Specification
DESCRIPTION
A METHOD FOR PRODUCING AN L-AMINO ACID USING A BACTERIUM OF THE ENTEROBACTERIACEAE FAMILY
Technical field
The present invention relates to the microbiological industry, and specifically to a method for producing an L-amino acid such as L-threonine, L-Iysine, L-histidine, L-phenylalanine, L-arginine, L-tryptophan, L-glutamic acid and L-leucine by fermentation using a bacterium with an enhanced activity of alcohol dehydrogenase.
Background 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 acid production yields have been reported, including transformation of microorganisms with recombinant DNA (U.S. Patent No. 4,278,765). Other techniques for enhancing production yields include increasing the activities of enzymes involved in amino acid biosynthesis and/or desensitizing the target enzymes to feedback inhibition by the resulting L-amino acid (U.S. Patent Nos. 4,346,170, 5,661,012, and 6,040,160).
By optimizing the main biosynthetic pathway of a desired compound, further improvement of L-amino acid producing strains can be accomplished. Typically, this is accomplished via supplementation of the bacterium with increasing amounts of a carbon source such as sugars, for example, glucose. Despite the efficiency of glucose transport by PTS, access to the carbon source in a highly productive strain still may be insufficient. Another way to increase productivity of L-amino acid producing strains and decrease the cost of the target L-amino acid is to use an alternative source of carbon, such as alcohol, for example, ethanol.
Alcohol dehydrogenase (ethanol oxidoreductase, AdhE) oiEscherichia coli is a multifimctional enzyme that catalyses fermentative production of ethanol by two sequential NADH-dependent reductions of acetyl-CoA, as well as deactivation of pyruvate formate-lyase, which cleaves pyruvate to acetyl-CoA and formate.
AdhE is abundantly synthesized (about 3x10 copies per cell) during anaerobic growth in the presence of glucose and forms helical structures, called spirosomes, which are around 0.22 irni long and contain 40-60 AdhE molecules (Kessler, D., Herth, W., and Knappe, J., J. Biol. Chem., 267, 18073-18079 (1992)). When the E. coli cell culture is shifted from anaerobic to aerobic conditions, transcription of the adhE gene is reduced and maintained within 10% of the range found under anaerobiosis (Chen, Y. M., and Lin, E. C. C, J. Bacteriol. 173, 8009-8013 (1991); Leonardo, M. R., Cunningham, P. R., and Clark, D. P., J. Bacteriol. 175,870-878 (1993); Mikulskis, A., Aristarkhov, A., and Lin, E. C. C, J. Bacteriol. 179, 7129-7134 (1997); Membrillo-Hemandez, J., and Lin, E. C. C, J. Bacteriol. 181,7571-7579 (1999)). Translation is also regulated and requires RNase III (Membrillo-Hemandez, J., and Lin, E. C. C, J. Bacteriol. 181, 7571-7579 (1999); Aristarkhov, A. et al, J. Bacteriol. 178,4327-4332 (1996)). AdhE has been identified as one of the major targets when £. co/;'cells are subjected to hydrogen peroxide stress (Tamarit, J., Cabiscol, E., and Ros, J., J. Biol. Chem. 273,3027-3032 (1998)).
Despite the reversibility of the two NADH-coupled reactions catalyzed by AdhE, wild-type E. coli is unable to grow in the presence of ethanol as the sole source of carbon and energy, because the adhE gene is transcribed aerobically at lowered levels (Chen, Y. M. and Lin, E. C. C, J. Bacteriol. 73, 8009-8013 (1991); Leonardo, M. R., Cunningham, P. R. & Clark, D. P., J. Bacteriol. 175 870-878 (1993)) and the half-life of the AdhE protein is shortened during aerobic metabolism by metal-catalyzed oxidation (MCO).
Mutants of £. coli capable of aerobic growth on ethanol as the sole carbon and energy source have been isolated and characterized (mutants with the substitution Ala267Thr grew in the presence of ethanol with a doubling time of 240 min; with ■flie substitutions Ala267Thr and GJu568Lys, a doubling time of 90 min al 37°C) (MembrilJo-Hemandez, J. et al, J. Biol. Chem. 275,33869-33875 (2000); HoIIand-Staley, C. A. et al, J. Bacteriol. 182,6049-6054 (2000)). Apparently, when the two sequential reactions are catalyzed in a direction opposite to that of the physiological one, acetyl-CoA fomiation is rate-limiting for vwld-type AdhE. The tradeoff for improving the Vmax by the A267T substitution in AdhE is decreased thermal enzyme stability and increased sensitivity to MCO damage. The second amino acid substitution, E568K, in AdhE (A267T/E568K) partially restored protein stability and resistance to MCO damage without further improvement of catalytic efficiency in substrate oxidation.
However, there have been no reports to date of using a bacterium of the Enterobacleriaceae family which has an enhanced activity of either native alcohol
dehydrogenase or mutant alcohol dehydrogenase resistant to aerobic inactivation for increasing the production of L-amino acids by fermentation in a culture medium containing ethanoj.
SUMMARY OF THE INVENTION Objects of the present invention include enhancing the productivity of L-amino acid-producing strains and providing a method for producing non-aromatic or aromatic L-amino acids using these strains.
This aim was achieved by finding that expressing either the native or mutant adhE gene which encodes alcohol dehydrogenase tmder the control of a promoter which fimctions under an aerobic cultivation condition enhances production of L-amino acids^ for example, L-threonine, L-lysine, L-histidJne, L-phenylalanine, L-arginine, L-tryptophan, L-glutamic acid, and/or L-ieucine.
It is an object of the present invention to provide a method for producing an L-amino acid comprising;
A) cultivating in a culture medium containing ethanol an L-amino acid-pmducing bacterium of die Enterobacteriaceae family having an alcohol dehydrogenase, and 6) isolating the L-amino acid from the culture medium,
wherein the gene encoding said alcohol dehydrogenase is expressed under the control of a non-native promoter which functions under aerobic cultivation conditions.
It is a further object of the present invention to provide the method described above, wherein said non-native promoter is selected from the group consisting of Pijc, PIBC. Piqi, Ptrc, PR, andPL.
It is a fitfther object of the present invention to provide the method described above, wherein said alcohol dehydrogenase is resistant to aerobic inactivation.
It is a further object of the present invention to provide the method described above, wherein said alcohol dehydrogenase originates from a bacterium selected from the group consisting oi Escherichia coli, Erwinia carotovora. Salmonella typhimurium. Shigella Jlexneri. Yersinia peslis, Pantoea anarmtis, Laciobacillus planlarum, and Lactococcus lactis.
It is a further object of the present invention to provide the method described above, wherein said alcohol dehydrogenase comprises the amino acid sequence set forth in SEQ ID NO: 2, except the glutamic acid residue at position 568 is replaced with another amino acid residue other than an aspartic acid residue.
It is a further object of the present invention to provide the method described above, wherein said alcohol dehydrogenase comprises the amino acid sequence set forth in SEQ ID KO: 2, except the glutamic acid residue at position 568 is replaced with a lysine residue.
It is a further object of the present invention to provide the method described above, wherein said alcohol dehydrogenase has at least one additional mutation which is able to improve the growth of said bacterium in a liquid medium which contains ethanol as the sole carbon source.
It is a further object of the present invention to provide the method described above, wherein said additional mutation is selected from the group consisting of:
A) replacement of the glutamic acid residue at position 560 in SEQ ID NO; 2 with another amino acid residue;
B) replacement of the phenylalanine residue at position 566 in SEQ ID NO: 2 with another amino acid residue,-
C) replacement of the glutamic acid residue, the methionine residue, the tyrosine residue, the isoleucine residue, and die alanine residue at positions 22,236,461, 554, and 786, respectively, in SEQ ID NO; 2 with other amino acid residues; and
D) combinations thereof.
II is a further object of the present invention to provide the method described above, wherein said additional mutation is selected from the group consisting of:
A) replacement of the glutamic acid residue at position 560 in SEQ ID NO: 2 with a lysine residue;
B) replacement of the phenylalanine residue at position 566 in SEQ ID NO: 2 with a valine residue;
C) replacement of the glutamic acid residue, the methionine residue, the tyrosine residue, the isoleucine residue, and the alanine residue at positions 22,236,461, 554, and 786 in SEQ ID NO: 2 with a glycine residue, a valine residue, a cysteine residue, a serine residue, and a valine residue, respectively; and
D) combinations thereof.
It is a fiirther object of the present invention to provide the method described above, wherein said bacterium belongs to the genus selected from the group consisting of Escherichia. Enterobacler, Erwinia, Klebsiella. Panloea, Providencia, Salmonella, Serratia, Shigella, and Morganella.
It is a further object of the present invention to provide the method described above, wherein said L-amiao acid is selected from a group consisting of L-threonine, L-lysine, L-hisfidine, L-phenylalanine, L-arginine, L-tiyptophan, L-glutamic acid, and L-leucine.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS Alcohol dehydrogenase is a Fe^*-dependent multifimcfional protein with an acetaldehyde-CoA dehydrogenase activity at the N-terminal, an iron-dependent alcohol dehydrogenase activity at the C-terminal, and a pyruvate-formate lyase deactivase activity. Synonyms include B1241, AdhC, and Ana, Under aerobic conditions, the half-life of the active AdhE protein is shortened during aerobic metabolism by metal-catalyzed oxidation.
In the present invention, the phrase "activity of alcohol dehydrogenase" means an activity of catalyzing the reaction of NAD~dependant oxidation of alcohols into aldehydes or ketones. Alcohol dehydrogenase (EC 1.1.1.1) works well with ethanol, n-propanol, and n-butanol. Activity of alcohol dehydrogenase can be detected and measured by, for example, the method described by Membrillo-Hemandez, J. et al (J. Biol. Chem. 275,33869-33875 (20OO)). Alcohol dehydrogenase is encoded by the adhE gene, and any adhE gene derived from or native to bacteria belonging to the genus Escherichia, Erwinia, Klebsiella, Salmonella, Shigella, Yershinia, Pantoeo, Lactobacillus, and Lactococcus may be used as the alcohol dehydrogenase gene in the present invention. Specific examples of the source of the adhE gene include bacterial strains such as Escherichia coli, Erwinia carotovora. Salmonella enterica. Salmonella typhimurium. Shigella flexneri. Yersinia pseudotuberculosis, Pantoea ananalis, [^cfobacillus planlarum and Lactococcus lactis. The wild-type adhE gene which encodes alcohol dehydrogenase from Escherichia coli has been elucidated (nucleotide numbers complementary to numbers 1294669 to 1297344 in the sequence of GenBank accession NC_000913.2, gi: 49175990). The adhE gene is located between the>c/iG snAychE ORFs on the chromosome of £■. coli K-12. Other adhE genes which encode alcohol dehydrogenases have also been elucidated: adhE gene from Erwinia carotovora (nucleotide numbers 2634501 to 2637176 in the sequence of GenBank accession NC_004547.2; gi: 50121254); adhE gene from Salmonella enterica (nucleotide numbers 1718612 to 1721290 in the sequence of GenBank accession NC_004631.1; gi; 29142095); adhE gene from Salmonella typhimurium (nucleotide numbers 1 to 2637 in the sequence of GenBank accession U68173.1;gi: 1519723); adhEgms from Shigella flexneri (nucleotide numbers complement to numbers J290816 fo ]293491in the sequence of GenBank accession NC_004741.1, gi: 30062760); adhE gene from
Yersinia pseudotuberculosis (nucleotide numbers complement to numbers 2478099 to 2480774 in the sequence of GenBank accession NC_006155.1; gi: 51596429), adhE gene from Pantoea ananatis (SEQ ID NO: 29), adhE gene from Lactobaccillusplantarum (UniProtKB Entry: Q88RY9_LACPL), adhE gene from Lactococcus lactis MG1363 (EMBL accession no. AJ001007), and the like (See Figure 2). The nucleotide sequence of the adhE gene from Escherichia coli is represented by SEQ JD NO;). The amino acid sequence encoded by this adhE gene is represented by SEQ ID NO: 2.
TTierefore, the adhE gene can be obtained by PCR (polymerase chain reaction; refer to White, T.J. etal. Trends Genet., 5, 185 (1989)) utilizing primers prepared based on the known nucleotide sequence of the gene from the £", coli chromosome. Genes coding for alcohol dehydrogenase from other microorganisms can be obtained in a similar manner.
The adhE gene derived from Escherichia coli is exemplified by a DNA which encodes the following protein (A) or (B):
(A) a protein which has the amino acid sequence shown in SEQ ID NO: 2; or
(B) a variant protein of the amino acid sequence shown in SEQ ID NO: 2, which has an activity of alcohol dehydrogenase.
The adhE gene derived from Pantoea ananatis is exemplified by a DNA which encodes the following protein (A) or (B):
(A) a protein which has the amino acid sequence shown in SEQ ID NO: 30; or
(B) a variant protein of the amino acid sequence shown in SEQ ID NO: 30, which has an activity of alcohol dehydrogenase.
The adhE gene derived from Shigella flexneri is exemplified by a DNA which encodes the following protein (A) or (B):
(A) a protein which has the amino acid sequence shown in SEQ ID NO: 53; or
(B) a variant protein of the amino acid sequence shown in SEQ ID NO: S3, which has an activity of alcohol dehydrogenase.
The adhE gene derived from Yersiniapestis is exemplified by a DNA which encodes the following protein (A) or (B):
(A) a protein which has the amino acid sequence shown in SEQ ID NO; 54; or
(B) a variant protein of (he amino acid sequence shown Jn SEQ ID NO: 54, which has an activity of alcohol dehydrogenase.
The adhE gene derived from Erwinia carotovora is exemplified by a DNA which encodes the following protein (A) or (B):
(A) a protein which has the amino acid sequence shown in SEQ ID NO: 55; or
(B) a variant protein of the amino acid sequence shown in SEQ ID NO: 55, which has an activity of alcohol dehydrogenase.
The adhE gene derived from Salmonella typkimurium is exemplified by a DNA which encodes the following protein (A) or (B):
(A) a protein which has the amino acid sequence shown in SEQ ID NO: 56; or
(B) a variant protein of the amino acid sequence shown in SEQ ID NO: 56, which has an activity of alcohol dehydrogenase.
Tlie adhE gene derived from Lactobacillus planlarum is exemplified by a DNA which encodes the following protein (A) or (B):
(A) a protein which has the amino acid sequence shown in SEQ ID NO: 57; or
(B) a variant protein of the amino acid sequence shown in SEQ ID NO: 57, which has an activity of alcohol dehydrogenase.
The adhE gene derived from Lactococcus lactis is exemplified by a DNA which encodes the following protein (A) or (B):
(A) a protein which has the amino acid sequence shown in SEQ ID NO: 58; or
(B) a variant protein of the amino acid sequence shown in SEQ ID NO: 58, which has an activity of alcohol dehydrogenase.
The phrase "variant protein" as used in the present invention means a protein which has changes in the sequence, whether they are deletions, insertions, additions, or substitutions of amino acids, but still maintains alcohol dehydrogenase activity at a useful level. 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 residue. The number ofchanges may be 1 to 30, preferably 1 to 15, and more preferably 1 to 5, relative to the protein (A). These changes in the variants are conservative mutations that preserve the function of the protein. In other words, these changes can occur in regions of the protein which are not critical for the function of the protein. This is because some amino acids have high homology to one another so the three dimensional structure or activity is not affected by such a change. Therefore, the protein variant (B) may be one which has an identity of not less than 70 %, preferably not less than 80 %, and more preferably not less than 90 %, and most preferably not less than 95 % with respect to the entire amino acid sequence of alcohol dehydrogenase shown in SEQ ID NO. 2, as long as the activity of the alcohol dehydrogenase is maintained.
Homology between two amino acid sequences can be determined using the well-known methods, for example, the computer program BLAST 2.0, which calculates three parameters: score, identity, and similarity.
The substitution, deletion, insertion, or addition of one or several amino acid residues should be conservative mutation(s) so that the activity is maintained. The representative conservative mutation is a conservative substitution. Exampies of conservative substitutions include substitution of Ser or Thr for Ala, substitution of Gin, His or Lys for Arg, substitution of Glu, Gin, Lys, His or Asp for Asn, substitution of Asn, Glu or Gin for Asp, substitution of Ser or AJa for Cys, substitution of Asn, Glu, Lys, His, Asp or Arg for Gin, substitution of Asn, Ghi, Lys or Asp for Glu, substitution of Pro for Gly, substitution of Asn» Lys, Gin, Ai^ or Tyr for His, substitution of Leu, Met, Val or Phe for lie, substitution of He, Met, Val or Phe for Leu, substitution of Asn, Glu, Gin, His or Arg for Lys, substitution of He, Leu, Val or Phe for Met, substitution of Tip, Tyr, Met, He 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, He or Leu for Val.
Data comparing the primary sequences of alcohol dehydrogenase ftom Escherichia coli. Shigella jlexneri, ParUoea ananatis, yersinia pestis, Envinia caroiovora. Salmonella typhimurium (Gram negative bacteria); and Lactobacillus plantarum, Lactococcus lactis (Gram positive bacteria) show a high level of homology among these proteins (see Figure 2). From this point of view, substitutions or deletions of the amino acid residues which are identical (marked by asterisk) in all the above-mentioned proteins could be crucial for their fLmction. It is possible to replace similar (marked by colon) amino acids residues by the similar amino acid residues without deterioration of the protein activity. But modifications of other non-conserved amino acid residues may not lead to alteration of the activity of alcohol dehydrogenase.
The DNA which encodes substantially the same protein as the alcohol dehydrogenase described above may be obtained, for example, by modifymg the nucleotide sequence of DNA encoding alcohol dehydrogenase (SEQ ID NO; 1), for example, by means of site-directed mutagenesis so that the nucleotide sequence responsible for one or more amino acid residues at a specified site is deleted, substituted, inserted, or added. DNA modified as described above may be obtained by conventionally known mutation treatments. Such treatments include hydroxylamine treatment of the DNA encoding proteins of present invention, or treatment of the bacterium containing the DNA with UV irradiation or a reagent such as N-methyl-N'-nitro-N-nitrosoguanidine or nitrous acid.
A DNA encoding substantially the same protein as alcohol dehydrogenase can be obtained by expressing DNA having a mutation as described above in an appropriate cell, and investigating the activity of any expressed product. A DNA encoding substantially the same protein as alcohol dehydrogenase can also be obtained by isolating a DNA that is able to hybridize with a probe having a nucleotide sequence which contains, for example, the nucleotide sequence shown as SEQ ID NO: 1, under stringent conditions, and encodes a protein having alcohol dehydrogenase activity. The "stringent conditions" referred to herein are conditions under which so-caJJed specific hybrids are formed, and non-specific hybrids ais not formed. For example, stringent conditions can be exemplified by conditions under which DNAs having high homology, for example, DNAs having identity of not less than 50%, preferably not less than 60%, more preferably not less than 70%, still more preferably not less than 80%, fiirther preferably not less than 90%, most preferably not less than 95%, are able to hybridize with each other, but DNAs having identity lower than the above are not able to hybridize with each other. Alternatively, stringent conditions may be exemplified by conditions under which DNA is able to hybridize at a salt concentration equivalent to ordinary washing conditions in Southern hybridization, i.e., 1 x SSC, 0.1% SDS, preferably 0.1 x SSC, 0.1% SDS, at 60''C. Duration of vrashing depends on the type of membrane used for blotting and, as a rule, what is recommended by the manufacturer. For example, reconmiended duration of washing for the Hybond^^ N+ nylon membrane (Amersham) under stringent conditions is ] 5 minutes. Preferably, washing may be performed 2 to 3 times.
A partial sequence of the nucleotide sequence of SEQ ID NO: 1 can also be used as a probe. Probes may be prepared by PCR using primers based on the nucleotide sequence of SEQ ID NO: 1, and a DNA fragment containing the nucleotide sequence of SEQ ID NO: 1 as a template. When a DNA fragment having a length of about 300 bp is used as the probe, the hybridization conditions for washing include, for example, SCC, 2 x SSC and 0.1% SDS.
The substitution, deletion, insertion, or addition of nucleotides as described above also includes mutations which naturally occur (mutant or variant), for example, due to variety in the species or genus of bacterium, and which contains the alcohol dehydrogenase.
A wild-type alcohol dehydrogenase may be subject to nietal catalyzed oxidatation. Although such a wild-type alcohol dehydrogenase can be used, a mutant alcohol dehydrogenase which is resistjint to aerobic inactivation is preferable in the present invention. The phrase "mutant alcohol dehydrogenase which is resistant to aerobic inactivation" means
thai the mutant alcohol dehydrogenase maintains its activity under aerobic conditions, or the activity is reduced by a negligible amount compared to the wild-type alcohol dehydrogenase. In case of the adhE gene ofE. colU the wild-type alcohol dehydrogenase comprises the amino acid sequence set forth in SEQ ID NO: 2. An example of a mutation in alcohol dehydrogenase of SEQ ID NO: 2 which results in the protein being resistant to aerobic inactivation is replacement of the glutamic acid residue at position 568 with a lysine residue . However, introduction of a mutation into the adhE gene, for example at position 568 in SEQ ID NO: 2, may lead to delay of growth in a liquid medium containing ethanol as a cartion source, and in such a case, it is preferable that the mutant alcohol dehydrogenase have at least one additional mutation which is able to improve the growth of the bacterium in a liquid medium which contains ethanol as the sole carbon source. For example, the growth of £ coH is improved when the glutamic acid residue at position 568 in the alcohol dehydrogenase of SEQ ID NO: 2 is replaced by another amino acid residue by introducing an additional mutation selected from the group consisting of:
A) replacement of the glutamic acid residue at position 560 in SEQ ID NO: 2 with another amino acid residue, e.g., a lysine residue;
B) replacement of the phenylalanine residue at position 566 in SEQ ID NO: 2 with another amino add residue, e.g., a valine residue;
C) replacement of the glutamic acid residue, the methionine residue, the tyrosine residue, the isoleucine residue, and the alanine residue at positions 22,236,461, 554, and 786, respectively, in SEQ ID NO: 2 with other amino acid residues, e.g., a glycine residue, a valine residue, a cysteine residue, a serine residue, and a valine residue, respectively; and
D) combinations thereof.
The reference to position numbers in a sequence, for example, the phrase "amino acid residues at positions 22, 236, 554, 560, 566, 568 and 786" refers to positions of the^e residues in the amino acid sequence of tiie wild-type AdhE from E. colt. However, the position of an amino acid residue may change. For example, if an amino acid residue is inserted at the N-ierminus portion, the amino acid residue inherently located at position 22 becomes position 23. In such a case, the amino acid residue at original position 22 is the amino acid residue at position 22 in the present invention.
The mutant AdhE may include deletion, substitution, insertion, or addition of one or several amino acids at one or a pluralily of positions other than positions identified in A) to C) above, provided that the AdhE activity is not lost or reduced.
The mutant AdhE and mutant adhE gene according to the present invention can be obtained from the wild-type adhE gene, for example, by site-specific mutagenesis using ordinary methods, such as PCR (polymerase chain reaction; refer to White, T.S. ef al., Trends Genet., 5,185 (1989)) utilizing primers prepared based on the nucleotide sequence of the gene.
Transcription of the adhE gene in wild-type E. coli is induced only under anaerobic conditions, largely in response to elevated levels of reduced NADH (Leonardo, M. R., Cunningham, P. R. & Clark, D. P., J. Bacteriol. 175 870-878 (1993)).
In the present invention, a bacteria! strain used for producing an L-amino acid is modified so that expression of the adhE gene is controlled by a non-native promoter, i.e., a promoter that does not control the expression of the adhE gene in a wild-type stram. Such modification can be achieved by replacing the native promoter of the adhE gene on the choTomosome with a non-native promoter which lunclions under an aerobic cultivation condition so that the adhE gene is operably linked with the non-native promoter. As a non-native promoter which functions under aerobic cultivation conditions, any promoter which can express the adhE gene above a certmn level under aerobic cultivation conditions may be used. With reference to the level of the AdhE protein in the present invention, the activity of alcohol dehydrogenase in the cell free extract measured according to the method by Clark and Cronan (J. Bacteriol. 141 177-183 (1980)) should be 1.5unitsormore,preferably 5 unitsormore, and more preferably 10 units or more, per mg of protein. Aerobic cultivation conditions can be those usually used for cultivation of bacteria in which oxygen is supplied by methods such as shaking, aeration and agitation. Specifically, any promoter which is known to express a gene under aerobic cultivation conditions can be used. For example, promoters of the genes involved in glycosis, the pentose phosphate pathway, TCA cycle, amino acid biosynthetic pathways, etc. can be used. In addition, the Ptat promoter, the lac promoter, the trp promoter, the trc promoter, the PB, or the PL promoters of lambda phage are all known to be strong promoters which function under aerobic cultivation conditions, and are preferably used.
The use of a non-native promoter can be combined with the multiplication of gene copies. For example, inserting the adhE gene operably linked with a non-native promoter into a vector ihat is able to function in a bacterium of the Enierobacteriaceae family and introducing the vector into the bacterium increases the copy number of the gene in a cell. Preferably, low-
copy vectors are used. Examples of low-copy vectors include, but are not limited to, pSClOl, pMWIiS, pMWU9, and the like. The term "low copy vector" is used for vectors, th^ copy number of which is up to 5 copies per cej]. Increasing the copy number of the adhE gene can also be achieved by introducmg multiple copies of the gene into the chromosomal DNA of the bacterium by, for example, homologous recombination, Mu integration, and the like. Homologous recombination is carried out using a sequence which is present in multiple copies as targets on the chromosomal DNA. Sequences having multiple copies on the chromosomal DNA include, but are not limited to, repetitive DNA, or inverted repeats existing at the end of a transposable element. Also, as disclosed in U.S. Patent No. 5,595,889, it is possible to incorporate the adhE gene into a transposon, and allow it to be transferred to introduce multiple copies of the gene into the chromosomal DNA. In these instances, the adhE gens cm be placed under the control of a promoter wiiich functions under aerobic cultivation conditions. Alternatively, the effect of a promoter can be enhanced by, for example, introducing a mutation into the promoter to increase the transcriplion level of a gene located downstream of the promoter. Furthermore, it is known that the substitution of several nucleotides in the spacer between the ribosome binding site (RBS) and the start codon, especially the sequences immediately upstream of the start codon, profoundly affect the mRNA translatability. 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 et al, Annu, Rev. Microbiol., 35,365-403, 1981; Hui et al, EMBO J., 3,623-629,1984). Previously, it was shown that the rhtA23 mutation is an A-for-G substitution at the -1 position relative to the ATG start codon (ABSTRACTS of 17"^ International Congress of Biochemistry and Molecular Biology in conjugation with 1997 Annual Meeting of the American Society for Biochemistry and Molecular Biology, San Francisco, California August 24-29,1997, abstract No. 457). Therefore, it may be suggested that the rhlA23 mutation enhances rktA gene expression and, as a consequence, increases resistance to threonine, homoserine, and some other substances transported out of cells.
Moreover, it is eilso possible to introduce a nucleotide substitution into a promoter region of the adhE gene on the bacterial chromosome, which results in stronger promoter function. The alteration of the expression control sequence can be performed, for example, in the same manner as the gene substitution using a temperature-sensitive plasmid, as disclosed in International Patent Publication WO 00/1893 5 and Japanese Patent Application Laid-Open No. 3-215280.
In the present invention, "L-amino acid-producing bacterium" means a bacterium which has an ability to produce and secrete an L-amino add into a medium, when the bacterium is cultured in the medium. The L-amino acid-producing ability may be imparted or enhanced by breeding. The term "L-amino acid-producing bacterium" as used herein also means a bacterium which is able to produce and cause accumulation of an L-amino acid in a culture medium in an amount larger than a wild-^e or parental strain of the bacterium, for example, E. coli, such as £. coli K-12, and preferably means that the bacterium is able to cause accumulation in a medium of an amount not less than 0.5 g/L, more preferably not less than i .0 g/L of the target L-amino acid. The term "L-amino acid" includes L-alanine, L-arginine, L-asparagine, L-aspartic acid, L-cysteine, L-glutamic acid, L-glutamine, glycine, L-histidine, L-isoleucine, L-!eucine, L-lysine, L-methionine, L-phenylalanine, L-pro]ine, L-serine, L-tfireonine, L-tryptophan, L-tyrosine, and L-valine, L-threonine, L-Iysine, L-histidine, L-phenylalanine, L-arginine, L-tryptophan, L-glutamic acid, and L-leucine are particularly preferred.
The Enterobacteriaceae family includes bacteria belonging to the gen«a Escherichia, Enterohacter, Erwinia, Klebsiella, Pantoea, Photorhabdus, Providencia, Salmcnella, Serralia, Shigella, Morganella, Yersinia, etc.. Specifically, those classified into the Enterobacteriaceae family according to the taxonomy used by the NCBI (National Center for Biotechnology Information) database
{http://www.ncbj.nlm.nih.govyTaxonDmy/Browser/wwwtax.cgi?id=91347) can be used. A bacterium belonging to the gemus Escherichia or Pantoea is preferred. The phrase "a bacterium belonging to the genus Escherichia" means that the bacterium is classified into the genus Escherichia according to the classification known to a person skilled in the art of microbiology. Examples of a bacterium belonging to the genus Escherichia as used in the present invention include, but are not limited to, Escherichia coH (E. coli).
The bacterium belonging to the genus Escherichia that can be used in the present invention js not particularly limited, however, for example, bacteria described by Neidhardt, F,C. et a!. {Escherichia coli and Salmonella typhimurium, American Society for Microbiology, Washington D.C., 1208, Table 1) are encompassed by the present invention.
The bacterium belonging to the genus Pantoea means that the bacterium is classified into the genus Pantoea according to the classification known to a person skilled in the art of microbiology. Some species of Enterohacter agglomerans have been recently re-classified into
Pantoea agglomerans, Panioea ananatis, Pantoea stewariii, or the like, based on the nucJeoJide sequence analysis of J6S rRNA etc. (Int. J. Syst. Bactctiol, 43, 162-173 (1993)).
The bacterium of the present invention encompasses a strain of the Enterobacieriaceae femily which has an ability to produce an L-amino acid and has been modified so that tfie gene encoding an alcohol dehydrogenase is expressed under the control of a promoter which functions under aerobic cultivation conditions. In addition, the bacterium of the present invention encompasses a strain of the Enterobacteriaceae family which has an ability to produce an L-amino acid and does not have a native activity of alcohol dehydrogenase, but has been transformed with a DNA fragment encoding alcohol dehydrogenase.
hi the present invention, the amount of accumulated L-amino acid, for example, L-threonine, L-lysine, L-histidine, L-phenylalanine, L-argmine, L-tryptophan, L-g!utamic acid, or L-Ieucine, can be significantly increased in a culture medium containing ethanol as a carbon source as a result of expressing the gene encoding an alcohol dehydrogenase under the cmitrol of a promoter which functions under aerobic cultivation conditions.
L-amino acid-producing bacteria
As a bacterium of the present invention which is modified to have mutant alcohol dehydrogenase of the present invention, bacteria which are able to produce either an aromatic or a non-aromatic L-amino acids may be used.
The bacterium of the present invention can be obtained by introducimg the gene encoding the mutant alcoholdehydrogenase of the present invention in a bacterium which inherently has the ability to produce L-amino acids. Alternatively, the bacterium of present invention can be obtained by imparting the ability to produce L-amino acids to a bacterium already having the mutant alcohol dehydrogenase.
L-threonine-producing bacteria
Examples of parent strains which can be used to derive the L-threonine-producing bacteria of the present invention include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli TDH-6/pVIC40 (VKPM B-3996) (U.S. Patent No. 5,175,107. U.S. Patent No. 5,705,371), E. coli 472T23/pYN7 (ATCC 98081) (U.S. Patent No.5,631,157), E coli NRRL-21593 (U.S. Patent No. 5,939,307), £ co[i PERM BP-3756 (U.S. Patent No. 5,474,9 J 8), E. coli PERM BP-3519 and PERM BP-3520 (U.S. Patent No. 5,376,538), E. coli
MG442 (Gusyatiner et al., Genetika (in Russian), 14,947-956 (1978)), E. coli VL643 and VL2055 (EP 1149911 A), and the like.
The strain TDH-6 is deficient in the thrC gene, as well as being sucrose-assimilative, and the ilvA gene in this strain has a leaky mutation. This strain also has a mutation in the rhtA gene, which imparts resistance to high concentrations of threonine or homoserine. The strain B-3996 contains the plasmid pVIC40 which was obtained by inserting a thrA*BC operon which includes a mutant/ATV^ geneintoaRSFlOlO-derived vector. This mutant/fe.4 gene encodes aspartokinase homoserine dehydrogenase I which has substantially desensitized feedback iniiibition by threonine. Tlie strain B-3996 was deposited on November 19,1987 in the All-Um'on Scientific Center of Antibiotics (Russia, 117105 Moscow, Nagatinskaya Street, 3-A) under the accession number RIA 1867. The strain was also dqwsited in the Russian National Collection of Industrial Microorganisms (VKPM) (Russia, 117545 Moscow, 1 Dorozhny proezd, 1) on April 7,1987 under the accession number VKPM B-3996.
E. coli VKPM B-5318 (EP 0593792B) also may be used as a parent strain to derive L-threonine-producing bacteria of the present invention. The strain B-5318 is prototrophic with regard to isoleucine, and a temperature-sensitive lambda-phage CI repressor and PRpromoter replaces the regulatory region of the threonine operon in the plasmid pVIC40 harbored by the strain- The stiain VKPM B-5318 was deposited in the Russian National Collection of Industrial Microorganisms (VKPM) on May 3, 199(i under accession number of VKPM B-531S.
Preferably, the bacterium of the present invention is additionally modified to enhance expression of one or more of the following genes;
the mutant thrA gene which codes for aspartokinase-homoserine dehydrogenase 1 resistant to feed back inhibition by threonine; the thrB gene which codes for homoserine kinase; the thrC gene which codes for threonine synthase; the rhtA gene which codes for a putative transmembrane protein; the asd gene which codes for aspartate-p-semialdehyde dehydrogenase; and the aspC gene which codes for aspartate aminotransferase (aspartate transaminase); The thrA gene which encodes aspartokinase-homoserine dehydrogenase I of Escherichia coli hZiS been elucidated (nucleotide positions 337 to 2799, GenBank accession no.NC^000913.2, gi: 49175990). The thrA gene is located between the thrL and thrB genes on the chromosome of £, coli K-12. The thrB gene which encodes homoserine kinase of
Escherichia coli has been elucidated (nucleotide positions 2801 to 3733, GenBank accession NC_00O913.2, gi: 49175990). The thrB gene is located between the thrA and thrC genes on the chromosome ofE. coli K-12. The (/jrCgene which encodes threonine synthase of Escherichia coli has been elucidated (nucleotide positions 3734 to 5020, GenBank accession NC_0009I3.2, gi; 49175990). The thrC gene is located between the thrB gene and the ^'oaA'open reading &ame on the chromosome ofE. coli K-12. All three genes function as a single threonine operon. To eiJiance expression of the threonine operon, the attenuator region which affects the transcription is desirably removed from the operon (WO2005/049808, WO2003/097839).
A mutant ikrA gene which codes for aspartokinase homoserine dehydrogenase I resistant to feedback inhibition by threonine, as well as the ihrB and thrC genes can be obtained as one operon from the well-known plasmid pVIC40, which is present in the threonine producing E. coli strain VKPM B-3996. Plasmid pVIC40 is described in detail in U.S. Patent No. S.705,371.
The rhtA gene is located at J 8 min on the E. coli chromosome close to ihe glnfJPQ operon, which encodes components of the glutamine transport system. The rhtA gene is identical to ORPl (ybiF gene, nucleotide positions 764 to 1651, GenBank accession number AAA218541, gi:440181), and is located between the pexB and ompXgenes. The DNA sequence expressing a protein encoded by the ORFl has been designated the rhiA gene (riit: resistance to homoserine and threonine). Also, it is known that the rhtA23 mutation is an A-for-G substitution at position-1 with respect to the ATG start codon (ABSTRACTS of the l?"*" International Congress of Biochemistry and Molecular Biology in conjugation with Annual Meeting of the American Society for Biochemistry and Molecular Biology, San Francisco, California August 24-29, 1997, abstract No. 457, EP 1013765 A). Hereinafter, the rhtAl^ mutation is marked as rklA*.
The osiigene ofE. coli has already been elucidated (nucleotide positions 3572511 to 3571408, GenBank accession NC_000913.1, gi:16131307), and can be obtained by PCR (polymerase chain reaction; refer to White, T.J. et al.. Trends Genet., 5, 185 (1989)) utilizing primers prepared based on the nucleotide sequence of the gene. The asd genes of other microoiganisms can be obtained in a similar manner.
Also, the aspC gene of E. coli has already been elucidated (nucleotide positions 983742 to 984932, GenBank accession NC_000913.1, gi:16128895), and can be obtained by PCR. The aspC genes of other microorganisms can be obtained in a similar manner.
L-lysine-producing bacteria
Examples of L-lysine-producing bacteria belonging to the genus Escherichia include mutants having resistance to an L-lysine analogue. The L-lysine analogue inhibits growth of bacteria belonging to the genus Escherichia, but this inhibition is fully or partially desensitized when L-lysine is present in the medium. Examples of the L-lysine analogue include, but are not limited to, oxalysine, lysine hydroxamate, S-{2-aminoethyI)-L-cysteine (AEC), 7-methyllysine, a-chlorocaprolactam, and so forth. Mutants having resistance to these lysine analogues can be obtained by subjecting bacteria belonging to the genus Escherichia to a conventional artificial mutagenesis treatment. Specific examples of bacterial strains usefiil for producing L-Iysine include Escherichia coli A3U442 (PERM BP-J543, NRRL B-llUS; see U.S. Patent No. 4,M6, ] 70) and Escherichia coli VL6 Xl.ln these microorganisms, feedback inhibition of aspartokinase by L-Jysine is desensitized.
The strain WC196 may be used as an L-Iysine producing bacterium tii Escherichia coli. This bacterial strainw/asbredbyconferringAECresistance to the strain W3110, which was derived from Escherichia coli K-12. The resulting strain was designated Escherichia coli AJ13069 and was deposited at the National Institute of Bioscience and Human-Technology, Agency of industrial Science and Technology (currently National Institute of Advanced Industrial Science and Technology, International Patent Organism Depositary, Tsukuba Central 6, l-l.Higashi 1-Chome, Tsukuba-shi, Ibaraki-ken, 305-8566, Japan) on December 6,1994 andreceivedanaccessionnumberof PERM P-14690. Then, it was converted to an international deposit under the provisions of the Budapest Treaty on September 29,1995, and received an accession number of PERM BP-5252 (U.S. Patent No. 5,827,698).
Examples of parent strains w2iich can be used to derive L-lysine-producihg bacteria of the present invention also include strains in which expression of one or more genes encoding an L-lysine biosynlhetic enzyme are enhanced. Examples of such genes include, but are not limited to, genes encoding dihydrodipicolinate synthase (dapA), aspartokinase (lysC), dihydrodipicolinate reductase (dapB), diaminopimelate decarboxylase (lysA% diaminopimelate dehydrogenase (ddh) (U.S. Patent No. 6,040,160), phosphoenolpyrvate carboxylase (ppc), aspartate semialdehyde dehydrogenease (as'if), and aspartase (osp^) (EP 1253195 A). In addition, the parent strains may have an increased level of expression of the gene involved in energy efficiency (cyo) (EP 1170376 A), the gene encoding nicotinamide nucleotide transhydrogenase (pniAB) (U.S. Patent No. 5,830,716), theybjE gene (WO2005/073390), or combinations thereof.
Examples of parent strains for deriving L-Iysine-producing bacteria of the present invention also include strains having decreased or eliminated activity of an enzyme that catalyzes a reaction for generating a compound other than L-lysine by branching off from the biosynthetic pathway of L-lysine, Examples of the enzymes that catalyze a reaction for generating a compound other than L-Jysine by branching off from the biosynthetic pathway of L-lysine include homoserine dehydrogenase, lysine decarboxylase (U.S. Patent No. 5,827,698), and the malic enzyme (WO2005/010175).
Examples of L-Iysine producing strains include E. coli WC196AcadAAldc/pCABD2 (WO2006/078039). This strain was obtained by introducing the plasmid pCABD2, which is disclosed in U.S. Patent No. 6,040,160, into the strain WC196 with the disrupted cadA and IdcC genes, which encode lysine decarboxylase. The plasmid pCABD2 contains the dapA gene ofE. coli coding for a dihydrodipicolinate synthase having a mutation which desensitizes feedback inhibition by L-lysine, the lysC gene of E. coli coding for aspartokinase III having a mutation which desensitizes feedback inhibition by L-]ysine, the dapB gene £. coii coding for a dihydrodipicolinate reductase, and the ddh gene of Corynebacterium glutamicum coding for diaminopimelate dehydrogenase..
L-cysteine-producing bacteria
Examples of parent strains which can be used to derive L-cysteine-producing bacteria of the present invention include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli JMl 5 which is transformed with different cysE alleles coding for feedback-resistant serine acetyltransferases (U.S. Patent No. 6,218,168, Russian patent application 2003121601); £ coli W3110 vAach over-expresses genes which encode proteins suitable for secreting substances toxic for cells (U.S. Patent No. 5,972,663); £. coli strains having lowered cysteine desulfohydrase activity (JPl 1155571A2); E. coli W3110 with increased activity of a positive transcriptional regulator for cysteine regulon encoded by the cysB gene (WO0127307A1), and the like.
L-Ieucine-producing bacteria
Examples of parent strmns which can be used to derive L-leucine-producing bacteria of the present invention include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli strains resistant to leucine (for example, the strain 57 (VKPM B-73S6, U.S. Patent No. 6,124,121)) or leucine analogs including p-2-thienylaIanine, 3-hydroxyleucine, 4-
azaleucine, 5,5,5-trifluoroIeucine (JP 62-34397 B and JP 8-70879 A); E. coli strains obtained by the genetic engineering methods such as those described in WO96/06926; E. coli H-9068 (JP 8-70879 AX and the like.
The bacterium of the present invention may be improved by enhancing the expression of one or more genes involved in L-leucme biosynthesis. Examples include genes of the leuABCD operon, which are preferably represented by a mutant leuA gene coding for isopropyhnaJate synthase which is not subject to feedback inhibition by L-leucine (US Patent 6,403,342). In addition, the bacterium of the present invention may be improved by enhancing the expression of one or more genes coding for proteins which excrete L-amino acids from the bacterial cell. Examples of such genes include the b2682 and b2683 genes (ygaZH genes) (EP 1239041 A2).
L-histidine-producing bacteria
Examples of parent strains which can be used to derive L-histidine-producing bacteria of the present invention include, but are not limited to, strains belonging to the genus Escherichia, such as £. coli strain 24 (VKPM B-5945, RU2003677), £. coli strain 80 (VKPM B-7270,RU2119536), £: coftNRRLB-I2H6-BI2I2I (U.S. Patent No. 4,388,405), £ coli H-9342 (PERM BP-6675) and H-9343 (PERM BP-6676) (U.S. Patent No. 6,344,347), £, coli H-9341 {PERM BP-6674) (EP1085087), E. coli AI8O/pFM201 (U,S. Patent No. 6,258,554), and the like.
Examples of parent strains wliich can be used to derive L-histidine-producing bacteria of the present invention also include strains in which expression of one or more genes encoding an L-histidine biosynthetic enzyme are enhanced. Examples of such genes include genes encoding ATP phosphoribosyltransferase (hisG), phosphoribosyl AMP cyclohydrolase (hisi), phosphoribosyl-ATP pyrophosphohydrolase (hisIE), phosphoribosyJformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA), amidotransferase (hisH), histidinol phosphate aminotransferase {hisC), histidinol phosphatase {hisB), histidinol dehydrogenase (hisD), and so forth.
It is known that the L-histidjne biosynthetic enzymes encoded by hlsG and hisBHAFI are inhibited by L-histidine, and therefore an L-histidine-producing ability can also be efRciently enhanced by introducing a mutation into any of these genes which confer resistance to the feedback inhibition into enzymes encoded by the genes (Russian Patent Nos. 2003677 and2n9536}.
Specific examples of strains having an L-histidine-producing abih'ty include £". coli PERM P-5038 and 5048 which have been transformed with a vector carrying a DNA encoding an L-histidine-biosynthetic enzyme (JP 56-005099 A), E. coli strains transformed with rhi, a gene for an amino acid-exporter (EP10I6710A), E. coli 80 strain imparted with sulfaguanidine, DL-!,2,4-triazDle-3-aIanine, and streptomycin-resistance (VKPM B-7270, Russian Patent No. 2119536), and so forth.
L-glutamic acid-producing bacteria
Examples of parent strains which can be used to derive L-glutamic acid-producing bacteria of the present invention include, but are not limited to, strains belonging to the genus Escherichia, suchas £". coli VL334thrC*(EP 1172433). E. coliVL334 (VKPM B-I64I) is an I--isoIeucine and L-threonine auxotrophic strain having mutations in the thfC and iivA genes (U.S. Patent No. 4,278,765). A wild-type allele of the thrCgeae was transferred using general transduction with a bacteriophage PI grown on the wild-type £ co//strain K12 (VKPM B-7) cells. As a resuJt, an L-isoleucine auxotnDphjc strain VL334thrC* (VKPM B-S96I), which is able to produce L-glutamic acid, w^s obtained.
Examples of parent strains which can be used to derive the L-glutamic acid-producing bacteria of the present invention include, but are not limited (o, strains which arc deficient in a-Jtetoglutarale dehj'drogenase activity, or strains in which expression of one or more genes encoding an L-glutamic acid Wosynthetic enzyme are enhanced. Examples of such genes include genes encoding gJutamate dehydrogenase (gifh), glutamine synthetase (glnA), gJulamate synthetase (gUAB), isocitrate dehydrogenase (JcdA), aconilate hydratase (aCfiA, acnB\ citrate synthase igUA), phospboenolpyruvate carboxylase (ppc), pyravste dehydrogenase (pceEF, IpdA), pyruvate kinase (pykA,f^kF), phosphoenolpyiuvate synthase ippsA), enolase (eno), phosphoglyceromutase {pgmA. pgmJ), pbosphoglycerate kinase (pgk% glyceraldehyde-3-phophate dehydrogenase igapA), triose pho^hate isomerase (IpiA), fiuctose bisphosphaie aldolase {/hp\ phosphofructokinase ipJkA, pJkB\ glucose phosphate isomerase ipgi), and so forth.
Examples of strains which have been modified so that expression of the citrate synthetase gene and/or the phosphoenolpyruvate carboxylase gene are reduced, and/or are deficient in a-ketoglularate dehydrogenase activity include those disclosed inEP]078989A, EP955368A, and EP952221A.
Examples of parent strains which can be used to derive the L-glutamic acid-producing bacteria of the present invention also include strains having decreased or eliminated activity of an en2yme that catalyzes synthesis of a compound other than L-gJutamic acid by branching off from an L-glutamic acid biosynthesis pathway. Examples of such enzymes include jsocitrate lyase (aceA), a-ketoglutarate dehydrogenase (sucA), phosphotransacetylase (pia\ acetate kinase (ack), acetohydroxy acid synthase (ilvG), acetolactate synthase (iVv/), formate acetyltransferase (pft), lactate dehydrogenase {Idh), and glutamate decarboxylase igadAB). Bacteria belonging to the genus Escherichia deficient in a-ketoglutarate dehydrogenase activity or having a reduced a-ketoglufarale dehydrogenase activity and methods for obtaining them are described in U.S. Patent Nos. 5,378,616 and 5,573,945. Specifically, these strains include the following:
£•. co/iWSUOsucA-Km" E. coli AJ12624 (PERM BP-3853) E. coli AJ12628 (PERM BP-3854) £. co/i AJ12949 (PERM BP-4881)
E. coU W31J OsucA;:Km'^ is obtained by disrupting the a-ketoglutarate dehydrogenase gene (hereinafter referred to as "sucA gene'^ of £ coli W3110. This strain is completely deficient in the a-ketoglutarate dehydrogenase activity.
Other examples of L-glutamic acid-producing bacteria include those which belong to the genus Escherichia and have resistance to an aspartic acid antimetabolite. These strains can also be deficient in the a-ketoglutarate dehydrogenase activity and include, for example, £ coli AJ13199 (PERM BP-5807) fU,S. Patent No. 5.908,768), FFRMP-I2379, which additionally has a low L-glutamic acid decomposing ability (U.S. Patent No. 5,393,671), AJ13138 (PERM BP-5565) (U.S. Patent No. 6,110,714), and the like.
Examples of L-glutamic acid-producing bacteria, include mutant strains belonging to the genus Pantoea which are deficient in a-ketoglutarate dehydrogenase activity or have decreased a-ketoglutarate dehydrogenase activity, and can be obtained as described above. Such strains include Pantoea anana«'jAJ]3356. (U.S. Patent No. 6,331,419). Pantoea ananatis AJl 3356 was deposited at the National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology, Ministry of International Trade and Industry (currently. National Institute of Advanced Industrial Science and Technology, International Patent Organism Depositary, Central 6,1-1, Higashi l-Chome, Tsukuba-shi, Ibaraki-ken, 305-8566, Japan) on February 19,1998 under an accession number of PERM P-
16645. It was then converted to an intematipnal deposit under the provisions of Budapest Treaty on January U, 1999 and received an accession number of FERMBP-6615. Pan/oea ananatis AJ13356 is deficient in the a-ketoglutarate dehydrogenase activity as a result of disruption of the aKGDH-El subunjt gene {sucA). The above strain was identified as Enterobacter agglomerans when it was isolated and deposited as Enterobacter agghmerans AJ13356. However, it was recently re-classified as Pantoea ananatis on the basis of nucleotide sequencing of 16S rRNA and so forth. Although AJ13356 was deposited at the aforementioned depository as Enterobacter agghmerans, for the purposes of this specification, they are described as Pantoea ananatis.
L-pheny)a!anine-producing bacteria
Examples of parent strains which can be used to derive L-phenylalanine-producing bacteria of the present invention include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli AJ12739 (tyrA::TnlO, tyrR) (VKPM B-8197), E. coli HW1089 (ATCC 55371) harboring the m\x\mXpheA34 gene (U.S. Patent No. 5,354,672), E. coli MWEClOl-b (KR8903681), £. CO//NRRL B-12141, NRRL B-12145, NRRL B-12146 and NRRL B-12147 (U.S. Patent No. 4,407,952). Also, as a parent strain, E. coli K-12 [W3110 (tyrA)/pPHAB (PERM BP-3566), E. coli K.-12 [W3110 (tyrA)/pPHAD] (PERM BP-12659), E. coli K-12 [W3U0 (tyrA)/pPHATenn] (FERM BP-12662) and E. coli K-12 [W3110 {tyrA)/pBR-aroG4, pACMAB] named as AJ 12604 (FERM BP-3579) may be used (EP 488424 Bl). Furthermore, L-phenylatanine producing bacteria belonging to the genus Escherichia with anenhancedactivity of die protein encoded by the ^-fifW gene or the y^AiVj gene may also be used (U.S. patent applications 2003/0148473 A\ and 2003/0157667 AI).
L-tryptophan-producing bacteria
Examples of parent strains which can be used to derive the L-tryptophan-producing bacteria of the present invention include, but are not limited to, strains belonging to the genus Escherichia, such as E. coli JP4735/pMU3028 (DSMI0122) and JP60]5/plvrU91 (DSM10123) which is deficient in tryptophanyl-tRNA synthetase encoded by the mutant trpS gene (U.S. Patent No. 5,756,345), E. coli SV164 (pGH5) having a ser^ allele encoding phosphoglycerate dehydrogenase which is not subject to feedback inhibition by serine and a trpE allele encoding anthranilate sjiithase which is not subject to feedback inhibition by tryptophan (U.S. Patent No. 6,180,373), E. coli AGX17 (pGX44) (NRRL B-12263) and AGX6(pGX50)aroP (NRRL B-
12264) which is deficient in the enzyme tryptophanase (U.S. Patent No. 4,371,614), E. coli AGX] 7/pGX50,pACKG4-pps in which a phosphoenolpyruvate-producing abili^ is enhanced (WO970g333, U.S. Patent No. 6,319,696), and the like. L-tryptophan-producing bacteria belonging to the genus Escherichia which have enhanced activity of the protein encoded by the yedA ot yddG genes may also be used (U.S. patent applications 2003/0148473 Al and 2003/0157667 Al).
Examples of parent strains which can be used to derive the L-tryptophan-producing bacteria of the present invention also include strains in which one or more activities are enhanced of the following enzymes: anthranilate synthase (trpE), phosphoglycerate dehydrogenase (serA), and (ryptopban synthase (p-pAB). The anthranilate synthase and phosphoglycerate dehydrogenase are both subject to feedback inhibition by L-tryptophan and L-serine, therefore a mutation desensitizing the feedback inhibition may be introduced into these enzymes. Specific examples of straiiw having such a mutation include E. coli SV164 which harbors desensitized anthranilate synthase and a transforaiant strain obtained by introducing into £". coli SVI64 the pIasmidpGH5 (WO 94/08031), which contains a mutant serA gene encoding feedback-desensitizedphosphoglyceratedehydrogenase.
Examples of parent strains which can be used to derive the L-tryptophan-producing bacteria of the present invention also include strains which have been transformed with the tiyptophan operon containing a gene encoding desensitized anthranilate synthase (JP 57-71397 A, JP 62-244382 A, U.S. Patent No. 4,371,614). Moreover, L-tryptophan-producing ability may be imparted by enhancing expression of a gene which encodes tryptophan synthase, among tryptophan operons (trpBA). Tryptophan synthase consists of a and p subunits which are encoded by the trpA and trpB genes, respectively. In addition, L-tryptophan-producing ability may be improved by enhancing expression of the isocitrate tyase-malate synthase operon (WO2005/103275).
L-proline-producing bacteria
Examples of parent strains which can be used to derive L-proline-producing bacteria of the present invention include, but are not limited to, strains belonging lo the genus Escherichia, such as E. coli 702iIvA (VKPM B-8012) which is deficient in the ilvA gene and is able to produce L-proline (EP 1172433). The bacterium of the present invention may be improved by enhancing the expression of one or more genes involved in L-proline biosynthesis. Examples of such genes include theproB gene coding for glutamate kinase which is desensitized lo
feedback inhibition by L-proline (DE Patent 3127361). In addition, the bacterium of the present invention may be improved by enhancing the expression of one or more genes coding for proteins responsible for secreting L-amino acids from the bacterial cell. Such genes are ■ exemptified by the b2682 and b2683 genes (ygaZNgenes) (EP123904I A2).
Examples of bacteria belongmg to the genus Escherichia, which have an activity to produce L-proIine include the following £. coli strains: NRRL B-I2403 and NfRRL B-12404 (GB Patent 2075056), VKPM B-8012 (Russian patent application 2000124295), plasmid mutants described in DE Patent 3127361, plasmid mutants described by Bloom F.R. et al (The 15* Miami winter symposium, I983,p.34), and the like.
L-arginine-producing bacteria
Examples of parent strains which can be used to derive L-arginine-producing bacteria of the present invention include, but are not limited to, strains belonging to the genus Escherichia, such as £ coli strain 237 (VKPM B-7925) (U.S. Patent Application 2002/058315 Al) and derivatives thereof harboring mutant N-acetylglutamate synthase (Russian Patent Application No. 2001112869), E. coli strain 382 (VKPM B-7926) (EPl 17035SAI), an arginine-producing strain transformed wdth the argA gene encoding N-acetylglutamate synthetase (EP117036 i A1), and the like.
Examples of parent strains which can be used to derive L-arginine producing bacteria of the present invention also include strains in which expression of one or more genes encoding an L-arginine biosynthetic enzyme are enhanced. Examples of such genes include genes encoding N-acetylglutamyl phosphate reductase (argC), ornithine acetyl transferase (argj), N-acetylglutamate kinase (argS), acetylomithine transaminase (argD), ornithine carbamoyl transferase {argF), argininosuccinic acid synthetase {argG), argininosuccinic acid lyase (argff), carbamoyl phosphate synthetase (carAB), and so forth.
L-valine-producing bacteria
Example of parent strains which can be used to derive L-valine-producing bacteria of the present invention include, but are not limited to, strains which have been modified lo overexpress the ilvGMEDA operon (U.S. Patent No. 5,998,178). It is desirable to remove the region of the ilvGMEDA operon responsible for attenuation so that the produced L-valine cannot attenuate expression of the operon. Furthermore, the ilvA gene in the operon is desirably disrupted so that threonine deaminase aclivity is decreased.
Examples of parent strains which can be used to derive L-va!ine-prcducing bacteria of the present invention also include mutants of amino-acy] t-RNA synthetase (U.S. Patent No. 5,658,766). For example, £ coli VL1970, which has a mutation in the UeS gene encoding isoieucine tRNA synthetase, can be used. £ coli VL 1970 has been deposited in the Russian National Collection of Industrial VQcroorganisms (VKPM) (Russia, 117545 Moscow, ] Dorozhny Proezd, 1) on June 24,1988 under accession number VKPM B-4411.
Furthermore, mutants requiring lipoic acid for growth and/or lacking H*-ATPase can also be used as parent str^ns (WO96/06926).
L-isoleucine-producing bacteria
Examples of parent strains which can be used to derive L-isoleucine producing bacteria of the present invention include, but are not limited to, mutants having resistance to 6-dimethylaminopurine (JP 5-30A969 A), mutants having resistance to an isoieucine analogue such as tiiiaisoieucuie and isoieucine hydroxamate, and mutants additionally having resistance to DL-ethionine and/or arginine hydroxamate (J9 5-130882 A). In addition, recombinant strains transformed vnth genes encoding proteins involved in L-isoleucine biosynthesis, such as threonine deaminase and acetohydroxate synthase, can also be used as parent strains (JP 2-458 A, FR 0356739, and U.S. Patent No. 5,998,178).
The method for producing an L-amino acid of the present invention includes the steps of cultivating the bacterium of the present invention in a culture medium, allowing L-amino acid to accumulate in the culture medium, and collecting L-amino acid from the culture medium. Furthermore, the method of present invention includes a method for producing 1^ threonine, L-Jysiiie, L-histidine, L-phenyJalanine, L-arginine, L-tryptophan, L-glufamic acid, or L-leucine, including the steps of cultivating the bacterium of the present invention in a culture medium, allowing L-threonine, L-Iysine, L-histidine, L-phenyiaianine, L-arginine, L-tryptophan, L-glutamic acid, or L-leucine to accumulate in the culture medium, and collecting L-threonine, L-lysine, L-histidine, L-phenylalanine, L-arginine, L-tryptophan, L-glutamic acid, or L-leucine from the culture medium.
In the present invention, the cultivation, collection, and purification of L-amino acids from the medium and the tike may be performed by conventional fermentation methods wherein an L-amino acid is produced using a bacterium.
The culture medium may be either synthetic or natural, so long as the medium includes a carbon source, a nitrogen source, minerals, and if necessary, appropriate amounts of nutrients which the bacterium requires for growth. The carbon source may include various carbohydrates such as glucose and sucrose, various organic acids and alcohols, such as ethanol. According to the present invention ethanol can be used as the sole carbon source or mixed with carbohydrates, such as glucose and sucrose. As the nitrogen source, various Jimmonium salts such as ammonia and ammoiuum sulfate, other nitrogen compounds such as amines, a natural , nitrogen source such as peptone, soybean-hydrolysafe, and digested fermentative microorganisms can be used. As minerals, potassium monophosphate, magnesium sulfate, sodium chloride, ferrous sulfate, manganese sulfate, calcium chloride, and the like, can be used. As vitamins, thiamine, yeast extract, and the like may be used. Additional nutrients may be added to the medium, if necessary. For example, if the bacterium requires an L-amino acid for growth (L-amino acid auxotrophy), a sufficient amount of the L-amino acid may be added to the cultivation medium.
Tlie cultivation is preferably performed under aerobic conditions such as a shaidng culture, and stirring culture with aeration, at a temperature of 20 to 40°C, preferably 30 to 38°C. The pH of the culture is usually between 5 and 9, preferably between 6.5 and 7.2. The pH of the culture can be adjusted with ammonia, calcium carbonate, various acids, various bases, and buffers. Usually, a 1 to 5-day cultivation leads to accumulation of the target L-amino acid in the liquid medium.
After cultivation, solids such as cells can be removed from the liquid medium by centrifligatfon or membrane filtration, and then the target L-amino acid can be collected and purified by ion-exchange, concentration, and/or crystallization methods.
BRIEF DESCRIPTION OF THE DRAWINGS Figure 1 shows the structure of the upstream region of the adhE gene in the chromosome ofE. coli and the structure of an integrated DNA fragment,containing the cat gene and a Pnac promoter.
Figure 2 shows the alignment of the primary sequences of alcohol dehydrogenase from Escherichia coH (ADHE_ECOU, SEQ ID NO: 2), Shigella Jlexneri (Q83RN2^SHIFL, SEQ ID NO: 53), Pantoea ananatis (ADHE PANAN, SEQ ID NO: 30), Yersiniapestis (Q66AM7_YERPS, SEQ ID NO: 54), Erwinia carotovora (Q6D4R4_ERWCT, SEQ ID NO; 55), Salmonella typhimurium (P74880_SALTY, SEQ ID NO: 56), Lactobacillusplantarum
(Q88RY9_LACPL, SEQ ID NO: 57) and Laciococcus iacds (OS6282_9LACT, SEQ ID NO: 58). The alignment was done by using the PIR Multiple Alignment program (http://pir.georgetown.edu). TTie identical amino acids are marked by asterisk (*}, similar amino acids are marked by colon (:).
Figure 3 shows growth curves of modified strains grown on the minimal M9 medium containing ethanol (2% or 3%) as a sole carbon source.
Figure 4 shows growth curves of modified strains grown on the mim'mal M9 medium containing a mixture of glucose {0.1 weight %) and ethane! (0.1 volume %).
Figure 5 shows comparison of growth curves of strains having mutant adhE* gene under control of the native promoter, or PL-JDC promoter grown on the minimal M9 medium containing ethanol (2% or 3%) as a sole carbon source.
Examples
The present invention will be more concretely explained below with reference to the following non-limiting examples.
Example 1. Preparation of £. coli MG1655 Atdh, rhtA* The L-threonine producing E. coli strain MG1655 &tdh, rhtA* (pVIC40) vras constructed by inactivation of the native tdh gene encoding threonine dehydrogenase in E. coli MG1655 (ATCC 700926) using the cat gene followed by introduction of an rhtA23 mutation {rhtA*) which confers resistance to high concentrations of threonine (>40 mg/ml) and homoserine (>5 mg^ml). Then, (he resulting strain was transformed with plasmid pV!C40 Srom E. coli VKPM B-3996. The plasmid pVIC40 is described in detail in U.S. Patent No. 5,705,371.
To replace the native tdh gene, a DNA fragment canying the chloramphenicol resistance marker (Cm'*) encoded by the cat gene was integrated into the chromosome of £. CO/7MG1655 inplaceof tbe native gene by the method described by DatsenkoK,A, and Wanner B.L. (Proc. Natl. Acad. Sci. USA, 2000,97, 6640-6645) which is also called "Red-mediated integration" and/or "Red-driven mtegration". The recombinant plasmid pKD46 (Datsenko, K.A., Wanner, B.L., Proc. Natl. Acad. Sci. USA, 2000,97, 6640-6645) with the thermosensitiverepliconwasusedas the donor of the phage Vderived genes responsible for the Red-mediated recombination system. E. coli BW25n3 containing the recombinant plasmid pKD46 can be obtained from the E. coli Genetic Stock Center, Yale University, New Haven, USA, the accession number of which is CGSC7630.
A DNA fragment containing a Cm*^ marker encoded by the cat gene was obtained by PCR using the commercially available piasmid pACYC 184 (GenBank/EMBL accession number X06403, "Fermentas", Lithuania) as the template, and primers PI (SEQ ID NO; 3) and P2 (SEQ ID NO: 4). Primer PI contains 35 nucleotides homologous to the 5'-region of the tdh gene introduced into the primer for further integration into the bacterial chromosome. Primer P2 contains 32 nucleotides homologous to the 3'-region of the tdh gene introduced into the primer for further integration into the bacterial chromosome.
PCR was provided using the "Gene Amp PCR System 2700" ampiificatoiy (Applied Biosystems). The reaction mixture (total volume-50 jil) consisted of 5 ^iI of lOxPCR-buffer with 25 mM MgCl^ ("Fermentas", Lilhuania), 200 MM each of dNTP, 25 pmo] each of the exploited primers and I U of Taq-polymerase ("Fermentas", Lithuania). Approximately 5 ng of the piasmid DNA was added in the reaction mixture as a template DNA for the PCR amplification. The temperature profile was the following: initial DNA denaturation for 5 min at 95 "C, followed by 25 cycles of denaturation at 95 °C for 30 sec, annealing at 55 "C for 30 sec, elongation at 72 °C for 40 sec; and the final elongation for 5 min at 72 "C. Then, the amplified DNA fragment was purified by agarose gel-electrophoresis, extracted using "GenElute Spin Columns" (Sigma, USA), and precipitated by ethanol.
The obtained DNA fragment was used for eiectroporation and Red-mediated integration into the bacterial chromosome ofE. coli MG1655/pKX)46.
MG1655/pKD46 cells were grown overnight at 30 "C in liquid LB-medium containing arapicilJin (lOOng/ml), then diluted 1 ;100 by SOB-medium (Yeast extract, 5 g/l; NaCl, 0.5 g/1; Tryptone, 20 g/1; KCl, 2.5 mM; MgCh, 10 mM) containing ampicillin (100 \igfml) and L-arabinose (10 mM) (arabinose is used for inducing the piasmid containing the genes of the Red system) and grown at 30 °C to reach the optical density of the bacterial culture OD6oo=0.4-0.7. Tie gnawn cells from 10 ml of the bacterial culture were washed 3 times with ice-cold de-ionized water, followed by suspension in 100 ^il of the water. 10 ^1 of DNA fragment (100 ng) dissolved in the de-ionized water was added to the cell suspension. The eiectroporation was performed by "Bio-Rad" electroporator (USA) (No. 165-2098, veKion 2-89) according to the manufacturer's instructions. Shocked cells were added to 1-ml of SOC medium (Sambrook et al, "Molecular Cloning A Laboratory Manual, Second Edition", Cold Spring Harbor Laboratory Press (1989)), incubated for 2 hours at 37°C, and then were spread onto L-agar containing 25 ^g/ml of chloramphenicol. Colonies grown for 24 hours were tested for the
presence of Cm" marker instead of the native tdh gene by PCR using primers P3 (SEQ ID NO: 5) and P4 (SEQ ID NO: 6). For this purpose, a freshly isolated colony was suspended in 20|il water and then I fil of obtained suspeas'wn was used for PCR. The temperature profile was the following: initial DNA denaturation for 5 min at 95 "C; then 30 cycles of denaturation at 95 °C for 30 sec, annealing at 55 "C for 30 sec and elongation at 72 °C for 30 sec; the fmal elongation for 5 min at 72 "C. A few Cm" colonies tested contained the desired 1104 bp DNA fragment, confirming the presence of Cm" marker DNA instead of 1242 bp fragment of tdh gene. One of the obtained strains was cured of the thezmosensitive plasmid pKD46 by culturing at 37 "C and the resulting strain was named E. coH MG1655Atdh.
Then, the rhtA23 mutation from tiie strain VL614rhtA23 (Livshits V.A. et al, 2003, Res. Microbiol., 154:123-135) was introduced into the obtained strain MG1655 Atdh resulting in strain MG1655 Atdh, rhtA*. The rhtA23 is a mutation which confers resistance to high concentrations of threonine (>40 mg/ml) and homoserine (>5 mg/ml). For that purpose the strain MG1655 Atdh was infected with phage Plvir grown on the donor strain 'VL614rhtA23. The transductants were selected on M9 minimal medium containing 8 mg/ml homoserine and 0.4% glucose as the sole carbon source.
Example 2. Construction of £. coli MG1655::PL-tacadhE
E. coli MG1655::PL-iacadh was obtained by replacement of the native promoter region ofthearf/i£ gene in the strain MG1655 by Pi^uc promoter.
To replace the native promoter region of the adhE gene, the DNA fragment carrying a PL-MC promoter and chloramphenicoJ resistance marker (Cm^) encoded by the cat gene was integrated into the chromosome ofE. coli MG1655 in the place of the native promoter region by the method described by Datsenko K.A. and Wanner B.L. (Proc. Natl. Acad. Sci. USA, 2000,97, 6640-6645), which is also called "Red-mediated integration" and/or "Red-driven integration".
A fragment containing the PL^W promoter and the cat gene was obtained by PCR using chromosomal DNA of £. coli MG1655PL-iacxylE (WO2006/043730) as atemplate. The nucleotide sequence of the PL-IK promoter is presented in the Sequence listing (SEQ ID NO: 7). Primers P5 (SEQ ID NO: 8) and P6 (SEQ ID NO: 9) were used for PCR amplification. Primer P5 contains 40 nucleotides complementary to the region located 318 bp upstream of the start
codon of the adhE gene introduced into the primer for further integration into the bacterial chromosome and primer ?6 contains a 39 nucleotides identical to 5'-sequence of the adhE gene.
PCR was provided using the "Gene Amp PCR System 2700" ampJificatoiy (Applied Biosystems). The reaction mixture (total volume- 50 ^I) consisted of 5 n\ of 1 Ox PCR-buffer with 15 mM MgCl; ("Fermentas", Lithuania), 200 ^M each of dNTP, 25 pmol each of the exploited primers and 1 U of Taq-polymerase ("Fermentas", Lithuania). Approximately 20 ng of the E. coli MG1655pL.iac'£ylE genomic DNA was added in the reaction mixtures as a template for PCR.
The temperature profile was the follo\\ing: initial DNA denaturation for 5 min at 95 "C, followed by 35 cycles of denaturation at 95 "C for 30 sec, annealing at 54 °C for 30 sec, elongation at 72 "^C for 1.5 min and the final elongation for 5 min at 72 "C. Then, the amplified DNA fragment was purified by agarose gel-electrophoresis, extracted using "GenElute Spin Columns" ("Sigma", USA) and precipitated by ethanol. The obtained DNA fragment was used for electroporation and Red-mediated integration into the bacterial chromosome of the E. coli MGl655/pKD46.
MGI655/pKI>46 celis were grown overnight at 30 °C in the liquid LB-medium containing ampicillin (100 Hg/ml), then diluted 1:100 by SOB-medium (Yeast extract, 5 g/1; NaCl, 0.5 g/I; Tryptone, 20 g/1; KCl, 2.5 mM; MgCI;, 10 mM) containing ampicillin (100 tig/ml) and L-arabinose (10 mM) (arabinose is used for inducing the plasmid encoding genes of the Red system) and grown at 30 "C to reach the optica! density of the bacterial culture OD6oo=0.4-0.7. The grown cells from 10 ml of the bacterial culture were washed 3 times with ice-cold de-ionized water, followed by suspension in 100 fil of the water. 10 |il of DNA fragment (100 ng) dissolved in the de-ionized water was added to the cell suspension. The electroporation was performed by "Bio-Rad" electroporator (USA) (No. 165-2098, version 2-89) according to the manufacturer's instructions.
Shocked ceJJs were added to 1-ml ofSOC medium (Sambrook et aJ, "Molecular Cloning A Laboratory Manual, Second Edition", Cold Spring Harbor Laboratory Press (1989)), incubated for 2 hours at 3 7''C, and then were spread onto L-agar containing 25 fig/ml of chJoramphem"co!.
About 100 resulting clones were selected on M9 plates with 2% ethanol as the sole carbon source. Some clones which grew on M9 plates v;dth 2% ethanol in 36 hours were chosen and tested for the presence of Cm*^ marker instead of the native promoter region of the
adhE gene by PCR using primers P7 (SEQ ID NO: 10) and P8 (SEQ ID NO: 11). For this purpose, a freshly isolated colony was suspended in 20^1 water and then 1 jil of the obtained suspension was used for PCR. The temperature profile follows: initial DNA denaturation for 10 minat95 °C; then 30 cycles ofdenaturation at 95''C for 30 sec, annealing at 54 °C for 30 sec and elongation at 12°C for 1.5min; the final elongation for 1 min at ll^C. A few Cm** colonies tested contained the desired ~ISQ0 bp DNA fragment, confirming the presence of Cm** marker DNA instead of 520 bp native promoter region of adhE gene. One of the obtained strains was cured of the thermosensitive plasmid pKD46 by culturing at 37 °C and the resulting strain was named E. coli MG1655: :PL-iacadhE (See Figure 1).
Example 3. Construction ofE. coli MG1655Atdh, rhtA*, PuacadhE
E. coli MG1655Atdh, rhtA*, pL-tacadhE was obtained by transduction of the pL-iac
promoter from the strain MGI655::PL4acadhE into sfrain MGI655Atdh, rhtA*.
The strain MGl 655Atdh, rhtA* was infected with phage PI vir grown on the donor strain
MG1655::PMBcadhE, and the strain MG]655Atdh, rhtA*, PL-wcadhE was obtained. This strain
was checked for growth on M9 plates with 2% ethanol as the sole carbon source. The growth
rate was the same as for the strain MG1655::PL-iacadhE.
Example 4. The effect of increasing the adhE gent expression on L-threonine production
To evaluate the effect of enhancing expression of the adhE gene on L-threonine production, both E. coli strains MG1655Atdh, rhtA*, PL-tacadhE and MGI655Atdh, rhtA* were transformed with plasmid pVIC40.
The stram MGl 655Atdh, rhtA*, pL-iacadhE (pVlC40) and a parent strain MGl655Atdh, rhtA* (pVIC40) were each cultivated at 37 "C for 18 hours in a nutrient broth and 0.3 ml of each of the obtained ciiltures was inoculated into 3 ml of fermentation medium having the following composition in a 20x200 mm test tube and cultivated at 34°C for 48 hours vvith a rotary shaker. Data from at least 10 independent experiments are shown on Tables 1 and 2.
Femientation medium composition (g/1):
Ethanol 24 or 16
Glucose 0 (Table 1) or 3 (Table 2)
(NH4)2S04 16
K2HP04 0.7
MgS04-7H20 1.0
MnS04'5H20 0.01
FeS04-7H20 0.01
Thiamine hydrochloride 0.002
Yeast extract 1.0
L-isoleucine 0.01
CaCOi 33
MgS04'7H20 and CaCOj were each sterilized separately.
It can be seen from the Tables 1 and 2, MGl 655Atdh, rhtA*, PmcadhE was able to accumulate a higher amount of L-threonine as compared with MG1655Atdh, rhtA*. Moreover, MG1655Mdh, rhtA*, PnacadhE was able to grow on the medium containing ethanoJ as the sole carbon source and cause accumulation of L-threonine, whereas MG1655Atdh, rhtA* exhibited very poor growth and productivity in the medium containing ethanol as the sole carbon source.
Example 5. Construction of £. co//MG1655AadhE
This strain was consJnicled by inactivation of the native odhE gene in E. coU ViQlSbS by the kan gene.
To inactivate (or disrupt) the native adhE gene, the DNA fragment carrying kanamycin resistance marker (Km'') encoded by the kan gene, was integrated into the chromosome of £■. coli MG1655 (ATCC 700926) in place of the native gene by the method described by Dalsenko K.A, and Wanner B.L, (Proc. Natl. Acad. Sci. USA, 2000, 97, 6640-6645) which is also called "Red-mediated integration" and/or "Red-driven integration".
A DNA fragment containing a Km marker (Aan gene) was obtained by PCR using the commercially available plasmid pACYC177 (GenBank/EMBL accession number X06402, "Fennentas", Lithuania) as the template, and primere P9 (SEQ ID NO: 12) and PIO (SEQ ID NO: 13). Primer P9 contains 40 nucleotides homologous lo the region located 318 bp upstream of the start codcn of the adhE gene introduced into the primer for further integration into the bacterial chromosome. Primer PIG contains 41 nucleotides homologous to the 3'-region of the adhE gene introduced into the primer for further integration into the bacterial chromosome.
PCR was provided using the "Gene Amp PCR System 2700" amplificatory (Applied Biosystems). The reaction mixture (total volume - 50 \^X) consisted of 5 \k\ot\ Ox PCR-buffer
with 25 mM MgCb {"Fennentas", Lithuania), 200 ^M each of dNTP, 25 pmol each of the exploited primers and 1 U of Taq-polyraerase ("Fermentas", Lithuania). Approximately 5 ng of the piasmid DN^A was added in the reaction mixture as a template DNA for the PCR amplification. The temperature profile was the following: initial DNA denaturation for 5 min at 95 "C, followed by 25 cycles of denamration at 95 "C for 30 sec, annealing at 55 "C for 30 sec, elongation at 72 "C for 40 sec; and the final elongation for 5 min at 72 "C. Then, the amplified DNA fragment was purified by agarose gel-electrophoresis, extracted using "GenElute Spin Columns" ("Sigma", USA) and precipitated by ethano/.
The obtmned DNA fragment was used for electroporation and Red-mediated integration into the bacterial chromosome of the E. coli MG1655/pKD46.
MG1655/pKD46 cells were grown overnight at 30 °C in liquid LB-medium containing ampicillin (100 jig/ml), then diluted 1:100 by SOB-medium (Yeast extract, 5 g/1; NaCl, 0.5 g/1; Trj^tone, 20 g/I; KCI, 2.5 mM; MgCh, 10 raM) containing ampicillin (J 00 (ig/ml) and L-arabinose(10mM)(arabinose is used for inducing the piasmid encoding genes of Red system) and grown at 30 °C to reach the optical density of the bacterial culture OD6DO=0.4-0.7. The grown cells fvom 10 ml of the bacterial culture were washed 3 times by the ice-cold de-ionized water, followed by suspension in 100 jal of the water. 10 |il of DNA fragment (100 ng) dissolved in the de-ionized water was added to the cell suspension. The electroporation was performed by "Bio-Rad" electroporator (USA) (No. 165-2098, version 2-89) according to the manufacturer's instructions. Shocked cells were added to 1-mI of SOC mediimi (Sambrook et al, "Molecular Cloning A Laboratory Manual, Second Edition", Cold Spring Harbor Laboratory Press (1989)), incubated for 2 hours at 37°C, and then were spread onto L-agar containing 20 >ig/ml of kanamycin. Colonies grown within 24 hours were tested for the presence of Km^ marker instead of the native adhE gene by PCR using primers PI 1 (SEQ ID NO: 14) and Pi2 (SEQ ID NO: 15). For this purpose, a freshly isolated colony was suspended in 20^1 water and then 1 \i\ of obtained suspension was used for PCR. The temperature profile follows: initial DNA denaturation for 5 min at 95 °C; then 30 cycles of denaturation at 95 "C for 30 sec, annealing at 55 *'C for 30 sec and elongation at 72 "C for 30 sec; the final elongation for 5 min at 72 °C. A few Km** colonies tested contained the desired about 1030 bp DNA fragment, confirming the presence of Km*^ marker DNA instead of the 3135 bp fragment of adhE gene. One of the obtained strains was cured of the thermosensitive piasmid pKD46 by culturing at 37 °C and the resuhing strain was named E. coli MG1655AadhE.
Example 6. Construction of £ coli MGI655:;pL-iacadhE*
E, coli MG1655::PL-rtcadhE* was obtained by introduction of the Glu568Lys (E568K) mutation into the aJ/iiT gene. First, 1.05 kbp fragment of the adhE^cne carrying the E5681C mutation was obtained by PCR using the genomic DNA of £^. coli MG1655 as the template and primers P13 (SEQ ID NO: 16) and P12 (SEQ ID NO: 15). Primer P15 homologous to 1662-1701 bpand 1703-1730 bp regions oftheaifAf gene and includes the substitution g/a (position 1702bp)shownasboIdandprimerP12homolDgous to3'-endoftheo(i?j£gene. PCR was provided using the "Gene Amp PCR System 2700" ampjificatory (Applied Biosystems). The reaction mixture (total volume - 50 \i\) consisted of 5 (ilof lOxPCR-bufferwithMgCl; ("TaKaRa", Japan), 250 ^M each of dNTP, 25 pmol each of the exploited primers and 2.5 U of Pyrobest DNA polymerase ("TaKaRa", Japan). Approximately 20 ng of the E. coli MG1655 genomic DNA was added in the reaction mixtures as a template for PCR. The temperature profile was the following: initial DNA denaturation for 5 min at 95 "C^ followed by 35 cycles of denaturation at 95 "C for 30 sec, annealing at 54 "C for 30 sec, elongation at 72 °C for Imin and the final elongation for 5 min at 72 °C. TTie fragment obtained was purified by agarose gel-electrophoresis, extracted using "GenEIute Spin Columns" ("Sigma", USA) and precipitated with ethanol.
In the second step, the fragment containing the Pt-tac promoter with the mutant adhE gene and marked by the cat gene, which provides chloramphenicol resistance, was obtained by PCR using the genomic DNA ofE. coli MG1655::PL.iacadhE as the template (see Example 2), primer PU (SEQ ID NO: 14) and a 1.05 kbp fragment carrying a mutant sequence (see above) as a second primer. Primer P11 is homologous to the region located at 402-425 bp upstream of the start codon of the adhE gene. PCR was provided using the "Gene Amp PCR System 2700" amplificatory (Applied Biosystems). The reaction mixture (total volume - 50 \x\) consisted of 5 \i.{ of lOx PCR-buffer ("TaKaRa", Japan), 25mM MgCti, 250 jiM each of dNTP, 10 ng of the primerPU, Ipgofthe 1.05 kbp fragment as a second primer ^d2.5U of TaKaRa LA DNA polymerase ("TaKaRa", Japan). Approximately 20 ng of the E. coli MG1655::Pi,.iacaciliE genomic DNA was added to the reaction mixture as a template for PCR. The temperature profile was the following; initial DNA denaturation for 5 rain at 95 °C, followed by 35 cycles of denaturation at 95 "C for 30 sec, annealing at 54 "C for 30 sec, elongation at 72 ''C for 3.5 ■ min and the final elongation for 7 min at 72 "C. The resulting fragment was purified by agarose
gel-electrophoresis, extracted using "GenElute Spin Colunms" ("Sigma", USA) and precipitated by ethanol.
To replace the native region of the adhE gene, the DNA fragment carrying a PL-IW promoter with the mutant adfiE and chloramphem'col resistance marker (Cm") encoded by the cat gene (cat-PL-iacadhE*, 4.7 kbp) was integrated into the chromosome of £. coH MGI655AadhE by (he method described by Datsenko K.A. and Wanner B.L. (Proc. Nati. Acad. Sci. USA, 2000,97, 6640-6645) which is also called "Red-mediated integration" and/or "Red-driven integration". MG] 655 AadhE/pKD46 cells were grown overnight at 30 °C in iiquid LB-medium containing ampicillin (100 ^g/ml), then diluted 1:100 by SOB-mediimi (Yeast extract, 5 g/i; NaCi, 0.5 g/1; Tryptone, 20 g/1; KCJ, 2.5 mM; MgCh, 10 mM) containing ampicillin {100 jig/ml) and L-arabinose (10 mM) (arabinose is used for inducing the plasmid encoding genes of the Red system) and grown at 30 °C to reach the optical density of the bacterial culture OD60D=0.4-0.7. The grown cells from 10 ml of the bacterial culture were washed 3 times by the ice-cold de-ionized water, followed by suspension in 100 pi of the water. 10 [il of DNA fragment (300 ng) dissolved in the de-ionized water was added to the cell suspension. The electroporation was performed by "Bio-Rad" electroporator (USA) (No. 165-2098, version 2-89) according to the manufacturer's instructions.
Shocked cells were added to 1-ml of SOC medium (Sambrook et al, "Molecular Cloning A Laboratory Manual, Second Edition", Cold Spring Harbor Laboratory Press (19S9)), incubated for 2 hours at 37 °C, and then were spread onto L-agar containing 25 Mg/ml of chlorampheiucol.
The clones obtained were selected on M9 plates with 2% ethanol as the sole carbon source.
The runaway clone was chosen and the full gene sequence was verified. The row of mutations was revealed as follows: Glu568Lys (gag - aag), Ile554Ser (ate - age), Glu22Gly (gaa -gga), Met236Val (atg - gtg), Tyr461Cys (tac - tgc), AIa786Val (gca - gta). This clone was named MG1655::PL-iB(;adhE*.
Example 7. Construction ofR coli MG1655Aldh, rhtA*, Pt-ia^adhE* E. co//MGI655Atdh, rhtA*, PL.iB=adhE* was obtained by transduction of the pL-tac adhE* mutation from the strain MG1655::PL.tacadhE*.
The strain MGI 6S5i^idh, rhtA* was infected with phage PI vir grown on the donor strain
MG1655::PL^flEadhE* and the strain MG]655Atdh, rhtA*, PL-utadhE* was obtained. This strain was checked for growth on M9 plates with 2% ethanol as a sole carbon source. The growth rate was the same as for the strain MGI 655::PuacadhE*.
Example 8. Construction of E. coU MG1655Atdh, rhtA*, PL-ucadhE-Lys568 A second attempt to obtain a single mutant adhE having the Glu568Lys mutation was performed. For that purpose E. coli strain ]V[GI655Atdh, rhtA*, PL-iacadhE-wtA34 was constructed.
E. coli MG1655Atdh, rhtA*, PL-,acadhE-wtA34 was obtained by replacement of a 34bp fragment of the adhE gene (the region from 1668 to 1702 bp, inclusive of the triplet encoding GIu568) in E. coli MGI6554{dh, rhtA*, PuacadhE-wt (wt means a wild type) with kan gene. The kan gene was integrated into the chromosome ofE. coli MGI655Atdh, rhtA*, FL-iacadhE-wt by the method, described by Datsenko K.A, and Wanner B.L. (ProcNatl.Acad.Sci.USA, 2000,97, 6640-6645) which is also called "Red-mediated integration" and/or "Red-driven integralion".
A DNA fragment containing a Km"* marker encoded by the kan gene was obtained by PCR using the commercially available plasmid pACYC177 (GenBank/EMBL accession number X06402, "Fermentas", Lithuania) as the template, and primers F14 (SEQ ID NO: 17) andPlS (SEQ ID NO: IS). Primer P14 contains 41 nucleotides identical to the region fi^m 1627 to 1668 bp of adhE gene and primtr PJ 5 contains 39 nucleotides complementaiy to the region from 1702 to 1740 bp of adhE gene introduced into the primers for fiirther integration into the bacterial chromosome.
PCR was provided using the "Gene Amp PCR System 2700" amplificatory (Applied Biosystems). "Die reaction mixture (total volume - 50 p.1) consisted of 5 ^1 of 1 Ox PCR^buffer with 25 mM MgCI: ("Fermentas", Lithuania), 200 ^M each of dNTP, 25 pmol each of the exploited primers and I U of Taq-polymcrase ("Fermentas", Lithuania). Approximately 5 ng of the plasmid DNA was added in the reaction mixture as a template DNA for the PCR ampjifjcation. The temperature profile was the following: initial DNA denaturation for 5 min at 95 "C, followed by 25 cycles of denaturation at 95 "C for 30 sec, annealing at 55 °C for 30 sec, elongation at 72 °C 50 sec and the final elongation for 5 min at 72 *C. Then, the amplified DNA fragment was purified by agarose gel-electrophoresis, extracted using "GenEIute Spin Columns" ("Sigma", USA) and precipilaled by ethanol.
Colonies obtained were tested for the presence of Km marker by PCR using primers P16 (SEQ ID NO: 19) and P17 (SEQ ID NO: 20). For this purpose, a freshly isolated colony was suspended in 20|J1 water and then l^l of the obtained suspension was used for PCR. The temperature profile follows: initial DNA denaturation for 5 min at 95 "C; then 30 cycles of denaturation at 95 °C for 30 sec, annealing at 55 "C for 30 sec and elongation at 72^0 for 45 sec; the final elongation for 5 min at 72 "C. A few Km" colonies tested contained the desired 1200 bp DNA fragment, confinning the presence of Km"* marker DNA instead of 230 bp iiagment of native adhE gene. One of the obtained strains was cured of the thennosensitive plasmid pKD46 by culturing at 37 °C and the resulting strain was named as E. coli MG1655Atdh, rhtA*,PL.,acadhE-wtA34.
"Dien, to replace the kanamycm resistance marker (Km'*) encoded by kan gene with a fragment of the adhE gene encoding the Glu568Lys mutation, the oligonucleotides PI 8 (SEQ ID NO: 21) and P19 (SEQ ID NO: 22) carrying the appropriate mutation were integrated into the chromosome of £". coli MGl655Atdh, rhtA, PL-iwadhE-wt A34 by the method "Red-mediated integration" and/or "Red-driven integration" (Yu D., Sawitzke J. et ai., Recombineering with overlapping single-stranded DNA oligonucleotides: Testing of recombination intermediate, PNAS, 2003, 100(12), 7207-7212). Primer PI8 contains 75 nucleotides identical to the region from 1627 to 1702 bpoffl(a!ft£'gene and primer P19 contains 75 nucleotides complementary to the region ^om 166S to 1740 bp ofadhE gene, both primers inclusive of the triplet encoding Lys568 instead of Glu568.
The clones were selected on M9 minimal medium containing 2% ethanol and 25mg/ml succinate as a carbon source.
Colonies were tested for the absence of Km'' marker by PCR using primers P16 (SEQ ID NO; 19) and P17 (SEQ ID NO: 20). For this purpose, a freshly isolated colony was suspended in 20jil water and then I jil of the obtained suspension was used for PCR. The temperature profile follows: initial DNA denaturation for 5 min at 95 "^C; then 30 cycles of denaturation at 95 "C for 30 sec, annealing at 55 "C for 30 sec and elongation at 72" C for 25 sec; the final elongation for 5 min at 72 "C. A few Km^ colonies tested contained the desired 230 bp DNA fragment ofadhE gene, confirming the absence of Km'' marker DNA instead of 1200 bp fragment. Several of the obtained strains was cured of the ihermo sensitive plasmid pKD46 by culturing at 37 °C and the resulting strain was named as E. coli MG1655Atdh, rhtA, PL-iacadhE-Lys568.
The presence of the Glu568Lys mutation was confirmed by sequencing, for example, cl.l8 has a single mutation Glu568Lys. Addditionally it was found that some clones (#1,13) contained additional mutations: cl. I - Glu568Lys, Phe566VaJ,- cJ.13 - Glu568Lys, Giu560Lys.
For strains MG1655Atdh, rhtA*,PL-u,cadhE-Lys568 (cl.18), MG1655Atdh, rhtA*,PL. ucadhE-Lys568,Val566 (cl.l), MG1655Atdh, rhtA*,PuacadhE-Lys568,Lys560 (cl.l3) and MGI655Atdh, rhtA*,pL-iacadhE*, the growth curves were studied (Figures 3 and 4).
The strains were grown in M9 medium with ethanol as a sole carbon source and in M9 medium with glucose and efhanol (molar ratio 1:3)
Example 9. Construction of £. co/iMGieSSAtdh, rhtA*, adhE* The E. coli strain MG1655Atdh, rhtA*, adhE* was obtained by reconstruction of the native oc/ft£ promoter in strain MG1655Atdh, rhtA*, PuacadhE*. A DNA fragment carrying a pL-tao promoter and chloramphenicol resistance marker (Cm"*) encoded by cat gene in the chromosome of the strain MGI655Atdh, rhtA*, PmacadhE* was replaced by a fragment carrying native adhE promoter and kanamycin resistance marker (Km*^) encoded by the kan gene. Native P,dhE was obtMied by PCR using a DNA of the strain MG1655 as a template and primers P20 (SEQ ID NO: 23) and P21 (SEQ ID NO: 24). Primer P20 contains an EcoBJ recognition site at the 5'-end thereof, which is necessaary for further joining to the kan gene and primer P21 contains 30 nucleotides homologous to 5'-region of the adhE gene (from 50 bp to 20 bp).
A DNA fragment containing a Km" marker encoded by the kan gene was obtained by PCR using the commercially available plasmid pACYC177 (GenBank/EMBL accession number X06402, "Fennentas", Lithuania) as the tempJate, and primers P22 (SEQ ID NO: 25) and P23 (SEQ ID NO: 26). Primer P22 contains 41 nucleotides homologous to the region located 425 bp upstream of the start codonofthearfAE gene introduced into the primer for further integration into the bacterial chromosome and primer P23 contains an £coRI recognition site at the 3'-end thereof, which is necessary for further joining to the PadhE pTOmoter.
PCR were provided using the "Gene Amp PCR System 2700" amplificatory (Applied Biosystems). The reaction mixture (total volume-50 p,I) consisted of 5 \iX of lOxPCR-buffer with 25 mM MgCU ("Fermentas", Lithuania), 200 jxM each of dNTP, 25 pmol each of the exploited primers and 1 U of Taq-poiymerase ("Fermentas", Lithuania). Approximately 20 ng
of genomic DNA or 5 ng of the plasmid DNA were added in the reaction mixture as a template for the PCR amplification. The temperature profile was the following: initial DNA denaturation for 5 min at 95 °C, followed by 35 cycles of denaturation for PajhE or 25 cycles of denaturation for kan gene at 95 °C for 30 sec, annealing at 55 °C for 30 sec, elongation at 72 °C for 20 sec for Ptac promoter and 50 sec for kan gene; and die final elongation for 5 min at 72 °C. Then, the amplified DNA fragments were purified by agarose gel-electrophoresis, extracted using "GenElute Spin Columns" ("Sigma", USA) and precipitated by ethanol.
Each of the two above-described DNA fi^gments.was treated with EcoRl restrictase and ligated. The ligation product was amplified by PCR using primers P2I and P22. The amplified kan-PtdhE DNA fragment was purified by agarose gel-electrophoresis, extracted using "GenElute Spin Columns" ("Sigma", USA) and precipitated by ethanol. The obtained DNA fragment was used for electroporation and Red-mediated integration into the bacterial chromosome of the E. coU MGl 655Atdh::rbtA*, PL.BcadhE*/p)CD46,
MG1655Atdh::rhtA*,PL-tBcadhE*/pKD46 cells were grown overnight at 30 °C in the liquid LB-medium with addition of ampicillin (100 ^g/ml), then diluted l:100by theSOB-medium (Yeast extract, 5 g/I; NaCI, 0.5 g/l; Tryptone, 20 g/J; KCI, 2.5 mM; MgCh, 10 mM) with addition of ampicillin (100 ng/ml) and L-arabinose (10 mM) (arabinose was used for inducing the plasmid encoding genes of Red system) and grown at 30 "C to reach the optical density of the bacterial culture OD6OD=0.4-0.7. The grown cells from 10 ml of the bacterial culture were washed 3 times by the ice-cold de-ionized water, followed by suspending in 100 fil of the water. 10 ^1 of DNA fragment (100 ng) dissolved in the de-ionized water was added to the cell suspension. The electroporation was perfoimed by "Bio-Rad" electroporator (USA) (No. 165-2098, version 2-89) according to the manufacturer's instructions.
Shocked cells were added to 1-ml of SOC medixim (Sambrook et al, "Molecular Cloning A Laboratory Manual, Second Edition", Cold Spring Harbor Laboratory Press (1989)), incubated for 2 hours at 37 °C, and then were spread onto L-agar containing 20 {ig/mi of kanamycin.
Colonies grown within 24 h were tested for the presence of PadKE -Km" marker instead of pL-iao-Cm'^-marker by PCR using primers P24 (SEQ ID NO: 27) and P25 (SEQ ID NO: 28). For this purpose, a freshly isolated colony was suspended in 20^1 water and then Ijilof obtained suspension was used for PCR. The temperature profile follows: initial DNA denaturation for 5 min at 95 "C; then 30 cycles of denaturation at 95 °C for 30 sec, annealing at
54 "C for 30 sec and elongation at 72 ''C for 1.0 min; the final elongation for 5 min at 72 °C. A few Km** colonies tested contained the desired 1200 bp DNA fi-agment, confirming the presence of native PadhE promoter and FCm'* -marker DNA. Some of these fragments were sequenced. The structure of the native PadhE promoter was confirmed. One of the strains containing the mutant adhE gene under the control of anative promoter was cured of the thermosensitive plasmid pKD46 by culturing at 37 °C and the resulting strain vyas named as E. coiiUG16S5&tdh, rhtA*, adhE*.
The ability of all the obtained strains MG1655Atdh, rhtA*, PL-iwadhE; MG]655Atdh, rhtA*, PutscadhE*; MG1655Atdh, rhlA*, Pi^a^dhE-Lys568 (cI.I8); MG1655Atdh, rhtA*, PL-tacadhE-Lys568, Val566 (cl.l); MG1655Atdh, rhtA*, adhE* and parental strain MG1655Atdh, rhtA* to grow on the minimal medium M9 containing ethanol as a sole carbon source was investigated. It was shovra that the parental strain MG1655Atdh, rhtA* and the strain with enhanced expression of wild-type alcohol dehydrogenase were unable to grow on the medium cofltaining ethanol (2% or 3%) as a sole: carbon source (Figure 3, A and B). Strain MG1655Atdh, rhtA*. PL-tflcadhE-Lys568 (c!.18) containing the single mutation in the alcohol dehydrogenase described early (Membrillo-Hemandez, J. et al, J. Biol. Chem. 275,33869-33875 (2000)) exhibited very poor growth in the same medium. But strains containing mutations in the alcohol dehydrogenase in addition to mutation Glu568Lys exhibited good growth (Figure 3, A and B). All the above strains were able to grow on the minimal medium M9 containing a mixture of glucose and ethanol, but strains with enhanced expression of the mutant alcohol dehydrogenase containing mutations in addition to mutation Glu568Lys exhibited better growth (Figure 4).
It was also shown that strain MGl 655Atdh, rhtA*, adhE* containing the alcohol dehydrogenase vyith 5 mutations under the control of the native promoter was unable to grow on the minimal medium M9 containing ethanol (2% or 3%) as a sole carbon source. Enhanced expression of the gene encoding for said alcohol dehydrogenase is necessary for good growth (Figure 5).
Example 10. Theeffect of increasing the mutant ati/iE gene expression on L-threonine
production
To evaluate the effect of enhancing expression of the mutant adhE gene on threonine production, E. coli strains MG1655Atdh, rhtA*, pL.„cadhE; MG1655Atdh, rhtA*, PL-tacadhE*;
MG]655Atdh, rhtA*, PL.,acadhE-LyE568 (cl.l8); MG1655Atdh. rhtA*, PL-iacadhE-Lys568, VaI566 (cl.l); MG1655Atdh, rhtA*, adhE* and parental strain MG]655Atdh, rhU* were transfonned with plasmid pVlG40.
These strains and the parent strain MGl 6554tdh, rbiA* (pVIC40) were cuJtivaled at 37 "C for 18 hours in a nutrient broth and 0.3 ml of each of the obtained cultures was inoculated into 3 ml of fermentation medium (see Example 4) in a 20x200 mm test tube and cultivated at 34 "C for 48 hours with a rotary shaker. Data from at least 10 independent experiments are shown on Tables 1 and 2.
It can be seen from the Tables 1 and 2, mutant alcohol dehydrogenase was able to cause accumulation of a higher amount of L-threonine as compared with MGl 655Atdh, rhtA* in which neither expression of a wild-type nor a mutant alcohol dehydrogenase was increased or even with MG1655Atdh, rhtA*, or PL-wcadhE, in which expression of wild-type alcohol dehydrogenase was increased. Such higher accumulation of L-threonine during fermentation was observed in the medium containing either a mixture of glucose and ethanol, or just ethanol as the sole carbon source.
Table 1
Strain 3% ethanol 2% ethanol
OD540 Thr,g/1 OD„o Thr,g/1
MG1655Atdh,rhtA* CpVIC40) 1.6±0.1 <0.1 1.4±0.1 <0.1
MG]655Atdh, rhtA*,PL-i«adhE(wt) (pVIC40) 7.9±0.3 l.liO.l 7.6i0.2 0.9±0.1
MG1655Atdh,rhtA*.PL-,BcaahE-Lys568(pVIC40)(cI.I8) 14,7±0.3 3.3±0.1 13.7±0.4 2.3±0.3
MG1655Atdh, rhtA*, PL-,acadhE-Lys568, 14.2±0.4 3.2±0.2 ]2.5±0.3 2.1±0.3
Vai566(pVJC40) (cU)
MG1655Atdh, ihtA*, PL-.acadhE*(pVIC40) 17.0±0.3 3.9±0.2 ]4.3±0.3 2.8±0.1
MG1655Atdh, rhtA*, adhE*(pVIC40) 2.8±0.2 <0.I 2.1±0.1 <0.1
Table 2
Strain
MG1655Atdh, rhtA* (pVIC40) MG1655Atdh, rhtA*,Pui Cys) under the control of the ionstitutive promoter PL was introduced into the strain ESP217. The DNA fragment shown in SEQ ID NO: 51) was used for elecfroporation of the strain ESP217/pKD46 for the purpose of subsequent integration into the chromosome. This DNA fragment contained the 35nt-region, A'hich is necessary for integration into the chromosome and homologous to the upstream ■egion of the gene [euA. It also contained an excisable region complementary to the sequence )f chloramphenicol resistance marker cat, and the mutant leuA (Gly479 -> Cys) gene under the lontrol of the constitutive promoter PL- Elcctroporation was performed as described above. Selected Cm" recombinants contained the mutant gene leuA (Gly479 -> Cys) under the control jf the constitutive promoter PL integrated into the chromosome. Thus, the strain ESP220 was )btmned. The chloramphenicol resistance marker was eliminated from the stram ESP220 as iescribed above. As a result, the strain ESP22I was obtained.
Then, the DNA fragment shown in SEQ ID NO: 52 was used for elcctroporation of the itrain ESP221/pKX)46 for the purpose of subsequent integration into the chromosome. This DNA fragment contained the 35nt-region homologous to the upstream region of the gene tyr£, ji/hich is necessary for integration into the chromosome. It also contained an excisable region complementary to the sequence of chloramphenicol resistance marker cat and the gene tyrB with a modified reguIatory(-35) region. Electroporation was performed as described above. Selected Cm^ recombinants contained the gene tyrB with the modified regu]atoiy(-35) region. Fhus, the strain NS1390 was obtained. The chloramphenicol resistance marker was etiminaled Tom the strain NS1390 as described above. As a result, the strain NS1391 was obtained. >ucine producing strain NS1391 was used for fiirther work.
Example 16. The effect of increasing the mutant adhE gene expression on L-leucine production
To test the effect of enhanced expression of the adhE gene under the control of a Puac promoter on L-leucine production, DNA fragments from the chromosome of the above-iescribed strain MGl 655 PuacadhE* were transferred to the L-Ieucine producing £ colt strain NS1391 by Pl transduction (Miller, J.H. (1972) Experiments in Molecular Genetics, Cold Spring Harbor Lab. Press, Plainview, NY) to obtain the strain NS 1391 PL-u=adhE* .
Both E. coli strains^ NS1391 and NS139I Pt-tacadhE*, were cultured for IS-24 hours at ST'C on L-agar plates. To obtain a seed culture, the strains were grovwi on a rotary shaker (250 rpm) at 32°C for 18 hours in 20x200-mm test tubes containing 2 mi of L-broth suppjemented with 4% sucrose. Then, the fermentation medium-was inoculated ivith 0.2] ml of seed njateriai (J0%). TTie fennentation was performed in2mJ of a minimal fennentafion medium in 20x200-mm test tubes. Cells were grown for 48-72 hours at 32*^0 with shaking at 250 rpm. The amount of L-leucine was measured by paper chromatography (liquid phase composition: butanol -acetic acid-water = 4:1:1). The results of ten independent test tube fermentations are shown in Table 5. As follows from Table 5, NS1391 PuBcadhE* produced a higher amount of L-leucine, as compared with NSl 391 , in media containing different concentrations of ethanol.
The composition of the fermentation medium (g/1) (pH 7.2) was as follows:
Glucose 60.0
Ethanol 0/10.0/20.0/30.0
(NH4)2S04 25.0
K2HPO4 2.0
MgS04-7H20 J.O
Thiamine 0.01
CaC03 25.0
Glucose, ethanol and CaCOj were sterilized separately.
Example 17. The effect of the increasing the adhE gene expression on L-phenylalanine production
To lest the effect of enhanced expression of the adhE gene under the control of a pKac promoter on phenylalanine production, the DNA fragments from the chromosome of the above-described strains MG1655Atdh, rhtA*. PnacadhE; MG]655Atdh, rhtA*, PL-acadhE*; MG1655Atdh, rhtA', PnacadhE-LysSeS (cl.l8); MG1655Atdh, rhtA*, PL.iacadhE-Lys568, Val566 (cl.l); MG1655 Atdh, rhtA*, adhE* can be transferred to the phenylalanine-producing E. coli strain AJ12739 by Pi transduction (Miller, J.H. (J972) Experiments in Molecular Genetics, Cold Spring Harbor Lab. Press, Plainview, NY). The strain AJ12739 has been deposited in the Russian National Collection of Industrial Microorganisms (VKPM) (Russia, 117545 Moscow, ] Dorozhny proezd, ])onNovember 6,2001 underaccessionnumbw VKPM B-8197 and then converted to a deposit under the Budapest Treaty on August 23,2O02
The resulting strains and the parent strain AJ12739 can each be cultivated at 37 "C for 18 hours in a nutrient broth, and 0.3 ml of the obtained cultures can each be inoculated into 3 ml of a fermentation medium in a 20 x 200 mm test tube and cultivated at 37 °C for 48 hours with a rotary shaker. After cultivation, the amount of phenylalanine which accumulates in the medium can be determined by TLC. 10 x 15 cm TLC plates coated with 0.11 mm layers of Sorbfil silica gel without fluorescent mdicator (Stock Company Sorbpolymer, Krasnodar, Russia) can be used. The Sorbfil plates can be developed with a mobile phase: propan-2-ol: ethylacetate : 25% aqueous ammonia : water = 40 140 : 7 : 16 (v/v). A solution (2%) of ninhydrin in acetone can be used as a visualizing reagent.
Tlie composition of the fermentation medium (g/1):
Ethanol 20.0
(NIi()2S04 16.0
K2HP04 0.1
MgS04-7H20 1.0
FeSO4-7H30 O.OI
MnSOv5H20 O.Ol
Thiamine HCl 0.0002
Yeast extract 2.0
Tyrosine 0.125
CaCOj 20.0
Ethanol and magnesium sulfate are sterilized separately. CaCOs dry-heat sterilized at ISO °C for 2 hours. pH is adjusted to 7.0.
Example 18. The effect of increasing the at//i£ gene expression on L-tryptophan production
To test the effect of enhanced expression of the adhE gene under the control of a PL-WC promoter on tryptophan production, the DNA fragments from the chromosome of the above-described strains MG1655Atdh, rhtA*, pL-iacadhE; MG1655Atdh, rhtA*, PuacadhE*; MG]655Atdh, rhlA*, Pi..ucadhE-Lys568 (cJ.18); MG]655Atdh, rhtA*. PL-u«:adhE-Lys568, Val566(cl.l); MG1655Atdh, rhtA*, adhE* can be transferred to the tryptophan-producing £. coll strain SV164 (pGH5) by PI transduction (Miller, J.H. (1972) Experiments in Molecular Genetics, Cold Spring Harbor Lab. Press, Plainview, NY). The strain SVI64 has the i>-/j£"allele encoding anthranilate synthase which is not subject to feedback inhibition by tryptophan. The plasmid pGH5 harbors a mutant serA gene encoding phosphoglycerate dehydrogenase which is not subject to feedback inhibition by serine. The strain SVI64 (pGH5) is described in detail in U.S. Patent No. 6,180,373 or European patent 0662143.
The resulting strains and the parent strain SV164 (pGH5) can each be cultivated with shaking at 37 "C for 18 hours in 3 ml of nutrient broth supplemented with 20 mg/1 of tetracycline (marker of pGH5 plasmid). 0.3 ml of the obtained cultures can each be inoculated into 3 ml of a fermentation medium contaming tetracycline (20 mg/1) in 20 x 200 mm test tubes, and cultivated at 37 °C for 48 hours with a rotary shaker at 250 rpm. After cultivation, the amount of tryptophan which accumulates in the medium can be determined by TLC as described in Example 17. The fermentation medium components are set forth in Table 6, but should be sterilized in separate groups A, B, C, D, E, F, and H, as shown, to avoid adverse interactions during sterilization.
Example 19. The effect of the increasing the arfA£ gene expression on L-histidine production
To test the effect of enhanced expression of the adhE gene under the control of a Puac promoter on histidine production, the DNA fragments from the chromosome of the above-described strains MG!655Atdh, rhtA», pL-wcadhE; MG1655Atdh, rhlA*, PnacadhE*; MGI655Atdh, rhtA', PL.wcadhE-Lys568 (d.lS); MG1655Atdh, rhtA*, PLHBcadhE-Lys568, VaI566(cl.l); MG1655Atdh, rhtA', adhE* can be transferred to the histidine-producing £:. coli strain 80 by PI transduction (Miller, J.H. (1972) Experiments in Molecular Genetics, Cold Spring Harbor Lab. Press, Plainview, NY). The strain 80 has been described in Russian patent 2119536 and deposited in the Russian National Collection oflndustrial Microorganisms (Russia, 117545 Moscow, 1 Dorozhny proezd, 1) on October 15, 1999 under accession number VKPM B-7270 and then converted to a deposit under the Budapest Treaty on July 12,2004.
The resulting strains and the parent strain 80 can each be cultivated in L broth for 6 hours at 29 °C. Then, 0.1 ml ofobtained culture can each be inoculated into 2 ml of
fermentation medium in a 20x200mm test tube and cultivated for 65 hours at 29 "C with a rotary shaker (350 rpm). After cuHivalion, the amount of histidine which accumulates in the medium can be determined by paper chromatography. The paper can be developed with a mobile phase: n-butanol: acetic acid : water = 4:1:1 (v/v). A solution of ninhydrin (0.5%) in acetone can be used as a visualizing reagent.
The composition of the fermentation medium (pH 6.0) (g/1):
Ethanol 20.0
Mameno (soybean hydrolyzate) 0.2 as total nitrogen
L-proIine 1.0
(NH4)2S04 25.0
KH2PO4 2.0
MgSO^-THiO 1.0
FeSOrVHiO 0.01
MnS04 O.OI
Thiamine 0.001
Betaine 2.0
CaC03 60.0
EthanoJ, proline, betaine and CaCOj are steri]i2ed separately. pH is adjusted lo 6.0 before sterilization.
Example 20. The effect of increasing the adhE gene expression on L-glutamic acid production
To test the effect of enhanced expression of the adhE gene under the control of a pL-tac promoter on glutamic acid production, the DNA fragments from the chromosome of the above-described strains MG1655Atdh, rhtA*, Pu»cadhE; MG1655Atdh, rhtA*, PuacadhE*; MG1655Atdh, rhtA*. pL.[acadhE-Lys568 (cl.l8); MG1655Atdh, rhtA*, PL.ucadhE-Lys568, Val566 (cl.l); MG1655Atdh, rhtA*, adhE* can be transferred to the glutamic acid-producing E. coli strain VL334thTC* (EPl 172433) by PI transduction (Miller, J.H. (1972) Experiments in Molecular Genetics, Cold Spring Harbor Lab. Press, Plainview, NY). The strain VL334thrC'' has been deposited in the Russian National Collection of Industrial Microorganisms (VKPM) (Russia, 117545 Moscow, 1 Dorozhny proezd, 1) on December 6,2004 under the accession number VKPM B-8961 and then converted to a deposit under the Budapest Treaty on December 8, 2004.
The resulting strains and the parent strain VL334thrC* can each be cultivated with shaking at 37 "C for 18 hours in 3 ml of nutrient broth. 0.3 ml of the obtained cultures can each be inoculated info 3 ml of a fermentation medium in 20 x 200 mm test tubes, and cultivated at 37 °C for 48 hours with a rotary shaker at 250 ipm.
The composition of the fermentation medium (pH 7.2) (g/1):
Ethanol 20.0
Ammonium sulfate 25.0
KH2PO4 2.0
MgS04-7H30 1.0
Thiamine 0.0001
L-isoleucine 0.05
CaCOs 25.0
Ethanol and CaCOj were sterilized separately.
While the invention has been described in detail with reference to preferred embodiments thereof, it will be apparent to one skilled in the art that various changes can be made, and equivalents employed, without departing from the scope of the invention. Each of the aforementioned documents is incorporated by reference herein in its entirety. Industrial Applicability
According to the present invention, production of an L-amino acid by a bacterium of the Enterobacteriaceae family can be enhanced.
CLAIMS
]. A method for producing an L-amino acid comprising:
A) cultivating in a culture medium containing ethanol an L-amino acid-producing bacterium of the Enterobacieriaceae family having an alcohol dehydrogenase, and
B) isolating the L-amino acid from the culture medium,
wherein Ihe gene encoding said alcohol dehydrogenase is expressed under the control of a non-native promoter which fimctions under aerobic cultivation conditions.
2. The method according to claim 1, wherein said non-native promoter is selected from the group consisting of Pia^, Pi^c, Pt^, Ptrc, PR, and PL.
3. The method according to claim 1 or 2, wherein said alcohol dehydrogenase is resistant to aerobic inactivation.
4. The method according to any one of claims 1 to 3, wherein said alcohol dehydrogenase originates from a bacterium selected from the group consisting oi Escherichia coli, Erwinia carolovora, Salmonella typhimurium, Shigella Jlexneri, Yersinia pestis, Pantoea ananatis, Lactobacillus plantarum, and Lactococcus lactis.
5. The method according to any one of claims (to 4, wherein said alcohol dehydrogenase comprises the amino acid sequence set forth in SEQ ID NO: 2, except the glutamic acid residue at position 568 is replaced with another amino acid residue other than an aspartic acid residue.
6. The method according to any one of claims 1 to 4, wherein said alcohol dehydrogenase comprises the amino acid sequence set forth in SEQ ID NO: 2, except the glutamic acid residue at position 568 is replaced with a lysine residue.
7. The method according to claim 5 or 6, wherein said alcohol dehydrogenase has at least one additional mutation which is able to improve the growth of said bacterium in a liquid medium which contains ethanol as the sole carbon source.
8. The method according to claim 7, wherein said additional mutation is selected from the group consisting of:
A) replacement of the glutamic acid residue at position 560 in SEQ ID NO: 2 with another amino acid residue;
B) replacement of the phenylalanine residue at position 566 in SEQ ID NO: 2 with another amino acid residue;
C) replacement of the glutamic acid residue, the methionine residue, the tyrosine
residue, the isoleucine residue and the alanine residue at positions 22,236, 461,
554, and 786, respectively, in SEQ ID NO: 2 with other amino acid residues;
and
D) combinations thereof.
9. The method according to claim 7, wherein said additional mutation is selected from the group consisting of:
A) replacement of the glutamic acid residue at position 560 in SEQ ID NO: 2 with
a lysine residue;
B) replacement of the phenylalanine residue at position 566 in SEQ ID NO: 2 with
a valine residue;
C) replacement of the glutamic acid residue, the methionine residue, the tyrosine
residue, the isoleucine residue and the alanine residue at positions 22,236,461,
554, and 786, respectively, in SEQ ID NO: 2 with a glycine residue, a valine
residue, a cysteine residue, a serine residue, and a valine residue, respectively;
and
D) combinations thereof.
10. The mefiiod according to any one of claims 1 to 9, wherein said L-amino acid-
producing bacteriiun belongs to a genus selected from the group consisting of Escherichia,
Enterobacter, Erwinia, Klebsiella, Pantoea, Providencia, Salmonella, Serralia. Shigella, and
Morganella.
11. The method according to any one of claims 1 to 10, wherein said L-amino acid is
selected from the group consisting of L-threonine, L-Jysine, L-histidine, L-phenylalanine, L-
arginine, L-tiyptophan, L-glutamic acid, and L-leucine.