from the gene may contain, for example, an expression control region of the gene. The region to be deleted may be any region such as an N-terminus region, an internal region, or a C-terminus region. Deletion of a longer region can usually more surely inactivate the gene. Further, it is preferred that reading frames of the sequences upstream and downstream from the region to be deleted are not the same.
Disruption of a gene can also be attained by, for example, introducing a mutation for an amino acid substitution (missense mutation), a stop codon (nonsense mutation), a frame shift mutation which adds or deletes one or two nucleotide residues, or the like into the coding region of the gene on a chromosome (Journal of Biological Chemistry, 272:8611-8617 (1997); Proceedings of the National Academy of Sciences, USA, 95 5511-5515 (1998); Journal of Biological Chemistry, 26 116, 20833-20839 (1991)).
Disruption of a gene can also be attained by, for example, inserting another sequence into a coding region of the gene on a chromosome. Site of the insertion may be in any region of the gene. Usually, insertion of a longer region can usually more surely inactivate the gene. It is preferred that reading frames of the sequences upstream and downstream from the insertion site are not the same. The other sequence is not particularly limited so long as insertion of the sequence provides disruption of a gene, and examples thereof include, for example, a marker gene such as antibiotic resistance genes, and a gene useful for production of a target substance.
Such modification of a gene on a chromosome as described above can be attained by, for example, preparing a deficient type gene in which a partial sequence of the gene is deleted so that it cannot produce a protein that can normally function, and transforming a host with a recombinant DNA including the deficient type gene to cause homologous recombination between the deficient type gene and the wild-type gene on a chromosome and thereby substitute the deficient type gene for the wild-type gene on the chromosome. In this procedure, if a marker gene selected according to the characteristics of the host such as auxotrophy is included in the recombinant DNA, the operation becomes easy. The protein encoded by the deficient type gene has a conformation different from that of the wild-type protein, even if it is produced, and thus the function thereof is reduced or eliminated. Such gene disruption based on gene substitution utilizing homologous recombination has already been established, and there are methods of using a linear DNA such as a method called “Red driven integration” (Datsenko, K. A, and Wanner, B. L., Proc. Natl. Acad. Sci. USA, 97:6640-6645 (2000)), and a method utilizing 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)) (refer to WO2005/010175), a method of using a plasmid including a temperature sensitive replication origin, a method of using a plasmid capable of conjugative transfer, a method of utilizing a suicide vector not including a replication origin that functions in a host (U.S. Pat. No. 6,303,383, Japanese Patent Laid-open (Kokai) No. 05-007491), and so forth.
A mutation may also be introduced by, for example, a mutagenesis treatment. Examples of the mutagenesis treatment include usual mutation treatments such as X-ray irradiation, ultraviolet irradiation, and treatment with a mutation agent such as N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), ethyl methanesulfonate (EMS), and methyl methanesulfonate (MMS).
A reduction in the expression of a gene can be confirmed by confirming a reduction in the transcription amount of the gene or a reduction in the amount of the protein expressed from the gene.
A reduction in the transcription amount of a gene can be confirmed by comparing the amount of mRNA transcribed from the gene with that observed in a non-modified strain. Examples of the method for evaluating the amount of mRNA include Northern hybridization, RT-PCR, and so forth (Molecular Cloning, Cold spring Harbor Laboratory Press, Cold Spring Harbor (USA), 2001). The amount of mRNA is preferably decreased to, for example, 50% or less, 20% or less, 10% or less, 5% or less, or 0%, of that observed in a non-modified strain.
A reduction in the amount of a protein can be confirmed by Western blotting using antibodies (Molecular Cloning, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (USA) 2001). The amount of the protein is preferably decreased to, for example, 50% or less, 20% or less, 10% or less, 5% or less, or 0%, of that observed in a non-modified strain.
Disruption of a gene can be confirmed by determining nucleotide sequence of a part or the whole of the gene, restriction enzyme map, full length, or the like of the gene depending on the means used for the disruption.
Further, specific examples of the mutation to be introduced into the NCgl2954 gene include, for example, the mutations of (1) to (7) mentioned below. By the introduction of any of the mutations of (1) to (7) mentioned below, for example, expression of the NCgl2954 gene may be attenuated, or the NCgl2954 gene may be disrupted. The NCgl2954 gene not having any of the mutations of (1) to (7) mentioned below may also be referred to as “wild-type NCgl2954 gene”, and the NCgl2954 gene having any of the mutations of (1) to (7) mentioned below may also be referred to as “mutant NCgl2954 gene”. Further, a protein encoded by a wild-type NCgl2954 gene may also be referred to as “wild-type NCgl2954 protein”, and a protein encoded by a mutant NCgl2954 gene may also be referred to as “mutant NCgl2954 protein”. Examples of the wild-type NCgl2954 gene include the NCgl2954 genes exemplified above, and conservative variants thereof.
(1) Replacing the leucine residue at position 438 of a wild-type NCgl2954 protein with another amino acid residue
(2) Replacing the tryptophan residue at position 274 of a wild-type NCgl2954 protein with another amino acid residue
(3) Replacing the tyrosine residue at position 377 of a wild-type NCgl2954 protein with another amino acid residue
(4) Replacing the leucine residue at position 365 of a wild-type NCgl2954 protein with another amino acid residue
(5) Replacing the leucine residue at position 366 of a wild-type NCgl2954 protein with another amino acid residue
(6) Replacing the alanine residue at position 367 of a wild-type NCgl2954 protein with another amino acid residue
(7) Truncating the N-terminus of the wild-type NCgl2954 protein at position 368.
The “another amino acid residue” (i.e. amino acid residue existing after the substitution) is not particularly limited, so long as it is an amino acid residue other than the amino acid residue existing before the substitution. Specific examples of the “another amino acid residue” include lysine, ornithine, arginine, histidine, isoleucine, alanine, valine, leucine, glycine, threonine, serine, proline, phenylalanine, tyrosine, tryptophan, cysteine, methionine, glutamic acid, aspartic acid, glutamine, and asparagine residues, provided that they must be other than the amino acid residues existing before the substitution. The leucine residue at position 438 may be replaced with, for example, a proline residue. The tryptophan residue at position 274 may be replaced with, for example, an arginine residue. The leucine residue at the position 365 may be replaced with, for example, a serine residue. The leucine residue at the position 366 may be replaced with, for example, an arginine residue. The alanine residue at the position 367 may be replaced with, for example, a phenylalanine residue. The tyrosine residue at the position 377 may be replaced with, for example, an asparagine residue.
A mutant NCgl2954 gene may have one or more mutations selected from these mutations. For example, a mutant NCgl2954 gene may have the mutations of (4) to (7) mentioned above in combination. Specifically, for example, a mutant NCgl2954 gene produced from the wild-type NCgl2954 gene shown as SEQ ID NO: 13 by deletion of GC at the positions 1092 and 1093 encodes a mutant NCgl2954 protein corresponding to the wild-type NCgl2954 protein shown as SEQ ID NO: 14 in which the leucine-leucine-alanine residues at the positions 365 to 367 are replaced with serine-arginine-phenylalanine residues, and the protein is truncated at position 368.
An “amino acid residue at the position X of a wild-type NCgl2954 protein” referred to in the present invention means an amino acid residue corresponding to the amino acid residue at the position X of SEQ ID NO: 14, unless otherwise stated. That is, the mutations of (1) to (7) mentioned above may be described, in other words, as follows.
(1) Replacing an amino acid residue corresponding to the leucine residue at position 438 of SEQ ID NO: 14 with an amino acid residue other than a leucine residue;
(2) Replacing an amino acid residue corresponding to the tryptophan residue at position 274 of SEQ ID NO: 14 with an amino acid residue other than a tryptophan residue
(3) Replacing an amino acid residue corresponding to the tyrosine residue at position 377 of SEQ ID NO: 14 with an amino acid residue other than tyrosine residue
(4) Replacing an amino acid residue corresponding to the leucine residue at position 365 of SEQ ID NO: 14 with an amino acid residue other than a leucine residue
(5) Replacing an amino acid residue corresponding to the leucine residue at position 366 of SEQ ID NO: 14 with an amino acid residue other than a leucine residue
(6) Replacing an amino acid residue corresponding to the alanine residue at position 367 of SEQ ID NO: 14 with an amino acid residue other than an alanine residue
(7) Truncating the protein the position 368 of SEQ ID NO: 14 and the rest of the N-terminus of the protein.
The “position X” in an amino acid sequence is the X-th position counted from the N-terminus of the amino acid sequence, and the amino acid residue of the N-terminus is the amino acid residue at the position 1. That is, the position of amino acid residue is a relative position, and the absolute position thereof may shift due to deletion, insertion, addition, or the like of an amino acid residue or residues. For example, “the leucine residue at position 438 of a wild-type NCgl2954 protein” means an amino acid residue corresponding to the leucine residue at position 438 of SEQ ID NO: 14. When one amino acid residue is deleted on the N-terminus side with respect to the position 438, the 437th amino acid residue from the N-terminus shall be the “leucine residue at position 438 of a wild-type NCgl2954 protein”. Also, when one amino acid residue is inserted on the N-terminus side with respect to the position 438, the 439th amino acid residue counted from the N-terminus shall be the “leucine residue at position 438 of a wild-type NCgl2954 protein”.
Which amino acid residue is the “amino acid residue corresponding to the amino acid residue at the position X of SEQ ID NO: 14” in an arbitrary amino acid sequence can be determined by aligning the arbitrary amino acid sequence and the amino acid sequence of SEQ ID NO: 14. The alignment can be performed by, for example, using known gene analysis software. Specific examples of such software include DNASIS produced by Hitachi Solutions, GENETYX produced by Genetyx, and so forth (Elizabeth C. Tyler et al., Computers and Biomedical Research, 24 (1) 72-96, 1991; Barton G. J. et al., Journal of Molecular Biology, 198 (2), 327-37, 1987).
When a wild-type NCgl2954 protein has an amino acid sequence other than the amino acid sequence shown as SEQ ID NO: 14, the amino acid residues for which the mutations of (1) to (7) mentioned above are introduced may be, or may not be conserved in such an amino acid sequence. That is, for example, in a wild-type NCgl2954 protein, the “amino acid residue corresponding to the leucine residue at position 438 of SEQ ID NO: 14” need not be leucine residue. Therefore, for example, the “Replacing an amino acid residue corresponding to the leucine residue at position 438 of SEQ ID NO: 14 with a proline residue” is not limited to a mutation for replacing, in the case that the amino acid residue at that position of the wild-type NCgl2954 protein is leucine residue, the leucine residue with a proline residue, but may also include replacing, in the case that the amino acid residue at that position is not leucine residue, the amino acid residue (not being leucine residue) with a proline residue.
A mutant NCgl2954 gene can be obtained by modifying a wild-type NCgl2954 gene so that the modified gene should have any of the mutations mentioned above. The modification of DNA can be performed by a known method. Specifically, the modification of DNA can be performed by, for example, the site-specific mutagenesis method for introducing an objective mutation into a target site of DNA. Examples of the site-specific mutagenesis method include, for example, a method of using PCR (Higuchi, R., 61, in PCR Technology, Erlich, H. A. Eds., Stockton Press, 1989; Carter P., Meth., in Enzymol., 154, 382, 1987), and a method of using a phage (Kramer, W. and Frits, H. J., Meth. in Enzymol., 154, 350, 1987; Kunkel, T. A. et al., Meth. in Enzymol., 154, 367, 1987). Further, a mutant NCgl2954 gene can also be obtained by chemical synthesis.
<1-4> Method for Reducing Activity of Protein
Hereafter, the methods for reducing the activity of a protein will be explained.
The expression “the activity of a protein is reduced” means that the activity of the protein per cell is reduced as compared with that of a non-modified strain such as a wild-type strain and parent strain. The state that “the activity of a protein is reduced” also includes a state that the activity of the protein has completely disappeared. Specifically, the expression “the activity of a protein is reduced” means that the number of molecules of the protein per cell is reduced, and/or the function of each molecule of the protein is reduced as compared with those of a non-modified strain. That is, the term “activity” in the expression “the activity of a protein is reduced” is not limited to the catalytic activity of the protein, but may also mean the transcription amount of a gene (i.e. the amount of mRNA) encoding the protein or the translation amount of the protein (i.e. the amount of the protein). The state that “the number of molecules of the protein per cell is reduced” also includes a state that the protein does not exist at all. The state that “the function of each molecule of the protein is reduced” also includes a state that the function of each protein molecule has completely disappeared. The degree of the reduction in the activity of a protein is not particularly limited, so long as the activity is reduced as compared with that of a non-modified strain. The activity of a protein may be reduced to, for example, 50% or less, 20% or less, 10% or less, 5% or less, or 0% of that of a non-modified strain.
The modification for reducing the activity of a protein can be attained by, for example, reducing the expression of a gene encoding the protein. Further, the modification for reducing the activity of a protein can also be attained by, for example, disrupting the gene encoding the protein. Further, the modification for reducing the activity of a protein can also be performed by, for example, a mutagenesis treatment. Methods for reducing the expression of a gene, methods for disrupting a gene, and mutagenesis treatment are as described above.
When a protein functions as a complex consisting of a plurality of subunits, a part or all of the plurality of subunits may be modified, so long as the activity of the protein is eventually reduced. That is, for example, a part or all of a plurality of genes that encode the respective subunits may be disrupted or the like. Further, when there is a plurality of isozymes of a protein, a part or all of the activities of the plurality of isozymes may be reduced, so long as the activity of the protein is eventually reduced. That is, for example, a part or all of a plurality of genes that encode the respective isozymes may be disrupted or the like.
A reduction in the activity of a protein can be confirmed by measuring the activity of the protein. A reduction in the activity of a protein can also be confirmed by confirming a reduction in the expression of a gene encoding the protein, or by confirming disruption of such a gene.
The aforementioned methods for reducing the activity of a protein as mentioned above can be applied to reduction in the activities of arbitrary proteins such as an enzyme that catalyzes a reaction branching away from the biosynthesis pathway of an objective L-amino acid to generate a compound other than the objective L-amino acid, and reduction in the expression of arbitrary genes such as genes encoding those arbitrary proteins.
<1-5> Methods for Increasing Activity of Protein
Hereafter, the methods for increasing the activity of a protein will be explained.
The expression “the activity of a protein is increased” means that the activity of the protein per cell is increased as compared with that of a non-modified strain such as a wild-type strain and parent strain. The state that “the activity of a protein is increased” may also be expressed as “the activity of a protein is enhanced”. Specifically, the expression “the activity of a protein is increased” means that the number of molecules of the protein per cell is increased, and/or the function of each molecule of the protein is increased as compared with those of a non-modified strain. That is, the term “activity” in the expression “the activity of a protein is increased” is not limited to the catalytic activity of the protein, but may also mean the transcription amount of a gene (i.e. the amount of mRNA) encoding the protein, or the translation amount of the protein (i.e. the amount of the protein). Further, the state that “the activity of a protein is increased” includes not only a state that the activity of an objective protein is increased in a strain inherently having the activity of the objective protein, but also a state that the activity of an objective protein is imparted to a strain not inherently having the activity of the objective protein. Further, so long as the activity of the protein is eventually increased, the activity of an objective protein inherently contained in a host may be attenuated and/or eliminated, and then an appropriate type of the objective protein may be imparted to the host.
The degree of the increase in the activity of a protein is not particularly limited, so long as the activity of the protein is increased as compared with a non-modified strain. The activity of the protein may be increased 1.5 times or more, 2 times or more, or 3 times or more, as compared with that of a non-modified strain. Further, when the non-modified strain does not have the activity of the objective protein, it is sufficient that the protein is produced as a result of introduction of the gene encoding the protein, and for example, the protein may be produced to such an extent that the enzymatic activity can be measured.
The modification for increasing the activity of a protein is attained by, for example, increasing the expression of a gene encoding the protein. The state that “the expression of a gene is increased” may also be referred to as “the expression of a gene is enhanced”. The expression of a gene may be increased 1.5 times or more, 2 times or more, or 3 times or more, as compared with that of a non-modified strain. Further, the state that “the expression of a gene is increased” includes not only when the expression amount of an objective gene is increased in a strain that inherently expresses the objective gene, but also when the gene is introduced into a strain that does not inherently express the objective gene, and expressed therein. That is, the phrase “the expression of a gene is increased” may also mean, for example, that an objective gene is introduced into a strain that does not possess the gene, and is expressed therein.
The expression of a gene can be increased by, for example, increasing the copy number of the gene.
The copy number of a gene can be increased by introducing the gene into the chromosome of a host. A gene can be introduced into a chromosome by, for example, using homologous recombination (Miller, J. H., Experiments in Molecular Genetics, 1972, Cold Spring Harbor Laboratory). Only one copy, or two or more copies of a gene may be introduced. For example, by performing homologous recombination using a sequence which is present in multiple copies on a chromosome as a target, multiple copies of a gene can be introduced into the chromosome. Examples of such a sequence which is present in multiple copies on a chromosome include repetitive DNAs, and inverted repeats located at the both ends of a transposon. Alternatively, homologous recombination may be performed by using an appropriate sequence on a chromosome such as a gene unnecessary for the target substance production as a target. Homologous recombination can be performed by, for example, a method of using a linear DNA such as Red-driven integration (Datsenko, K. A., and Wanner, B. L., Proc. Natl. Acad. Sci. USA, 97:6640-6645 (2000)), a method of using a plasmid including a temperature sensitive replication origin, a method of using a plasmid capable of conjugative transfer, a method of using a suicide vector not including a replication origin that functions in a host, or a transduction method using a phage. Further, a gene can also be randomly introduced into a chromosome by using a transposon or Mini-Mu (Japanese Patent Laid-open (Kokai) No. 2-109985, U.S. Pat. No. 5,882,888, EP 805867 B1).
Introduction of a target gene into a chromosome can be confirmed by Southern hybridization using a probe having a sequence complementary to the whole gene or a part thereof, PCR using primers prepared on the basis of the sequence of the gene, or the like.
Further, the copy number of a gene can also be increased by introducing a vector containing the gene into a host. For example, the copy number of a target gene can be increased by ligating a DNA fragment containing the target gene with a vector that functions in a host to construct an expression vector of the gene, and transforming the host with the expression vector. The DNA fragment containing the target gene can be obtained by, for example, PCR using the genomic DNA of a microorganism having the target gene as the template. As the vector, a vector autonomously replicable in the cell of the host can be used. The vector is preferably a multi-copy vector. Further, the vector preferably has a marker such as an antibiotic resistance gene for selection of transformant. The vector may be, for example, a vector derived from a bacterial plasmid, a vector derived from a yeast plasmid, a vector derived from a bacteriophage, cosmid, phagemid, or the like. Specific examples of vector autonomously replicable in coryneform bacteria include pHM1519 (Agric. Biol. Chem., 48, 2901-2903 (1984)); pAM330 (Agric. Biol. Chem., 48, 2901-2903 (1984)); plasmids obtained by improving these and having a drug resistance gene; plasmid pCRY30 described in Japanese Patent Laid-open (Kokai) No. 3-210184; plasmids pCRY21, pCRY2KE, pCRY2KX, pCRY31, pCRY3KE, and pCRY3KX described in Japanese Patent Laid-open (Kokai) No. 2-72876 and U.S. Pat. No. 5,185,262; plasmids pCRY2 and pCRY3 described in Japanese Patent Laid-open (Kokai) No. 1-191686; pAJ655, pAJ611, and pAJ1844 described in Japanese Patent Laid-open (Kokai) No. 58-192900; pCG1 described in Japanese Patent Laid-open (Kokai) No. 57-134500; pCG2 described in Japanese Patent Laid-open (Kokai) No. 58-35197; and pCG4 and pCG11 described in Japanese Patent Laid-open (Kokai) No. 57-183799.
When a gene is introduced, it is sufficient that the gene is expressibly harbored by the bacterium of the present invention. Specifically, it is sufficient that the gene is introduced so that it is expressed under control by a promoter sequence that functions in the bacterium of the present invention. The promoter may be a promoter derived from the host, or a heterogenous promoter. The promoter may be the native promoter of the gene to be introduced, or a promoter of another gene. As the promoter, for example, such a stronger promoter as mentioned later may also be used.
A terminator for termination of gene transcription may be located downstream of the gene. The terminator is not particularly limited so long as it functions in the bacterium of the present invention. The terminator may be a terminator derived from the host, or a heterogenous terminator. The terminator may be the native terminator of the gene to be introduced, or a terminator of another gene. Specific examples of the terminator include, for example, trpA terminator.
Vectors, promoters, and terminators available in various microorganisms are disclosed in detail in “Fundamental Microbiology Vol. 8, Genetic Engineering, KYORITSU SHUPPAN CO., LTD, 1987”, and those can be used.
Further, when two or more genes are introduced, it is sufficient that the genes each are expressibly harbored by the bacterium of the present invention. For example, all the genes may be carried by a single expression vector or a chromosome. Further, the genes may be separately carried by two or more expression vectors, or separately carried by a single or two or more expression vectors and a chromosome. An operon constituted by two or more genes may also be introduced. The case of “introducing two or more genes” include, for example, cases of introducing respective genes encoding two or more kinds of enzymes, introducing respective genes encoding two or more subunits constituting a single enzyme complex, and a combination of the foregoing cases.
The gene to be introduced is not particularly limited so long as it encodes a protein that functions in the host. The gene to be introduced may be a gene derived from the host, or may be a heterogenous gene. The gene to be introduced can be obtained by, for example, PCR using primers designed on the basis of the nucleotide sequence of the gene, and using the genomic DNA of an organism having the gene, a plasmid carrying the gene, or the like as a template. The gene to be introduced may also be totally synthesized, for example, on the basis of the nucleotide sequence of the gene (Gene, 60(1), 115-127 (1987)).
In addition, when a protein functions as a complex consisting of a plurality of subunits, a part or all of the plurality of subunits may be modified, so long as the activity of the protein is eventually increased. That is, for example, when the activity of a protein is increased by increasing the expression of a gene, the expression of a part or all of genes that encode the subunits may be enhanced. It is usually preferable to enhance the expression of all of the genes encoding the subunits. Further, the subunits constituting the complex may be derived from a single kind of organism or two or more kinds of organisms, so long as the complex has a function of the objective protein. That is, for example, genes of the same organism encoding a plurality of subunits may be introduced into a host, or genes of different organisms encoding a plurality of subunits may be introduced into a host.
Further, the expression of a gene can be increased by improving the transcription efficiency of the gene. The transcription efficiency of a gene can be improved by, for example, replacing the promoter of the gene on a chromosome with a stronger promoter. The “stronger promoter” means a promoter providing an improved transcription of a gene compared with an inherently existing wild-type promoter of the gene. Examples of stronger promoters usable in coryneform bacteria include the artificially modified P54-6 promoter (Appl. Microbiol. Biotechnolo., 53, 674-679 (2000)), pta, aceA, aceB, adh, and amyE promoters inducible in coryneform bacteria with acetic acid, ethanol, pyruvic acid, or the like, cspB, SOD, and tuf (EF-Tu) promoters, which are potent promoters capable of providing a large expression amount in coryneform bacteria (Journal of Biotechnology, 104 (2003) 311-323; Appl. Environ. Microbiol., 2005 December; 71 (12):8587-96), as well as lac promoter, tac promoter, and trc promoter. Further, as the stronger promoter, a highly-active type of an existing promoter may also be obtained by using various reporter genes. For example, by making the −35 and −10 regions in a promoter region closer to the consensus sequence, the activity of the promoter can be enhanced (WO00/18935). Examples of highly active-type promoter include various tac-like promoters (Katashkina J I et al., Russian Federation Patent Application No. 2006134574) and pnlp8 promoter (WO2010/027045). 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., 1, 105-128 (1995)), and so forth.
Further, the expression of a gene can be increased by improving the translation efficiency of the gene. The translation efficiency of a gene can be improved by, for example, replacing the Shine-Dalgarno (SD) sequence (also referred to as ribosome binding site (RBS)) for the gene on a chromosome with a stronger SD sequence. The “stronger SD sequence” means a SD sequence that provides an improved translation of mRNA compared with the inherently existing wild-type SD sequence of the gene. Examples of stronger SD sequences include, for example, RBS of the gene 10 derived from phage T7 (Olins P. O. et al, Gene, 1988, 73, 227-235). Further, it is known that substitution, insertion, or deletion of several nucleotides in a spacer region between RBS and the start codon, especially in a sequence immediately upstream of the start codon (5′-UTR), significantly affects the stability and translation efficiency of mRNA, and hence, the translation efficiency of a gene can also be improved by modifying them.
These expression control sequences can be modified by, for example, a method of using a temperature sensitive vector, or the Red driven integration method (WO2005/010175).
The translation efficiency of a gene can also be improved by, for example, modifying codons. In Escherichia coli etc., a clear codon bias exists among the 61 amino acid codons found within the population of mRNA molecules, and the level of cognate tRNA appears directly proportional to the frequency of codon usage (Kane, J. F., Curr. Opin. Biotechnol., 6 (5), 494-500 (1995)). That is, if there is a large amount of mRNA containing an excess amount of rare codons, a translational problem may arise. According to the recent researches, it is suggested that clusters of AGG/AGA, CUA, AUA, CGA, or CCC codons may especially reduce both the quantity and quality of a synthesized protein. Such a problem occurs especially at the time of expression of a heterologous gene. Therefore, in the case of heterogenous expression of a gene or the like, the translation efficiency of the gene can be improved by replacing a rare codon present in the gene with a synonymous codon more frequently used. Codons can be replaced by, for example, the site-specific mutation method for introducing an objective mutation into an objective site of DNA. Examples of the site-specific mutation method include the method utilizing PCR (Higuchi, R., 61, in PCR Technology, Erlich, H. A. Eds., Stockton Press (1989); Carter, P., Meth. in Enzymol., 154, 382 (1987)), and the method utilizing phage (Kramer, W. and Frits, H. J., Meth. in
Enzymol., 154, 350 (1987); Kunkel, T. A. et al., Meth. in Enzymol., 154, 367 (1987)). Alternatively, a gene fragment in which objective codons are replaced may be totally synthesized. Frequencies of codons in various organisms are disclosed in the “Codon Usage Database” (kazusa.or.jp/codon; Nakamura, Y. et al, Nucl. Acids Res., 28, 292 (2000)).
Further, the expression of a gene can also be increased by amplifying a regulator that increases the expression of the gene, or deleting or attenuating a regulator that reduces the expression of the gene.
Such methods for increasing the gene expression as mentioned above may be used independently or in an arbitrary combination.
Further, the modification that increases the activity of a protein can also be attained by, for example, enhancing the specific activity of the enzyme. Enhancement of the specific activity also includes desensitization to feedback inhibition. That is, when a protein is subject to feedback inhibition by a metabolite, the activity of the protein can be increased by making the bacterium harbor a gene encoding a mutant protein that has been desensitized to the feedback inhibition. In the present invention, “desensitization to feedback inhibition” includes attenuation and elimination of the feedback inhibition. A protein showing an enhanced specific activity can be obtained by, for example, searching various organisms. Further, a highly-active type of an existing protein may also be obtained by introducing a mutation into the existing protein. The mutation to be introduced may be, for example, substitution, deletion, insertion, or addition of one or several amino acid residues at one or several position of the protein. The mutation can be introduced by, for example, such a site-specific mutation method as mentioned above. The mutation may also be introduced by, for example, a mutagenesis treatment. Examples of the mutagenesis treatment include irradiation of X-ray, irradiation of ultraviolet, and a treatment with a mutation agent such as N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), ethyl methanesulfonate (EMS), and methyl methanesulfonate (MMS). Further, a random mutation may be induced by directly treating DNA in vitro with hydroxylamine. Enhancement of the specific activity may be independently used, or may be used in an arbitrary combination with such methods for enhancing gene expression as mentioned above.
The method for the transformation is not particularly limited, and conventionally known methods can be used. There can be used, for example, a method of treating recipient cells with calcium chloride so as to increase the permeability thereof for DNA, which has been reported for the Escherichia coli K-12 strain (Mandel, M. and Higa, A., J. Mol. Biol., 1970, 53, 159-162), and a method of preparing competent cells from cells which are in the growth phase, followed by transformation with DNA, which has been reported for Bacillus subtilis (Duncan, C. H., Wilson, G. A. and Young, F. E., Gene, 1977, 1:153-167). Alternatively, there can also be used a method of making DNA-recipient cells into protoplasts or spheroplasts, which can easily take up recombinant DNA, followed by introducing a recombinant DNA into the DNA-recipient cells, which is known to be applicable to Bacillus subtilis, actinomycetes, and yeasts (Chang, S. and Choen, S. N., 1979, Mol. Gen. Genet., 168:111-115; Bibb, M. J., Ward, J. M. and Hopwood, O. A., 1978, Nature, 274:398-400; Hinnen, A., Hicks, J. B. and Fink, G. R., 1978, Proc. Natl. Acad. Sci. USA, 75:1929-1933). Further, the electric pulse method reported for coryneform bacteria (Japanese Patent Laid-open (Kokai) No. 2-207791) can also be used.
An increase in the activity of a protein can be confirmed by measuring the activity of the protein.
An increase in the activity of a protein can also be confirmed by confirming an increase in the expression of a gene encoding the protein. An increase in the expression of a gene can be confirmed by confirming an increase in the transcription amount of the gene, or by confirming an increase in the amount of a protein expressed from the gene.
An increase of the transcription amount of a gene can be confirmed by comparing the amount of mRNA transcribed from the gene with that of a non-modified strain such as a wild-type strain or parent strain. Examples of the method for evaluating the amount of mRNA include Northern hybridization, RT-PCR, and so forth (Sambrook, J., et al., Molecular Cloning A Laboratory Manual/Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (USA), 2001). The amount of mRNA may increase, for example, 1.5 times or more, 2 times or more, or 3 times or more, as compared with that of a non-modified strain.
An increase in the amount of a protein can be confirmed by Western blotting using antibodies (Molecular Cloning, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (USA), 2001). The amount of the protein may increase, for example, 1.5 times or more, 2 times or more, or 3 times or more, as compared with that of a non-modified strain.
The aforementioned methods for increasing the activity of a protein can be used for enhancement of the activities of arbitrary proteins such as L-amino acid biosynthesis enzymes, and enhancement of the expression of arbitrary genes such as genes encoding those arbitrary proteins.
<2> Method for Producing Target Substance
<2-1> Method for Producing Target Substance
The method of the present invention is a method for producing a target substance that includes culturing the bacterium of the present invention in a medium containing xylose to produce and accumulate the target substance in the medium or cells of the bacterium, and collecting the target substance from the medium or cells. In the present invention, one kind of target substance may be produced, or two or more kinds of target substances may be produced.
The medium to be used is not particularly limited, so long as it contains xylose, the bacterium of the present invention can proliferate in it, and a target substance can be produced. As the medium, for example, a usual medium used for culture of bacteria and so forth can be used. The medium may contain, in addition to xylose, carbon source, nitrogen source, phosphate source, and sulfur source, as well as components selected from other various organic components and inorganic components as required. Types and concentrations of the medium components may be appropriately determined according to various conditions such as type of the bacterium to be used and type of the target substance to be produced.
As xylose, pure xylose such as purified xylose may be used, or a mixture containing xylose and other components may be used. Examples of such a mixture include hydrolysates of plant biomass. Such plant biomass is not particularly limited so long as it contains xylose as a constituent sugar. Examples of plant biomass include wood biomass and herb biomass. Specific examples of plant biomass include, for example, rice straw, chaff, and sugarcane bagasse. By subjecting the plant biomass to such a treatment as hydrothermal decomposition treatment, concentrated acid hydrolysis, diluted acid hydrolysis, hydrolysis with an enzyme such as cellulase, and alkaline treatment, a processed product containing xylose can be obtained. Such a processed product can be used as the carbon source, as it is, or after it is subjected to purification etc., appropriately.
As the method for treating plant biomass, hydrothermal decomposition treatment is preferred. Plant biomass may be subjected to a treatment such as hydrothermal decomposition treatment, as it is, or after it is subjected to pretreatment such as steaming and blasting, appropriately. For example, plant biomass may be ground into a size of 5 mm or smaller, and then subjected to a treatment such as hydrothermal decomposition treatment. The hydrothermal decomposition can be performed by using, for example, pressurized hot water of preferably 175 to 240° C., more preferably 200 to 230° C. Since hemicellulose components, cellulose, and lignin components dissolve at temperatures around 140° C. or higher, around 230° C. or higher, and around 140° C. or higher, respectively, a temperature within the aforementioned ranges is preferred for sufficiently dissolving the hemicellulose components.
The aforementioned hydrothermal decomposition treatment can be performed by countercurrently contacting plant biomass with pressurized hot water. Such a treatment can be performed by using the apparatuses disclosed in Japanese Patent Nos. 4436429, 4524351, and 4427583. By the hydrothermal decomposition treatment of plant biomass, the lignin components and hemicellulose components are transferred into hot water from the plant biomass, and cellulose components remain as solid content.
The reaction pressure of the hydrothermal decomposition treatment is preferably higher than the saturation vapor pressure of water at the selected temperature by 0.1 to 0.5 MPa, so that water in the inside of the apparatus becomes pressurized hot water. Reaction time is usually 20 minutes or shorter, preferably 3 to 15 minutes.
Then, the hot water is separated from the solid content, and hemicellulose contained in the hot water is subjected to a saccharification treatment. The saccharification of hemicellulose can be performed by enzymatic decomposition using a saccharification enzyme, or by sulfuric acid decomposition using sulfuric acid. In the present invention, enzymatic decomposition is preferred.
The saccharification enzyme is not particularly limited so long as a saccharification enzyme that can decompose hemicellulose to generate xylose is chosen. Specific examples of the saccharification enzyme include hemicellulase. Hemicellulase is a generic term for referring to enzymes that catalyze hydrolysis of glycosidic bonds contained in hemicellulose. Hemicellulose means polysaccharides constituting cell walls of land plant cells except for cellulose and pectin, and the main component of hemicellulose is xylan. Xylan is a heteropolysaccharide consisting of a backbone comprising xylose as a constituent sugar, and side chains comprising arabinose etc. and binding to the backbone. The main components of hemicellulase are endo-1,4-β-xylanase (EC 3.2.1.8), β-1,4-xylosidase (EC 3.2.1.37), and so forth, but hemicellulase also contains other glycosidic bond hydrolysis enzymes. Examples of commercially available hemicellulase include Cellic Htec (Novozymes), and so forth. Spezyme CP (Genencor, derived from Trichoderma reesei), which is a cellulase, Novozyme 188 (Novozyme, derived from Aspergillus niger), which is a β-glucosidase, and so forth may also be used as hemicellulase. If these enzymes are made to act on hemicellulose, xylose, arabinose, and so forth are generated. Further, not only hemicellulose, but also cellulose may be transferred into or contaminate the hot water, and therefore glucose may be generated by the saccharification treatment. In the present invention, such by-products as glucose obtained by the saccharification treatment may also be used as a carbon source, in addition to xylose.
The enzymatic reaction can be performed in an appropriate aqueous solvent such as water and buffers. The solvent used for the enzymatic reaction may be water used for the hydrothermal treatment itself. The reaction conditions, such as reaction temperature and pH, may be as described in descriptions attached to commercially available enzymes, or appropriately determined by performing preliminary experiments etc. For example, when Spezyme CP or Novozyme 188 mentioned above is used, examples of the reaction conditions are conditions of 45 to 60° C. and pH 4.5 to 6.5. Amount of the enzyme may usually be 20 to 120 FPU (filter paper unit) based on the substrate solid amount, and the reaction time may usually be, for example, 24 to 144 hours. The enzymatic reaction may be statically performed, or it may be performed with stirring. Further, in advance of the enzymatic reaction, a pretreatment such as delignification and partial decomposition of hemicellulose may be performed.
When the saccharification is performed by sulfuric acid decomposition, sulfuric acid concentration may be usually 0.1 to 5% by weight, preferably 1 to 4% by weight. The decomposition temperature may be usually 100 to 140° C., preferably around 120° C. The decomposition time may be usually 30 minutes to 3 hours, preferably around 1 hour. After the decomposition, sulfuric acid can be removed by an ion exchange resin treatment, or the like.
The sugar solution containing xylose obtained by the saccharification treatment may be used as the carbon source, as it is, or after it is subjected to such a treatment as concentration, dilution, drying, fractionation, and purification, appropriately. For example, a component such as xylose may be purified from the sugar solution to a desired extent, and then used as the carbon source.
The sugar solution obtained by the saccharification treatment may contain substances that inhibit growth and metabolism of microorganisms. Such inhibitory substances are mainly nonvolatile non-saccharide substances having a molecular weight of 3000 or smaller. Therefore, it is preferred that the sugar solution be subjected to a treatment for removing such inhibitory substances, and then used as the carbon source. Examples of the treatment for removing such inhibitory substances include adsorbent treatment, gel filtration, membrane treatment, and so forth. The sugar solution may be subjected to a treatment for removing inhibitory substances, as it is, or after it is subjected to concentration or dilution, appropriately.
Examples of adsorbent that can be used for the adsorbent treatment include, for example, activated carbon, ion exchange resins, synthetic adsorptive resins, zeolite, and silica gel. The adsorbent is preferably an adsorbent that selectively adsorbs such inhibitory substances as mentioned above. Although the adsorbent treatment can be performed as a batch treatment or by using a column, it is preferable to use a column. In the case of the batch treatment, the adsorbent is put into a vessel containing the sugar solution, and then the adsorbent and the sugar solution are separated. When a column is used, the sugar solution is flown through a column filled with the adsorbent, a washing solution is flown through the column if needed, and flow-through solution (non-adsorbed fraction) is collected. The adsorbent treatment may be performed only once, or may be repeated twice or more. Also, one kind of adsorbent may be used, or two or more kinds of adsorbents may be used in combination for the adsorbent treatment.
The sugar solution from which inhibitory substances are removed can be used as the carbon source, as it is, or after it is subjected to concentration, dilution, drying, fractionation, purification, etc., appropriately.
Various components generated by the saccharification treatment may be further subjected to isomerization, decomposition, or the like by a chemical reaction or enzymatic reaction depending on type of use.
The solid content remained after the hot water was separated from a biomass raw material subjected to the hydrothermal treatment may also be used. That is, if cellulose in such solid content is enzymatically treated with cellulase or the like, a sugar solution containing hexoses such as glucose can be obtained. In addition to xylose, such a sugar solution or a processed product thereof may be used as the carbon source.
In the method of the present invention, xylose may be or may not be used as a sole carbon source. That is, in the method of the present invention, in addition to xylose, another carbon source may be used together. The other carbon source is not particularly limited, so long as the bacterium of the present invention can utilize, and a target substance can be produced. Specific examples of the other carbon source include, for example, saccharides such as glucose, fructose, sucrose, lactose, galactose, arabinose, blackstrap molasses, hydrolysate of starch, and hydrolysate of biomass, organic acids such as acetic acid, fumaric acid, citric acid, succinic acid, and malic acid, alcohols such as glycerol, crude glycerol, and ethanol, and aliphatic acids. When another carbon source is used, ratio of xylose in the total carbon source may be, for example, 5% by weight or more, 10% by weight or more, or 20% by weight or more, preferably 30% by weight or more, more preferably 50% by weight or more. As the other carbon source, one kind of carbon source may be used, or two or more kinds of carbon sources may be used in combination.
The concentration of the carbon source in the medium is not particularly limited, so long the bacterium of the present invention can proliferate in the medium, and a target substance can be produced. The concentration of the carbon source in the medium is preferably made as high as possible in such a range that the production of the target substance is not inhibited. The initial concentration of the carbon source in the medium may be, for example, usually 1 to 30% (W/V), preferably 3 to 10% (W/V). Along with consumption of the carbon source accompanying advance of the fermentation, the carbon source may be supplementarily added.
Specific examples of the nitrogen source include, for example, ammonium salts such as ammonium sulfate, ammonium chloride, and ammonium phosphate, organic nitrogen sources such as peptone, yeast extract, meat extract, and soybean protein decomposition products, ammonia, and urea. Ammonia gas or aqueous ammonia used for adjusting pH may also be used as the nitrogen source. As the nitrogen source, a single kind of nitrogen source may be used, or two or more kinds of nitrogen sources may be used in combination.
Specific examples of the phosphate source include, for example, phosphoric acid salts such as potassium dihydrogenphosphate and dipotassium hydrogenphosphate, and phosphoric acid polymers such as pyrophosphoric acid. As the phosphate source, a single kind of phosphate source may be used, or two or more kinds of phosphate sources may be used in combination.
Specific examples of the sulfur source include, for example, inorganic sulfur compounds such as sulfates, thiosulfates, and sulfites, and sulfur-containing amino acids such as cysteine, cystine, and glutathione. As the sulfur source, a single kind of sulfur source may be used, or two or more kinds of sulfur sources may be used in combination.
Specific examples of other various organic components and inorganic components include, for example, inorganic salts such as sodium chloride and potassium chloride; trace metals such as iron, manganese, magnesium, and calcium; vitamins such as vitamin B1, vitamin B2, vitamin B6, nicotinic acid, nicotinamide, and vitamin B12; amino acids; nucleic acids; and organic components containing those such as peptone, casamino acid, yeast extract, and soybean protein decomposition product. As other various organic components and inorganic components, a single kind of component may be used, or two or more kinds of components may be used in combination.
Further, when an auxotrophic mutant that requires an amino acid or the like for growth thereof is used, it is preferable to supplement a required nutrient to the medium. For example, in many of L-lysine-producing bacteria, the L-lysine biosynthetic pathway is enhanced and the L-lysine degrading ability is attenuated. Therefore, when such an L-lysine-producing bacterium is cultured, for example, one or more kinds of amino acids selected from L-threonine, L-homoserine, L-isoleucine, and L-methionine are preferably added to the medium.
Further, when L-glutamic acid is produced by using a coryneform bacterium, it is preferable to, for example, restrict the amount of biotin in the medium, or add a surfactant or penicillin to the medium. It is also preferable to add an appropriate amount of a commercially available antifoam to the medium in order to suppress foaming at the time of the culture.
Culture conditions are not particularly limited, so long as the bacterium of the present invention can proliferate, and a target substance can be produced. The culture can be performed with, for example, usual conditions used for culture of coryneform bacteria. The culture conditions may be appropriately determined depending on various conditions such as type of bacterium to be used and type of target substance to be produced.
The culture can be performed by using a liquid medium. At the time of the culture, the bacterium of the present invention cultured on a solid medium such as agar medium may be directly inoculated into a liquid medium, or the bacterium of the present invention cultured in a liquid medium as seed culture may be inoculated into a liquid medium for main culture. That is, the culture may be performed as separate seed culture and main culture. In such a case, the culture conditions of the seed culture and the main culture may be or may not be the same. Amount of the bacterium of the present invention contained in the medium at the time of the start of the culture is not particularly limited. For example, a seed culture broth showing an OD660 of 4 to 8 may be added to a medium for main culture at a ratio of 0.1 to 30 mass %, or 1 to 10 mass %, at the time of the start of the culture.
The culture can be performed as batch culture, fed-batch culture, continuous culture, or a combination of these. The medium used at the time of the start of the culture is also referred to as “starting medium”. The medium supplied to a culture system (fermentation tank) in fed-batch culture or continuous culture is also referred to as “feed medium”. Further, to supply a feed medium to a culture system in fed-batch culture or continuous culture is also referred to as to “feed”. Further, when the culture is performed as separate seed culture and main culture, for example, both the seed culture and the main culture may be performed as batch culture. Alternatively, for example, the seed culture may be performed as batch culture, and the main culture may be performed as fed-batch culture or continuous culture.
In the present invention, the medium components each may be contained in the starting medium, feed medium, or the both. The types of the components contained in the starting medium may be or may not be the same as the types of the components contained in the feed medium. The concentration of each component contained in the starting medium may be or may not be the same as the concentration of the component contained in the feed medium. Further, two or more kinds of feed media containing different types and/or different concentrations of components may be used. For example, when medium is intermittently fed a plurality of times, the types and/or concentrations of components contained in the feed media may be or may not be the same.
The concentration of xylose in the medium is not particularly limited, so long as the bacterium of the present invention can use xylose as the carbon source. Xylose may be contained in the medium at a concentration of, for example, 10 w/v % or lower, 5 w/v % or lower, or 2 w/v % or lower. Also, xylose may be contained in the medium at a concentration of, for example, 0.2 w/v % or higher, 0.5 w/v % or higher, or 1.0 w/v % or higher. Xylose may be contained in the starting medium, feed medium, or the both at a concentration within the range exemplified above.
When xylose is contained in the feed medium, xylose may be contained in the feed medium at such a concentration that, for example, the xylose concentration in the medium after feeding is 5 w/v % or lower, 2 w/v % or lower, or 1 w/v % or lower. When xylose is contained in the feed medium, xylose may be contained in the feed medium at such a concentration that, for example, the xylose concentration in the medium after feeding is 0.01 w/v % or higher, 0.02 w/v % or higher, or 0.05 w/v % or higher.
When xylose is used as a sole carbon source, xylose may be contained at a concentration within the range exemplified above. When another carbon source is used together, xylose may also be contained at a concentration within the range exemplified above. When another carbon source is used together, xylose may also be contained at a concentration within a range defined by appropriately modifying the range exemplified above on the basis of, for example, ratio of xylose in the total carbon source, or the like.
Xylose may be or may not be contained within a certain range over the whole period of culture. For example, xylose may run short during a partial period of culture. The term “run short” means that the amount of xylose is smaller than the required amount, and it may means, for example, that the concentration in the medium becomes zero. The term “partial period of culture” may refer to, for example, 1% or less, 5% or less, 10% or less, 20% or less, 30% or less, or 50% or less of the whole period of the culture. When the culture is performed as separate seed culture and main culture, the term “whole period of the culture” may mean the whole period of the main culture. It is preferred that, during a period when xylose runs short, another carbon source exists in a sufficient amount. Even if xylose runs short during a partial period of culture as described above, culture performed under such a condition is included in the scope of the expression “culture of a bacterium in a medium containing xylose”, so long as there is a culture period where the culture is performed in a medium containing xylose.
Concentration of various components such as xylose can be measured by gas chromatography (Hashimoto, K. et al., Biosci. Biotechnol. Biochem., 1996, 70:22-30) or HPLC (Lin, J. T. et al., J. Chromatogr. A., 1998, 808:43-49).
The culture can be, for example, aerobically performed. For example, the culture can be performed as aeration culture or shaking culture. The oxygen concentration can be controlled to be, for example, 5 to 50%, or about 10%, of the saturated oxygen concentration. pH of the medium may be, for example, 3 to 10, preferably 4.0 to 9.5. During the culture, pH of the medium can be adjusted as required. pH of the medium can be adjusted by using various alkaline and acidic substances such as ammonia gas, aqueous ammonia, sodium carbonate, sodium bicarbonate, potassium carbonate, potassium bicarbonate, magnesium carbonate, sodium hydroxide, calcium hydroxide, and magnesium hydroxide. The culture temperature may be, for example, 20 to 45° C., preferably 25 to 37° C. The culture period may be, for example, 10 to 120 hours. The culture may be continued, for example, until the carbon source contained in the medium is consumed, or until the bacterium of the present invention loses the activity. By culturing the bacterium of the present invention under such conditions as described above, a target substance is accumulated in cells of the bacterium and/or the medium.
In the fed-batch culture or continuous culture, feeding of the feed medium may be continued over the whole period of the culture or only during a partial period of the culture. In the fed-batch culture or continuous culture, feeding may be intermittently performed a plurality of times.
When feeding is intermittently performed a plurality of times, the feeding may be repeatedly started and stopped so that the period for one time of feeding is, for example, 30% or shorter, 20% or shorter, or10% or shorter, of the total period of the feeding of the plurality of times.
Further, when feeding is intermittently performed a plurality of times, the carbon source concentration in the fermentation medium can also be automatically maintained at a low level by controlling the feeding so that the second and following feedings are started when the carbon source in the fermentation medium is depleted in the non-feeding periods immediately before the respective feedings (U.S. Pat. No. 5,912,113). Depletion of the carbon source can be detected on the basis of, for example, elevation of pH, or elevation of dissolved oxygen concentration.
In the continuous culture, extraction of the culture medium may be continued over the whole period of the culture or only during a partial period of the culture. Further, in the continuous culture, extraction of the culture medium may be intermittently performed a plurality of times. Extraction and feeding of the culture medium may be or may not be simultaneously performed. For example, after extracting the culture medium, feeding may be performed, or after performing feeding, the culture medium may be extracted. It is preferred that the volume of the culture medium to be extracted is equal to the volume of the medium to be fed. The expression “the volume of the culture medium to be extracted is equal to the volume of the medium to be fed equal volume” mentioned above may mean that the volume of the culture medium to be extracted is, for example, 93 to 107% of the volume of the medium to be fed.
When the culture medium is continuously extracted, the extraction is preferably started at the same time as or after the start of the feeding. For example, within 5 hours, preferably 3 hours, more preferably 1 hour, after the start of the feeding, the extraction can be started.
When the culture medium is intermittently extracted, it is preferred that, when the target substance concentration reaches a predetermined level, a part of the culture medium is extracted to collect the target substance, and then a fresh medium is fed to continue the culture.
Further, after the target substance is collected from the extracted culture medium, the cells can be reused by recycling filtration residue containing the cells into the fermentation tank (French Patent No. 2669935).
Moreover, when L-glutamic acid is produced, the culture can be performed by using a liquid medium adjusted to satisfy a condition under which L-glutamic acid is precipitated, while precipitating L-glutamic acid in the medium. Examples of the condition under which L-glutamic acid is precipitated include, for example, pH 5.0 to 3.0, preferably pH 4.9 to 3.5, more preferably pH 4.9 to 4.0, particularly preferably around pH 4.7 (EP 1078989 A). The culture may be performed at a pH value within the aforementioned ranges over the whole period of culture, or only during a partial period of culture. The term “partial period of culture” may refer to, for example, 50% or more, 70% or more, 80% or more, 90% or more, 95% or more, or 99% or more, of the whole period of culture.
When a basic amino acid such as L-lysine is produced, there may be employed a method in which the basic amino acid is produced by fermentation using bicarbonate ions and/or carbonate ions as major counter ions for the basic amino acid (Japanese Patent Laid-open (Kokai) No. 2002-65287, U.S. Patent Published Application No. 20020025564, EP 1813677 A). By such a method, a basic amino acid can be produced while reducing the amount(s) of sulfate ions and/or chloride ions to be used, which have been conventionally used as counter ions for a basic amino acid.
Production of the target substance can be confirmed by known methods used for detection or identification of compounds. Examples of such methods include, for example, HPLC, LC/MS, GC/MS, and NMR. These methods can be used in an appropriate combination.
The produced target substance can be collected by known methods used for separation and purification of compounds. Examples of such methods include, for example, ion-exchange resin method, membrane treatment, precipitation, and crystallization. These methods can be used in an appropriate combination. When the target substance is accumulated in bacterial cells, the bacterial cells can be disrupted with, for example, ultrasonic waves or the like, and then the target substance can be collected by the ion exchange resin method or the like from the supernatant obtained by removing the cells from the cell-disrupted suspension by centrifugation. The target substance to be collected may be a free compound, a salt thereof, or a mixture thereof. Examples of the salt include, for example, sulfate, hydrochloride, carbonate, ammonium salt, sodium salt, and potassium salt. For example, L-lysine may be free L-lysine, L-lysine sulfate, L-lysine hydrochloride, L-lysine carbonate, or a mixture of these. Also, for example, L-glutamic acid may be free L-glutamic acid, sodium L-glutamate (monosodium L-glutamate, MSG), ammonium L-glutamate (monoammonium L-glutamate), or a mixture of these. For example, in the case of L-glutamic acid, monosodium L-glutamate (MSG) can be obtained by adding an acid to the fermentation broth to crystallize ammonium L-glutamate contained therein, and then by adding an equimolar of sodium hydroxide to the crystals. In addition, decolorization can be performed by using activated carbon before and/or after the crystallization (see, Tetsuya KAWAKITA, “Industrial Crystallization for Monosodium L-Glutamate.”, Bulletin of the Society of Sea Water Science, Japan, Vol. 56:5). Also, for example, specific examples of salt of inosinic acid include sodium inosinate (5′-IMP disodium salt). Also, for example, specific examples of salt of guanylic acid include sodium guanylate (5′-GMP disodium salt).
When the target substance is precipitated in the medium, it can be collected by centrifugation, filtration, or the like. The target substance precipitated in the medium may also be isolated together with the target substance dissolving in the medium, after the target substance dissolving in the medium is crystallized.
The collected target substance may contain such components as bacterial cells, medium components, moisture, and by-product metabolites of the bacterium in addition to the target substance. Purity of the collected target substance may be, for example, 30% (w/w) or higher, 50% (w/w) or higher, 70% (w/w) or higher, 80% (w/w) or higher, 90% (w/w) or higher, or 95% (w/w) or higher.
When the L-amino acid is L-glutamic acid, for example, the monosodium L-glutamate crystal can be used as an umami seasoning. The monosodium L-glutamate crystal can be used as a seasoning in combination with a nucleic acid such as 5′-GMP disodium salt and 5′-IMP disodium salt, which also have umami taste.
<2-2> Method for Producing Purine Nucleotide
When a purine nucleoside is produced by the bacterium of the present invention, a purine nucleotide can be produced by using the purine nucleoside. The present invention thus provides a method for producing a purine nucleotide comprising culturing the bacterium of the present invention having a purine nucleoside-producing ability in a medium to produce and accumulate the purine nucleoside in the medium, phosphorylating the purine nucleoside to generate a purine nucleotide, and collecting the purine nucleotide.
In this method, a purine nucleotide corresponding to the purine nucleoside to be used is produced. That is, for example, inosinic acid can be produced from inosine, guanylic acid can be produced from guanosine, xanthylic acid can be produced from xanthosine, and adenylic acid can be produced from adenosine. In the present invention, one kind of purine nucleotide may be produced, or two or more kinds of purine nucleotides may be produced.
The purine nucleoside may be phosphorylated in a state that it is contained in the medium, or phosphorylated after it is collected from the medium. The purine nucleoside may also be phosphorylated after being subjected to a pretreatment, appropriately. Examples of the pretreatment include, for example, purification, dilution, concentration, crystallization, drying, grinding, dissolution, and so forth. These pretreatments may be performed in an appropriate combination. For example, a culture broth containing a purine nucleoside may be used as it is for the phosphorylation, or a purine nucleoside purified to a desired extent from such a culture broth may be used for the phosphorylation.
The method for phosphorylating the purine nucleoside is not particularly limited. The phosphorylation can be performed by, for example, known methods.
The phosphorylation can be performed, for example, chemically. Such chemical phosphorylation can be performed by using a phosphorylating agent such as phosphoryl chloride (POC13) (Yoshikawa et al., Studies of phosphorylation, III, Selective phosphorylation of unprotected nucleosides, Bull. Chem. Soc. Jpn., 1969, 42:3505-3508).
The phosphorylation can also be performed by using, for example, a microorganism or enzyme. That is, by allowing a microorganism having a nucleoside-5′-phosphate-producing ability to act on a purine nucleoside and a phosphate donor, a purine nucleotide can be produced (Japanese Patent Laid-open (Kolai) No. 07-231793). Further, by allowing a phosphorylation enzyme to act on a purine nucleoside and a phosphate donor, a purine nucleotide can be produced.
Specific examples of microorganisms having a nucleoside-5′-phosphate-producing ability include, for example, such strains as mentioned below (Japanese Patent Laid-open (Kokai) No. 07-231793).
Escherichia blattae JCM 1650
Serratia ficaria ATCC 33105
Klebsiella planticola IFO 14939 (ATCC 33531)
Klebsiella pneumoniae IFO 3318 (ATCC 8724)
Klebsiella terrigena IFO 14941 (ATCC 33257)
Morganella morganii IFO 3168
Enterobacter aerogenes IFO 12010
Enterobacter aerogenes IFO 13534 (ATCC 13048)
Chromobacterium fluviatile IAM 13652
Chromobacterium violaceum IFO 12614
Cedecea lapagei JCM 1684
Cedecea davisiae JCM 1685
Cedecea neteri JCM 5909
Examples of the phosphorylation enzyme include, for example, phosphatase, nucleoside kinase, and nucleoside phosphotransferase. The phosphorylation enzyme may be or may not be a purified enzyme. For example, a fraction containing a phosphorylation enzyme, such as culture of a microorganism that produces the phosphorylation enzyme, culture supernatant separated from the culture, cells separated from the culture, processed product of the cells of the microorganism, and partially purified products of these, may be used as the phosphorylation enzyme.
Examples of the nucleoside kinase include, for example, inosine-guanosine kinase. Specific examples of a method using inosine-guanosine kinase include, for example, the method for producing a purine nucleotide using an Escherichia bacterium introduced with a gene encoding inosine-guanosine kinase of Escherichia coli (WO91/08286), and the method for producing a purine nucleotide using Corynebacterium ammoniagenes introduced with a gene encoding inosine-guanosine kinase of Exiguobacterium acetylicum (WO96/30501).
Examples of the phosphatase include, for example, acid phosphatase. Examples of acid phosphatase include, for example, the acid phosphatase disclosed in Japanese Patent Laid-open (Kokai) No. 2002-000289. Preferred examples of acid phosphatase include, for example, the mutant acid phosphatase showing increased affinity for nucleosides (Japanese Patent Laid-open (Kokai) No. 10-201481), the mutant acid phosphatase showing reduced nucleotidase activity (WO96/37603), and the mutant acid phosphatase showing reduced phosphoric acid ester hydrolysis activity (Japanese Patent Laid-open (Kokai) No. 2001-245676).
Examples of the phosphate donor include, for example, polyphosphoric acid, phenyl phosphate, acetyl phosphate, carbamyl phosphate, ATP, and dATP (deoxy-ATP). Examples of polyphosphoric acid include, for example, pyrophosphoric acid, tripolyphosphoric acid, trimetaphosphoric acid, tetrametaphosphoric acid, and hexametaphosphoric acid. The phosphate donors each may be a free compound, a salt thereof, or a mixture of them. Examples of the salt include, for example, sodium salt and potassium salt. The phosphate donor can be appropriately chosen depending on type of the microorganism to be used and type of the phosphorylation enzyme to be used, etc. Further, when ATP or dATP is used as the phosphate donor, a recycling system therefor can also be used in combination (WO91/08286, WO96/30501).
Production of a purine nucleotide can be confirmed by known methods used for detection or identification of compounds. Examples of such methods include, for example, HPLC, LC/MS, GC/MS, and NMR. These methods can be used in an appropriate combination.
The produced purine nucleotide can be collected by known methods used for separation and purification of compounds. Examples of such methods include, for example, ion-exchange resin method, membrane treatment, precipitation, and crystallization. These methods can be used in an appropriate combination. The collected purine nucleotide may be a free compound, a salt thereof, or a mixture of them. The collected purine nucleotide may contain such components as phosphorylation enzyme, phosphate donor, bacterial cells, medium components, moisture, and by-product metabolites of the bacterium, in addition to the purine nucleotide. The purine nucleotide may be purified in a desired degree. Purity of the purine nucleotide may be, for example, 30% (w/w) or higher, 50% (w/w) or higher, 70% (w/w) or higher, 80% (w/w) or higher, 90% (w/w) or higher, or 95% (w/w) or higher.
Hereafter, the present invention will be more specifically explained with reference to the following non-limiting examples.
(1) Media
Compositions and preparation methods of the media used in this example are shown below.
LB Medium
The LB medium contained 10 g/L of polypeptone, 5 g/L of yeast extract, and 5 g/L of NaCl. The medium was adjusted to pH 7.0 with NaOH. The LB agar medium further contained 15 g/L of agar.
CM-Dex Medium
The CM-Dex medium contained 10 g/L of polypeptone, 10 g/L of yeast extract, 5 g/L of glucose, 1 g/L of KH2PO4, 3 g/L of urea, 0.4 g/L of MgSO4.7H2O, 0.01 g/L of FeSO4.7H2O, 0.01 g/L of MnSO4.5H2O, and 1.2 g/L (T-N) of bean filtrate (soybean hydrolysate). The medium was adjusted to pH 7.5 with KOH. The CM-Dex agar medium further contained 15 g/L of agar.
S10 Agar Medium
The S10 medium contained 100 g/L of sucrose, 10 g/L of polypeptone, 10 g/L of yeast extract, 1 g/L of KH2PO4, 3 g/L of urea, 0.4 g/L of MgSO4.7H2O, 0.01 g/L of FeSO4.7H2O, 0.01 g/L of MnSO4.5H2O, 1.2 g/L (T-N) of bean filtrate, and 10 μg/L of biotin. The medium was adjusted to pH 7.5 with KOH. The S10 agar medium further contained 15 g/L of agar.
Xylose Minimal Medium
The xylose minimal medium contained 2.5 g/L, 5.0 g/L, or 10 g/L of xylose, 2.5 g/L of (NH4)2SO4, 0.5 g/L of KH2PO4, 0.25 g/L of MgSO4.7H2O, 2 g/L of urea, 10 mg/L of MnSO4.4H2O, 50 μg/L of biotin, 100 μg/L of vitamin B1-HCl, 15 mg/L of protocatechuic acid, 0.02 mg/L of CuSO4, 10 mg/L of CaCl2), and 40 g/L of MOPS. The medium was adjusted to pH 7.0 with KOH.
Seed Medium
The seed medium contained 60 g/L of glucose, 1.45 g/L of K3PO4, 1.45 g/L of KOH, 0.9 g/L of MgSO4.7H2O, 0.01 g/L of FeSO4.7H2O, 2 g/L of sodium succinate.6H2O, 8.55 mg/L of para-aminobenzoic acid, 8.55 mg/L of ascorbic acid, 200 μg/L of vitamin B1-HCl, 60 μg/L of biotin, 1.54 g/L (T-N) of bean filtrate, 0.28 g/L of DL-methionine, 5 mL/L of Fermol, and 25 mg/L of kanamycin. The medium was adjusted to pH 7.2 with ammonia gas.
Glucose Main Medium
The glucose main medium contained 90 g/L of glucose, 3.46 g/L of KH2PO4, 1 g/L of MgSO4.7H2O, 0.01 g/L of FeSO4.7H2O, 0.01 g/L of MnSO4.5H2O, 23 mg/L of vitamin B1-HCl, 0.35 g/L (T-N) of bean filtrate, 15 mL/L of Fermol, and 25 mg/L of kanamycin. The medium was adjusted to pH 7.2 with ammonia gas.
Xylose Main Medium
The xylose main medium was the same as the glucose main medium, except 90 g/L of glucose was replaced with 100 g/L of xylose.
Glucose/Xylose Main Medium
The glucose/xylose main medium was the same as the glucose main medium, except 90 g/L of glucose was replaced with 45 g/L of glucose and 45 g/L of xylose.
(2) Construction of C. glutamicum that is Able to Assimilate Xylose
By transforming the C. glutamicum ATCC 13869 strain with a plasmid pVK9Peftu_xylAB carrying the xylAB genes encoding the xylose isomerase and xylulokinase of E. coli, a xylose assimilability-imparted strain, C. glutamicum ATCC13869/pVK9Peftu_xylAB strain, was constructed. The procedures are shown below.
(2-1) Construction of pVK9Peftu_xylAB
An expression plasmid pVK9Peftu_xylAB for the xylAB genes of E. coli was constructed as follows. pVK9Peftu_xylAB contains a sequence consisting of a promoter sequence of the elongation factor Tu (EF-Tu) gene tuf of C. glutamicum (WO2008/114721, henceforth referred to as “Peftu”), and the xylAB genes of E. coli ligated downstream of the promoter sequence.
By PCR using the chromosomal DNA of the E. coli MG1655 strain as the template, as well as the primers xylA_SP(2)_4691-80-12 (SEQ ID NO: 1) and xylAB_ASP_4691-80-13 (SEQ ID NO: 2), a DNA fragment containing the xylAB genes (xylAB fragment) was obtained. Further, by PCR using the chromosomal DNA of the C. glutamicum ATCC 13869 strain as the template, as well as the primers EFTU_SP_4691-80-1 (SEQ ID NO: 3) and EFTU_ASP_4691-80-2 (SEQ ID NO: 4), a DNA fragment containing Peftu (Peftu fragment) was obtained. PrimeSTAR HS DNA Polymerase (Takara Bio) was used for PCR, and the reactions were performed according to the protocol attached to the enzyme.
The xylAB fragment and Peftu fragment obtained as described above were mixed with pVK9 (Japanese Patent Laid-open (Kokai) No. 2007-97573, Published U.S. Patent Application No. 20050196846) treated with XbaI, and used for in-fusion reaction with Clontech In-Fusion HD Cloning Kit (Takara Bio) according to the protocol attached to the kit, and E. coli JM109 was transformed with the reaction mixture. The transformants were subjected to selection by culturing them overnight at 37° C. on the LB agar medium (containing 40 mg/L of kanamycin). The objective plasmid pVK9Peftu_xylAB was obtained from an obtained transformant. The nucleotide sequences of the cloned EF-Tu promoter (Peftu) and xylAB genes are shown as SEQ ID NOS: 9 and 10, respectively.
(2-2) Transformation of C. glutamicum
By the electric pulse method (Japanese Patent Laid-open (Kokai) No. 2-207791), the C. glutamicum ATCC 13869 strain was transformed with pVK9Peftu_xylAB. The transformants were subjected to selection by culturing them overnight at 31.5° C. on the CM-Dex agar medium (containing 25 mg/L of kanamycin) to obtain a xylose assimilability-imparted strain, C. glutamicum ATCC13869/pVK9Peftu_xylAB strain.
(3) Growth of C. glutamicum that is Able to Assimilate Xylose in Xylose Minimal Medium
The C. glutamicum ATCC13869/pVK9Peftu_xylAB strain as described above, was cultured in the minimal medium containing xylose as a sole carbon source (xylose minimal medium).
The cells of the C. glutamicum ATCC13869/pVK9Peftu_xylAB strain were spread on the CM-Dex agar medium (containing 25 mg/L kanamycin), and cultured overnight at 31.5° C. After the culture, the cells in about 1-cm square on the agar medium were scraped together, suspended in 1 mL of the 0.25% (w/v) xylose minimal medium, and inoculated in 5 mL of each of the 0.25% (w/v), 0.5% (w/v), and 1.0% (w/v) xylose minimal media (all containing 25 mg/L of kanamycin) contained in a culture tube so as to obtain an absorbance of 0.01 at a wavelength of 660 nm (OD660). Culture was performed at a culture temperature of 31.5° C. with shaking at a velocity of 70 rpm by using a small shaking culture apparatus, TVS062CA (Advantec Toyo), and OD660 was measured over time.
The growth patterns in the respective media are shown in
(4) Acquisition of Mutant Strain Showing Improved Proliferation Rate in Xylose Minimal Medium
The culture broth by the culture for 60 hours in the 0.25% (w/v) xylose minimal medium obtained in (3) mentioned above (
As a result of culturing some clones obtained as described above in the xylose minimal medium in the same manner as that of (3) mentioned above, there was obtained a mutant strain (XM strain) of which proliferation rate did not significantly reduce even in a medium of low xylose concentration (
(5) Analysis of Mutation Point of Xylose Assimilability-Improved Mutant Strain
Six mutant strains, including the XM strain, showing improved proliferation rate in the xylose minimal medium were obtained by the same test as that of (4) mentioned above. The nucleotide sequences of the chromosomal DNAs of the obtained 6 mutant strains were compared with that of the parent strain by using MiSeq 2000 (Illumina). As a result, a mutation causing mutation of translated amino acid was detected in the NCgl2954 gene on the chromosome for all the mutant strains (Table 1).
(6) Construction of NCgl2954 Gene-Deficient Strain of C. glutamicum
(6-1) Construction of Plasmid pBS4SΔNCgl2954 for Deletion of NCgl2954 Gene
A plasmid pBS4SΔNCgl2954 for deletion of the NCgl2954 gene was prepared as follows.
First, PCR was performed by using the chromosomal DNA of the C. glutamicum ATCC 13869 strain as the template, as well as the primers delta_2954_F1 (SEQ ID NO: 5) and delta_2954_MR (SEQ ID NO: 6) to amplify a DNA fragment containing a NCgl2954 gene upstream region. Further, PCR was performed by similarly using the chromosomal DNA of the C. glutamicum ATCC 13869 strain as the template, as well as the primers delta_2954_MF (SEQ ID NO: 7) and delta_2954_R1 (SEQ ID NO: 8) to amplify a DNA fragment containing a NCgl2954 gene downstream region. PrimeSTAR HS DNA Polymerase was used for PCR, and the reactions were performed according to the protocol attached to the enzyme.
The two DNA fragments obtained above were mixed with the plasmid pBS4S (Japanese Patent Laid-open (Kokai) No. 2007-97573, U.S. Published Patent Application No. 20050196846) treated with XbaI, and used for in-fusion reaction with Clontech In-Fusion HD Cloning Kit (Takara Bio) according to the protocol attached to the kit, and E. coli JM109 was transformed with the reaction mixture. The transformants were subjected to selection by culturing them overnight at 37° C. on the LB agar medium (containing 40 mg/L of kanamycin). A plasmid pBS4SΔNCgl2954 corresponding to pBS4S in which the upstream and downstream sequences of the NCgl2954 gene were inserted was obtained from an obtained transformant.
(6-2) Acquisition of NCgl2954 Gene-Deficient Strain
The C. glutamicum ATCC 13869 strain was transformed with pBS4SΔNCgl2954 by the electric pulse method, and cultured at 31.5° C. for two nights on the CM-Dex agar medium (containing 25 mg/L kanamycin) to obtain a one-time recombinant in which pBS4SΔNCgl2954 was incorporated into the chromosome. The obtained one-time recombinant was subcultured on the S10 agar medium to obtain a two-time recombinant C. glutamicum ATCC13869ΔNCgl2954 strain deficient in the NCgl2954 gene region.
(7) Growth of NCgl2954 Gene-Deficient Strain in Xylose Minimal Medium
In the same manner as that of (2-2) mentioned above, the C. glutamicum ATCC13869ΔNCgl2954 strain was transformed with pVK9Peftu_xylAB to obtain a xylose assimilability-imparted and NCgl2954 gene-deficient strain (C. glutamicum ATCC13869ΔNCgl2954/pVK9Peftu_xylAB strain). Growth of this strain in the 0.25% (w/v), 0.5% (w/v), and 1.0% (w/v) xylose minimal media was verified in the same manner as that of (3) mentioned above.
The NCgl2954 gene-deficient strain did not show such marked reduction of proliferation rate as that shown by the wild-type strain (C. glutamicum ATCC13869/pVK9Peftu_xylAB strain) even in a low concentration xylose minimal medium, and showed a specific proliferation rate comparable to that of the XM strain (
(8) Influence of Deficiency of NCgl2954 Gene on Glutamic Acid Production Using Xylose as Carbon Source
A glutamic acid fermentation test was performed with the NCgl2954 gene-deficient strain (C. glutamicum ATCC13869ΔNCgl2954/pVK9Peftu_xylAB strain) and the wild-type strain (C. glutamicum ATCC13869/pVK9Peftu_xylAB strain) under biotin limitation in a medium containing xylose to verify influence of deficiency of the NCgl2954 gene on glutamic acid production using xylose as the carbon source.
(8-1) Culture Conditions and Analysis Conditions
The glutamic acid fermentation test was performed by using a jar fermenter. Each strain was cultured overnight at 31.5° C. on the CM-Dex agar medium (containing 25 mg/L kanamycin). After the culture, the cells in 1-cm square on the agar medium were scraped together, and inoculated to 250 mL of the seed medium contained in the jar fermenter. Culture was performed at a culture temperature of 31.5° C., pH 7.2 (adjusted by addition of ammonia gas), aeration rate of 250 mL/min, and stirring number of 700 rpm, and continued until glucose in the medium was completely consumed. Each seed culture broth obtained as described above was inoculated (10% (v/v)) to each of the main media (glucose, xylose, and glucose/xylose) so as to obtain a final volume of 250 mL, and culture was performed at a culture temperature of 31.5° C., pH 7.2 (adjusted by addition of ammonia gas), aeration rate of 250 mL/minute, and stirring number of 700 rpm.
The culture broth was sampled over time, and OD620 of the culture broth, glucose concentration, xylose concentration, and glutamic acid concentration of the culture supernatant were measured. OD620 of the culture broth was measured by using U-2900 (Hitachi High-Technologies). The glutamic acid concentration and glucose concentration in the culture supernatant were measured by using Biotech Analyzer AS-310 (Sakura SI). The xylose concentration in the culture supernatant was measured by using an HPLC system (Pump L-7100, Autosampler L-7200 (both from Hitachi High-Technologies), and Column oven CO 705 (GL Sciences)). The HPLC analysis conditions were as follows: column, SHODEX (SUGAR-G and SUGAR SH1011 (Showa Denko)); column temperature, 50° C.; eluent, H2O; flow rate, 1.0 mL/minute; and detection, RI Detector (Hitachi High-Technologies).
(8-2) Results of Glutamic Acid Production in Glucose Medium
In the glucose medium, both the wild-type strain and the NCgl2954 gene-deficient strain completely consumed glucose contained in the medium after the culture of 11 hours, and difference in glucose consumption rate or glutamic acid productivity was not observed between both the strains (
(8-3) Results of glutamic acid production in xylose medium
In the xylose medium, the wild-type strain left 40 g/L of xylose in the medium even after the culture of 11 hours, and the amount of the accumulated glutamic acid at that time was 6.4 g/L (
(8-4) Results of Glutamic Acid Production in Glucose/Xylose Medium
In the glucose/xylose medium, the wild-type strain left 11 g/L of xylose in the medium even after the culture of 11 hours, and the glutamic acid accumulation amount at that time was 16.5 g/L (
(9) Construction of NXA Pathway-Introduced C. glutamicum
C. glutamicum into which the genes of the NXA pathway have been introduced can be obtained by transformation with the plasmid pVK9Peftu_ccrNXA (WO2013/069634A1). pVK9Peftu_ccrNXA contains a sequence consisting of the EF-Tu promoter (Peftu) of C. glutamicum, and the xylXABCD genes encoding the NXA pathway of C. crescentus CB15 (ATCC 19089) and ligated downstream of the promoter. The yagF gene encoding the xylonate dehydratase of E. coli was introduced into the chromosomes of C. glutamicum ATCC 13869 and ATCC13869ΔNCgl2954, and the resultant strains were further transformed with pVK9Peftu_ccrNXA to construct strains that can produce L-glutamic acid from xylose through the NXA pathway. The procedures are shown below.
(9-1) Construction of pBS4SΔxylB_yagF
In order to introduce the yagF gene encoding the xylonate dehydratase of E. coli into the xylB gene region encoding xylulokinase on the chromosome of C. glutamicum ATCC 13869 strain, plasmid pBS4SΔxylB_yagF was constructed as follows.
First, PCR was performed by using the chromosomal DNA of the C. glutamicum ATCC 13869 strain as the template, as well as the primers xylB_F1 (SEQ ID NO: 27) and xylB_MR (SEQ ID NO: 28) to amplify a DNA fragment containing a xylB gene upstream region. PCR was performed by similarly using the chromosomal DNA of the C. glutamicum ATCC 13869 strain as the template, as well as the primers xylB (SEQ ID NO: 29) and xylB_R1 (SEQ ID NO: 30) to amplify a DNA fragment containing a xylB gene downstream region. PrimeSTAR HS DNA Polymerase (Takara Bio) was used for PCR, and the reactions were performed according to the protocol attached to the enzyme.
The two DNA fragments obtained above were mixed with the plasmid pBS4S (Japanese Patent Laid-open (Kokai) No. 2007-97573, U.S. Published Patent Application No. 20050196846) treated with XbaI, and used for in-fusion reaction with Clontech In-Fusion HD Cloning Kit according to the protocol attached to the kit, and the E. coli DH5α strain was transformed with the reaction mixture. The transformants were subjected to selection by culturing them overnight at 37° C. on the LB agar medium (containing 40 mg/L of kanamycin). Plasmids were extracted from the obtained transformants, and a plasmid pBS4SΔxylB corresponding to pBS4S in which the upstream and downstream sequences of the xylB gene were inserted was obtained. In pBS4SΔxylB, the XbaI recognition sequence was inserted between the upstream and downstream sequences of the xylB gene.
Then, PCR was performed by using the chromosomal DNA of the E. coli MG1655 strain as the template, as well as the primers PcspB_yagF_fw (SEQ ID NO: 31) and yagF_xylB_rv (SEQ ID NO: 32) to amplify a DNA fragment containing the yagF gene. PCR was also performed by using the chromosomal DNA of the C. glutamicum ATCC 13869 strain as the template, as well as the primers xylB_PcspB_fw (SEQ ID NO: 33) and PcspB_rv (SEQ ID NO: 34) to amplify a DNA fragment containing the promoter region of the cspB gene (henceforth referred to as “PcspB”). PrimeSTAR HS DNA Polymerase (Takara Bio) was used for PCR, and the reactions were performed according to the protocol attached to the enzyme.
The two DNA fragments obtained above were mixed with the plasmid pBS4SΔxylB treated with XbaI, and used for in-fusion reaction with Clontech In-Fusion HD Cloning Kit (Takara Bio) according to the protocol attached to the kit, and the E. coli DH5α strain was transformed with the reaction mixture. The transformants were subjected to selection by culturing them overnight at 37° C. on the LB agar medium (containing 40 mg/L of kanamycin). Plasmids were extracted from the obtained transformants, and a plasmid pBS4SΔxylB_yagF in which a sequence consisting of PcspB and the yagF gene ligated downstream from PcspB was inserted between the upstream and downstream sequences of the xylB gene was obtained. The nucleotide sequences of the cloned cspB promoter (PcspB) and yagF gene are shown as SEQ ID NOS: 47 and 19, respectively.
(2-2) Transformation of C. glutamicum
The C. glutamicum ATCC 13869 strain was transformed with pBS4SΔxylB_yagF by the electric pulse method, and cultured at 31.5° C. for two nights on the CM-Dex agar medium (containing 25 mg/L kanamycin) to obtain a one-time recombinant in which pBS4SΔxylB_yagF was incorporated into the chromosome. The obtained one-point recombinant was subcultured on the S10 agar medium, and a strain into which the yagF gene was introduced as intended was selected by PCR from strains that grew on the S10 agar medium and showed kanamycin sensitivity. The strain obtained as described above was designated as ATCC13869+D strain. In this strain, the xylB gene region on the chromosome is replaced with the yagF gene.
Then, the ATCC13869+D strain was transformed with pVK9Peftu_ccrNXA, and by selection of the transformants on the CM-Dex agar medium (containing 25 mg/L kanamycin), an NXA pathway-introduced strain, ATCC13869+D/pVK9Peftu_ccrNXA strain, was obtained.
The same procedures as described above were used for the ATCC13869ΔNCgl2954 strain to obtain ATCC13869ΔNCgl2954+D strain in which the yagF gene was introduced into the chromosome, and this strain was transformed with pVK9Peftu_ccrNXA to obtain an NXA pathway-introduced strain, ATCC13869ΔNCgl2954+D/pVK9Peftu_ccrNXA strain.
(10) Influence of Deficiency of NCgl2954 Gene on Glutamic Acid Production Via NXA Pathway
In order to confirm effect of deficiency of the NCgl2954 gene on glutamic acid production from xylose via the NXA pathway, a glutamic acid fermentation test under biotin limitation was performed. The culture conditions and analysis conditions are as shown in (8-1).
As a result of culture in the xylose medium, the NCgl2954 gene-deficient strain was able to consume xylose and produce glutamic acid at improved rates, as compared with the strain having an intact NCgl2954 gene (
According to the present invention, xylose assimilability of coryneform bacteria can be improved, and a target substance such as L-amino acids and nucleic acids can be efficiently produced from a raw material containing xylose.
Explanation of Sequence Listing
SEQ ID NO: 1, Primer xylA_SP(2)_4691-80-12
SEQ ID NO: 2, Primer xylAB_ASP_4691-80-13
SEQ ID NO: 3, Primer EFTU_SP_4691-80-1
SEQ ID NO: 4, Primer EFTU_ASP_4691-80-2
SEQ ID NO: 5, Primer delta_2954_F1
SEQ ID NO: 6, Primer delta_2954_MR
SEQ ID NO: 7, Primer delta_2954_MF
SEQ ID NO: 8, Primer delta_2954_R1
SEQ ID NO: 9, Nucleotide sequence of EF-Tu promoter (Peftu)
SEQ ID NO: 10, Nucleotide sequence of xylose operon (xylAB operon) of E. coli K-12 MG1655 strain
SEQ ID NO: 11, Amino acid sequence of XylA protein of E. coli K-12 MG1655 strain
SEQ ID NO: 12, Amino acid sequence of XylB protein of E. coli K-12 MG1655 strain
SEQ ID NO: 13, Nucleotide sequence of NCgl2954 gene of C. glutamicum ATCC 13869 strain
SEQ ID NO: 14, Amino acid sequence of protein encoded by NCgl2954 gene of C. glutamicum ATCC 13869 strain
SEQ ID NO: 15, Nucleotide sequence of xylB gene of Sphingomonas elodea
SEQ ID NO: 16, Amino acid sequence of XylB protein of Sphingomonas elodea
SEQ ID NO: 17, Nucleotide sequence of xylC gene of Sphingomonas elodea
SEQ ID NO: 18, Amino acid sequence of XylC protein of Sphingomonas elodea
SEQ ID NO: 19, Nucleotide sequence of yagF gene of Escherichia coli K-12 MG1655 strain
SEQ ID NO: 20, Amino acid sequence of YagF protein of Escherichia coli K-12 MG1655 strain
SEQ ID NO: 21, Nucleotide sequence of xylX gene of Sphingomonas elodea
SEQ ID NO: 22, Amino acid sequence of XylX protein of Sphingomonas elodea
SEQ ID NO: 23, Nucleotide sequence of ycbD gene of Bacillus subtilis
SEQ ID NO: 24, Amino acid sequence of YcbD protein of Bacillus subtilis
SEQ ID NO: 25, Nucleotide sequence of the yggB gene of C. glutamicum ATCC 13869 strain
SEQ ID NO: 26, Amino acid sequence of YggB protein of C. glutamicum ATCC 13869 strain
SEQ ID NOS: 27 to 34, Primers
SEQ ID NO: 35, Nucleotide sequence of xylB gene of C. glutamicum ATCC 13869 strain
SEQ ID NO: 36, Amino acid sequence of XylB protein of C. glutamicum ATCC 13869 strain
SEQ ID NO: 37, Nucleotide sequence of xylX gene of Caulobacter crescentus CB15 strain
SEQ ID NO: 38, Amino acid sequence of XylX protein of Caulobacter crescentus CB15 strain
SEQ ID NO: 39, Nucleotide sequence of xylA gene of Caulobacter crescentus CB15 strain
SEQ ID NO: 40, Amino acid sequence of XylA protein of Caulobacter crescentus CB15 strain
SEQ ID NO: 41, Nucleotide sequence of xylB gene of Caulobacter crescentus CB15 strain
SEQ ID NO: 42, Amino acid sequence of XylB protein of Caulobacter crescentus CB15 strain
SEQ ID NO: 43, Nucleotide sequence of xylC gene of Caulobacter crescentus CB15 strain
SEQ ID NO: 44, Amino acid sequence of XylC protein of Caulobacter crescentus CB15 strain
SEQ ID NO: 45, Nucleotide sequence of xylD gene of Caulobacter crescentus CB15 strain
SEQ ID NO: 46, Amino acid sequence of XylD protein of Caulobacter crescentus CB15 strain
SEQ ID NO: 47, Nucleotide sequence of cspB promoter (PcspB)
| Number | Date | Country | Kind |
|---|---|---|---|
| 2013-220609 | Oct 2013 | JP | national |
This application is a Continuation of, and claims priority under 35 U.S.C. § 120 to, International Application No. PCT/JP2014/078234, filed Oct. 23, 2014, and claims priority therethrough under 35 U.S.C. § 119 to Japanese Patent Application No. 2013-220609, filed Oct. 23, 2013, the entireties of which are incorporated by reference herein. Also, the Sequence Listing filed electronically herewith is hereby incorporated by reference (File name: 2016-04-21T_US-546_Seq_List; File size: 128 KB; Date recorded: Apr. 21, 2016).
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| Number | Date | Country | |
|---|---|---|---|
| 20160222394 A1 | Aug 2016 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/JP2014/078234 | Oct 2014 | US |
| Child | 15134674 | US |
