US20100311136A1 - Recombinant yeast and branched alcohol production method using recombinant yeast - Google Patents

Recombinant yeast and branched alcohol production method using recombinant yeast Download PDF

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US20100311136A1
US20100311136A1 US12/794,393 US79439310A US2010311136A1 US 20100311136 A1 US20100311136 A1 US 20100311136A1 US 79439310 A US79439310 A US 79439310A US 2010311136 A1 US2010311136 A1 US 2010311136A1
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gene
yeast
recombinant yeast
yhfr
branched alcohol
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Satoshi Yoneda
Masayoshi Muramatsu
Shusei Obata
Ai Inoue
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Toyota Motor Corp
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • C12N9/1241—Nucleotidyltransferases (2.7.7)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/52—Genes encoding for enzymes or proenzymes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0006—Oxidoreductases (1.) acting on CH-OH groups as donors (1.1)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/02—Preparation of oxygen-containing organic compounds containing a hydroxy group
    • C12P7/04—Preparation of oxygen-containing organic compounds containing a hydroxy group acyclic

Definitions

  • the present invention relates to a recombinant yeast having a predetermined gene introduced therein and a branched alcohol production method using the recombinant yeast.
  • 2-methyl-1-butenol can be synthesized by causing the expression of the nudF gene or yhfR gene of Bacillus subtilis in Escherichia coli .
  • expression products of the nudF gene and the yhfR gene convert dimethylallyl-diphosphate or isopentenyl diphosphate into 2-methyl-3-butene-1-ol ( Appl. Environ. Microbiol. 73, 6277-83 (2007)).
  • the amino acid synthesis pathway is used for synthesizing a branched alcohol with a certain chain length such as 2-methyl-1-butanol or 3-methyl-1-butanol, which is appropriate for automotive fuel and the like.
  • branched alcohol production with the use of the amino acid synthesis pathway the supply shortage of amino acids necessary for microorganism growth is a matter of concern.
  • mass-production of branched alcohol which is a product of interest.
  • a method involving the use of the nudF gene or the yhfR gene of Bacillus subtilis is advantageous because it does not involve the use of the amino acid synthesis pathway.
  • the resulting branched alcohol has unsaturated bonds, and therefore the oxidative stability is poor when such alcohol is used as fuel, which is problematic.
  • a step of adding hydrogen to synthesized branched alcohol for example.
  • such step is cost-consuming, which is also problematic.
  • a desired branched alcohol can be produced by causing the expression of the ADP-ribose pyrophosphatase gene and/or the yhfR gene in a yeast in which a gene encoding hydroxymethyl glutaryl-CoA (HMG-CoA) reductase has been expressed to a high degree. This has led to the completion of the present invention.
  • HMG-CoA hydroxymethyl glutaryl-CoA
  • the recombinant yeast of the present invention is a recombinant yeast in which a hydroxymethyl glutaryl-CoA reductase gene has been expressed to a high degree, and the ADP-ribose pyrophosphatase gene and/or the yhfR gene are introduced so as to be expressed therein.
  • the nudF gene of Bacillus subtilis is preferably used as the ADP-ribose pyrophosphatase gene.
  • the yhfR gene of Bacillus subtilis is preferably used as the above yhfR gene.
  • the HMG1 gene of Saccharomyces cerevisiae is preferably used as the above hydroxymethyl glutaryl-CoA reductase gene.
  • a host is preferably a yeast having a mevalonic acid pathway, more preferably a yeast of the genus Saccharomyces , and most preferably Saccharomyces cerevisiae.
  • branched alcohols and particularly saturated branched alcohols such as 2-methyl-1-butanol and 3-methyl-1-butanol, can be collected from the medium.
  • the recombinant yeast of the present invention has an excellent feature of producing a desired branched alcohol that can be used as an automotive fuel and a resin material. With the use of the recombinant yeast of the present invention, the above branched alcohol can be produced at low cost.
  • FIG. 1 shows the nucleotide sequence of a DNA fragment optimized to serve as a codon for Saccharomyces cerevisiae based on the nucleotide sequences of the nudF gene and the yhfR gene from Bacillus subtilis registered with GenBank.
  • FIG. 2 is a characteristic chart showing results of GC/MS analysis of 2-methyl-1-butanol with the use of a host yeast and recombinant yeasts of the YPH499 strain.
  • FIG. 3 is a characteristic chart showing results of GC/MS analysis of 3-methyl-1-butanol with the use of a host yeast and recombinant yeasts of the YPH499 strain.
  • the recombinant yeast of the present invention is obtained by introducing the ADP-ribose pyrophosphatase gene and/or the yhfR gene into a yeast in which the hydroxymethyl glutaryl-CoA (HMG-CoA) reductase gene has been expressed to a high degree.
  • the recombinant yeast of the present invention is a yeast that has been modified in a manner such that the HMG-CoA gene expression level and the expression level(s) of the ADP-ribose pyrophosphatase gene and/or the yhfR gene become greater than those of a wild-type yeast.
  • the ADP-ribose pyrophosphatase gene of the present invention is not particularly limited, and therefore a gene from any organism can be used. Specifically, any gene can be used as the ADP-ribose pyrophosphatase gene, regardless of its origin, as long as it is a gene encoding ADP-ribose pyrophosphatase specified with the enzyme commission number EC 3.6.1.13.
  • An example of the ADP-ribose pyrophosphatase gene is the nudF gene (SEQ ID NO: 1) of Bacillus subtilis .
  • SEQ ID NO: 2 represents the amino acid sequence of a protein encoded by the nudF gene of Bacillus subtilis.
  • the “ADP-ribose pyrophosphatase gene” of the present invention includes a gene homologous to a Bacillus subtilis -derived gene.
  • a homologous gene can refer to a gene that has evolved and branched from a common ancestor gene.
  • genes include a homologous gene (ortholog) for two different species and a homologous gene (paralog) generated as a result of overlapping branching in a single species.
  • the ADP-ribose pyrophosphatase gene of the present invention is not limited to Bacillus subtilis -derived genes.
  • the ADP-ribose pyrophosphatase gene includes a gene encoding a protein having an amino acid sequence with a similarity of, for example, 70% or more, preferably 80% or more, more preferably 90% or more, and most preferably 95% or more to the amino acid sequence represented by SEQ ID NO: 2 and having ADP-ribose pyrophosphatase activity.
  • a similarity value refers to a value determined as a default setting with the use of a computer program (the BLAST (Basic Local Alignment Search Tool) program) and a database containing gene sequence information.
  • Examples of the gene encoding a protein having a high similarity to the amino acid sequence (SEQ ID NO: 2) of Bacillus subtilis -derived ADP-ribose pyrophosphatase include the gene specified as “GK2320” of Geobacillus kaustophilus HTA426, the gene specified as “OB1851” of Oceanobacillus iheyensis HTE831, the gene specified as “BSPH — 1706” of Lysinibacillus sphaericus C3-41, the gene specified as “LIN2079” of Listeria innocua Clip11262, the gene specified as “AMET — 2521” of Alkaliphilus metalliredigens QYMF, the gene specified as “EF2696” of Alkaliphilus metalliredigens QYMF, the gene specified as “TTE1310” of Thermoanaerobacter tengcongensis MB4T, the gene specified as “SA1330” of Staphylococcus au
  • the ADP-ribose pyrophosphatase gene of the present invention is also possible to use a gene from an organism with unknown genomic information as the ADP-ribose pyrophosphatase gene of the present invention.
  • the genome is extracted from an organism of interest or the cDNA library of an organism of interest is constructed, followed by isolation of a genomic region or cDNA that hybridizes to at least a portion of a polynucleotide complementary to the nucleotide sequence represented by SEQ ID NO: 1 under stringent conditions.
  • stringent conditions used herein refers to conditions that cause formation of a so-called specific hybrid but not a non-specific hybrid.
  • such conditions include hybridization at 45° C. with 6 ⁇ SSC (sodium chloride/sodium citrate) and the subsequent washing at 50° C. to 65° C. with 0.2 to 1 ⁇ SSC and 0.1% SDS.
  • the conditions include hybridization at 65° C. to 70° C. with 1 ⁇ SSC and the subsequent washing at 65° C. to 70° C. with 0.3 ⁇ SSC.
  • Hybridization can be performed by a conventionally known method such as the method described in J. Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory (1989).
  • the ADP-ribose pyrophosphatase gene of the present invention is not particularly limited to wild-type genes from a variety of organisms as described above.
  • a mutant ADP-ribose pyrophosphatase gene that has been artificially mutated may also be used.
  • An example of a mutant ADP-ribose pyrophosphatase gene is a gene encoding a protein having an amino acid sequence derived from the amino acid sequence encoded by the wild-type ADP-ribose pyrophosphatase gene by deletion, substitution, addition, or insertion of 1 or more amino acid(s) and having ADP-ribose pyrophosphatase activity.
  • ADP-ribose pyrophosphatase gene encoding a protein having an amino acid sequence derived from the amino acid sequence (SEQ ID NO: 2) of Bacillus subtilis -derived ADP-ribose pyrophosphatase by deletion, substitution, addition, or insertion of, for example, 1 to 20 amino acids, preferably 1 to 10 amino acids, more preferably 1 to 7 amino acids, further preferably 1 to 5 amino acids, and particularly preferably 1 to 3 amino acids and having ADP-ribose pyrophosphatase activity.
  • deletion, substitution, or addition of amino acids can be carried out by modifying the nucleotide sequence encoding the above wild-type ADP-ribose pyrophosphatase gene by a technique known in the art.
  • Mutagenesis of the nucleotide sequence can be carried out by a known technique such as the Kunkel method, the gapped duplex method, or a method similar to either thereof with the use of, for example, a mutagenesis kit (e.g., Mutant-K and Mutant-G (product names; TAKARA Bio Inc.)) for a site-specific mutagenesis method, an LA PCR in vitro Mutagenesis series kit (product name, TAKARA Bio Inc.), or the like.
  • a mutagenesis kit e.g., Mutant-K and Mutant-G (product names; TAKARA Bio Inc.)
  • an LA PCR in vitro Mutagenesis series kit product name, TAKARA Bio Inc.
  • a method using agents that cause chemical mutation such as EMS (ethyl methanesulfonate), 5-bromouracil, 2-aminopurine, hydroxylamine, N-methyl-N′-nitro-N-nitrosoguanidine, and other carcinogenic compounds, or a method involving treatment with radioactive rays such as X-rays, ⁇ -rays, ⁇ -rays, and ⁇ -rays, an ion beam, or ultraviolet rays may be used.
  • agents that cause chemical mutation such as EMS (ethyl methanesulfonate), 5-bromouracil, 2-aminopurine, hydroxylamine, N-methyl-N′-nitro-N-nitrosoguanidine, and other carcinogenic compounds
  • radioactive rays such as X-rays, ⁇ -rays, ⁇ -rays, and ⁇ -rays, an ion beam, or ultraviolet rays
  • the yhfR gene of the present invention includes a Bacillus subtilis -derived yhfR gene, a gene homologous to the yhfR gene from an organism other than Bacillus subtilis , and a gene encoding a protein having a high similarity to the protein encoded by the yhfR gene of Bacillus subtili .
  • SEQ ID NO: 3 represents the yhfR gene from Bacillus subtilis .
  • SEQ ID NO: 4 represents the amino acid sequence of a protein encoded by the yhfR gene.
  • the yhfR gene from Bacillus subtilis has been known as a gene encoding a protein highly homologous to phosphoglycerate mutase, although the functions thereof have not been accurately identified (Pearson C. L. et al., J Bacteriol (2000) 182:4121-4123). Therefore, the yhfR gene of the present invention can also be referred to as a gene encoding phosphoglycerate mutase.
  • a gene homologous to the yhfR gene found in an organism other than Bacillus subtilis can be referred to as a gene that has evolved and branched from a common ancestor gene.
  • genes include a homologous gene (ortholog) for two different species and a homologous gene (paralog) generated as a result of overlapping branching in a single species.
  • Genes encoding proteins having a high similarity to the protein encoded by the yhfR gene of Bacillus subtilis include a gene encoding a protein having an amino acid sequence with a similarity of, for example, 70% or more, preferably 80% or more, more preferably 90% or more, and most preferably 95% or more to the amino acid sequence represented by SEQ ID NO: 4.
  • a similarity value refers to a value determined as a default setting with the use of a computer program (the BLAST (Basic Local Alignment Search Tool) program) and a database containing gene sequence information.
  • Examples of a gene encoding a protein having a sequence with a high similarity to the amino acid sequence (SEQ ID NO: 4) of the protein encoded by a Bacillus subtilis -derived yhfR gene include the gene specified as “OB0337” of Oceanobacillus iheyensis HTE831, the gene specified as “EXIG — 2819” of Exiguobacterium sibiricum 255-15, the gene specified as “KRAD — 3374” of Kineococcus radiotolerans SRS30216, the gene specified as “PTH — 1315” of Pelotomaculum thermopropionicum SI, the gene specified as “ARTH — 0069” of Arthrobacter sp.
  • FB24 the gene specified as “DARO — 0602” of Dechloromonas aromatica , the gene specified as “LIN0293” of Listeria innocua Clip11262, the gene specified as “STH2126” of Symbiobacterium thermophilum IAM 14863, the gene specified as “KPN — 04850” of Klebsiella pneumoniae ATCC 700721, and the gene specified as “EBA1038” of Azoarcus sp. EbN1.
  • identifiers capable of identifying such genes are registered in the “Entry” section in the KEGG database.
  • yhfR gene of the present invention it is also possible to use a gene from an organism with unknown genomic information as the yhfR gene of the present invention.
  • the technique described in the “ADP-ribose pyrophosphatase gene” section can be applied to the yhfR gene from an organism with unknown genomic information.
  • the yhfR gene of the present invention is not limited to wild-type genes from a variety of organisms as described above. Therefore, a mutant yhfR gene that has been artificially mutated can also be used.
  • a mutant yhfR gene is a gene encoding a protein having an amino acid sequence derived from the amino acid sequence encoded by the wild-type yhfR gene by deletion, substitution, addition, or insertion of 1 or more amino acid(s).
  • mutant yhfR gene encoding a protein having an amino acid sequence derived from the amino acid sequence (SEQ ID NO: 4) of the Bacillus subtilis -derived yhfR gene by deletion, substitution, addition, or insertion of, for example, 1 to 20 amino acids, preferably 1 to 10 amino acids, more preferably 1 to 7 amino acids, further preferably 1 to 5 amino acids, and particularly preferably 1 to 3 amino acids.
  • deletion, substitution, or addition of amino acids can be carried out by a technique described in the aforementioned “ADP-ribose pyrophosphatase gene” section.
  • the HMG-CoA reductase gene of the present invention which has been expressed to a high degree in a host, is not particularly limited. Therefore, a gene from any organism can be used. Specifically, regardless of the origin, any gene can be used as the HMG-CoA reductase gene as long as it is a gene encoding an enzyme specified as EC 1.1.1.34.
  • the HMG-CoA reductase is an enzyme involved in the mevalonic acid pathway in which dimethylallyl diphosphate is biosynthesized from acetyl-CoA, such enzyme reducing 3-hydroxy-3-methyl glutaryl-CoA to result in mevalonic acid.
  • the mevalonic acid pathway is known as a metabolic pathway found in substantially all organisms.
  • a gene from any organism, which has the mevalonic acid pathway can be used as the HMG-CoA reductase gene of the present invention.
  • examples of the HMG-CoA reductase gene that can be used include the HMG1 gene and the HMG2 gene from Saccharomyces cerevisiae , the HMG-CoA reductase gene from Streptomyces sp. CL190 (S Takahashi et al., (1999) J. Bacteriol., 181, 1256-1263), and other genes from a variety of organisms.
  • the HMG1 gene from Saccharomyces cerevisiae has a function of imparting a prenylalcohol production capacity to yeast as a result of promotion of the expression thereof in yeast, which is disclosed in, for example, JP Patent No. 3894119, JP Patent No.
  • HMG1 genes disclosed in JP Patent No. 3894119, JP Patent No. 3838033, and JP Patent No. 3918185 and the mutant HMG1 gene can be used.
  • the recombinant yeast of the present invention can cause high expression of the HMG-CoA reductase gene by incorporating the above HMG-CoA reductase gene into a vector so as to result in high expression of the gene and introducing the obtained expression vector into a host yeast described below.
  • high expression of the HMG-CoA reductase gene may be caused by modifying the promoter region of the HMG-CoA reductase gene that is endogenously present in a host yeast described below.
  • a host yeast into which the aforementioned HMG-CoA reductase gene, the ADP-ribose pyrophosphatase gene, and/or the yhfR gene are(is) introduced is not particularly limited. Examples thereof include ascomycetous yeast of Ascomycetes, basidiomycetous yeast of Basidiomycetes, and deuteromycetouts yeast of Deuteromycetes. Examples of yeast that can be used include: ascomycetous yeast, and particularly budding yeast, such as Saccharomyces cerevisiae known as bakers' yeast, Candida utilis , or Pichia pastris ; and fission yeast such as Shizosaccharomyces pombe .
  • yeasts haploid yeast or diploid yeast known as so-called laboratory yeast may be used.
  • a multiploid yeast having the chromosome structure of a diploid or greater polyploid yeast known as so-called practical yeast may be used.
  • examples of yeasts that can be used include the A451 strain, the EUG8 strain, the EUG12 strain, the EUG27 strain, the YPH499 strain, the YPH500 strain, the W303-1A strain, the W303-1B strain, and the AURGG101 strain.
  • yeast in which the expression of the HMG-CoA reductase gene has been strengthened disclosed in JP Patent No. 3894119, JP Patent No. 3838033, and JP Patent No. 3918185 described above.
  • the recombinant yeast of the present invention may be produced by introducing the ADP-ribose pyrophosphatase gene and/or the yhfR gene into yeast in which the expression of the HMG-CoA reductase gene has been strengthened.
  • the phrase “the expression of the HMG-CoA reductase gene has been strengthened” means that the expression level (i.e. “amount”) of the HMG-CoA reductase gene is significantly improved.
  • the term “significantly” refers to a situation in which the expression amount of the HMG-CoA reductase gene is increased to a statistically significant extent compared with that of yeast not being strengthened the expression of the gene, e.g. wild-type yeast.
  • Any conventionally known technique may be used for introducing the above HMG-CoA reductase gene, the ADP-ribose pyrophosphatase gene, and/or the yhfR gene into the aforementioned host yeast.
  • plasmid DNA, bacteriophage, retrotransposon DNA, yeast artificial chromosome DNA (YAC: yeast artificial chromosome), and the like which can be genetically retained in a host yeast, are constructed.
  • plasmid DNA examples include: YCp-type Escherichia coli -yeast shuttle vectors such as pRS413, pRS414, pRS415, pRS416, YCp50, pAUR112, and pAUR123; YEp-type Escherichia coli -yeast shuttle vectors such as pYES2 and YEp13; YIp-type Escherichia coli -yeast shuttle vectors such as pRS403, pRS404, pRS405, pRS406, pAUR101, and pAUR135; Escherichia coli -derived plasmids (e.g.: Co1E plasmids such as pBR322, pBR325, pUC18, pUC19, pUC118, pUC119, pTV118N, pTV119N, pBluescript, pHSG298, pHSG396, and pTrc99A
  • Examples of phage DNA include ⁇ phages (Charon4A, Charon21A, EMBL3, EMBL4, ⁇ gt10, ⁇ gt11, and ⁇ ZAP), ⁇ X174, M13 mp 18, and M13 mp 19.
  • Examples of retrotransposons include a Ty factor.
  • Examples of YAC vectors include pYACC2.
  • any promoter for stable expression or promoter for inducible expression may be used as a transcription promoter that causes the HMG-CoA reductase gene, the ADP-ribose pyrophosphatase gene, and the yhfR gene to be expressed in a host cell.
  • a promoter for stable expression is, for example, a transcription promoter for a gene involved in a major metabolic pathway, such promoter having transcription activity regardless of growth conditions and the like.
  • a promoter for inducible expression is a promoter that induces transcription under specific growth conditions.
  • Any transcription promoter may be used as long as it exhibits activity in the aforementioned host yeast.
  • a GAL1 promoter, a GAL10 promoter, a TDH3 (GAP) promoter, an ADH1 promoter, a TEF2 promoter, and the like can be used for expression in yeast.
  • cis elements such as enhancers, splicing signals, polyA addition signals, selection markers, and the like can be ligated to such promoters.
  • selection markers include: marker genes with non-auxotrophic phenotypes such as URA3, LEU2, TRP1, HIS3, ADE2, and LYS2; and antibiotic-resistant genes such as Ampr, Tetr, Cmr, Kmr, AUR1-C, can1, Bla, Shble, and Neo.
  • a terminator from any gene may be used as long as it exhibits activity in the aforementioned host yeast.
  • Examples of terminators for expression in yeast include the ADH1 terminator and the CYC1 terminator.
  • any conventional method known as a yeast transformation method can be applied as a method for introducing a plasmid incorporating the HMG-CoA reductase gene, the ADP-ribose pyrophosphatase gene, and the yhfR gene into a host yeast.
  • Specific examples of such method that can be carried out include, but are not limited to, an electroporation method described in “ Meth. Enzym., 194, p182 (1990),” a spheroplast method described in “ Proc. Natl. Acad. Sci. USA, 75 p. 1929 (1978),” a lithium acetate method described in “ J. Bacteriology, 153, p. 163 (1983),” and methods described in “ Proc. Natl. Acad. Sci. USA, 75 p. 1929 (1978)” and “ Methods in yeast genetics, 2000 Edition: A Cold Spring Harbor Laboratory Course Manual.”
  • PCR polymerase chain reaction
  • Southern hybridization method it is possible to confirm whether or not a gene has been introduced into a host yeast by the PCR (polymerase chain reaction) method, the Southern hybridization method, or the like.
  • PCR may be carried out by preparing DNA from a recombinant yeast and designing a primer specific to an introduced gene. Thereafter, PCR amplification products are subjected to agarose gel electrophoresis, polyacrylamide gel electrophoresis, capillary electrophoresis, or the like. Then, staining with ethidium bromide, an SYBR Green solution, or the like or DNA detection with a UV detector is carried out such that amplification products can be detected with peaks, thereby confirming introduced DNA.
  • PCR is carried out using primers that have been preliminarily labeled with a fluorescent dye or the like so as to detect amplification products.
  • the recombinant yeast of the present invention produced as above can produce saturated branched alcohols such as 2-methyl-1-butanol and 3-methyl-1-butanol in a medium when cultured in an ordinary medium.
  • WO 2007/139925 reports that Escherichia coli into which the nudF gene or the yhfR gene of Bacillus subtilis have been introduced can synthesize unsaturated branched alcohols such as 3-methyl-2-butene-1-ol and 3-methyl-3-butene-1-ol.
  • the recombinant yeast of the present invention has an unpredictable effect of producing saturated branched alcohols such as 2-methyl-1-butanol and 3-methyl-1-butanol.
  • saturated branched alcohols such as 2-methyl-1-butanol and 3-methyl-1-butanol produced in a medium can be isolated/produced by a known method such as distillation.
  • a distillation method When unsaturated branched alcohols are isolated/purified by a distillation method, a polymerization reaction via unsaturated bonds in a molecular chain or a chemical reaction with other components takes place in some cases, which might result in reduction of branched alcohol productivity.
  • unsaturated branched alcohols have lower acid stability than saturated branched alcohols, it is necessary to reduce unsaturated bonds for conversion into saturated branched alcohols.
  • Saccharomyces cerevisiae capable of causing high expression of the HMG-CoA reductase gene was produced first. Specifically, the HMG-CoA reductase gene derived from the Saccharomyces cerevisiae DBY746 strain was introduced into the Saccharomyces cerevisiae YPH499 strain. A detailed explanation is as follows.
  • a CYC1 transcription terminator CYC1t fragment was prepared by PCR with the use of a pair of primers designed as shown below.
  • XhoI-Tcyc1FW (SEQ ID NO: 5) 5′ TGC ATC TCG AGG GCC GCA TCA TGT AAT TAG 3′
  • ApaI-Tcyc1RV (SEQ ID NO: 6) 5′ CAT TAG GGC CCG GCC GCA AAT TAA AGC CTT CG 3′
  • PCR reaction solution was a solution (50 ml) containing 1 ⁇ pfu buffer with MgSO 4 (Promega), 10 nmol dNTP, a Pfu DNA polymerase (Promega) (1.5 u), and a perfect match polymerase enhancer (Stratagene) (1 ml).
  • PCR thermal cycles were as follows: 95° C. for 2 minutes; 30 cycles of 95° C. for 45 seconds, 60° C. for 30 seconds, and 72° C. for 1 minute; and 72° C. for 5 minutes.
  • the resulting solution was stored as a stock solution at 4° C.
  • DNA amplified by PCR was cleaved with XhoI and ApaI, followed by purification of a 260-bp DNA fragment by agarose gel electrophoresis. Then, pRS404 and pRS406 (Stratagene) were separately prepared and a purified DNA fragment was inserted into the XhoI-ApaI site of each thereof.
  • the obtained plasmids were referred to as pRS404Tcyc and pRS406Tcyc, respectively.
  • a DNA fragment containing a TDH3p (GAP) promoter was prepared by PCR with the use of genomic DNA of the Saccharomyces cerevisiae YPH499 strain (Stratagene) as a template and a pair of primers designed as shown below.
  • genomic DNA a “GenTLE Kun” yeast genomic DNA preparation kit (TAKARA Bio Inc.) was used for the genomic DNA.
  • SacI-Ptdh3FW (SEQ ID NO: 7) 5′ CAC GGA GCT CCA GTT CGA GTT TAT CAT TAT CAA 3′ SacII-Ptdh3RV: (SEQ ID NO: 8) 5′ CTC TCC GCG GTT TGT TTG TTT ATG TGT GTT TAT TC 3′
  • genomic DNA (0.46 mg) as a template and the above pair of primers (100 pmol each) were used.
  • the reaction solution used for PCR was a solution (100 ml) containing 1 ⁇ ExTaq buffer (TAKARA Bio Inc.), dNTP (20 nmol), ExTaq DNA polymerase (TAKARA Bio Inc.) (0.5 u), and a perfect match polymerase enhancer (1 ml).
  • PCR thermal cycles were as follows: 95° C. for 2 minutes; 30 cycles of 95° C. for 45 seconds, 60° C. for 1 minute, and 72° C. for 2 minutes; and 72° C. for 4 minutes.
  • the resulting solution was stored as a stock solution at 4° C.
  • DNA amplified by PCR was cleaved with SacI and SacII. Then, a 680-bp DNA fragment was purified by agarose gel electrophoresis. The obtained DNA fragment was designated as TDH3p.
  • pYES2 (Invitrogen) was cleaved with SspI and NheI.
  • a 1.5-kbp fragment containing a 2 ⁇ m DNA replication origin (2 ⁇ m ori) was purified by agarose gel electrophoresis and blunt-ended with a Klenow enzyme. The obtained DNA fragment was designated as 2 ⁇ m OriSN.
  • 2 ⁇ m OriSN was inserted into the BAP (bacterial alkaline phosphatase, TAKARA Bio Inc.)-treated NaeI site of each of pRS404Tcyc and pRS406Tcyc obtained in (1) above.
  • the reaction product was transformed into an E. coli SURE2 strain according to a general method.
  • Transformed Escherichia coli was cultured according to a general method for preparation of plasmid DNA.
  • the obtained plasmid DNA was cleaved with DraIII and EcoRI or with PstI and PvuII, followed by agarose gel electrophoresis. Then, the insertion of 2 ⁇ m on and the direction of insertion were checked.
  • Plasmids obtained by separately inserting 2 ⁇ m on into pRS404Tcyc and pRS406Tcyc obtained in (1) above in the same direction with pYES2 were designated as pRS434Tcyc2 ⁇ m Ori and pRS436Tcyc2 ⁇ m Ori, respectively.
  • TDH3p (a DNA fragment containing a transcription promoter) obtained in (2) above was inserted into the SacI-SacII site of each of pRS434Tcyc2 pmOri and pRS436Tcyc2 ⁇ m Ori.
  • the finally obtained plasmids were designated as pRS434GAP and pRS436GAP, respectively.
  • a pRS504 vector was produced by introducing the Sacharomyces cerevisiae rDNA sequence into pRS434GAP produced in (4) above.
  • rDNA sequence Nieto A et al. (1999) Biotechnol. Prog., 15 (3), 459-66 was used as a reference.
  • a PCR reaction was carried out as in the above case with the use of primers shown below.
  • AatTRP1-50F (SEQ ID NO: 9) 5′-TTT CCG ACG TCC ACG TGA GTA TAC GTG ATT AAG-3′
  • TRP1d-R (SEQ ID NO: 10) 5′-AGG CAA GTG CAC AAA CAA TAC TT-3′
  • PCR was carried out with the use of pRS434GAP produced in (4) above as a template DNA, AatTRP1-50F, and TRP1d-R for amplification of a 0.8-kb TRP1d fragment. Then, PCR was carried out with the use of phosphorylated primers shown below and genomic DNA of the Saccharomyces cerevisiae YPH499 (ATCC 204679) strain for amplification of a portion of rDNA; namely, a 1.3-kb fragment (R47).
  • R4 (SEQ ID NO: 11) 5′-ATG AGA GTA GCA AAC GTA AGT CTA A-3′
  • K-R7 (SEQ ID NO: 12) 5′-TGA CTG GTA CCT TTC CTC TAA TCA GGT TCC ACC-3′
  • TRP1d and R47 fragments were purified by agarose gel electrophoresis, followed by ligation. PCR was carried out using the resulting reaction solution as a template and AatTRP1-50F and K-R7 primers for amplification of a 2.0-kb fragment (TR47) comprising TRP1d and R47 ligated to each other. TR47 was further purified by agarose gel electrophoresis, followed by subcloning into a pCR-Blunt 11 TOPO vector (Invitrogen). The obtained vector was designated as TOPO-TR47. As a result of sequencing of the TR47 fragment, it was confirmed that no mutation was contained therein.
  • TOPO-TR47 and pRS434GAP were digested with restriction enzymes Aat11 and Kpn1 such that a 3.2-kb fragment comprising a TR47 fragment and a TDH3 promoter was excised therefrom, followed by ligation.
  • the obtained plasmid was referred to as pRS504.
  • Inverse PCR was carried out using pRS436GAP produced in (4) above as template DNA and a pair of primers that had been phosphorylated with T4 polynucleotide kinase for amplification of a 4.7-kb fragment.
  • T7-F (SEQ ID NO: 13) 5′-GCG TAA TAC GAC TCA CTA TAG GG-3′ 2um-R: (SEQ ID NO: 14) 5′-CCT GAT GCG GTA TTT TCT CCT TAC-3′
  • the obtained fragment was subjected to self-ligation, followed by degradation and removal of the template DNA with DpnI.
  • a plasmid pRS436-2 ⁇ m comprising pRS436GAP from which 2 ⁇ m Ori had been removed was produced.
  • PCR was carried out with the use of Aat-TY1F and Sse-TY2R primers shown below and genomic DNA of the Saccharomyces cerevisiae YPH499 (ATCC 204679) strain.
  • the amplified fragment was designated as T12.
  • Aat-TY1F (SEQ ID NO: 15) 5′-GAC GTC TGT TGG AAT AAA AAT CCA CTA TCG-3′
  • Sse-TY2R (SEQ ID NO: 16) 5′-CCT GCA GGA TTC CGT TTT ATA TGT TTA TAT TCA TTG-3′
  • PCR was carried out using primers shown below and genomic DNA of the Saccharomyces cerevisiae YPH499 (ATCC 204679) strain.
  • the amplified fragment was designated as T34.
  • SAC 1-TY3F (SEQ ID NO: 17) 5′-GAG CTC GAG GAA TAA TCG TAA TAT TAG TAT GTA-3′
  • Sse-TY4R (SEQ ID NO: 18) 5′-GCG CGC TGA GAA ATT TGT GGG TAA TTA GAT AAT-3′
  • Each of the amplified T12 and T34 fragments was a portion of the LTR sequence of YOLWTy1-1 (chromosome XV; from coordinates 117, 702 to 123, 627).
  • the amplified T12 and T34 fragments were separately subcloned into a pCR-Blunt II TOPO vector.
  • the obtained vectors were designated as TOPO-T12 and TOPO-T34, respectively.
  • the vectors were subjected to sequencing, and thus no PCR error was confirmed therein.
  • TOPO-T12 was digested with AatII and Sse83871.
  • a T12 fragment was excised therefrom, followed by ligation into the AatII-Sse8387I site of pRS436-2 ⁇ m.
  • a plasmid pDIT12 was produced.
  • TOPO-T34 was digested with the use of SacI and BssHII. A T34 fragment was excised therefrom, followed by ligation into the SacI-BssHII site of pDIT12. Thus, a plasmid pDI626 was produced.
  • PCR was carried out using a “Quick-Clone cDNA” cDNA library from Saccharomyces cerevisiae DBY746 (Clonetech) as a template and the pair of primers shown below.
  • the PCR reaction solution was a solution (50 ⁇ l) containing Perfect Match (Stratagene) (1 ⁇ l), a 10 ⁇ ExTaq buffer (TAKARA Bio Inc.) (5 ⁇ l), a 2.5 mM dNTP mix (4 ⁇ l), 5 U/ ⁇ l ExTaq (TAKARA Bio Inc.) (1 ⁇ l), and Primers 1 and 2 (10 pmol each).
  • PCR thermal cycles were as follows: 30 cycles of 94° C. for 45 seconds, 55° C. for 1 minute, and 72° C. for 2 minutes.
  • the amplified fragment (approximately 3.2 kb) was subjected to T/A cloning into a pT7Blue-T vector for determination of the nucleotide sequence of the HMG1 region.
  • the sequence was found to be different from the HMG1 gene sequence from Saccharomyces cerevisiae registered with GenBank (http://www.neb.nih.gov/Genbank/index.html) at 12 sites. Of these, 3 sites were confirmed to have a mutation that could influence the amino acid sequence (S68F, L607S, and H909R).
  • the produced plasmid DNA was designated as pT7HMG1.
  • pT7HMG1 was cleaved with Sma1, ApaL1, and Sal1 and then a 3.2-kbp fragment was prepared by agarose electrophoresis. The fragment was inserted into the Sma1-Sal1 site of a pALTER-1 (Promega) vector such that pALHMG1 was produced. After alkaline denaturation, pALHMG1 was subjected to annealing with mutated oligos (Oligos 1 to 3) shown below, an Amp repair oligo (Promega), and a Tet knockout oligo (Promega).
  • the resultant was introduced into the Escherichia coli ES1301 strain (Promega). Subsequently, a transformant retaining a site-specifically mutated plasmid was subjected to enrichment culture with 125 ⁇ g/ml ampicillin such that plasmid DNA was prepared.
  • the plasmid was designated as pALHMG106.
  • pALHMG106 produced in (7) above was cleaved with SmaI and SalI. Then, a 3.2-kb HMG1 gene fragment was purified by agarose electrophoresis. The fragment was inserted into the SmaI-SalI site of pRS434GAP produced in (4) above such that pRS434GAP-HMG1 was obtained. Next, PCR was carried out with the use of pRS434GAP-HMG1 as a template and primers shown below for amplification of a fragment between the initiation codon and the Tth111I site (647 by reckoned from the ATG initiation codon) of the HMG1 gene.
  • SacHMG1-F (SEQ ID NO: 24) 5′-CCG CGG AAC AAA ATG CCG CCG CTA TTC AAG GG-3′ TthHMG647R: (SEQ ID NO: 25) 5′-GAC CCG GTC TTC CTC ATG TC-3′
  • the SacHMG1-F primer With the use of the SacHMG1-F primer, the AACAAA sequence and the SacII site were added upstream of the HMG1 initiation codon.
  • the PCR product was subcloned into a pMCR2.1-TOPO vector (Invitrogen) and it was confirmed to have no PCR error by sequencing.
  • a SacII-Tth111I fragment was excised from the obtained vector so as to be replaced by a SacII-Tth111I fragment of pRS434GAP-HMG1.
  • the obtained plasmid was designated as pRS434GAPa-HMG1.
  • pRS434GAPa-HMG1 was digested with SacII and XhoI.
  • a 3.2-kb HMG1 fragment was excised therefrom, followed by ligation into the SacII-XhoI site of pRS504 produced in (5) above.
  • the obtained plasmid was designated as pRS504HMG1.
  • pRS504HMG1 (20 ⁇ g) produced in (8) above was cleaved with BstPI for linearization.
  • Linearized pRS504HMG1 was recovered by ethanol precipitation and dissolved in sterile water (5 ⁇ l).
  • pRS504HMG1 was introduced into Saccharomyces cerevisiae YPH499 (Stratagene) with the use of a Frozen EZ yeast transformation kit (Zymoresearch).
  • the obtained strain was designated as HMG1/YPH499.
  • GGGCCGCGGACTAGTGCCGCCACC and GGGTCTAGAACTAGTGCCGCCACC were added to the non-translation region upstream of ORF of the nudF gene and that of the yhfR gene, respectively.
  • GATATCGTCGACGGGG and GAATTCGTCGACGGGG were added to the non-translation region downstream of ORF of the nudF gene and that of the yhfR gene, respectively (capital letters in FIG. 1 ).
  • a DNA fragment of the nudF gene represented by SEQ ID NO: 26 was digested with SpeI and SalI and inserted into the SpeI-SalI site of the pDI626 produced in (6) above.
  • the obtained plasmid was designated as PDI626NUDF.
  • a DNA fragment of the yhfR gene represented by SEQ ID NO: 27 was digested with SpeI and SalI and inserted into the SpeI-SalI site of pDI626 produced in (6) above.
  • the obtained plasmid was designated as PDI626YHFR.
  • PDI626NUDF and PDI626YHFR (22 ⁇ g each) obtained above was cleaved with AatII and BssHII for linearization.
  • Linearized PDI626NUDF and PDI626YHFR were separately recovered by ethanol precipitation and dissolved in sterile water (5 ⁇ l).
  • PDI626NUDF and PDI626YHFR were separately introduced into Saccharomyces cerevisiae YPH499 (Stratagene).
  • a strain grown in a uracil-free yeast minimal medium (BIO 101) was collected as a strain having the nudF gene or yhfR gene introduced therein. PCR was carried out in order to confirm the occurrence of gene introduction.
  • the obtained strains were designated as the NUDF/YPH499 strain and the YHFR/YPH499 strain, respectively.
  • PDI626NUDF and PDI626YHFR (22 ⁇ g each) obtained in (10) above were cleaved with AatII and BssHII, respectively, for linearization.
  • Linearized PDI626NUDF and PDI626YHFR were introduced into HMG1/YPH499 produced in (9) above in a similar manner.
  • a transgenic strain was obtained. After confirmation of gene introduction by PCR, the obtained strains were designated as the NUDF/HMG1/YPH499 strain and the YHFR/HMG1/YPH499 strain, respectively.
  • the NUDF/YPH499 strain and YHFR/YPH499 strain produced in (10) above and the NUDF/HMG1/YPH499 strain, the YHFR/HMG1/YPH499 strain, and the Saccharomyces cerevisiae YPH499 strain produced in (11) above were precultured in an SD medium (-Trp, -Ura) at 30° C.
  • an SD medium (-Trp, -Ura) at 30° C.
  • a 2-ml SD medium (-Trp, -Ura) contained in a sterile disposable glass test tube (IWAKI) was inoculated separately with each preculture solution (1%). Each tube was covered with an aluminium cap and subjected to shake culture at 30° C. under aerobic conditions.
  • Ethyl acetate (2 ml) and methanol (0.3 ml) were added to each test tube cryopreserved at ⁇ 30° C. after the above culture, followed by agitation with a vortex mixer. Centrifugation was carried out with a centrifuge (Beckman Coulter, Inc.) (room temperature, 1200 rpm, 5 minutes) for separation of the solvent phase and the aqueous phase. Each solvent phase was transferred to a 2-ml vial bottle for a gas chromatograph mass spectrometer (GC/MS), to which a 1% undecanol solution (dissolved in ethanol) (10 ⁇ l) had been added as an internal standard.
  • GC/MS gas chromatograph mass spectrometer
  • FIG. 2 shows GC/MS analysis results.
  • FIG. 3 shows results of comparison of the samples regarding the ratio of the 3-methyl-1-butanol area to the internal standard area, provided that the 3-methyl-1-butanol area was determined based on profiles obtained as GC/MS analysis results with the use of a database containing GC/MS mass spectrometry patterns. As shown in FIGS.
  • the recombinant yeast of the present invention can produce 2-methyl-1-butanol and 3-methyl-1-butanol. Therefore, it can be used for production of automotive fuel and the like containing the butanols as components.

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Abstract

This invention provides a recombinant yeast that can produce branched alcohol appropriate for automotive fuel and the like and a branched alcohol production method whereby branched alcohol can be produced at low cost with the use of the recombinant yeast.
A recombinant yeast in which a hydroxymethyl glutaryl-CoA reductase gene has been expressed to a high degree and the ADP-ribose pyrophosphatase gene and/or the yhfR gene are introduced so as to be expressed therein is provided.

Description

    BACKGROUND OF THE INVENTION
  • 1. Field of the Invention
  • The present invention relates to a recombinant yeast having a predetermined gene introduced therein and a branched alcohol production method using the recombinant yeast.
  • 2. Background Art
  • In recent years, the following problems have been arising regarding ethanol used as automotive fuel: the energy density thereof is low and the characteristics thereof significantly differ from those of conventional petroleum fuel. Therefore, studies have been conducted to produce butanol or the like, which is an alcohol with an extended carbon chain length serving as fuel characteristically closer to petroleum fuel, by a fermentative production method with the use of Escherichia coli and yeast (see WO 2007/041269 and WO 2008/052991). In addition, since a gasoline fuel with the high octane number of such a straight-chain alcohol is preferably used, fuels comprising 2-methyl-1-butanol, 3-methyl-1-butanol, and the like have been also studied (Nature 451, 86-89, (2008)).
  • Meanwhile, it has been reported that 2-methyl-1-butenol can be synthesized by causing the expression of the nudF gene or yhfR gene of Bacillus subtilis in Escherichia coli. In addition, it has been revealed that expression products of the nudF gene and the yhfR gene convert dimethylallyl-diphosphate or isopentenyl diphosphate into 2-methyl-3-butene-1-ol (Appl. Environ. Microbiol. 73, 6277-83 (2007)). Further, it has been reported that 3-methyl-2-butene-1-ol and 3-methyl-3-butene-1-ol can be synthesized by causing the expression of the above genes in Escherichia coli in a similar manner (WO 2007/139925).
    • SUMMARY OF THE INVENTION
  • It is generally thought that the amino acid synthesis pathway is used for synthesizing a branched alcohol with a certain chain length such as 2-methyl-1-butanol or 3-methyl-1-butanol, which is appropriate for automotive fuel and the like. However, regarding branched alcohol production with the use of the amino acid synthesis pathway, the supply shortage of amino acids necessary for microorganism growth is a matter of concern. There are still problems for mass-production of branched alcohol, which is a product of interest. In addition, a method involving the use of the nudF gene or the yhfR gene of Bacillus subtilis is advantageous because it does not involve the use of the amino acid synthesis pathway. However, the resulting branched alcohol has unsaturated bonds, and therefore the oxidative stability is poor when such alcohol is used as fuel, which is problematic. In addition, it is possible to reduce unsaturated bonds with a step of adding hydrogen to synthesized branched alcohol, for example. However, such step is cost-consuming, which is also problematic.
  • In view of the above circumstances, it is an object of the present invention to provide a recombinant yeast that can produce branched alcohol appropriate for automotive fuel and the like. It is another object of the present invention to provide a branched alcohol production method whereby branched alcohol can be produced at low cost with the use of the recombinant yeast.
  • As a result of intensive studies in order to achieve the above object, the present inventors have found that a desired branched alcohol can be produced by causing the expression of the ADP-ribose pyrophosphatase gene and/or the yhfR gene in a yeast in which a gene encoding hydroxymethyl glutaryl-CoA (HMG-CoA) reductase has been expressed to a high degree. This has led to the completion of the present invention.
  • Specifically, the recombinant yeast of the present invention is a recombinant yeast in which a hydroxymethyl glutaryl-CoA reductase gene has been expressed to a high degree, and the ADP-ribose pyrophosphatase gene and/or the yhfR gene are introduced so as to be expressed therein. For the recombinant yeast of the present invention, the nudF gene of Bacillus subtilis is preferably used as the ADP-ribose pyrophosphatase gene. In addition, for the recombinant yeast of the present invention, the yhfR gene of Bacillus subtilis is preferably used as the above yhfR gene. Further, for the recombinant yeast of the present invention, the HMG1 gene of Saccharomyces cerevisiae is preferably used as the above hydroxymethyl glutaryl-CoA reductase gene.
  • In addition, for the recombinant yeast of the present invention, a host is preferably a yeast having a mevalonic acid pathway, more preferably a yeast of the genus Saccharomyces, and most preferably Saccharomyces cerevisiae.
  • By culturing the above recombinant yeast of the present invention, branched alcohols, and particularly saturated branched alcohols such as 2-methyl-1-butanol and 3-methyl-1-butanol, can be collected from the medium.
    • EFFECTS OF THE INVENTION
  • The recombinant yeast of the present invention has an excellent feature of producing a desired branched alcohol that can be used as an automotive fuel and a resin material. With the use of the recombinant yeast of the present invention, the above branched alcohol can be produced at low cost.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIG. 1 shows the nucleotide sequence of a DNA fragment optimized to serve as a codon for Saccharomyces cerevisiae based on the nucleotide sequences of the nudF gene and the yhfR gene from Bacillus subtilis registered with GenBank.
  • FIG. 2 is a characteristic chart showing results of GC/MS analysis of 2-methyl-1-butanol with the use of a host yeast and recombinant yeasts of the YPH499 strain.
  • FIG. 3 is a characteristic chart showing results of GC/MS analysis of 3-methyl-1-butanol with the use of a host yeast and recombinant yeasts of the YPH499 strain.
    •  DESCRIPTION OF THE PREFERRED EMBODIMENTS
  • Hereinafter, the recombinant yeast of the present invention and the branched alcohol production method using the recombinant yeast are described in detail.
  • The recombinant yeast of the present invention is obtained by introducing the ADP-ribose pyrophosphatase gene and/or the yhfR gene into a yeast in which the hydroxymethyl glutaryl-CoA (HMG-CoA) reductase gene has been expressed to a high degree. In other words, the recombinant yeast of the present invention is a yeast that has been modified in a manner such that the HMG-CoA gene expression level and the expression level(s) of the ADP-ribose pyrophosphatase gene and/or the yhfR gene become greater than those of a wild-type yeast.
    • ADP-Ribose Pyrophosphatase Gene
  • The ADP-ribose pyrophosphatase gene of the present invention is not particularly limited, and therefore a gene from any organism can be used. Specifically, any gene can be used as the ADP-ribose pyrophosphatase gene, regardless of its origin, as long as it is a gene encoding ADP-ribose pyrophosphatase specified with the enzyme commission number EC 3.6.1.13. An example of the ADP-ribose pyrophosphatase gene is the nudF gene (SEQ ID NO: 1) of Bacillus subtilis. SEQ ID NO: 2 represents the amino acid sequence of a protein encoded by the nudF gene of Bacillus subtilis.
  • The “ADP-ribose pyrophosphatase gene” of the present invention includes a gene homologous to a Bacillus subtilis-derived gene. In general, a homologous gene can refer to a gene that has evolved and branched from a common ancestor gene. Such genes include a homologous gene (ortholog) for two different species and a homologous gene (paralog) generated as a result of overlapping branching in a single species.
  • In addition, the ADP-ribose pyrophosphatase gene of the present invention is not limited to Bacillus subtilis-derived genes. The ADP-ribose pyrophosphatase gene includes a gene encoding a protein having an amino acid sequence with a similarity of, for example, 70% or more, preferably 80% or more, more preferably 90% or more, and most preferably 95% or more to the amino acid sequence represented by SEQ ID NO: 2 and having ADP-ribose pyrophosphatase activity. Herein, such a similarity value refers to a value determined as a default setting with the use of a computer program (the BLAST (Basic Local Alignment Search Tool) program) and a database containing gene sequence information.
  • Examples of the gene encoding a protein having a high similarity to the amino acid sequence (SEQ ID NO: 2) of Bacillus subtilis-derived ADP-ribose pyrophosphatase include the gene specified as “GK2320” of Geobacillus kaustophilus HTA426, the gene specified as “OB1851” of Oceanobacillus iheyensis HTE831, the gene specified as “BSPH—1706” of Lysinibacillus sphaericus C3-41, the gene specified as “LIN2079” of Listeria innocua Clip11262, the gene specified as “AMET—2521” of Alkaliphilus metalliredigens QYMF, the gene specified as “EF2696” of Alkaliphilus metalliredigens QYMF, the gene specified as “TTE1310” of Thermoanaerobacter tengcongensis MB4T, the gene specified as “SA1330” of Staphylococcus aureus N315, the gene specified as “DRED—1901” of Desulfotomaculum reducens MI-1, and the gene specified as “PTH—1329” of Pelotomaculum thermopropionicum SI. In addition, identifiers that allow the identification of such genes are registered in the “Entry” section in the KEGG database.
  • Further, it is also possible to use a gene from an organism with unknown genomic information as the ADP-ribose pyrophosphatase gene of the present invention. For instance, the genome is extracted from an organism of interest or the cDNA library of an organism of interest is constructed, followed by isolation of a genomic region or cDNA that hybridizes to at least a portion of a polynucleotide complementary to the nucleotide sequence represented by SEQ ID NO: 1 under stringent conditions. Thus, the ADP-ribose pyrophosphatase gene of the organism can be identified/isolated. The term “stringent conditions” used herein refers to conditions that cause formation of a so-called specific hybrid but not a non-specific hybrid. For example, such conditions include hybridization at 45° C. with 6×SSC (sodium chloride/sodium citrate) and the subsequent washing at 50° C. to 65° C. with 0.2 to 1×SSC and 0.1% SDS. Alternatively, the conditions include hybridization at 65° C. to 70° C. with 1×SSC and the subsequent washing at 65° C. to 70° C. with 0.3×SSC. Hybridization can be performed by a conventionally known method such as the method described in J. Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory (1989).
  • Furthermore, the ADP-ribose pyrophosphatase gene of the present invention is not particularly limited to wild-type genes from a variety of organisms as described above. A mutant ADP-ribose pyrophosphatase gene that has been artificially mutated may also be used. An example of a mutant ADP-ribose pyrophosphatase gene is a gene encoding a protein having an amino acid sequence derived from the amino acid sequence encoded by the wild-type ADP-ribose pyrophosphatase gene by deletion, substitution, addition, or insertion of 1 or more amino acid(s) and having ADP-ribose pyrophosphatase activity. An example of such gene that can be used is a mutant ADP-ribose pyrophosphatase gene encoding a protein having an amino acid sequence derived from the amino acid sequence (SEQ ID NO: 2) of Bacillus subtilis-derived ADP-ribose pyrophosphatase by deletion, substitution, addition, or insertion of, for example, 1 to 20 amino acids, preferably 1 to 10 amino acids, more preferably 1 to 7 amino acids, further preferably 1 to 5 amino acids, and particularly preferably 1 to 3 amino acids and having ADP-ribose pyrophosphatase activity.
  • Moreover, deletion, substitution, or addition of amino acids can be carried out by modifying the nucleotide sequence encoding the above wild-type ADP-ribose pyrophosphatase gene by a technique known in the art. Mutagenesis of the nucleotide sequence can be carried out by a known technique such as the Kunkel method, the gapped duplex method, or a method similar to either thereof with the use of, for example, a mutagenesis kit (e.g., Mutant-K and Mutant-G (product names; TAKARA Bio Inc.)) for a site-specific mutagenesis method, an LA PCR in vitro Mutagenesis series kit (product name, TAKARA Bio Inc.), or the like. In addition, as a mutagenesis method, a method using agents that cause chemical mutation such as EMS (ethyl methanesulfonate), 5-bromouracil, 2-aminopurine, hydroxylamine, N-methyl-N′-nitro-N-nitrosoguanidine, and other carcinogenic compounds, or a method involving treatment with radioactive rays such as X-rays, α-rays, β-rays, and γ-rays, an ion beam, or ultraviolet rays may be used.
  • yhfR Gene
  • The yhfR gene of the present invention includes a Bacillus subtilis-derived yhfR gene, a gene homologous to the yhfR gene from an organism other than Bacillus subtilis, and a gene encoding a protein having a high similarity to the protein encoded by the yhfR gene of Bacillus subtili. SEQ ID NO: 3 represents the yhfR gene from Bacillus subtilis. SEQ ID NO: 4 represents the amino acid sequence of a protein encoded by the yhfR gene. The yhfR gene from Bacillus subtilis has been known as a gene encoding a protein highly homologous to phosphoglycerate mutase, although the functions thereof have not been accurately identified (Pearson C. L. et al., J Bacteriol (2000) 182:4121-4123). Therefore, the yhfR gene of the present invention can also be referred to as a gene encoding phosphoglycerate mutase.
  • In general, a gene homologous to the yhfR gene found in an organism other than Bacillus subtilis can be referred to as a gene that has evolved and branched from a common ancestor gene. Such genes include a homologous gene (ortholog) for two different species and a homologous gene (paralog) generated as a result of overlapping branching in a single species.
  • Genes encoding proteins having a high similarity to the protein encoded by the yhfR gene of Bacillus subtilis include a gene encoding a protein having an amino acid sequence with a similarity of, for example, 70% or more, preferably 80% or more, more preferably 90% or more, and most preferably 95% or more to the amino acid sequence represented by SEQ ID NO: 4. Herein, such a similarity value refers to a value determined as a default setting with the use of a computer program (the BLAST (Basic Local Alignment Search Tool) program) and a database containing gene sequence information.
  • Examples of a gene encoding a protein having a sequence with a high similarity to the amino acid sequence (SEQ ID NO: 4) of the protein encoded by a Bacillus subtilis-derived yhfR gene include the gene specified as “OB0337” of Oceanobacillus iheyensis HTE831, the gene specified as “EXIG—2819” of Exiguobacterium sibiricum 255-15, the gene specified as “KRAD—3374” of Kineococcus radiotolerans SRS30216, the gene specified as “PTH—1315” of Pelotomaculum thermopropionicum SI, the gene specified as “ARTH—0069” of Arthrobacter sp. FB24, the gene specified as “DARO—0602” of Dechloromonas aromatica, the gene specified as “LIN0293” of Listeria innocua Clip11262, the gene specified as “STH2126” of Symbiobacterium thermophilum IAM 14863, the gene specified as “KPN—04850” of Klebsiella pneumoniae ATCC 700721, and the gene specified as “EBA1038” of Azoarcus sp. EbN1. In addition, identifiers capable of identifying such genes are registered in the “Entry” section in the KEGG database.
  • Further, it is also possible to use a gene from an organism with unknown genomic information as the yhfR gene of the present invention. The technique described in the “ADP-ribose pyrophosphatase gene” section can be applied to the yhfR gene from an organism with unknown genomic information.
  • Furthermore, the yhfR gene of the present invention is not limited to wild-type genes from a variety of organisms as described above. Therefore, a mutant yhfR gene that has been artificially mutated can also be used. For example, an example of a mutant yhfR gene is a gene encoding a protein having an amino acid sequence derived from the amino acid sequence encoded by the wild-type yhfR gene by deletion, substitution, addition, or insertion of 1 or more amino acid(s). As an example of such gene, it is possible to use a mutant yhfR gene encoding a protein having an amino acid sequence derived from the amino acid sequence (SEQ ID NO: 4) of the Bacillus subtilis-derived yhfR gene by deletion, substitution, addition, or insertion of, for example, 1 to 20 amino acids, preferably 1 to 10 amino acids, more preferably 1 to 7 amino acids, further preferably 1 to 5 amino acids, and particularly preferably 1 to 3 amino acids.
  • Further, deletion, substitution, or addition of amino acids can be carried out by a technique described in the aforementioned “ADP-ribose pyrophosphatase gene” section.
    • HMG-CoA Reductase Gene
  • The HMG-CoA reductase gene of the present invention, which has been expressed to a high degree in a host, is not particularly limited. Therefore, a gene from any organism can be used. Specifically, regardless of the origin, any gene can be used as the HMG-CoA reductase gene as long as it is a gene encoding an enzyme specified as EC 1.1.1.34. The HMG-CoA reductase is an enzyme involved in the mevalonic acid pathway in which dimethylallyl diphosphate is biosynthesized from acetyl-CoA, such enzyme reducing 3-hydroxy-3-methyl glutaryl-CoA to result in mevalonic acid. The mevalonic acid pathway is known as a metabolic pathway found in substantially all organisms. A gene from any organism, which has the mevalonic acid pathway, can be used as the HMG-CoA reductase gene of the present invention.
  • For instance, examples of the HMG-CoA reductase gene that can be used include the HMG1 gene and the HMG2 gene from Saccharomyces cerevisiae, the HMG-CoA reductase gene from Streptomyces sp. CL190 (S Takahashi et al., (1999) J. Bacteriol., 181, 1256-1263), and other genes from a variety of organisms. In addition, the HMG1 gene from Saccharomyces cerevisiae has a function of imparting a prenylalcohol production capacity to yeast as a result of promotion of the expression thereof in yeast, which is disclosed in, for example, JP Patent No. 3894119, JP Patent No. 3838033, and JP Patent No. 3918185. In the present invention, the HMG1 genes disclosed in JP Patent No. 3894119, JP Patent No. 3838033, and JP Patent No. 3918185 and the mutant HMG1 gene can be used.
  • In addition, the recombinant yeast of the present invention can cause high expression of the HMG-CoA reductase gene by incorporating the above HMG-CoA reductase gene into a vector so as to result in high expression of the gene and introducing the obtained expression vector into a host yeast described below. Alternatively, high expression of the HMG-CoA reductase gene may be caused by modifying the promoter region of the HMG-CoA reductase gene that is endogenously present in a host yeast described below.
    • Host Yeast
  • In the present invention, a host yeast into which the aforementioned HMG-CoA reductase gene, the ADP-ribose pyrophosphatase gene, and/or the yhfR gene are(is) introduced is not particularly limited. Examples thereof include ascomycetous yeast of Ascomycetes, basidiomycetous yeast of Basidiomycetes, and deuteromycetouts yeast of Deuteromycetes. Examples of yeast that can be used include: ascomycetous yeast, and particularly budding yeast, such as Saccharomyces cerevisiae known as bakers' yeast, Candida utilis, or Pichia pastris; and fission yeast such as Shizosaccharomyces pombe. In addition, as a yeast, haploid yeast or diploid yeast known as so-called laboratory yeast may be used. Alternatively, a multiploid yeast having the chromosome structure of a diploid or greater polyploid yeast known as so-called practical yeast may be used. In the case of S. cerevisiae, examples of yeasts that can be used include the A451 strain, the EUG8 strain, the EUG12 strain, the EUG27 strain, the YPH499 strain, the YPH500 strain, the W303-1A strain, the W303-1B strain, and the AURGG101 strain.
  • Also, it is possible to use yeast in which the expression of the HMG-CoA reductase gene has been strengthened disclosed in JP Patent No. 3894119, JP Patent No. 3838033, and JP Patent No. 3918185 described above. Specifically, the recombinant yeast of the present invention may be produced by introducing the ADP-ribose pyrophosphatase gene and/or the yhfR gene into yeast in which the expression of the HMG-CoA reductase gene has been strengthened. Here, the phrase “the expression of the HMG-CoA reductase gene has been strengthened” means that the expression level (i.e. “amount”) of the HMG-CoA reductase gene is significantly improved. Here, the term “significantly” refers to a situation in which the expression amount of the HMG-CoA reductase gene is increased to a statistically significant extent compared with that of yeast not being strengthened the expression of the gene, e.g. wild-type yeast.
    • Transformation of Host Yeast
  • Any conventionally known technique may be used for introducing the above HMG-CoA reductase gene, the ADP-ribose pyrophosphatase gene, and/or the yhfR gene into the aforementioned host yeast. For example, when each such gene is introduced, plasmid DNA, bacteriophage, retrotransposon DNA, yeast artificial chromosome DNA (YAC: yeast artificial chromosome), and the like, which can be genetically retained in a host yeast, are constructed. Examples of plasmid DNA include: YCp-type Escherichia coli-yeast shuttle vectors such as pRS413, pRS414, pRS415, pRS416, YCp50, pAUR112, and pAUR123; YEp-type Escherichia coli-yeast shuttle vectors such as pYES2 and YEp13; YIp-type Escherichia coli-yeast shuttle vectors such as pRS403, pRS404, pRS405, pRS406, pAUR101, and pAUR135; Escherichia coli-derived plasmids (e.g.: Co1E plasmids such as pBR322, pBR325, pUC18, pUC19, pUC118, pUC119, pTV118N, pTV119N, pBluescript, pHSG298, pHSG396, and pTrc99A; p15A plasmids such as pACYC177 and pACYC184; and pSC101 plasmids such as pMW118, pMW119, pMW218, and pMW219); and Bacillus subtilis-derived plasmids (e.g., pUB110 and pTP5). Examples of phage DNA include λ phages (Charon4A, Charon21A, EMBL3, EMBL4, λgt10, λgt11, and λZAP), φX174, M13 mp 18, and M13 mp 19. Examples of retrotransposons include a Ty factor. Examples of YAC vectors include pYACC2.
  • In addition, as a transcription promoter that causes the HMG-CoA reductase gene, the ADP-ribose pyrophosphatase gene, and the yhfR gene to be expressed in a host cell, any promoter for stable expression or promoter for inducible expression may be used. A promoter for stable expression is, for example, a transcription promoter for a gene involved in a major metabolic pathway, such promoter having transcription activity regardless of growth conditions and the like. A promoter for inducible expression is a promoter that induces transcription under specific growth conditions.
  • Any transcription promoter may be used as long as it exhibits activity in the aforementioned host yeast. For example, a GAL1 promoter, a GAL10 promoter, a TDH3 (GAP) promoter, an ADH1 promoter, a TEF2 promoter, and the like can be used for expression in yeast. Further, if desired, cis elements such as enhancers, splicing signals, polyA addition signals, selection markers, and the like can be ligated to such promoters. In addition, examples of selection markers include: marker genes with non-auxotrophic phenotypes such as URA3, LEU2, TRP1, HIS3, ADE2, and LYS2; and antibiotic-resistant genes such as Ampr, Tetr, Cmr, Kmr, AUR1-C, can1, Bla, Shble, and Neo.
  • As a transcription terminator, a terminator from any gene may be used as long as it exhibits activity in the aforementioned host yeast. Examples of terminators for expression in yeast include the ADH1 terminator and the CYC1 terminator.
  • Meanwhile, any conventional method known as a yeast transformation method can be applied as a method for introducing a plasmid incorporating the HMG-CoA reductase gene, the ADP-ribose pyrophosphatase gene, and the yhfR gene into a host yeast. Specific examples of such method that can be carried out include, but are not limited to, an electroporation method described in “Meth. Enzym., 194, p182 (1990),” a spheroplast method described in “Proc. Natl. Acad. Sci. USA, 75 p. 1929 (1978),” a lithium acetate method described in “J. Bacteriology, 153, p. 163 (1983),” and methods described in “Proc. Natl. Acad. Sci. USA, 75 p. 1929 (1978)” and “Methods in yeast genetics, 2000 Edition: A Cold Spring Harbor Laboratory Course Manual.”
  • It is possible to confirm whether or not a gene has been introduced into a host yeast by the PCR (polymerase chain reaction) method, the Southern hybridization method, or the like. For instance, PCR may be carried out by preparing DNA from a recombinant yeast and designing a primer specific to an introduced gene. Thereafter, PCR amplification products are subjected to agarose gel electrophoresis, polyacrylamide gel electrophoresis, capillary electrophoresis, or the like. Then, staining with ethidium bromide, an SYBR Green solution, or the like or DNA detection with a UV detector is carried out such that amplification products can be detected with peaks, thereby confirming introduced DNA. Alternatively, PCR is carried out using primers that have been preliminarily labeled with a fluorescent dye or the like so as to detect amplification products.
    • Branched Alcohol Production
  • The recombinant yeast of the present invention produced as above can produce saturated branched alcohols such as 2-methyl-1-butanol and 3-methyl-1-butanol in a medium when cultured in an ordinary medium. WO 2007/139925 reports that Escherichia coli into which the nudF gene or the yhfR gene of Bacillus subtilis have been introduced can synthesize unsaturated branched alcohols such as 3-methyl-2-butene-1-ol and 3-methyl-3-butene-1-ol. When compared with the above, it can be said that the recombinant yeast of the present invention has an unpredictable effect of producing saturated branched alcohols such as 2-methyl-1-butanol and 3-methyl-1-butanol.
  • In addition, saturated branched alcohols such as 2-methyl-1-butanol and 3-methyl-1-butanol produced in a medium can be isolated/produced by a known method such as distillation. When unsaturated branched alcohols are isolated/purified by a distillation method, a polymerization reaction via unsaturated bonds in a molecular chain or a chemical reaction with other components takes place in some cases, which might result in reduction of branched alcohol productivity. In addition, since unsaturated branched alcohols have lower acid stability than saturated branched alcohols, it is necessary to reduce unsaturated bonds for conversion into saturated branched alcohols. Meanwhile, even if saturated branched alcohols produced by the recombinant yeast of the present invention are isolated/purified by a distillation method, it is possible to avoid loss due to the above polymerization reaction or chemical reaction. Therefore, when branched alcohols are produced with the use of the recombinant yeast of the present invention, excellent productivity can be achieved. When branched alcohol is produced with the use of the recombinant yeast of the present invention, low-cost production can be achieved. This is because a step of reducing unsaturated bonds can be omitted.
    • EXAMPLES
  • The present invention is hereafter described in greater detail with reference to the following examples, although the technical scope of the present invention is not limited thereto.
    • Example 1 Production of the HMG1/YPH499 Strain
  • In this Example, Saccharomyces cerevisiae capable of causing high expression of the HMG-CoA reductase gene was produced first. Specifically, the HMG-CoA reductase gene derived from the Saccharomyces cerevisiae DBY746 strain was introduced into the Saccharomyces cerevisiae YPH499 strain. A detailed explanation is as follows.
  • (1) Preparation of pRS404Tcyc and pRS406Tcyc
  • A CYC1 transcription terminator CYC1t fragment was prepared by PCR with the use of a pair of primers designed as shown below.
  • XhoI-Tcyc1FW:
    (SEQ ID NO: 5)
    5′ TGC ATC TCG AGG GCC GCA TCA TGT AAT TAG 3′
    ApaI-Tcyc1RV:
    (SEQ ID NO: 6)
    5′ CAT TAG GGC CCG GCC GCA AAT TAA AGC CTT CG 3′
  • In addition, pYES2 (Invitrogen) (0.1 mg) as a PCR template and the above pair of primers (50 pmol each) were used. The PCR reaction solution was a solution (50 ml) containing 1×pfu buffer with MgSO4 (Promega), 10 nmol dNTP, a Pfu DNA polymerase (Promega) (1.5 u), and a perfect match polymerase enhancer (Stratagene) (1 ml). PCR thermal cycles were as follows: 95° C. for 2 minutes; 30 cycles of 95° C. for 45 seconds, 60° C. for 30 seconds, and 72° C. for 1 minute; and 72° C. for 5 minutes. The resulting solution was stored as a stock solution at 4° C.
  • Thereafter, DNA amplified by PCR was cleaved with XhoI and ApaI, followed by purification of a 260-bp DNA fragment by agarose gel electrophoresis. Then, pRS404 and pRS406 (Stratagene) were separately prepared and a purified DNA fragment was inserted into the XhoI-ApaI site of each thereof. The obtained plasmids were referred to as pRS404Tcyc and pRS406Tcyc, respectively.
    • (2) Production of a TDH3p Fragment
  • A DNA fragment containing a TDH3p (GAP) promoter was prepared by PCR with the use of genomic DNA of the Saccharomyces cerevisiae YPH499 strain (Stratagene) as a template and a pair of primers designed as shown below. In addition, for the genomic DNA, a “GenTLE Kun” yeast genomic DNA preparation kit (TAKARA Bio Inc.) was used.
  • SacI-Ptdh3FW:
    (SEQ ID NO: 7)
    5′ CAC GGA GCT CCA GTT CGA GTT TAT CAT TAT CAA 3′
    SacII-Ptdh3RV:
    (SEQ ID NO: 8)
    5′ CTC TCC GCG GTT TGT TTG TTT ATG TGT GTT TAT
    TC 3′
  • For PCR, genomic DNA (0.46 mg) as a template and the above pair of primers (100 pmol each) were used. In addition, the reaction solution used for PCR was a solution (100 ml) containing 1×ExTaq buffer (TAKARA Bio Inc.), dNTP (20 nmol), ExTaq DNA polymerase (TAKARA Bio Inc.) (0.5 u), and a perfect match polymerase enhancer (1 ml). PCR thermal cycles were as follows: 95° C. for 2 minutes; 30 cycles of 95° C. for 45 seconds, 60° C. for 1 minute, and 72° C. for 2 minutes; and 72° C. for 4 minutes. The resulting solution was stored as a stock solution at 4° C.
  • Thereafter, DNA amplified by PCR was cleaved with SacI and SacII. Then, a 680-bp DNA fragment was purified by agarose gel electrophoresis. The obtained DNA fragment was designated as TDH3p.
    • (3) Production of a 2 μm OriSN Fragment
  • pYES2 (Invitrogen) was cleaved with SspI and NheI. A 1.5-kbp fragment containing a 2 μm DNA replication origin (2 μm ori) was purified by agarose gel electrophoresis and blunt-ended with a Klenow enzyme. The obtained DNA fragment was designated as 2 μm OriSN.
  • (4) Production of pRS434GAP and pRS436GAP
  • 2 μm OriSN was inserted into the BAP (bacterial alkaline phosphatase, TAKARA Bio Inc.)-treated NaeI site of each of pRS404Tcyc and pRS406Tcyc obtained in (1) above. The reaction product was transformed into an E. coli SURE2 strain according to a general method. Transformed Escherichia coli was cultured according to a general method for preparation of plasmid DNA. The obtained plasmid DNA was cleaved with DraIII and EcoRI or with PstI and PvuII, followed by agarose gel electrophoresis. Then, the insertion of 2 μm on and the direction of insertion were checked. Plasmids obtained by separately inserting 2 μm on into pRS404Tcyc and pRS406Tcyc obtained in (1) above in the same direction with pYES2 were designated as pRS434Tcyc2 μm Ori and pRS436Tcyc2 μm Ori, respectively.
  • Then, TDH3p (a DNA fragment containing a transcription promoter) obtained in (2) above was inserted into the SacI-SacII site of each of pRS434Tcyc2 pmOri and pRS436Tcyc2 μm Ori. The finally obtained plasmids were designated as pRS434GAP and pRS436GAP, respectively.
  • (5) Production of pRS504
  • A pRS504 vector was produced by introducing the Sacharomyces cerevisiae rDNA sequence into pRS434GAP produced in (4) above. For the rDNA sequence, Nieto A et al. (1999) Biotechnol. Prog., 15 (3), 459-66 was used as a reference. A PCR reaction was carried out as in the above case with the use of primers shown below.
  • AatTRP1-50F:
    (SEQ ID NO: 9)
    5′-TTT CCG ACG TCC ACG TGA GTA TAC GTG ATT AAG-3′
    TRP1d-R:
    (SEQ ID NO: 10)
    5′-AGG CAA GTG CAC AAA CAA TAC TT-3′
  • Specifically, first, PCR was carried out with the use of pRS434GAP produced in (4) above as a template DNA, AatTRP1-50F, and TRP1d-R for amplification of a 0.8-kb TRP1d fragment. Then, PCR was carried out with the use of phosphorylated primers shown below and genomic DNA of the Saccharomyces cerevisiae YPH499 (ATCC 204679) strain for amplification of a portion of rDNA; namely, a 1.3-kb fragment (R47).
  • R4:
    (SEQ ID NO: 11)
    5′-ATG AGA GTA GCA AAC GTA AGT CTA A-3′
    K-R7:
    (SEQ ID NO: 12)
    5′-TGA CTG GTA CCT TTC CTC TAA TCA GGT TCC ACC-3′
  • Next, the TRP1d and R47 fragments were purified by agarose gel electrophoresis, followed by ligation. PCR was carried out using the resulting reaction solution as a template and AatTRP1-50F and K-R7 primers for amplification of a 2.0-kb fragment (TR47) comprising TRP1d and R47 ligated to each other. TR47 was further purified by agarose gel electrophoresis, followed by subcloning into a pCR-Blunt 11 TOPO vector (Invitrogen). The obtained vector was designated as TOPO-TR47. As a result of sequencing of the TR47 fragment, it was confirmed that no mutation was contained therein. Subsequently, TOPO-TR47 and pRS434GAP were digested with restriction enzymes Aat11 and Kpn1 such that a 3.2-kb fragment comprising a TR47 fragment and a TDH3 promoter was excised therefrom, followed by ligation. The obtained plasmid was referred to as pRS504.
  • (6) Production of a pDI626 Vector
  • Inverse PCR was carried out using pRS436GAP produced in (4) above as template DNA and a pair of primers that had been phosphorylated with T4 polynucleotide kinase for amplification of a 4.7-kb fragment.
  • T7-F:
    (SEQ ID NO: 13)
    5′-GCG TAA TAC GAC TCA CTA TAG GG-3′
    2um-R:
    (SEQ ID NO: 14)
    5′-CCT GAT GCG GTA TTT TCT CCT TAC-3′
  • The obtained fragment was subjected to self-ligation, followed by degradation and removal of the template DNA with DpnI. Thus, a plasmid pRS436-2 μm comprising pRS436GAP from which 2 μm Ori had been removed was produced.
  • Next, PCR was carried out with the use of Aat-TY1F and Sse-TY2R primers shown below and genomic DNA of the Saccharomyces cerevisiae YPH499 (ATCC 204679) strain. The amplified fragment was designated as T12.
  • Aat-TY1F:
    (SEQ ID NO: 15)
    5′-GAC GTC TGT TGG AAT AAA AAT CCA CTA TCG-3′
    Sse-TY2R:
    (SEQ ID NO: 16)
    5′-CCT GCA GGA TTC CGT TTT ATA TGT TTA TAT TCA
    TTG-3′
  • Similarly, PCR was carried out using primers shown below and genomic DNA of the Saccharomyces cerevisiae YPH499 (ATCC 204679) strain. The amplified fragment was designated as T34.
  • SAC 1-TY3F:
    (SEQ ID NO: 17)
    5′-GAG CTC GAG GAA TAA TCG TAA TAT TAG TAT GTA-3′
    Sse-TY4R:
    (SEQ ID NO: 18)
    5′-GCG CGC TGA GAA ATT TGT GGG TAA TTA GAT AAT-3′
  • Each of the amplified T12 and T34 fragments was a portion of the LTR sequence of YOLWTy1-1 (chromosome XV; from coordinates 117, 702 to 123, 627). The amplified T12 and T34 fragments were separately subcloned into a pCR-Blunt II TOPO vector. The obtained vectors were designated as TOPO-T12 and TOPO-T34, respectively. The vectors were subjected to sequencing, and thus no PCR error was confirmed therein. TOPO-T12 was digested with AatII and Sse83871. A T12 fragment was excised therefrom, followed by ligation into the AatII-Sse8387I site of pRS436-2 μm. Thus, a plasmid pDIT12 was produced. Similarly, TOPO-T34 was digested with the use of SacI and BssHII. A T34 fragment was excised therefrom, followed by ligation into the SacI-BssHII site of pDIT12. Thus, a plasmid pDI626 was produced.
    • (7) Cloning of the “HMG1” HMG-CoA Reductase Gene
  • PCR was carried out using a “Quick-Clone cDNA” cDNA library from Saccharomyces cerevisiae DBY746 (Clonetech) as a template and the pair of primers shown below.
  • (SEQ ID NO: 19)
    Primer 1: 5′-ATG CCG CCG CTA TTC AAG GGA CT-3′
    (SEQ ID NO: 20)
    Primer 2: 5′-TTA GGA TTT AAT GCA GGT GAC GG-3′
  • In addition, the PCR reaction solution was a solution (50 μl) containing Perfect Match (Stratagene) (1 μl), a 10×ExTaq buffer (TAKARA Bio Inc.) (5 μl), a 2.5 mM dNTP mix (4 μl), 5 U/μl ExTaq (TAKARA Bio Inc.) (1 μl), and Primers 1 and 2 (10 pmol each). PCR thermal cycles were as follows: 30 cycles of 94° C. for 45 seconds, 55° C. for 1 minute, and 72° C. for 2 minutes.
  • The amplified fragment (approximately 3.2 kb) was subjected to T/A cloning into a pT7Blue-T vector for determination of the nucleotide sequence of the HMG1 region. As a result of comparison, the sequence was found to be different from the HMG1 gene sequence from Saccharomyces cerevisiae registered with GenBank (http://www.neb.nih.gov/Genbank/index.html) at 12 sites. Of these, 3 sites were confirmed to have a mutation that could influence the amino acid sequence (S68F, L607S, and H909R). The produced plasmid DNA was designated as pT7HMG1.
  • Next, in order to correct PCR errors, pT7HMG1 was cleaved with Sma1, ApaL1, and Sal1 and then a 3.2-kbp fragment was prepared by agarose electrophoresis. The fragment was inserted into the Sma1-Sal1 site of a pALTER-1 (Promega) vector such that pALHMG1 was produced. After alkaline denaturation, pALHMG1 was subjected to annealing with mutated oligos (Oligos 1 to 3) shown below, an Amp repair oligo (Promega), and a Tet knockout oligo (Promega). The resultant was introduced into the Escherichia coli ES1301 strain (Promega). Subsequently, a transformant retaining a site-specifically mutated plasmid was subjected to enrichment culture with 125 μg/ml ampicillin such that plasmid DNA was prepared.
  • (SEQ ID NO: 21)
    Oligo 1: 5′-CCA AAT AAA GAC TCC AAC ACT CTA TTT-3′
    (SEQ ID NO: 22)
    Oligo 2: 5′-GAA TTA GAA GCA TTA TTA AGT AGT GGA-3′
    (SEQ ID NO: 23)
    Oligo 3: 5′-GGA TTT AAC GCA CAT GCA GCT AAT TTA-3′
  • As a result of analysis of the nucleotide sequence of the prepared plasmid DNA, the aforementioned mutations at 3 sites were confirmed to have been corrected. The plasmid was designated as pALHMG106.
  • (8) Production of pRS504HMG1
  • pALHMG106 produced in (7) above was cleaved with SmaI and SalI. Then, a 3.2-kb HMG1 gene fragment was purified by agarose electrophoresis. The fragment was inserted into the SmaI-SalI site of pRS434GAP produced in (4) above such that pRS434GAP-HMG1 was obtained. Next, PCR was carried out with the use of pRS434GAP-HMG1 as a template and primers shown below for amplification of a fragment between the initiation codon and the Tth111I site (647 by reckoned from the ATG initiation codon) of the HMG1 gene.
  • SacHMG1-F:
    (SEQ ID NO: 24)
    5′-CCG CGG AAC AAA ATG CCG CCG CTA TTC AAG GG-3′
    TthHMG647R:
    (SEQ ID NO: 25)
    5′-GAC CCG GTC TTC CTC ATG TC-3′
  • With the use of the SacHMG1-F primer, the AACAAA sequence and the SacII site were added upstream of the HMG1 initiation codon. The PCR product was subcloned into a pMCR2.1-TOPO vector (Invitrogen) and it was confirmed to have no PCR error by sequencing. A SacII-Tth111I fragment was excised from the obtained vector so as to be replaced by a SacII-Tth111I fragment of pRS434GAP-HMG1. The obtained plasmid was designated as pRS434GAPa-HMG1. pRS434GAPa-HMG1 was digested with SacII and XhoI. A 3.2-kb HMG1 fragment was excised therefrom, followed by ligation into the SacII-XhoI site of pRS504 produced in (5) above. The obtained plasmid was designated as pRS504HMG1.
    • (9) Production of the HMG1/YPH499 Strain
  • pRS504HMG1 (20 μg) produced in (8) above was cleaved with BstPI for linearization. Linearized pRS504HMG1 was recovered by ethanol precipitation and dissolved in sterile water (5 μl). pRS504HMG1 was introduced into Saccharomyces cerevisiae YPH499 (Stratagene) with the use of a Frozen EZ yeast transformation kit (Zymoresearch). A strain grown in a tryptophan-free YNB yeast minimal medium (Difco) was subjected to colony PCR such that the HMG1 gene was confirmed to have been introduced therein. The obtained strain was designated as HMG1/YPH499.
  • (10) Production of the NUDF/YPH499 strain and the YHFR/YPH499 Strain
  • A DNA fragment (FIG. 1) optimized for a codon of Saccharomyces cerevisiae based on the nucleotide sequences of the nudF gene and the yhfR gene from Bacillus subtilis registered with GenBank (http://www.neb.nih.gov/Genbank/index.html) was synthesized (Operon Biotechnologies).
  • In addition, GGGCCGCGGACTAGTGCCGCCACC and GGGTCTAGAACTAGTGCCGCCACC were added to the non-translation region upstream of ORF of the nudF gene and that of the yhfR gene, respectively. Further, GATATCGTCGACGGGG and GAATTCGTCGACGGGG were added to the non-translation region downstream of ORF of the nudF gene and that of the yhfR gene, respectively (capital letters in FIG. 1).
  • A DNA fragment of the nudF gene represented by SEQ ID NO: 26 was digested with SpeI and SalI and inserted into the SpeI-SalI site of the pDI626 produced in (6) above. The obtained plasmid was designated as PDI626NUDF. In addition, a DNA fragment of the yhfR gene represented by SEQ ID NO: 27 was digested with SpeI and SalI and inserted into the SpeI-SalI site of pDI626 produced in (6) above. The obtained plasmid was designated as PDI626YHFR.
  • Each of PDI626NUDF and PDI626YHFR (22 μg each) obtained above was cleaved with AatII and BssHII for linearization. Linearized PDI626NUDF and PDI626YHFR were separately recovered by ethanol precipitation and dissolved in sterile water (5 μl). With the use of a Frozen EZ yeast transformation kit (Zymoresearch), PDI626NUDF and PDI626YHFR were separately introduced into Saccharomyces cerevisiae YPH499 (Stratagene). A strain grown in a uracil-free yeast minimal medium (BIO 101) was collected as a strain having the nudF gene or yhfR gene introduced therein. PCR was carried out in order to confirm the occurrence of gene introduction. The obtained strains were designated as the NUDF/YPH499 strain and the YHFR/YPH499 strain, respectively.
    • (11) Production of the NUDF/HMG1/YPH499 Strain and the YHFR/HMG1/YPH499 Strain
  • PDI626NUDF and PDI626YHFR (22 μg each) obtained in (10) above were cleaved with AatII and BssHII, respectively, for linearization. Linearized PDI626NUDF and PDI626YHFR were introduced into HMG1/YPH499 produced in (9) above in a similar manner. As a result of obtaining a uracil-independent strain, a transgenic strain was obtained. After confirmation of gene introduction by PCR, the obtained strains were designated as the NUDF/HMG1/YPH499 strain and the YHFR/HMG1/YPH499 strain, respectively.
    • (12) Branched Alcohol Synthesis Analysis Culture Test
  • The NUDF/YPH499 strain and YHFR/YPH499 strain produced in (10) above and the NUDF/HMG1/YPH499 strain, the YHFR/HMG1/YPH499 strain, and the Saccharomyces cerevisiae YPH499 strain produced in (11) above were precultured in an SD medium (-Trp, -Ura) at 30° C. Next, a 2-ml SD medium (-Trp, -Ura) contained in a sterile disposable glass test tube (IWAKI) was inoculated separately with each preculture solution (1%). Each tube was covered with an aluminium cap and subjected to shake culture at 30° C. under aerobic conditions.
    • Extraction and Analysis
  • Ethyl acetate (2 ml) and methanol (0.3 ml) were added to each test tube cryopreserved at −30° C. after the above culture, followed by agitation with a vortex mixer. Centrifugation was carried out with a centrifuge (Beckman Coulter, Inc.) (room temperature, 1200 rpm, 5 minutes) for separation of the solvent phase and the aqueous phase. Each solvent phase was transferred to a 2-ml vial bottle for a gas chromatograph mass spectrometer (GC/MS), to which a 1% undecanol solution (dissolved in ethanol) (10 μl) had been added as an internal standard. Each bottle was sealed with a Teflon-coated aluminium cap, followed by GC/MS analysis. At this time, 2-methyl-1-butanol serving as a standard solution was analyzed for quantification based on the TIC peak area ratio of the standard solution to undecanol used as the internal standard. GC/MS analysis was carried out with the use of an HP6890/5973 GC/MS system (Hewlett-Packard Development Company, L.P.) under the conditions listed in table 1.
    • [Table 1] <GC/MS Analysis Conditions>
      • Inlet temperature: 260° C.
      • Detector temperature: 260° C.
      • Injection Parameters
      • Mode: Automatic injection
      • Sample volume: 2 μl
      • Instances of washing: 3 times with methanol
        • Twice with chloroform
      • Split ratio: 20:1
      • Column: Hewlett-Packard Development Company, L.P. HP-5MS (0.25 mm×30 M; film thickness: 0.25 μm)
      • Carrier gas: Helium: 1.0 ml/min
      • Oven temperature rise conditions: Retention at 45° C. for 1 minute Temperature rise at 5° C./minute to 60° C.
        • 100° C./minute to 320° C.; retention for 3.4 minutes
  • FIG. 2 shows GC/MS analysis results. In addition, FIG. 3 shows results of comparison of the samples regarding the ratio of the 3-methyl-1-butanol area to the internal standard area, provided that the 3-methyl-1-butanol area was determined based on profiles obtained as GC/MS analysis results with the use of a database containing GC/MS mass spectrometry patterns. As shown in FIGS. 2 and 3, it has been revealed that 2-methyl-1-butanol and 3-methyl-1-butanol, which are saturated branched alcohols, can be produced with the use of a recombinant yeast that has been modified such that the expression level of the HMG-CoA gene and the expression levels of ADP-ribose pyrophosphatase gene and/or the yhfR gene become higher than those of a wild-type yeast.
  • The recombinant yeast of the present invention can produce 2-methyl-1-butanol and 3-methyl-1-butanol. Therefore, it can be used for production of automotive fuel and the like containing the butanols as components.

Claims (15)

1. A recombinant yeast in which a hydroxymethyl glutaryl-CoA reductase gene has been expressed to a high degree and the ADP-ribose pyrophosphatase gene and/or the yhfR gene are introduced so as to be expressed therein.
2. The recombinant yeast according to claim 1, wherein the ADP-ribose pyrophosphatase gene is the nudF gene of Bacillus subtilis.
3. The recombinant yeast according to claim 1, wherein the yhfR gene is the yhfR gene of Bacillus subtilis.
4. The recombinant yeast according to claim 1, wherein the hydroxymethyl glutaryl-CoA reductase gene is the HMG1 gene of Saccharomyces cerevisiae.
5. The recombinant yeast according to claim 1, which is a yeast having a mevalonic acid pathway.
6. The recombinant yeast according to claim 1, which is a yeast of the genus Saccharomyces.
7. The recombinant yeast according to claim 1, which is Saccharomyces cerevisiae.
8. A branched alcohol production method, comprising culturing the recombinant yeast according to claim 1 and collecting a branched alcohol from the medium.
9. The branched alcohol production method according to claim 8, wherein the ADP-ribose pyrophosphatase gene in the recombinant yeast is the nudF gene of Bacillus subtilis.
10. The branched alcohol production method according to claim 8, wherein the yhfR gene in the recombinant yeast is the yhfR gene of Bacillus subtilis.
11. The branched alcohol production method according to claim 8, wherein the hydroxymethyl glutaryl-CoA reductase gene in the recombinant yeast is the HMG1 gene of Saccharomyces cerevisiae.
12. The branched alcohol production method according to claim 8, wherein the recombinant yeast is a yeast having a mevalonic acid pathway.
13. The branched alcohol production method according to claim 8, wherein the recombinant yeast is a yeast of the genus Saccharomyces.
14. The branched alcohol production method according to claim 8, wherein the recombinant yeast is Saccharomyces cerevisiae.
15. The branched alcohol production method according to claim 8, wherein 2-methyl-1-butanol and 3-methyl-1-butanol is collected as the branched alcohol.
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US9340793B2 (en) 2011-01-20 2016-05-17 Toyota Jidosha Kabushiki Kaisha Recombinant yeast and substance production method using the same
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CN118813437A (en) * 2024-09-02 2024-10-22 深圳良合生物科技有限公司 A high-lysine-producing yeast strain and its construction method and application

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