# Patent

## Title
Method for producing L-isoleucine using a bacterium of the family Enterobacteriaceae having overexpressed the cycA gene

## Abstract

The present invention provides a method for producing L-isoleucine by fermentation using a bacterium belonging to the family Enterobacteriaceae which has been modified to overexpress the cycA gene. The method also allows reducing the amount of byproduct amino acids that are produced during fementative production of L-isoleucine using Enterobacteriaceae bacterium having an L-isoleucine-producing ability.

## Background
This application claims priority under 35 U.S.C. § 119 to Russian Patent Application No. 2015114955, filed Apr. 22, 2015, the entirety of which is incorporated by reference herein. Also, the Sequence Listing filed electronically herewith is hereby incorporated by reference (File name: 2016-04-13T_US-543_Seq_List; File size: 18 KB; Date recorded: Apr. 13, 2016).
BACKGROUND OF THE INVENTION
Field of the Invention
The present invention relates generally to the microbiological industry, and specifically to a method for producing L-isoleucine by fermentation of a bacterium of the family Enterobacteriaceae which has been modified to overexpress the cycA gene, so that production of byproduct amino acid(s) of L-isoleucine is reduced.
Brief Description of the Related Art
Conventionally, L-amino acids are industrially produced by fermentation methods utilizing strains of microorganisms obtained from natural sources, or mutants thereof. Typically, the microorganisms are modified to enhance production yields of L-amino acids.
Many techniques to enhance L-amino acids production yields have been reported, including transformation of microorganisms with recombinant DNA (see, for example, U.S. Pat. No. 4,278,765 A) and alteration of expression regulatory regions such as promoters, leader sequences, and/or attenuators, or others known to the person skilled in the art (see, for example, US20060216796 A1 and WO9615246 A1). Other techniques for enhancing production yields include increasing the activities of enzymes involved in amino acid biosynthesis and/or desensitizing the target enzymes to the feedback inhibition by the resulting L-amino acid (see, for example, WO9516042 A1, EP0685555 A1 or U.S. Pat. Nos. 4,346,170 A, 5,661,012 A, and 6,040,160 A).
Another method for enhancing L-amino acids production yields is to attenuate expression of a gene or several genes which are involved in degradation of the target L-amino acid, genes which divert the precursors of the target L-amino acid from the L-amino acid biosynthetic pathway, genes involved in the redistribution of the carbon, nitrogen, and phosphate fluxes, and genes encoding toxins, etc.
L-isoleucine is an essential amino acid in humans and other animals, and it can be used as a material for various medicinal drugs. For example, L-isoleucine can be used as a nutritional supplement to promote nutrition. L-isoleucine has two chiral centers in its carbon backbone, one of which is its central (alpha) carbon atom and the other is its beta carbon atom in the side chain. It is therefore difficult to industrially synthesize the L-isomer; that is, the 2S,3S-isomer of isoleucine by a chemical synthetic method with a high grade of purity at a low price.
L-isoleucine can be produced from its various precursors, such as, for example, alpha-aminobutyric acid (αABA), alpha-hydroxybutyric acid (αHBA), threonine, aspartic acid, or fumaric acid, when a microorganism is cultured in a medium containing the precursor, a carbon source, a nitrogen source, and other nutrients (U.S. Pat. Nos. 3,058,888, 3,262,861, and 3,231,478).
A method for producing L-isoleucine by native immobilization of cells of the Brevibacterium flavum strain AB-07 that can metabolize precursors in biosynthetic pathways of L-isoleucine, such as alpha-aminobutyric acid (αABA) and alpha-ketobutyric acid (αKBA), has been developed (Terasawa M. et al., Depression of by-product formation during L-isoleucine production by a living-cell reaction process, Appl. Microbiol. Biotechnol., 1991, 35(3):348-351). Furthermore, the living cell reaction (LCR) process was applied to the immobilized cells of the Corynebacterium glutamicum (formerly Brevibacterium flavum) strain MJ-233 to produce L-isoleucine from ethanol as the energy source and αKBA as the precursor (overviewed in Jojima, T., Inui, M. and Yukawa, H. Amino acids, branched chain, L-isoleucine//Encyclopedia of industrial biotechnology: bioprocess, bioseparation, and cell technology, pp. 1-6, M. C. Flickinger (ed.), John Wiley & Sons, Inc., 2010). However, these methods require the use of expensive precursors and, therefore, are not considered useful for industrial production of L-isoleucine at a low price.
Furthermore, methods for producing L-isoleucine have been disclosed which include a method utilizing Escherichia coli (E. coli) resistant to isoleucine analogs (Japanese Patent Laid-open Publication No. 5-130882), a method utilizing a recombinant strain of E. coli integrated with a DNA-fragment encoding threonine deaminase (Japanese Patent Laid-open Publication No. 2-458), a method utilizing the mutant microorganisms belonging to the genus Corynebacterium resistant to methyllysine (Japanese Patent Laid-open Publication No. 61-15696) or amino-hydroxyvaleric acid (AHVA) (U.S. Pat. No. 3,767,529), and a method utilizing a recombinant strain of Corynebacterium glutamicum transformed with a gene encoding homoserine dehydrogenase (Japanese Patent Laid-open Publication No. 60-12995). It is also known that L-isoleucine-producing ability can be imparted by introducing the thrABC operon containing the thrA gene encoding aspartate kinase I/homoserine dehydrogenase I derived from E. coli, of which inhibition by L-threonine is substantially desensitized, and the ilvGMEDA operon containing the ilvA gene encoding threonine deaminase, of which inhibition by L-isoleucine is substantially desensitized and from which a region required for attenuation is removed (EP0685555 B1).
It has also been reported that the ability to produce substances such as L-amino acids can be improved by increasing enzymatic activity of nicotinamide nucleotide transhydrogenase (also referred to as “transhydrogenase”) in microbial cells, so that the producing ability of the microorganism for reduced nicotinamide adenine dinucleotide phosphate (NADPH) is increased (WO9511985 A1). In this reference, an example of improvement of L-isoleucine-producing ability of E. coli by the increase of the transhydrogenase activity is also mentioned. A further method for producing L-isoleucine discloses the use of a bacterium belonging to the genus Escherichia that has been modified to enhance the intracellular phosphoenolpyruvate carboxylase and transhydrogenase activities (EP1179597 B1).
However, a well-known disadvantage of L-isoleucine production by fermentation of a microorganism is the accumulation of byproduct amino acids in a relatively large amount as compared with the amount of the L-isoleucine that is produced (Terasawa M. et al., 1991; Komatsubara, S. Amino acids: genetically engineered Serratia marcescens/Recombinant microbes for industrial and agricultural applications, pp. 474-477, Y. Murooka and T. Imanaka (eds.), Marcel Dekker, Inc., 1994; Terasawa, M. and Yukawa, H. Industrial production of biochemicals by native immobilization//Industrial application of immobilized biocatalysts, pp. 44-52, A. Tanaka, T. Tosa and T. Kobayashi (eds.), Marcel Dekker, Inc., 1993; Jojima T. et al., 2010). Byproduct amino acids, such as, for example, valine (Val), leucine (Leu), alanine (Ala), glycine (Gly), norvaline (nVal), O-ethyl-homoserine (O-EH) and alpha-aminobutyric acid (αABA), can accumulate considerably in fermentation liqueur during fermentation of L-isoleucine-producing microorganisms. Because the physicochemical characteristics of the byproduct amino acids produced during L-isoleucine fermentation are very similar to those of L-isoleucine, it is very difficult to isolate L-isoleucine with a sufficient grade of purity at a reasonable price using ordinary separation methods such as, for example, chromatography. It is therefore of particular importance to reduce the production of byproduct amino acids in the method for producing L-isoleucine by fermentation. From the viewpoint of industrial production, the improvement of a method for producing L-isoleucine by fermentation of L-isoleucine-producing microorganisms that are devoid of or produce less byproduct amino acids represents a great challenge since such an improved method has the potential to produce L-isoleucine with the high grade of purity at a low price.
A method for reducing production of byproducts of a target substance by deleting or attenuating the biosynthesis system of the byproduct has been reported (for example, “Amino acid fermentation” Gakkai Shuppan Center, p. 4, 1986). However, in this method, when a microorganism is cultured, the aforementioned byproduct needs to be added to the medium in the amount necessary for growth of the microorganism. Further methods for reducing production of byproduct amino acids, such as L-tryptophan, L-phenylalanine, L-isoleucine and/or L-valine (EP1484410 A1) or L-glutamic acid (EP 2360263 A1), by enhancing a system for cell uptake of the byproduct of a target substance have been also disclosed. For example, the cell system for L-leucine uptake (LivK) was enhanced in E. coli to reduce by-production of L-leucine when the bacterium was cultivated to produce L-isoleucine as the target substance (EP1484410 A1).
However, no data has been previously reported that demonstrates the effect of overexpression of the cycA gene on production of L-isoleucine and byproduct amino acids by fermentation of an L-isoleucine-producing bacterium of the family Enterobacteriaceae.
SUMMARY OF THE INVENTION
An improved method of producing L-isoleucine by fermentation of a bacterium of the family Enterobacteriaceae is described herein. According to the presently disclosed subject matter, production of L-isoleucine by fermentation of a bacterium of the family Enterobacteriaceae can be increased. Specifically, production of L-isoleucine by fermentation of a bacterium of the family Enterobacteriaceae can be improved by overexpressing the cycA gene in the bacterium, so that the production of L-isoleucine by the modified bacterium can be increased. Increase of L-isoleucine production can be an absolute amount, or a relative amount to the byproduct amino acid(s). Furthermore, when L-isoleucine is produced by fermentation of a bacterium of the family Enterobacteriaceae, production of byproduct amino acids can be reduced. Specifically, the method for producing L-isoleucine by fermentation of a bacterium of the family Enterobacteriaceae can be improved by overexpressing the cycA gene in the bacterium, so that the production of byproduct amino acid(s) such as L-leucine, L-valine, L-norleucine, L-norvaline and alpha-aminobutyric acid by the modified bacterium can be reduced. Reduction of byproduct amino acid production can be an absolute amount of byproduct amino acid(s), or relative to the amount of L-isoleucine produced. Therefore, in an embodiment, a larger amount of L-isoleucine with respect to the byproduct amino acid(s) can be produced, and as a result of simplifying the purification process of the L-isoleucine produced by the method described herein, the produced L-isoleucine is at a high grade of purity and is produced at a low price.
It is one aspect of the present invention to provide a method for producing L-isoleucine comprising:
(i) cultivating a bacterium of the family Enterobacteriaceae which has an ability to produce L-isoleucine in a culture medium to produce the L-isoleucine in the culture medium or the bacterial cells, or both; and
(ii) collecting the L-isoleucine from the culture medium or the bacterial cells, or both,
wherein the bacterium has been modified to overexpress the cycA gene.
It is a further aspect of the present invention to provide the method as described above, wherein the cycA gene encodes a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence of SEQ ID NO: 2;
(B) a protein comprising the amino acid sequence of SEQ ID NO: 2, but which includes one or more mutations comprising substitution, deletion, insertion and/or addition of one or several amino acid residues, and wherein said protein has the activity of a transporter having the amino acid sequence of SEQ ID NO: 2; and
(C) a protein having a homology of not less than 70% with respect to the entire amino acid sequence of SEQ ID NO: 2 and having the activity of the transporter having the amino acid sequence of SEQ ID NO: 2.
It is a further aspect of the present invention to provide the method as described above, wherein the cycA gene is a DNA selected from the group consisting of:
(A) a DNA comprising the nucleotide sequence of SEQ ID NO: 1;
(B) a DNA encoding a protein comprising the amino acid sequence of SEQ ID NO: 2, but which includes one or more mutations comprising substitution, deletion, insertion and/or addition of one or several amino acid residues, and wherein said protein has the activity of the transporter having the amino acid sequence of SEQ ID NO: 2; and
(C) a DNA which is a variant nucleotide sequence of SEQ ID NO: 1 due to the degeneracy of the genetic code.
It is a further aspect of the present invention to provide the method as described above, wherein the cycA gene is overexpressed by increasing the copy number of the cycA gene and/or by modifying an expression regulatory region of the cycA gene, so that the expression of the gene is enhanced as compared with a non-modified bacterium.
It is a further aspect of the present invention to provide the method as described above, wherein the bacterium belongs to the genus Escherichia. 
It is a further aspect of the present invention to provide the method as described above, wherein the bacterium is Escherichia coli. 
It is a further aspect of the present invention to provide the method as described above, wherein the bacterium belongs to the genus Pantoea. 
It is a further aspect of the present invention to provide the method as described above, wherein the bacterium is Pantoea ananatis. 
It is a further aspect of the present invention to provide the method as described above, wherein an amount of a byproduct amino acid is reduced as compared with a non-modified bacterium.
It is a further aspect of the present invention to provide the method as described above, wherein the byproduct amino acid is selected from the group consisting of L-valine, L-leucine, L-norvaline, L-norleucine, alpha-aminobutyric acid and a combinations thereof.


DESCRIPTION OF THE PREFERRED EMBODIMENTS
The present invention is described in detail below.
1. Bacterium
Any L-isoleucine-producing bacterium belonging to the family Enterobacteriaceae and modified to overexpress the cycA gene can be used. The phrase “an L-isoleucine-producing bacterium” can mean a bacterium of the family Enterobacteriaceae which has an ability to produce, excrete or secrete, and/or cause accumulation of L-isoleucine in a culture medium and/or the bacterial cells when the bacterium is cultured in the medium.
The phrase “an L-isoleucine-producing bacterium” can also mean a bacterium which has an ability to produce, excrete or secrete, and/or cause accumulation of L-isoleucine in a culture medium in an amount larger than a wild-type or parental strain, such as E. coli K-12, and can also mean a bacterium that is able to cause accumulation in the medium of an amount, for example, not less than 0.1 g/L, not less than 0.5 g/L, or not less than 1.0 g/L of L-isoleucine.
Furthermore, the bacterium belonging to the family Enterobacteriaceae and modified to overexpress the cycA gene, which has an ability to produce L-isoleucine, can also be used. The bacterium may inherently have the ability to produce L-isoleucine or may be modified to have an ability to produce L-isoleucine by using a mutation method or DNA recombination techniques. The bacterium can be obtained by overexpressing the cycA gene in a bacterium that inherently has the ability to produce L-isoleucine, or in a bacterium that has already been imparted with the ability to produce L-isoleucine. Alternatively, the bacterium can be obtained by imparting the ability to produce L-isoleucine to a bacterium already modified to overexpress the cycA gene. Also, the bacterium can acquire the ability to produce L-isoleucine by being modified to overexpress the cycA gene.
The phrase “an ability to produce L-isoleucine” can mean the ability of a bacterium of the family Enterobacteriaceae to produce, excrete or secrete, and/or cause accumulation of L-isoleucine in a culture medium and/or the bacterial cells to such a level that the L-isoleucine can be collected from the culture medium and/or the bacterial cells when the bacterium is cultured in the medium.
The bacterium can produce L-isoleucine either alone or as a mixture of L-isoleucine and one or more kinds of amino acids that are different from L-isoleucine, such as, for example, amino acids in L-form (also referred to as L-amino acids). Furthermore, the bacterium can produce L-isoleucine either alone or as a mixture of L-isoleucine and one or more kinds of hydroxycarboxylic acids.
Furthermore, a bacterium belonging to the family Enterobacteriaceae, which has an ability to produce L-isoleucine and has been modified to overexpress the cycA gene, such that production of byproduct amino acid(s) is reduced as compared with a non-modified strain, for example, a wild-type or parental strain as described hereinafter, can be used. Specifically, the bacterium can be used, which has been modified to overexpress the cycA gene and which is able to produce one, two, or more kinds of byproduct amino acids of L-isoleucine production at a lower level than a non-modified strain, or in which by-production of one, two, or more kinds of byproduct amino acids of L-isoleucine is reduced as compared with a non-modified strain.
The phrase “able to produce byproduct amino acids of L-isoleucine production” as used herein with regard to a bacterium can mean the ability of a bacterium of the family Enterobacteriaceae to produce, excrete or secrete, and/or cause accumulation of one, two, or more kinds of byproduct amino acids of L-isoleucine production in a culture medium or the bacterial cells, or both, to such a level that the one, two or more byproduct amino acids of L-isoleucine production can be collected from the culture medium and/or the bacterial cells when the bacterium is cultured in the medium. The phrase “a byproduct amino acid of L-isoleucine production” is explained hereinafter.
The phrase “amino acid” can mean an organic compound containing at least one amino group (NH2) and at least one carboxyl group (COOH). An L-amino acid is a non-limiting example of an amino acid.
The phrase “L-amino acid” can mean L-alanine, L-arginine, L-asparagine, L-aspartic acid, L-citrulline, L-cysteine, L-glutamic acid, L-glutamine, glycine, L-histidine, L-isoleucine, L-leucine, L-lysine, L-methionine, L-ornithine, L-phenylalanine, L-proline, L-serine, L-threonine, L-tryptophan, L-tyrosine, and L-valine. Other non-limiting examples of an L-amino acid include norvaline (nVal) or L-norvaline, norleucine (nLeu) or L-norleucine, 0-ethyl-homoserine (O-EH) or O-ethyl-L-homoserine, and alpha-aminobutyric acid (αABA) or L-alpha-aminobutyric acid.
The phrase “amino acid” or “L-amino acid” can refer not only to an amino acid in a free form, but may also include a salt or a hydrate of the amino acid, or an adduct formed by the amino acid and another organic or inorganic compound. The phrase “amino acid” can mean, for example, sodium, potassium, ammonium, monochlorhydrate, and so forth salts of an amino acid such as, for example, monochlorhydrate salt of L-lysine (L-lysine.HCl) or monochlorhydrate salt of L-arginine (L-arginine.HCl). An example of a hydrate of an amino acid includes L-cysteine monohydrate (L-Cys×H2O).
The phrase “hydroxycarboxylic acid” can mean an organic compound containing at least one hydroxyl group (OH) and at least one carboxylic group (COOH). An alpha-hydroxycarboxylic acid is an example of a hydroxycarboxylic acid. Specific and non-limiting examples of alpha-hydroxycarboxylic acids include L-lactic acid, citric acid, and L-alpha-hydroxybutyric acid (αHBA).
The phrase “a byproduct amino acid of L-isoleucine production” can refer to one, two or more byproduct amino acids of L-isoleucine and can mean a substance, such as, for example, an organic compound, which is different from L-isoleucine and which is produced as a byproduct, co-product, or side-product during the production of L-isoleucine by fermentation of a bacterium belonging to the family Enterobacteriaceae that has an ability to produce L-isoleucine. The phrase “a byproduct amino acid of L-isoleucine production” can also refer to a substance that can be produced and excreted or secreted by a bacterium of the family Enterobacteriaceae, that has an ability to produce L-isoleucine, during fermentation of the bacterium to produce L-isoleucine, such that the substance accumulates in a culture medium or the bacterial cells, or both, to such a level that the substance can be collected from the culture medium and/or the bacterial cells when the bacterium is cultured in the medium. An amount of a byproduct amino acid of L-isoleucine production in the culture medium and/or the bacterial cells can be lower, equal or higher than the amount of L-isoleucine produced by fermentation of a bacterium belonging to the family Enterobacteriaceae that has an ability to produce L-isoleucine. However, the amount of a byproduct amino acid of L-isoleucine production in the culture medium and/or the bacterial cells is preferably lower than the amount of L-isoleucine.
Specific examples of a byproduct amino acid of L-isoleucine production include, but are not limited to, an intermediate in a biosynthetic pathway of L-isoleucine or a product of another biosynthetic pathway that branches off from the biosynthetic pathway of L-isoleucine, and so forth, or their combination. The intermediate is not limited to an intermediate in the biosynthetic pathway of L-isoleucine, and it also may be a precursor, an intermediate or a substrate in a metabolic pathway of other one, two or more substances, for example, a precursor, an intermediate or a substrate in a biosynthetic pathway of a branched-chain L-amino acid when the target substance is L-isoleucine.
The phrase “a branched-chain L-amino acid” can refer to the L-amino acids such as L-valine, L-leucine, and L-isoleucine, and may also refer to L-norvaline and L-norleucine. As pyruvic acid (may be also referred to as “alpha-ketopropionic acid”) is a precursor in the biosynthetic pathway of L-isoleucine, a byproduct of L-isoleucine can be the product of another biosynthetic pathway that branches off from pyruvic acid in the biosynthetic pathway of L-isoleucine. A byproduct amino acid of L-isoleucine is a particular example of the product of another biosynthetic pathway that branches off from pyruvic acid in the biosynthetic pathway of L-isoleucine, and can include L-valine and L-leucine that have the common precursor 2-oxoisovaleric acid (may be also referred to as “alpha-ketoisovaleric acid”), L-norvaline and L-norleucine that have the common precursor 2-oxovaleric acid (may be also referred to as “alpha-ketovaleric acid”), which 2-oxoisovaleric acid and 2-oxovaleric acid have the common precursor pyruvic acid.
A non-limiting example of an intermediate in a metabolic pathway of a substance, that is different from L-isoleucine, includes alpha-aminobutyric acid (αABA), which is an intermediate in the biosynthetic pathway of ophthalmic acid.
Therefore, a byproduct amino acid of L-isoleucine may be, but is not limited to, L-valine, L-leucine, L-norvaline, L-norleucine, alpha-aminobutyric acid (αABA) or a combination thereof, in a method for producing L-isoleucine by fermentation of a bacterium belonging to the family Enterobacteriaceae and modified to overexpress the cycA gene, as described hereinafter.
The bacteria belonging to the family Enterobacteriaceae can be from the genera Enterobacter, Enwinia, Escherichia, Klebsiella, Morganella, Pantoea, Photorhabdus, Providencia, Salmonella, Yersinia, and so forth, and can have the ability to produce L-isoleucine. Specifically, those classified into the family Enterobacteriaceae according to the taxonomy used in the NCBI (National Center for Biotechnology Information) database (www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=543) can be used. Examples of bacteria from the family Enterobacteriaceae which can be modified include a bacterium of the genus Escherichia, Enterobacter or Pantoea. 
Escherichia bacteria which can be modified to obtain Escherichia bacteria in accordance with the presently disclosed subject matter are not particularly limited, and specifically, those described in the work of Neidhardt et al. can be used (Bachmann, B. J., Derivations and genotypes of some mutant derivatives of E. coli K-12, p. 2460-2488. In F. C. Neidhardt et al. (ed.), E. coli and Salmonella: cellular and molecular biology, 2nd ed. ASM Press, Washington, D.C., 1996). The species E. coli is a particular example. Specific examples of E. coli include E. coli W3110 (ATCC 27325), E. coli MG1655 (ATCC 47076), and so forth, which are derived from the prototype wild-type strain, E. coli K-12 strain. These strains are available from, for example, the American Type Culture Collection (P.O. Box 1549, Manassas, Va. 20108, United States of America). That is, registration numbers are given to each of the strains, and the strains can be ordered by using these registration numbers (refer to www.atcc.org). The registration numbers of the strains are listed in the catalogue of the American Type Culture Collection.
Examples of the Enterobacter bacteria include Enterobacter agglomerans, Enterobacter aerogenes, and so forth. Examples of the Pantoea bacteria include Pantoea ananatis (P. ananatis), and so forth. Some strains of Enterobacter agglomerans were recently reclassified into Pantoea agglomerans, Pantoea ananatis or Pantoea stewartii on the basis of nucleotide sequence analysis of 16S rRNA, etc. A bacterium belonging to either genus Enterobacter or Pantoea may be used so long as it is a bacterium classified into the family Enterobacteriaceae. When a Pantoea ananatis strain is bred by genetic engineering techniques, Pantoea ananatis AJ13355 strain (FERM BP-6614), AJ13356 strain (FERM BP-6615), AJ13601 strain (FERM BP-7207) and derivatives thereof can be used. These strains were identified as Enterobacter agglomerans when they were isolated, and deposited as Enterobacter agglomerans. However, they were recently re-classified as Pantoea ananatis on the basis of nucleotide sequencing of 16S rRNA and so forth as described above.
L-Isoleucine-Producing Bacteria
Examples of L-isoleucine-producing bacteria or parental strains which can be used to derive L-isoleucine-producing bacteria include, but are not limited to, mutants having resistance to 6-dimethylaminopurine (JP 5-304969 A), mutants having resistance to an isoleucine analogue such as thiaisoleucine and isoleucine hydroxamate, and mutants additionally having resistance to DL-ethionine and/or arginine hydroxamate (JP 5-130882 A). In addition, recombinant strains transformed with genes encoding proteins involved in L-isoleucine biosynthesis, such as threonine deaminase and acetohydroxate synthase, can also be used as L-isoleucine-producing bacteria or parental strains thereof (JP 2-458 A, EP0356739 A1, and U.S. Pat. No. 5,998,178). Example of L-isoleucine-producing bacteria or parental strains thereof also includes E. coli K-12 strain 44-3-15 Scr (VKPM B-12149).
The bacterium of the present invention belonging to the family Enterobacteriaceae has been modified to overexpress the cycA gene.
The cycA gene (synonyms: dagA, ECK4204, JW4166, ytfD) of E. coli encodes the D-alanine/D-serine/glycine transporter CycA (KEGG, Kyoto Encyclopedia of Genes and Genomes, entry No. b4208; Protein Knowledgebase, UniProtKB/Swiss-Prot, accession No. P0AAE0). The cycA gene (GenBank, accession No. NC_000913.3; nucleotide positions: 4429864 to 4431276; Gene ID: 948725) is located between the fklB gene on the same strand and the ytfE gene on the opposite strand on the chromosome of E. coli strain K-12. The nucleotide sequence of the cycA gene of E. coli strain K-12 (SEQ ID NO: 1) and the amino acid sequence of the CycA protein of E. coli strain K-12 (SEQ ID NO: 2) encoded by the cycA gene are known. That is, the cycA gene may have the nucleotide sequence of SEQ ID NO: 1, and the CycA protein may have the amino acid sequence of SEQ ID NO: 2. The phrase “a gene or protein has a nucleotide or amino acid sequence” encompasses cases where a gene or protein comprises the nucleotide or amino acid sequence, and cases where a gene or protein consists of the nucleotide or amino acid sequence.
The CycA protein encoded by the cycA gene is a member of the amino acid-polyamine-organocation (APC) superfamily of amino acid transporters (AAT) (transporter classification (TC) number 2.A.3.1). It is suggested that CycA functions as a proton/serine (or alanine, or glycine) symporter. The CycA transporter is involved in the uptake of glycine, serine and alanine (Robbins J. C. and Oxender D. L. Transport systems for alanine, serine, and glycine in Escherichia coli K-12, J. Bacteriol., 1973, 116(1):12-18; Lee M. et al., Transport properties of merodiploids covering the dagA locus in Escherichia coli K-12, J. Bacteriol., 1975, 122(3):1001-1005). The transport activity of CycA towards cycloserine was also found (Wargel R. J. et al., Mechanism of D-cycloserine action: transport systems for D-alanine, D-cycloserine, L-alanine, and glycine, J. Bacteriol., 1970, 103(3):778-788). No transport activity was found for L-leucine and L-proline (Lee M. et al., 1975). The homologues of CycA from different bacteria of the family Enterobacteriaceae are known, examples of which are described hereinafter.
The phrase “a bacterium modified to overexpress the cycA gene” can mean that the bacterium has been modified in such a way that in the modified bacterium the total activity of the cycA gene product such as CycA protein is increased as compared with, or the expression level of the cycA gene is higher than that level in, a non-modified strain, for example, a wild-type or parental strain as described above and hereinafter. Examples of a non-modified strain serving as a reference for the above comparison can include a wild-type strain of a microorganism belonging to the genus Escherichia such as the E. coli MG1655 strain (ATCC 47076), W3110 strain (ATCC 27325), or a microorganism belonging to the genus Pantoea such as the P. ananatis AJ13355 strain (FERM BP-6614), and so forth.
The phrase “the cycA gene is overexpressed” can mean that the total activity of the cycA gene product such as the CycA protein is increased as compared with a non-modified strain. The total activity of the cycA gene product such as the CycA protein is increased by, for example, increasing the expression level of the cycA gene as compared with a non-modified strain as described hereinafter, or increasing the activity per molecule (may be referred to as a specific activity) of the protein encoded by the cycA gene as compared with a wild-type protein. The bacterium can be modified so that the activity of the CycA protein per cell is increased to 150% or more, 200% or more, 300% or more, of the activity of a non-modified strain.
The phrase “activity of a transporter” can mean the activity of transporting an amino acid, such as, for example, an achiral amino acid and/or an L-amino acid and/or a D-amino acid, such as glycine, D-alanine, L-alanine, and D-serine, which can be transported in a bacterium belonging to the family Enterobacteriaceae. The phrase “activity of a transporter” can also mean the activity of transporting an amino acid, which can be transported in a bacterium belonging to the family Enterobacteriaceae, utilizing the protein having an activity of a transporter having the amino acid sequence of SEQ ID NO: 2.
The phrase “activity of a transporter having the amino acid sequence of SEQ ID NO: 2” can mean the activity of a protein having the amino acid sequence of SEQ ID NO: 2 of transporting an amino acid, which can be transported utilizing the protein having the amino acid sequence of SEQ ID NO: 2 in a bacterium belonging to the family Enterobacteriaceae. It is also acceptable that the phrase “activity of a transporter having the amino acid sequence of SEQ ID NO: 2” can mean the activity of the CycA protein having the amino acid sequence of SEQ ID NO: 2 of transporting the amino acid, which can be transported utilizing the CycA protein in a bacterium belonging to the family Enterobacteriaceae. Specifically, the phrases “activity of a transporter” and “activity of a transporter having the amino acid sequence of SEQ ID NO: 2” can mean the activity of the CycA protein having the amino acid sequence of SEQ ID NO: 2 of transporting an amino acid in the bacterium belonging to the family Enterobacteriaceae, such as, for example, glycine, D-alanine, L-alanine or D-serine, and so forth, or their combination, as long as said one or more amino acids can be transported utilizing the CycA in the bacterium.
The activity of a transporter can be determined by evaluating the transporter activity of CycA. The activity of a transporter can also be determined as a specific activity of the protein per unit weight such as mg or μg. For example, a radioactive labeled amino acid such as, for example, [2-14C]glycine can be used to measure uptake of the amino acid (Lee M. et al., 1975; Ghrist A. C. and Stauffer G. V. The Escherichia coli glycine transport system and its role in the regulation of the glycine cleavage enzyme system, Microbiol., 1995, 141(Pt 1):133-140). The protein concentration can be determined by the Bradford protein assay using bovine serum albumin as a standard (Bradford M. M., Anal. Biochem., 1976, 72:248-254).
The phrase “the cycA gene is overexpressed” can also mean that the expression level of the cycA gene is higher than that level in a non-modified strain. Therefore, the phrase “the cycA gene is overexpressed” can be equivalent to the phrase “expression of the cycA gene is enhanced”. The bacterium can be modified so that the expression amount of the cycA gene per cell is increased to 150% or more, 200% or more, 300% or more, of the expression amount of a non-modified strain.
Methods which can be used to enhance expression of the cycA gene include, but are not limited to, increasing the cycA gene copy number, such as the cycA gene copy number in the chromosome of the bacterium and/or in the autonomously replicating plasmid harbored by the bacterium. The cycA gene copy number can be increased by, for example, introducing the cycA gene into the chromosome of the bacterium and/or introducing an autonomously replicating vector containing the cycA gene into the bacterium.
Examples of the vectors include, but are not limited to, broad-host-range plasmids such as pMW118/119, pBR322, pUC19, and the like. The cycA gene can also be introduced into the chromosomal DNA of a bacterium by, for example, homologous recombination, Mu-driven integration, or the like. Only one copy, or two or more copies of the cycA gene may be introduced. For example, homologous recombination can be carried out using sequence with multiple copies in the chromosomal DNA to introduce multiple copies of the cycA gene into the chromosomal DNA. Sequences with multiple copies in the chromosomal DNA include, but are not limited to, repetitive DNA or inverted repeats present at the end of a transposable element. In addition, it is possible to incorporate the cycA gene into a transposon and allow it to be transferred to introduce multiple copies of the cycA gene into the chromosomal DNA. By using Mu-driven integration, more than 3 copies of the gene can be introduced into the chromosomal DNA during a single act (Akhverdyan V. Z. et al., Biotechnol. (Russian), 2007, 3:3-20).
Additional methods which can be used to enhance expression of the cycA gene include increasing the expression level of the cycA gene by modification of expression regulatory region(s) of the cycA gene. Expression regulatory region(s) of the cycA gene can be modified by, for example, replacing the native expression regulatory region(s) of cycA gene with native and/or modified foreign expression regulatory region(s). Expression regulatory region(s) can also be referred to as Expression regulatory sequence(s). Expression regulatory regions can be exemplified by promoters, enhancers, attenuators and termination signals, anti-termination signals, ribosome-binding sites (RBS) and other expression control elements (e.g., regions to which repressors or inducers bind and/or binding sites for transcriptional and translational regulatory proteins, for example, in the transcribed mRNA). Such regulatory regions are described, for example, in Sambrook J., Fritsch E. F. and Maniatis T., “Molecular Cloning: A Laboratory Manual”, 2nd ed., Cold Spring Harbor Laboratory Press (1989). Modifications of regions controlling gene(s) expression can be combined with increasing the copy number of the gene(s) (see, for example, Akhverdyan V. Z. et al., Appl. Microbiol. Biotechnol., 2011, 91:857-871; Tyo K. E. J. et al., Nature Biotechnol., 2009, 27:760-765).
The exemplary promoters suitable for enhancing the cycA gene expression can be the potent promoters that are stronger than the native cycA promoter. For example, the lac promoter, the trp promoter, the trc promoter, the tac promoter, the PR or the PL promoters of lambda phage are all known to be potent promoters. Potent promoters providing a high level of gene expression in a bacterium belonging to the family Enterobacteriaceae can be used. Alternatively, the effect of a promoter can be enhanced by, for example, introducing a mutation into the promoter region of the cycA gene to obtain a stronger promoter function, thus resulting in the increased transcription level of the cycA gene located downstream of the promoter. Furthermore, it is known that substitution of several nucleotides in the Shine-Dalgarno (SD) sequence, and/or in the spacer between the SD sequence and the start codon, and/or a sequence immediately upstream and/or downstream from the start codon in the ribosome-binding site greatly affects the translation efficiency of mRNA. For example, a 20-fold range in the expression levels was found, depending on the nature of the three nucleotides preceding the start codon (Gold L. et al., Annu. Rev. Microbiol., 1981, 35:365-403; Hui A. et al., EMBO J., 1, 1984, 3:623-629).
The copy number, presence or absence of the gene can be measured, for example, by restricting the chromosomal DNA followed by Southern blotting using a probe based on the gene sequence, fluorescence in situ hybridization (FISH), and the like. The level of gene expression can be determined by measuring the amount of mRNA transcribed from the gene using various well-known methods, including Northern blotting, quantitative RT-PCR, and the like. The amount of the protein encoded by the gene can be measured by known methods including SDS-PAGE followed by immunoblotting assay (Western blotting analysis), or mass spectrometry analysis of the protein samples, and the like.
Methods for manipulation with recombinant molecules of DNA and molecular cloning such as preparation of plasmid DNA, digestion, ligation and transformation of DNA, selection of an oligonucleotide as a primer, incorporation of mutations, and the like may be ordinary methods well-known to the person skilled in the art. These methods are described, for example, in Sambrook J., Fritsch E. F. and Maniatis T., “Molecular Cloning: A Laboratory Manual”, 2nd ed., Cold Spring Harbor Laboratory Press (1989) or Green M. R. and Sambrook J. R., “Molecular Cloning: A Laboratory Manual”, 4th ed., Cold Spring Harbor Laboratory Press (2012); Bernard R. Glick, Jack J. Pasternak and Cheryl L. Patten, “Molecular Biotechnology: principles and applications of recombinant DNA”, 4th ed., Washington, D.C., ASM Press (2009).
There may be some differences in DNA sequences between the genera, species or strains of the family Enterobacteriaceae. Therefore, the cycA gene is not limited to the gene shown in SEQ ID NO: 1, but may include genes which are variant nucleotide sequences of or homologous to SEQ ID NO: 1, and which encode the CycA protein.
The phrase “a variant protein” can mean a protein which has one or more mutations in the sequence compared with the amino acid sequence of SEQ ID NO: 2, whether they are substitutions, deletions, insertions, and/or additions of one or several amino acid residues, but which still maintains an activity or function similar to that of the CycA protein, such as the activity of a transporter as described above, or of which the three-dimensional structure is not significantly changed relative to the wild-type protein. The number of changes in the variant protein depends on the position in the three-dimensional structure of the protein or the type of amino acid residues. It can be, but is not strictly limited to, 1 to 50, in another example 1 to 30, in another example 1 to 15, in another example 1 to 10, and in another example 1 to 5, in SEQ ID NO: 2. This is because some amino acids have high homology to one another, so that the activity or function of a protein is not affected by a change between such amino acids, or the three-dimensional structure of a protein is not significantly changed relative to the wild-type protein by a change between such amino acids. Therefore, the variant proteins encoded by the cycA gene may have a homology, defined as the parameter “identity” when using the computer program BLAST, of not less than 70%, not less than 75%, not less than 80%, not less than 85%, not less than 90%, not less than 95%, not less than 98%, or not less than 99% with respect to the entire amino acid sequence shown in SEQ ID NO: 2, as long as the activity or function of the CycA protein is maintained, or the three-dimensional structure of CycA protein is not significantly changed relative to the wild-type CycA protein.
The exemplary substitution, deletion, insertion, and/or addition of one or several amino acid residues can be a conservative mutation(s). The representative conservative mutation is a conservative substitution. The conservative substitution can be, but is not limited to, a substitution, wherein substitution takes place mutually among Phe, Trp and Tyr, if the substitution site is an aromatic amino acid; among Ala, Leu, Ile and Val, if the substitution site is a hydrophobic amino acid; between Glu, Asp, Gln, Asn, Ser, His and Thr, if the substitution site is a hydrophilic amino acid; between Gln and Asn, if the substitution site is a polar amino acid; among Lys, Arg and His, if the substitution site is a basic amino acid; between Asp and Glu, if the substitution site is an acidic amino acid; and between Ser and Thr, if the substitution site is an amino acid having hydroxyl group. Examples of conservative substitutions include substitution of Ser or Thr for Ala, substitution of Gln, His or Lys for Arg, substitution of Glu, Gln, Lys, His or Asp for Asn, substitution of Asn, Glu or Gln for Asp, substitution of Ser or Ala for Cys, substitution of Asn, Glu, Lys, His, Asp or Arg for Gln, substitution of 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.
The exemplary substitution, deletion, insertion, and/or addition of one or several amino acid residues can also be a non-conservative mutation(s) provided that the mutation(s) is/are compensated by one or more secondary mutation(s) in the different position(s) of amino acids sequence so that the activity or function similar to that of the CycA protein, such as the activity of a transporter as described above, is maintained, or the three-dimensional structure of CycA protein is not significantly changed relative to the wild-type CycA protein.
To evaluate the degree of protein or DNA homology, several calculation methods can be used, such as BLAST search, FASTA search and ClustalW method. The BLAST (Basic Local Alignment Search Tool, www.ncbi.nlm.nih.gov/BLAST/) search is the heuristic search algorithm employed by the programs blastp, blastn, blastx, megablast, tblastn, and tblastx; these programs ascribe significance to their findings using the statistical methods of Karlin S. and Altschul S. F. (“Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes” Proc. Natl. Acad. Sci. USA, 1990, 87:2264-2268; “Applications and statistics for multiple high-scoring segments in molecular sequences”. Proc. Natl. Acad. Sci. USA, 1993, 90:5873-5877). The computer program BLAST calculates three parameters: score, identity and similarity. The FASTA search method is described by Pearson W. R. (“Rapid and sensitive sequence comparison with FASTP and FASTA”, Methods Enzymol., 1990, 183:63-98). The ClustalW method is described by Thompson J. D. et al. (“CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice”, Nucleic Acids Res., 1994, 22:4673-4680).
Protein homologues of CycA (CycA homologues) can also be used as the CycA protein. Examples of CycA homologues include CycA homologues of various organisms such as bacteria of the family Enterobacteriaceae. For example, the CycA homologues from different bacteria of the family Enterobacteriaceae are known, that have the activity of a transporter as described above. Examples of such CycA homologues of the family Enterobacteriaceae are described hereinafter (Table 1) with indication of a homology value (as “identity”, that is the identity of amino acids), taxonomy data, and accession and sequence record numbers of amino acid sequences in the NCBI database (National Center for Biotechnology Information, www.ncbi.nlm.nih.gov/protein/). Furthermore, variant proteins of such CycA homologues can also be used as the CycA protein. The aforementioned descriptions concerning variant proteins of the CycA protein of SEQ ID NO: 2, e.g. those regarding mutations and sequence identity, can be applied mutatis mutandis to variant proteins of CycA homologues.
The phrase “the CycA” or “the CycA protein” is not limited to the wild-type CycA proteins such as the CycA protein of SEQ ID NO: 2 and CycA homologues of Table 1, but can correctively refer to the wild-type CycA proteins and variant proteins thereof.









TABLE 1







Accession No.*;




Sequence


Identity
Organism
record (GI) No.*

















100%
Escherichia coli
YP_492350.1;



(strain K-12)
388480155


93%
Klebsiella pneumoniae
WP_015959296.1;




506439579


100%
Shigella sonnei (strain Ss046)
Q3YUD9;




123615489


95%
Salmonella enterica
WP_000228328.1;




446150473


94%
Enterobacter aerogenes
WP_015368603.1;




505181501


95%
Citrobacter freundii MGH 56
KDF09506.1;




635727731


74%
Pantoea ananatis
WP_013025298.1;




502790322


100%
Klebsiella pneumoniae IS22
CDK72727.1;




571213503


76%
Pantoea sp. At-9b
WP_013508580.1;




503273919


96%
Enterobacter cloacae
WP_014168338.1;




503934344


74%
Erwinia amylovora ATCC BAA-2158
CBX80271.1;




312172014


100%
Escherichia coli O145:H28
AHG17723.1;



(strain RM13516)
573937918


77%
Dickeya dadantii
WP_013318563.1;




503083691


99%
Shigella flexneri
WP_000228331.1;




446150476


69%
Morganella morganii
WP_024473835.1;




639125696


86%
Serratia marcescens
WP_019456240.1;




518286032





*in the NCBI database (National Center for Biotechnology Information, www.ncbi.nlm.nih.gov/)






The cycA gene can be any gene encoding CycA protein. For example, the cycA gene can be a variant nucleotide sequence. The phrase “a variant nucleotide sequence” can mean a nucleotide sequence which encodes a variant protein as described above, or a nucleotide sequence which encodes any wild-type CycA protein using any synonymous amino acid codons according to the standard genetic code table (see, e.g., Lewin B., “Genes VIII”, 2004, Pearson Education, Inc., Upper Saddle River, N.J. 07458). Therefore, the cycA gene can be a variant nucleotide sequence due to the degeneracy of the genetic code, such as a variant nucleotide sequence of SEQ ID NO: 1 due to the degeneracy of the genetic code.
The phrase “a variant nucleotide sequence” can also mean, but is not limited to, a nucleotide sequence which hybridizes under stringent conditions with the nucleotide sequence complementary to the sequence shown in SEQ ID NO: 1, or a probe which can be prepared from the nucleotide sequence under stringent conditions provided that it encodes active or functional protein. “Stringent conditions” include those under which a specific hybrid, for example, a hybrid having homology, defined as the parameter “identity” when using the computer program BLAST, of not less than 70%, not less than 75%, not less than 80%, not less than 85%, not less than 90%, not less than 95%, not less than 96%, not less than 97%, not less than 98%, or not less than 99% is formed, and a non-specific hybrid, for example, a hybrid having homology lower than the above is not formed. For example, stringent conditions can be exemplified by washing one time or more, or in another example, two or three times, at a salt concentration of 1×SSC (standard sodium citrate or standard sodium chloride), 0.1% SDS (sodium dodecyl sulphate), or in another example, 0.1×SSC, 0.1% SDS at 60° C. or 65° C. Duration of washing depends on the type of membrane used for blotting and, as a rule, should be what is recommended by the manufacturer. For example, the recommended duration of washing for the Amersham HybondTM-N+ positively charged nylon membrane (GE Healthcare) under stringent conditions is 15 minutes. The washing step can be performed 2 to 3 times. As the probe, a part of the sequence complementary to the sequence shown in SEQ ID NO: 1 may also be used. Such a probe can be produced by PCR using oligonucleotides as primers prepared on the basis of the sequence shown in SEQ ID NO: 1 and a DNA fragment containing the nucleotide sequence as a template. The length of the probe is recommended to be >50 bp; it can be suitably selected depending on the hybridization conditions, and is usually 100 bp to 1 kbp. For example, when a DNA fragment having a length of about 300 bp is used as the probe, the washing conditions after hybridization can be exemplified by 2×SSC, 0.1% SDS at 50° C., 60° C. or 65° C.
As the gene encoding the CycA protein of the species E. coli has already been elucidated (see above), the cycA gene, such as genes encoding the wild-type CycA proteins or variant proteins thereof, can be obtained by PCR (polymerase chain reaction; refer to White T. J. et al., The polymerase chain reaction, Trends Genet., 1989, 5:185-189) from a microorganism harboring a wild-type cycA gene, for example, a bacterium belonging to the family Enterobacteriaceae, utilizing primers prepared based on the nucleotide sequence of the cycA gene; or the site-directed mutagenesis method by treating a DNA containing the wild-type cycA gene in vitro, for example, with hydroxylamine, or a method for treating a microorganism harboring a wild-type cycA gene, for example, a bacterium belonging to the family Enterobacteriaceae, with ultraviolet (UV) irradiation or a mutating agent such as N-methyl-N′-nitro-N-nitrosoguanidine (NTG) and nitrous acid usually used for the such treatment; or chemically synthesized as full-length gene structure. Thus, genes encoding the wild-type CycA proteins such as the CycA protein of E. coli and CycA protein homologues of other microorganisms of the family Enterobacteriaceae or genes encoding variant proteins thereof can be obtained.
The phrase “the cycA gene” is not limited to the wild-type cycA genes such as the cycA gene of SEQ ID NO: 1 and genes encoding CycA homologues of Table 1, but can correctively refer to the native cycA genes and genes encoding variant CycA proteins.
The phrase “a wild-type protein” can mean a native protein naturally produced by a wild-type or parent bacterial strain of the family Enterobacteriaceae, for example, by the wild-type E. coli MG1655 strain. A wild-type protein can be encoded by the “wild-type gene”, which can be present in genome of a wild-type bacterium.
The above descriptions concerning variants of the genes and proteins can also be applied mutatis mutandis to arbitrary proteins such as L-isoleucine biosynthesis enzymes and genes coding for them.
The bacterium can have, in addition to the properties already mentioned, other specific properties such as various nutrient requirements, drug resistance, drug sensitivity, and drug dependence, without departing from the scope of the present invention.
2. Method
A method of the present invention includes the method for producing L-isoleucine. The method for producing L-isoleucine can include the steps of cultivating the bacterium in a culture medium to allow L-isoleucine to be produced, excreted or secreted, and/or accumulated in the culture medium or in the bacterial cells, or both, and collecting L-isoleucine from the culture medium and/or the bacterial cells. L-isoleucine can be produced in a free form or as a salt thereof, or as a mixture thereof. That is, the phrase “L-isoleucine” may refer to L-isoleucine in a free form, a salt thereof, or a mixture thereof. For example, sodium, potassium, ammonium, and the like salts or an inner salt such as zwitterion of L-isoleucine can be produced by the method. This is possible as amino acids can react under fermentation conditions with each other or a neutralizing agent such as an inorganic or organic acidic or alkaline substance in a typical acid-base neutralization reaction to form a salt that is the chemical feature of amino acids which is apparent to one skilled in the art.
Moreover, the method of the present invention for producing L-isoleucine further includes a method for reducing production of byproduct amino acid(s) of L-isoleucine. The method for reducing production of byproduct amino acid(s) of L-isoleucine can include the steps of cultivating the bacterium in a culture medium to allow L-isoleucine to be produced, excreted or secreted, and/or accumulated in the culture medium or in the bacterial cells, or both, collecting and, if necessary, purifying L-isoleucine from the culture medium and/or the bacterial cells.
The cultivation of the bacterium, and collection and purification of L-isoleucine from the medium and the like may be performed in a manner similar to conventional fermentation methods wherein L-isoleucine is produced using a microorganism. The culture medium for production of the L-isoleucine can be either a synthetic or natural medium such as a typical medium that contains a carbon source, a nitrogen source, a sulphur source, a phosphorus source, inorganic ions, and other organic and inorganic components as required. As the carbon source, saccharides such as glucose, sucrose, lactose, galactose, fructose, arabinose, maltose, xylose, trehalose, ribose, and hydrolyzates of starches; alcohols such as ethanol, glycerol, mannitol, and sorbitol; organic acids such as gluconic acid, fumaric acid, citric acid, malic acid, and succinic acid; fatty acids, and the like can be used. As the nitrogen source, inorganic ammonium salts such as ammonium sulfate, ammonium chloride, and ammonium phosphate; organic nitrogen such as of soy bean hydrolysate; ammonia gas; aqueous ammonia; and the like can be used. Furthermore, peptone, yeast extract, meat extract, malt extract, corn steep liquor, and so forth can also be utilized. The medium may contain one or more types of these nitrogen sources. The sulphur source can include ammonium sulphate, magnesium sulphate, ferrous sulphate, manganese sulphate, and the like. The medium can contain a phosphorus source in addition to the carbon source, the nitrogen source and the sulphur source. As the phosphorus source, potassium dihydrogen phosphate, dipotassium hydrogen phosphate, phosphate polymers such as pyrophosphoric acid and so forth can be utilized. Vitamins such as vitamin B 1, vitamin B2, vitamin B6, nicotinic acid, nicotinamide, vitamin B12, required substances, for example, organic nutrients such as nucleic acids such as adenine and RNA, amino acids, peptone, casamino acid, yeast extract, and the like may be present in appropriate, even if trace, amounts. Other than these, small amounts of calcium phosphate, iron ions, manganese ions, and so forth may be added, if necessary.
Cultivation can be performed under aerobic conditions for 16 to 72 h, or for 32 to 68 h; the culture temperature during cultivation can be controlled within 30 to 45° C., or within 30 to 37° C.; and the pH can be adjusted between 5 and 8, or between 6 and 7.5. The pH can be adjusted by using an inorganic or organic acidic or alkaline substance, as well as ammonia gas.
After cultivation, L-isoleucine can be collected from the culture medium. Also, after cultivation, the cells can be disrupted with, for example, supersonic waves or the like, the supernatant can be obtained by removing solids such as the cells and the cell-disrupted suspension (also referred to as cell debris) by, for example, centrifugation or membrane filtration, and then L-isoleucine can be collected from the supernatant. Collection of L-isoleucine from the culture medium or the supernatant etc can be performed by any combination of conventional techniques such as concentration, ion-exchange chromatography, and crystallization.
The collected L-isoleucine may contain, for example, microbial cells, medium components, moisture, by-product metabolites of the microorganism, and so forth, in addition to L-isoleucine. Purity of the collected L-isoleucine can be 50% or higher, 85% or higher, or 95% or higher (U.S. Pat. No. 5,431,933, Japanese Patent No. 1214636, U.S. Pat. Nos. 4,956,471, 4,777,051, 4,946,654, 5,840,358, 6,238,714, U.S. Patent Published Application No. 2005/0025878).
EXAMPLES
The present invention will be more specifically explained below with reference to the following non-limiting examples.
Example 1. Construction of the E. coli L-Isoleucine-Producing Strain Modified to Overexpress the cycA Gene
1.1 Construction of the E. coli MG1655 Strain Having Modified a Regulatory Region of cycA
The cycA gene in E. coli was overexpressed using the method developed by Datsenko K. A. and Wanner B. L. called “λRed/ET-mediated integration” (Datsenko K. A. and Wanner B. L., Proc. Natl. Acad. Sci. USA, 2000, 97(12):6640-6645). According to this procedure, the PCR primers P1 (SEQ ID NO: 3) and P2 (SEQ ID NO: 4), which are homologous to both regions adjacent to the cycA gene and regions adjacent to the cat gene conferring chloramphenicol resistance (CmR) and the PL promoter in the template chromosome, were constructed. The chromosome of the chloramphenicol-resistant E. coli strain BW25113 cat-PL-yddG, which contains the early PL promoter region of phage lambda (Giladi H. et al., Identification of an UP element within the IHF binding site at the PL1-PL2 tandem promoter of bacteriophage lambda, J. Mol. Biol., 1996, 260(4):484-491), was used as the template in PCR reaction. The E. coli strain BW25113 cat-PL-yddG can be constructed as described in detail in EP1449918 A1. The E. coli strain BW25113 can be obtained from the Coli Genetic Stock Center (Yale University, New Haven, USA) as CGSC7636.
Conditions for PCR were as follows: denaturation for 3 min at 95° C.; profile for 35 cycles: 1 min at 95° C., 1 min at 58° C., 1 min at 72° C.; final elongation for 5 min at 72° C. The obtained DNA-fragment 1 (1,964 bp) (SEQ ID NO: 5) was purified in an agarose gel and used for electroporation of the strain E. coli MG1655 (ATCC 47076) containing the plasmid pKD46 with a temperature-sensitive replication origin. E. coli MG1655 is available from the American Type Culture Collection (P.O. Box 1549, Manassas, Va. 20108, United States of America). The plasmid pKD46 (Datsenko K. A. and Wanner B. L., Proc. Natl. Acad. Sci. USA, 2000, 97(12):6640-6645) includes a 2,154 nt (31088-33241) DNA-fragment of phage λ (GenBank, accession No. J02459) and contains genes of the λRed homologous recombination system (γ, β, and exo genes) under the control of arabinose-inducible ParaB promoter. The plasmid pKD46 is necessary to integrate the DNA-fragment into the chromosome of strain E. coli MG1655.
Electrocompetent cells were prepared as follows: E. coli MG1655 cells were grown overnight at 30° C. in LB-medium (Sambrook, J. and Russell, D. W. “Molecular Cloning: A Laboratory Manual”, 3rd ed., Cold Spring Harbor Laboratory Press (2001)) containing ampicillin (100 mg/L), and the culture was diluted 100 times with 5 mL of SOB-medium (Sambrook J., Fritsch E. F. and Maniatis T., “Molecular Cloning: A Laboratory Manual”, 2nd ed., Cold Spring Harbor Laboratory Press (1989)) containing ampicillin (100 mg/L) and L-arabinose (1 mM). The diluted culture was grown with aeration (250 rpm) at 30° C. to an OD600 of about 0.6 and then made electrocompetent by concentrating 100-fold and washing three times with ice-cold deionized H2O. Electroporation was performed using 70 μL of cells and about 100 ng of the DNA-fragment 1. Then, cells were incubated with 1 mL of SOC-medium (Sambrook J., Fritsch E. F. and Maniatis T., “Molecular Cloning: A Laboratory Manual”, 2nd ed., Cold Spring Harbor Laboratory Press (1989)) at 37° C. for 2.5 h, placed onto the plates containing LB-medium (Sambrook, J. and Russell, D. W. “Molecular Cloning: A Laboratory Manual”, 3rd ed., Cold Spring Harbor Laboratory Press (2001)), agar (1.5%) and chloramphenicol (20 mg/L), and grown at 37° C. to select CmR-recombinants. To eliminate the pKD46 plasmid, 1 passage on L-agar with chloramphenicol (20 mg/L) at 42° C. was performed, and the obtained colonies were tested for sensitivity to ampicillin. Thus the strain E. coli MG1655 cat-PL-cycA was obtained.
1.2. Verification of a Modification of the Regulatory Region of cycA Gene
Cells containing a heterologous promoter region of the cycA gene marked with CmR-gene (cat) were verified by PCR using locus-specific primers P3 (SEQ ID NO: 6) and P4 (SEQ ID NO: 7). Conditions for PCR were as follows: denaturation for 3 min at 95° C.; profile for 20 cycles: 30 sec at 95° C., 30 sec at 60° C., 2 min at 72° C.; final elongation for 5 min at 72° C. DNA-fragment 2, obtained in the reaction with the chromosomal DNA from the parent strain E. coli MG1655 as the template, was 457 bp in length (SEQ ID NO: 8). DNA-fragment 3, obtained in the reaction with the chromosomal DNA from the strain E. coli MG1655 cat-PL-cycA as a template, was 2,174 bp in length (SEQ ID NO: 9).
1.3. Construction of the E. coli L-Isoleucine-Producing Strain
The cycA gene under control of PL promoter was introduced into the L-isoleucine-producing E. coli K-12 strain 44-3-15 Scr (U.S. Pat. Nos. 6,960,455 B2 and 7,179,623 B2; Russian Patent No. 2212447 C2). The E. coli K-12 strain 44-3-15 Scr (also referred to as E. coli 44-3-15 Scr) was deposited in the Russian National Collection of Industrial Microorganisms (VKPM, Russian Federation, 117545 Moscow, 1st Dorozhny Proezd, 1) on Dec. 17, 2014 according to the provisions of the Budapest Treaty under the accession number of VKPM B-12149. The E. coli 44-3-15 Scr has a mutation in the ilvG gene (ilvG5) that results in restoration of acetohydroxy acid synthase II activity, a mutation in the ilvA gene (ilvA7434) that results in threonine deaminase insensitivity to feedback inhibition by isoleucine (Gavrilova et al., Biotechnologiya (in Russian), 1988, 4:600-608), and is resistant to chloramphenicol (CmR). Before introduction into the E. coli 44-3-15 Scr, the CmR-marker upstream of the PL promoter in the expression cassette cat-PL-cycA was replaced with the kanamycin resistance (KmR) marker using λRed integration (Datsenko K. A. and Wanner B. L., Proc. Natl. Acad. Sci. USA, 2000, 97(12):6640-6645). According to this procedure, the PCR primers P5 (SEQ ID NO: 10) and P6 (SEQ ID NO: 11), which are homologous to both regions adjacent to the cat gene and the kan gene conferring kanamycin resistance (KmR) in the template plasmid, were constructed. The plasmid pMW118-(λattL-KmR-λattR) was used as the template in the PCR reaction (EP2100957 A1).
Conditions for PCR were as follows: denaturation for 3 min at 95° C.; profile for 35 cycles: 30 sec at 94° C., 30 sec at 57° C., 1 min 30 sec at 72° C.; final elongation for 5 min at 72° C. The obtained DNA-fragment 4 (1,541 bp) (SEQ ID NO: 12) was purified in an agarose gel and used for electroporation of the strain E. coli MG1655 cat-PL-cycA (Example 1.1) containing the plasmid pKD46 (Datsenko K. A. and Wanner B. L., Proc. Natl. Acad. Sci. USA, 2000, 97(12):6640-6645). The cells of E. coli MG1655 strain, that harbor the kan-PL-cycA cassette, were selected on the plates containing LB-medium, agar (1.5%) and kanamycin (40 mg/L). Thus, the kanamycin-resistant chloramphenicol-sensitive strain E. coli MG1655 kan-PL-cycA was obtained.
The replacement of the CmR-marker upstream of the PL-cycA construct was verified by PCR. For this purpose, the primers P3 (SEQ ID NO: 6) and P4 (SEQ ID NO: 7) were used. Conditions for PCR were as follows: denaturation for 3 min at 95° C.; profile for 20 cycles: 30 sec at 95° C., 30 sec at 60° C., 2 min at 72° C.; final elongation for 5 min at 72° C. DNA-fragment 3, obtained in the reaction with the chromosomal DNA from the parent strain E. coli MG1655 cat-PL-cycA as the template, was 2,174 bp in length (SEQ ID NO: 9). DNA-fragment 5, obtained in the reaction with the chromosomal DNA from the strain E. coli MG1655 kan-PL-cycA as a template, was 2,087 bp in length (SEQ ID NO: 13).
Then, the expression cassette kan-PL-cycA was introduced into the L-isoleucine producing strain E. coli 44-3-15 Scr by P1-transduction (Miller J. H. “Experiments in molecular genetics”, Cold Spring Harbor Laboratory, Cold Spring Harbor (1972)). Cells of the E. coli 44-3-15 Scr strain that harbor the kan-PL-cycA cassette were selected on the plates containing LB-medium, agar (1.5%) and kanamycin (40 mg/L). Thus, the L-isoleucine producing strain E. coli 44-3-15 Scr kan-PL-cycA was obtained. The replacement of a promoter region of the cycA gene was verified by PCR as described above.
Example 2. By-Production of L-Valine Using the E. coli 44-3-15 Scr Kan-PL-cycA Strain
The modified E. coli 44-3-15 Scr kan-PL-cycA and the control E. coli 44-3-15 Scr strains were each cultivated at 32° C. for 18 hours in LB-medium (also referred to as lysogenic broth or Luria-Bertani medium as described in Sambrook, J. and Russell, D. W. “Molecular Cloning: A Laboratory Manual”, 3rd ed., Cold Spring Harbor Laboratory Press (2001)). Then, 0.2 mL of the obtained culture was inoculated into 2 mL of a fermentation medium in 20×200-mm test tubes and cultivated at 32° C. for 66 hours on a rotary shaker at 250 rpm to an OD550 of about 29 until glucose was consumed.
The composition of the fermentation medium (g/L) was as follows:
















Glucose
60.0



(NH4)2SO4
15.0



KH2PO4
1.5



MgSO4•7H2O
1.0



Thiamine-HCl
0.1



L-threonine
4.0



CaCO3
25.0



LB-medium
10% (v/v)










The fermentation medium was sterilized at 116° C. for 30 min, except that glucose and CaCO3 were sterilized separately as follows: glucose at 110° C. for 30 min and CaCO3 at 116° C. for 30 min. The pH was adjusted to 7.0 by KOH solution.
After cultivation, the accumulated L-isoleucine and L-valine were measured using thin-layer chromatography (TLC). TLC plates (10×20 cm) were coated with 0.11-mm layers of Sorbfil silica gel containing non-fluorescent indicator (Sorbpolymer, Krasnodar, Russian Federation). Samples were applied onto the plates with the Camag Linomat 5 sample applicator. The Sorbfil plates were developed with a mobile phase consisting of propan-2-ol:ethylacetate:25% aqueous ammonia:water (16:16:5:10, v/v). A solution of ninhydrin (2%, w/v) in acetone was used as the visualizing reagent. After development, plates were dried and scanned with the Camag TLC Scanner 3 in absorbance mode with detection at 520 nm using winCATS software (version 1.4.2).
The results of four independent test-tube fermentations are shown in Table 2. The amount of L-valine was determined as a relative value based on the value for L-isoleucine as a control, which was taken as 100%. As it can be seen from the Table 2, the modified E. coli 44-3-15 Scr kan-PL-cycA strain was able to accumulate a higher amount of L-isoleucine as compared with the parent E. coli 44-3-15 Scr strain. Table 2 also shows that the modified E. coli 44-3-15 Scr kan-PL-cycA strain was able to accumulate less L-valine as compared with the parent E. coli 44-3-15 Scr strain.











TABLE 2








L-Ile,
L-Val,



Strain
g/L
% of L-Ile









E. coli 44-3-15 Scr
13.7
23.5



E. coli 44-3-15 Scr kan-PL-cycA
14.0
16.0










Example 3. By-Production of Alpha-Aminobutyric Acid and Norvaline Using the E. coli 44-3-15 Scr kan-PL-cycA Strain
The modified E. coli 44-3-15 Scr kan-PL-cycA and the control E. coli 44-3-15 Scr strains were each cultivated at 32° C. for 18 hours in LB-medium. Then, 0.2 mL of the obtained culture was inoculated into 2 mL of a fermentation medium in 20×200-mm test tubes and cultivated at 32° C. for 66 hours on a rotary shaker at 250 rpm to an OD550 of about 29 until glucose consumption. The fermentation medium was supplemented with chlorsulfuron (CAS number 64902-72-3) to decrease biosynthesis of branched-chain L-amino acids by inhibiting acetolactate synthase (AHAS) to demonstrate the effect from overexpression of cycA on by-production of alpha-aminobutyric acid and norvaline (Gedi V. and Yoon M.-Y., Bacterial acetohydroxyacid synthase and its inhibitors—a summary of their structure, biological activity and current status, FEBS J., 2012, 279(6):946-963).
The composition of the fermentation medium (g/L) was as follows:
















Glucose
60.0



(NH4)2SO4
15.0



KH2PO4
1.5



MgSO4•7H2O
1.0



Thiamine-HCl
0.1



Chlorsulfuron
20 μM



CaCO3
25.0



LB-medium
10% (v/v)










The fermentation medium was sterilized at 116° C. for 30 min, except that glucose and CaCO3 were sterilized separately as follows: glucose at 110° C. for 30 min and CaCO3 at 116° C. for 30 min. The pH was adjusted to 7.0 by KOH solution.
After cultivation, the accumulated L-isoleucine, alpha-aminobutyric acid and norvaline were measured using high-performance liquid chromatography (HPLC) (Auxiliary example).
The results of three independent test-tube fermentations are shown in Table 3. The amount of alpha-aminobutyric acid (αABA) and norvaline (nVal) was determined as a relative value based on the value for L-isoleucine as a control, which was taken as 100%. As it can be seen from the Table 3, the modified E. coli 44-3-15 Scr kan-PL-cycA strain was able to accumulate a lower amount of αABA and nVal as compared with the parent E. coli 44-3-15 Scr strain.










TABLE 3






L-Ile,
αABA,
nVal,


Strain
mg/L
% of L-Ile
% of L-Ile


















E. coli 44-3-15 Scr
270
274
337


E. coli 44-3-15 Scr kan-PL-cycA
113
<9
105









Auxiliary Example. Chromatographic Analysis for L-Isoleucine, Alpha-Aminobutyric Acid and Norvaline
The Waters AccQ-Tag Method was used for the analysis. The AccQ-Tag Method is a precolumn derivatization technique for determination of amino acids. The HPLC system Agilent 1100 gradient system (Agilent Technologies) equipped with fluorescence detector and connected to computer loaded with “ChemStation B.02.01 SR2” chromatography software (Agilent Technologies) was used. The detector settings were as follows: excitation wavelength at 250 nm, emission wavelength at 395 nm. A 5 μL sample injection loop was used for all runs. Waters AccQ-Tag Amino Acid Analysis Column (3.9×150 mm) equipped with a guard column was used to resolve the amino acid derivatives obtained in the AccQ-Fluor derivatization reaction using the AccQ-Fluor Reagent Kit (Waters, WAT052880). The column was equilibrated at 37° C., and a mobile-phase at a flow-rate of 0.8 mL/min was applied. The mobile phase contained the following eluents: A—aqueous buffer Waters AccQ-Tag Eluent A (Waters, WAT052890), B—HPLC-grade acetonitrile, and C—Milli-Q water. The gradient was as shown in the Table 4. The curve No. 6 corresponds to a linear segment and No. 11 to a step function.












TABLE 4






Start time of



Curve


Step
a step, min
Eluent A, %
Eluent B, %
Eluent C, %
type




















1
0
100
0
0
0


2
0.4
100
0
0
6


3
0.5
99
1
0
6


4
18.0
95
5
0
6


5
19.0
91
9
0
6


6
28.0
78
17
5
6


7
35.0
78
17
5
11


8
36.0
0
60
40
11


9
38.0
0
60
40
11


10
39.0
100
0
0
11


11
47.0
99
1
0
11









INDUSTRIAL APPLICABILITY
The method of the present invention is useful for the production of L-isoleucine in a higher amount with the high grade of purity.
While the invention has been described in detail with reference to preferred embodiments thereof, it will be apparent to one skilled in the art that various changes can be made, and equivalents employed, without departing from the scope of the invention. All the cited references herein are incorporated as a part of this application by reference.

## Claims

1. A method for producing L-isoleucine comprising:
(i) cultivating an Escherichia coli bacterium that produces L-isoleucine in a culture medium or in cells of the bacterium, or both; and
(ii) collecting the L-isoleucine from the culture medium or the cells, or both,
wherein the bacterium has been modified to overexpress a cycA gene by increasing the copy number of the cycA gene and/or by modifying an expression regulatory region of the cycA gene, so that the expression of said gene is enhanced as compared with a non-modified bacterium.

2. The method of claim 1, wherein said cycA gene encodes a protein selected from the group consisting of:
(A) a protein comprising the amino acid sequence of SEQ ID NO: 2;
(B) a protein comprising the amino acid sequence of SEQ ID NO: 2, having 1 to 10 mutations comprising substitution, deletion, insertion and/or addition of one or several amino acid residues, and wherein said protein has the activity of a transporter having the amino acid sequence of SEQ ID NO: 2; and
(C) a protein having at least 90% homology with the amino acid sequence of SEQ ID NO: 2 and having the activity of a transporter.

3. The method of claim 1, wherein said cycA gene is a DNA selected from the group consisting of:
(A) a DNA comprising the nucleotide sequence of SEQ ID NO: 1;
(B) a DNA encoding a protein comprising the amino acid sequence of SEQ ID NO: 2, having 1 to 10 mutations comprising substitution, deletion, insertion and/or addition of one or several amino acid residues, and wherein said protein has the activity of a transporter; and
(C) a DNA which is a variant nucleotide sequence of SEQ ID NO: 1 due to the degeneracy of the genetic code.

4. The method of claim 1, wherein the Escherichia coli bacterium further produces a byproduct amino acid in an amount less than that produced by a non-modified bacterium, wherein the byproduct amino acid is selected from the group consisting of L-valine, L-leucine, L-norvaline, L-norleucine, alpha-aminobutyric acid, and combinations thereof.