643
Views
6
CrossRef citations to date
0
Altmetric
Review

Progress in the genomics and genome-wide study of sake yeast

Pages 1463-1472 | Received 18 Jan 2019, Accepted 18 Feb 2019, Published online: 05 Mar 2019

References

  • Vaughan-Martini A, Martini A. Saccharomyces Meyen ex Reess (1870). In: Kurtsman CP, Fell JW, Boekhaut T, editors. The yeasts, a taxonomic study. 5th ed. London: Elsevier; 2011. p. 733–746.
  • Goffeau A, Barrell BG, Bussey H, et al. Life with 6000 genes. Science. 1996;274(5287):546–567.
  • Lashkari DA, DeRisi JL, McCusker JH, et al. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci USA. 1997;94(24):13057–13062.
  • Johnston M. Gene chips: array of hope for understanding gene regulation. Curr Biol. 1998;8(5):R171–174.
  • Cox KH, Pinchak AB, Cooper TG. Genomewide transcriptional analysis in S. cerevisiae by mini-array membrane hybridization. Yeast. 1999;15(8):708–713.
  • Winzeler EA, Shoemaker DD, Astromoff A, et al.. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 1999;285(5429):901–906.
  • Huh WK, Falvo JV, Gerke LC, et al. Global analysis of protein localization in budding yeast. Nature. 2003;425(6959):686–691.
  • Akao T, Yashiro I, Hosoyama A, et al. Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7. DNA Res. 2011;18(6):423–434.
  • Levy SE, Myers RM. Advancements in next-generation sequencing. Annu Rev Genomics Hum Genet. 2016;17:95–115.
  • Ogihara F, Kitagaki H, Wang Q, et al. Common industrial sake yeast strains have three copies of the AQY1–ARR3 region of chromosome XVI in their genomes. Yeast. 2008;25(6):419–432.
  • Wu H, Zheng X, Araki Y, et al. Global gene expression analysis of yeast cells during sake brewing. Appl Environ Microbiol. 2006;72(11):7353–7358.
  • Wu H, Watanabe T, Araki Y, et al. Disruption of ubiquitin-related genes in laboratory yeast strains enhances ethanol production during sake brewing. J Biosci Bioeng. 2009;107(6):636–640.
  • Watanabe D, Wu H, Noguchi C, et al. Enhancement of the initial rate of ethanol fermentation due to dysfunction of yeast stress response components Msn2p and/or Msn4p. Appl Environ Microbiol. 2011;77(3):934–941.
  • Urbanczyk H, Noguchi C, Wu H, et al. Sake yeast strains have difficulty in entering a quiescent state after cell growth cessation. J Biosci Bioeng. 2011;112(1):44–48.
  • Noguchi C, Watanabe D, Akao T, et al. Constitutive hyperphosphorylation of Hsf1p associated with defective ethanol stress response in sake yeast. Appl Environ Microbiol. 2012;78(2):385–392.
  • Watanabe D, Hashimoto N, Mizuno M, et al. Accelerated alcoholic fermentation caused by defective gene Expression related to glucose derepression in Saccharomyces cerevisiae. Biosci Biotechnol Biochem. 2013;77(11):2255–2262.
  • Shobayashi M, Ukena E, Fujii T, et al. Genome-wide expression profile of sake brewing yeast under shaking and static conditions. Biosci Biotechnol Biochem. 2007;71(2):323–335.
  • Kajiwara S, Aritomi T, Suga K, et al. Overexpression of the OLE1 gene enhances ethanol fermentation by Saccharomyces cerevisiae. Appl Microbiol Biotechnol. 2000;53(5):568–574.
  • You KM, Rosenfield CL, Knipple DC. Ethanol tolerance in the yeast Saccharomyces cerevisiae is dependent on cellular oleic acid content. Appl Environ Microbiol. 2003;69(3):1499–1503.
  • Yamada T, Shimoi H, Ito K. High expression of unsaturated fatty acid synthesis gene OLE1 in sake yeasts. J Biosci Bioeng. 2005;99(5):512–516.
  • Daum G, Lees ND, Bard M, et al. Biochemistry, cell biology and molecular biology of lipids of Saccharomyces cerevisiae. Yeast. 1998;14(16):1471–1510.
  • Inoue T, Iefuji H, Fujii T, et al. Cloning and characterization of a gene complementing the mutation of an ethanol-sensitive mutant of sake yeast. Biosci Biotechnol Biochem. 2000;64(2):229–236.
  • Tamura K, Gu Y, Wang Q, et al. A hap1 mutation in a laboratory strain of Saccharomyces cerevisiae results in decreased expression of ergosterol-related genes and cellular ergosterol content compared to sake yeast. J Biosci Bioeng. 2004;98(3):159–166.
  • Hirasawa T, Yoshikawa K, Nakakura Y, et al. Identification of target genes conferring ethanol stress tolerance to Saccharomyces cerevisiae based on DNA microarray data analysis. J Biotechnol. 2007;131(1):34–44.
  • Nitta A, Uchiyama H, Imamura T. Breeding of ethanol-tolerant sake yeasts from K1 Killer-resistant mutants. Seibutu Kougaku. 2000;78(3):77–81. (in Japanese).
  • Hara S, Nojiro K. A remarkably high alcohol-tolerant mutant: application to sake brwing (2). J Brew Soc Jpn. 1978;73(2):76–79. (in Japanese).
  • Kobayashi N, McEntee K. Identification of cis and trans components of a novel heat shock stress regulatory pathway in Saccharomyces cerevisiae. Mol Cell Biol. 1993;13(1):248–256.
  • Ogawa Y, Nitta A, Uchiyama H, et al. Tolerance mechanism of the ethanol-tolerant mutant of sake yeast. J Biosci Bioeng. 2000;90(3):313–320.
  • Ogawa Y. Characters of the ethanol-tolerant mutant of sake yeast. J Brew Soc Jpn. 2001;96(11):730–736. (in Japanese).
  • Watanabe M, Tamura K, Magbanua JP, et al. Elevated expression of genes under the control of stress response element (STRE) and Msn2p in an ethanol tolerance sake yeast Kyokai no.11. J Biosci Bioeng. 2007;104(3):163–170.
  • Asano T, Yano S, Takakura Y, et al. Isolation of strains with high malate and succinate productivity from α-ketoglutarate resistant mutants of sake yeast. J Brew Soc Jpn. 2003;98(3):217–220. (in Japanese).
  • Yano S, Asano T, Kurose N, et al. Characterization of an alpha-ketoglutarate-resistant sake yeast mutant with high organic acid productivity. J Biosci Bioeng. 2003;96(4):332–336.
  • Olesen J, Hahn S, Guarente L. Yeast HAP2 and HAP3 activators both bind to the CYC1 upstream activation site, UAS2, in an interdependent manner. Cell. 1987;51(6):953–961.
  • Oba T, Suenaga H, Nakayama S, et al. Properties of a high malic acid-producing strains of Saccharomyces cerevisiae isolated from sake mash. Biosci Biotechnol Biochem. 2011;75(10):2025–2029.
  • Koganemaru K, Kanda K, Yasuda M, et al. Gene expression concerning malate production of a cycloheximide-resistant mutant and industrial scale sake brewing. J Brew Soc Jpn. 2003;98(4):303–309. (in Japanese).
  • Kanai M, Mizunuma M, Fujii T, et al. A genetic method to enhance the accumulation of S-adenosylmethionine in yeast. Appl Microbiol Biotechnol. 2017;101(4):1351–1357.
  • Kanai M, Masuda M, Takaoka Y, et al. Adenosine kinase-deficient mutant of Saccharomyces cerevisiae accumulates S-adenosylmethionine because of an enhanced methionine biosynthesis pathway. Appl Microbiol Biotechnol. 2013;97(3):1183–1190.
  • Iefuji H, Yasuda N, Kanai M, et al. Method for breeding yeast strain highly accumulating S-adenosylmethionine. Japan Patent P641192. 2014 Nov 7 (in Japanese).
  • Inoue T, Iefuji H, Katsumata H. Characterization and isolation of mutants producing increased amounts of isoamyl acetate derived from hygromycin B-resistant sake yeast. Biosci Biotechnol Biochem. 2012;76(1):60–66.
  • Oba T, Yamamoto Y, Nomiyama S, et al. Properties of a trifluoroleucine-resistant mutant of Saccharomyces cerevisiae. Biosci Biotechnol Biochem. 2006;70(7):1776–1779.
  • Koganemaru K, Sumi T, Kanda K, et al. Beta-phenylethyl alcohol production by a mutant of sake yeast and its highly productive mechanism. J Brew Soc Jpn. 2003;93(3):201–209. (in Japanese).
  • Tsuboi H, Wakisaka Y, Hirotsune M, et al. Analysis of the pyruvate permease gene (JEN1) in glucose derepression yeast (Saccharomyces cerevisiae) isolated from a 2-deoxyglucose-tolerant mutant, and its application to sake making. Biosci Biotechnol Biochem. 2003;67(4):765–771.
  • Koganemaru K, Sumi T, Kanda K, et al. Improvement of the ethyl alcohol production ability of high malic acid sake yeast. J Brew Soc Jpn. 2004;99(5):365–373. (in Japanese).
  • Uehigashi H, Kato R, Sugiyama H, et al. Effect of deep seawater on sake yeast. J Brew Soc Jpn. 2006;101(2):117–124. (in Japanese).
  • Kato R, Uehigashi H. Study on making high-quality sake using DNA microarray analysis. The Report of the Works on Kochi Prefectural Industrial Technology Center. 2007; 38:1–7. (in Japanese).
  • Alexander J, Auðunsson GA, Benford D, et al. Ethyl carbamate and hydrocyanic acid in food and beverages1Scientific opinion of the panel on contaminants. EFSA J. 2007;551:1–41.
  • Dahabieh MS, Husnik JI, Van Vuuren HJ. Functional enhancement of sake yeast strains to minimize the production of ethyl carbamate in sake wine. J Appl Microbiol. 2010;109(3):963–973.
  • Kitamoto K, Oda-Miyazaki K, Gomi K, et al. Mutant isolation of non-urea producing sake yeast by positive selection. J Ferment Bioeng. 1993;75(5):359–363.
  • Ouchi K, Akiyama H. Non-foaming mutants of sake yeasts selection by cell agglutination method and by froth flotation method. Agr Biol Chem. 1971;35(7):1024–1032.
  • Ouchi K. History of non foaming yeasts. J Brew Soc Jpn. 2010;105(4):184–187. (in Japanese).
  • Shimoi H, Sakamoto K, Okuda M, et al. The AWA1 gene is required for the foam-forming phenotype and cell surface hydrophobicity of sake yeast. Appl Environ Microbiol. 2002;68(4):2018–2025.
  • Namise M, Hata Y, Shimoi H, et al. Genome-wide DNA marker of yeast Saccharomcyes cerevisiae. Japan Patent P2007-82431A. 2005 Sep 20. (in Japanese).
  • Wu H, Ito K, Shimoi H. Identification and characterization of a novel biotin biosynthesis gene in Saccharomyces cerevisiae. Appl Environ Microbiol. 2005;71(11):6845–6855.
  • Azumi M, Goto-Yamamoto N. AFLP analysis of type strains and laboratory and industrial strains of Saccharomyces sensu stricto and its application to phenetic clustering. Yeast. 2001;18(12):1145–1154.
  • Katou T, Namise M, Kitagaki H, et al. QTL mapping of sake brewing characteristics of yeast. J Biosci Bioeng. 2009;107(4):383–393.
  • Kanai M, Kawata T, Yoshida Y, et al. Sake yeast YHR032W/ERC1 haplotype contributes to high S-adenosylmethionine accumulation in sake yeast strains. J Biosci Bioeng. 2017;123(1):8–14.
  • Katou T, Kitagaki H, Akao T, et al. Brewing characteristics of haploid strains isolated from sake yeast Kyokai No. 7. Yeast. 2008;25(11):799–807.
  • Akao T. The genome analysis of sake yeast Kyokai no. 7 and foresights of sake yeast genomics. J Brew Soc Jpn. 2012;107(6):366–380. (in Japanese).
  • Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res. 1998;8(3):195–202.
  • Watanabe D, Araki Y, Zhou Y, et al. A loss-of-function mutation in the PAS kinase Rim15p is related to defective quiescence entry and high fermentation rates in Saccharomyces cerevisiae sake yeast strains. Appl Environ Microbiol. 2012;78(11):4008–4016.
  • Watanabe D, Zhou Y, Hirata A. Inhibitory role of Greatwall-like protein kinase Rim15p in alcoholic fermentation via upregulating the UDP-glucose synthesis pathway in Saccharomyces cerevisiae. Appl Environ Microbiol. 2016;82(1):340–351.
  • Akao T, Zhou Y, Watanabe D, et al. Development of DNA markers to differntiate good Kyokai sake yeast and other yeast strains. J Brew Soc Jpn. 2018;113(10):631–641. (in Japanese).
  • Negoro H, Kotaka A, Matsumura K, et al. Enhancement of malate-production and increase in sensitivity to dimethyl succinate by mutation of the VID24 gene in Saccharomyces cerevisiae. J Biosci Bioeng. 2016;121(6):665–671.
  • Negoro H, Sakamoto M, Kotaka A, et al. Mutation in the peroxin-coding gene PEX22 contributing to high malate production in Saccharomyces cerevisiae. J Biosci Bioeng. 2018;125(2):211–217.
  • Takahashi T, Ohara Y, Sawatari M, et al. Isolation and characterization of sake yeast mutants with enhanced isoamyl acetate productivity. J Biosci Bioeng. 2017;123(1):71–77.
  • Takahashi T, Ohara Y, Sueno K. Breeding of a sake yeast mutant with enhanced ethyl caproate productivity in sake brewing using rice milled at a high polishing ratio. J Biosci Bioeng. 2017;23(6):707–713.
  • Aikawa M, Suizu T, Ichikawa E, et al. Breeding of higher malic acid-productive mutants from Saccharomyces cerevisiae Kyokai No.7 (K7). Hakko-Kogaku. 1992;70(6):473–477. (in Japanese).
  • Inokoshi J, Tomoda H, Hashimoto H, et al. Cerulenin-resistant mutants of Saccharomyces cerevisiae with an altered fatty acid synthase gene. Mol Gen Genet. 1994;244(1):90–96.
  • Horie K, Oba T, Motomura S, et al. Breeding of a low pyruvate-producing sake yeast by isolation of a mutant resistant to ethyl alpha-transcyanocinnamate, an inhibitor of mitochondrial pyruvate transport. Biosci Biotechnol Biochem. 2010;74(4):843–847.
  • Kadowaki M, Fujimaru Y, Taguchi S. Chromosomal aneuploidy improves the brewing characteristics of sake yeast. Appl Environ Microbiol. 2017;83(24):e01620–17.
  • Tamura H, Okada H, Kume K, et al. Isolation of a spontaneous cerulenin-resistant sake yeast with both high ethyl caproate-producing ability and normal checkpoint integrity. Biosci Biotechnol Biochem. 2015;79(7):1191–1199.
  • Goshima T, Nakamura R, Kume K, et al. Identification of a mutation causing a defective spindle-assembly checkpoint in high ethyl-caproate producing sake yeast strain K1801. Biosci Biotechnol Biochem. 2016;80(8):1657–1662.
  • Ohnuki S, Okada H, Friedrich A, et al. Phenotypic diagnosis of lineage and differentiation during sake yeast breeding. G3 (Bethesda). 2017;7(8):2807–2820.
  • Watanabe D, Kajihara T, Sugimoto Y, et al. Nutrient signalling via the TORC1-greatwall-PP2AB55δ pathway responsible for the high initial rates of alcoholic fermentation in sake yeast strains of Saccharomyces cerevisiae. Appl Environ Microbiol. 2019;85(1):e02083–18.
  • Pavelka N, Rancati G, Zhu J, et al. Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. Nature. 2010;468:321–325.
  • Mulla W, Zhu J, Li R. Yeast: a simple model system to study complex phenomena of aneuploidy. FEMS Microbiol Rev. 2014;38(2):201–212.
  • Peter J, De Chiara M, Friedrich A, et al. Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature. 2018;556(7701):339–344.
  • Shimoi H, Hamazumi Y, Kawamura N, et al. Meiotic chromosomal recombination defect in sake yeasts. J Biosci Bioeng. 2018. DOI:10.1016/j.jbiosc.2018.07.027.
  • Nakazawa N, Ashikari T, Goto N, et al. Partial restoration of sporulation defect in sake yeasts, Kyokai No. 7 and No. 9, by increased dosage of the IME1 gene. J Ferment Bioeng. 1992;73(4):265–270.
  • Mori K, Kadooka C, Masuda C, et al. Genome sequence of Saccharomyces cerevisiae strain Kagoshima No. 2, used for brewing the Japanese distilled spirit shōchū. Genome Announc. 2017;5(41):pii:e01126-17.
  • Kajiwara Y, Mori K, Tashiro K, et al. Genomic sequence of Saccharomyces cerevisiae BAW-6, a yeast strain optimal for brewing barley shochu. Genome Announc. 2018;6(14):pii: e00228-18.
  • Futagami T, Kadooka C, Ando Y, et al. Multi-gene phylogenetic analysis reveals that shochu-fermenting Saccharomyces cerevisiae strains form a distinct sub-clade of the Japanese sake cluster. Yeast. 2017;34(10):407–415.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.