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Hotta N, Kotaka A, Matsumura K, Sasano Y, Hata Y, Harada T, Sugiyama M, Harashima S, Ishida H. Effect of yeast chromosome II aneuploidy on malate production in sake brewing. J Biosci Bioeng 2024; 137:24-30. [PMID: 37989703 DOI: 10.1016/j.jbiosc.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/08/2023] [Accepted: 10/31/2023] [Indexed: 11/23/2023]
Abstract
Chromosome aneuploidy is a common phenomenon in industrial yeast. Aneuploidy is considered one of the strategies to enhance the industrial properties of Saccharomyces cerevisiae strains. However, the effects of chromosomal aneuploidy on the brewing properties of sake have not been extensively studied. In this study, sake brewing was performed using a series of genome-wide segmental duplicated laboratory S. cerevisiae strains, and the effects of each segmentally duplicated region on sake brewing were investigated. We found that the duplication of specific chromosomal regions affected the production of organic acids and aromatic compounds in sake brewing. As organic acids significantly influence the taste of sake, we focused on the segmental duplication of chromosome II that alters malate levels. Sake yeast Kyokai No. 901 strains with segmental chromosome II duplication were constructed using a polymerase chain reaction-mediated chromosomal duplication method, and sake was brewed using the resultant aneuploid sake yeast strains. The results showed the possibility of developing sake yeast strains exhibiting low malate production without affecting ethanol production capacity. Our study revealed that aneuploidy in yeast alters the brewing properties; in particular, the aneuploidy of chromosome II alters malate production in sake brewing. In conclusion, aneuploidization can be a novel and useful tool to breed sake yeast strains with improved traits, possessing industrial significance.
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Affiliation(s)
- Natsuki Hotta
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan.
| | - Atsushi Kotaka
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
| | - Kengo Matsumura
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
| | - Yu Sasano
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Yoji Hata
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
| | - Tomoka Harada
- Department of Food Sciences and Biotechnology, Faculty of Life Sciences, Hiroshima Institute of Technology, 2-1-1 Miyake, Saeki-ku, Hiroshima 731-5193, Japan
| | - Minetaka Sugiyama
- Department of Food Sciences and Biotechnology, Faculty of Life Sciences, Hiroshima Institute of Technology, 2-1-1 Miyake, Saeki-ku, Hiroshima 731-5193, Japan
| | - Satoshi Harashima
- Department of Applied Microbial Technology, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Hiroki Ishida
- Research Institute, Gekkeikan Sake Co., Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
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Wang DY, Ren K, Tong SM, Ying SH, Feng MG. Pleiotropic effects of Ubi4, a polyubiquitin precursor required for ubiquitin accumulation, conidiation and pathogenicity of a fungal insect pathogen. Environ Microbiol 2020; 22:2564-2580. [PMID: 32056334 DOI: 10.1111/1462-2920.14940] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 12/15/2019] [Accepted: 02/11/2020] [Indexed: 11/30/2022]
Abstract
Ubi4 is a polyubiquitin precursor well characterized in yeasts but unexplored in insect mycopathogens. Here, we report that orthologous Ubi4 plays a core role in ubiquitin- and asexual lifestyle-required cellular events in Beauveria bassiana. Deletion of ubi4 led to abolished ubiquitin accumulation, blocked autophagic process, severe defects in conidiation and conidial quality, reduced cell tolerance to oxidative, osmotic, cell wall perturbing and heat-shock stresses, decreased transcript levels of development-activating and antioxidant genes, but light effect on radial growth under normal conditions. The deletion mutant lost insect pathogenicity via normal cuticle infection and was severely compromised in virulence via cuticle-bypassing infection due to a block of dimorphic transition critical for acceleration of host mummification. Proteomic and ubiquitylomic analyses revealed 1081 proteins differentially expressed and 639 lysine residues significantly hyper- or hypo-ubiquitylated in the deletion mutant, including dozens of ubiquitin-activating, conjugating and ligating enzymes, core histones, and many more involved in proteasomes, autophagy-lysosome process and protein degradation. Singular deletions of seven ubiquitin-conjugating enzyme genes exerted differential Ubi4-like effects on conidiation level and conidial traits. These findings uncover an essential role of Ubi4 in ubiquitin transfer cascade and its pleiotropic effects on the in vitro and in vivo asexual cycle of B. bassiana.
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Affiliation(s)
- Ding-Yi Wang
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Kang Ren
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Sen-Miao Tong
- College of Agricultural and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, China
| | - Sheng-Hua Ying
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ming-Guang Feng
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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Abstract
Completion of the whole genome sequence of a laboratory yeast strain Saccharomyces cerevisiae in 1996 ushered in the development of genome-wide experimental tools and accelerated subsequent genetic study of S. cerevisiae. The study of sake yeast also shared the benefit of such tools as DNA microarrays, gene disruption-mutant collections, and others. Moreover, whole genome analysis of representative sake yeast strain Kyokai no. 7 was performed in the late 2000s, and enabled comparative genomics between sake yeast and laboratory yeast, resulting in some notable finding for of sake yeast genetics. Development of next-generation DNA sequencing and bioinformatics also drastically changed the field of the genetics, including for sake yeast. Genomics and the genome-wide study of sake yeast have progressed under these circumstances during the last two decades, and are summarized in this article. Abbreviations: AFLP: amplified fragment length polymorphism; CGH: comparative genomic hybridization; CNV: copy number variation; DMS: dimethyl succinate; DSW: deep sea water; LOH: loss of heterozygosity; NGS: next generation sequencer; QTL: quantitative trait loci; QTN: quantitative trait nucleotide; SAM: S-adenosyl methionine; SNV: single nucleotide variation.
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Affiliation(s)
- Takeshi Akao
- a National Research Institute of Brewing , Higashi-hiroshima , Japan
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Peter JJ, Watson TL, Walker ME, Gardner JM, Lang TA, Borneman A, Forgan A, Tran T, Jiranek V. Use of a wine yeast deletion collection reveals genes that influence fermentation performance under low-nitrogen conditions. FEMS Yeast Res 2018; 18:4841842. [DOI: 10.1093/femsyr/foy009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 02/05/2018] [Indexed: 12/26/2022] Open
Affiliation(s)
- Josephine J Peter
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tommaso L Watson
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Michelle E Walker
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Jennifer M Gardner
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tom A Lang
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Anthony Borneman
- The Australian Wine Research Institute, Waite Campus, Urrbrae, SA 5064, Australia
| | - Angus Forgan
- The Australian Wine Research Institute, Waite Campus, Urrbrae, SA 5064, Australia
| | - Tina Tran
- The Australian Wine Research Institute, Waite Campus, Urrbrae, SA 5064, Australia
| | - Vladimir Jiranek
- Department of Wine and Food Science, School of Agriculture Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
- Australian Research Council Training Centre for Innovative Wine Production, The University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
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Nakagawa Y, Ogihara H, Mochizuki C, Yamamura H, Iimura Y, Hayakawa M. Development of intra-strain self-cloning procedure for breeding baker's yeast strains. J Biosci Bioeng 2017; 123:319-326. [DOI: 10.1016/j.jbiosc.2016.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/09/2016] [Accepted: 10/12/2016] [Indexed: 10/20/2022]
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Kaboli S, Miyamoto T, Sunada K, Sasano Y, Sugiyama M, Harashima S. Improved stress resistance and ethanol production by segmental haploidization of the diploid genome in Saccharomyces cerevisiae. J Biosci Bioeng 2015; 121:638-644. [PMID: 26690924 DOI: 10.1016/j.jbiosc.2015.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/25/2015] [Accepted: 10/27/2015] [Indexed: 12/21/2022]
Abstract
Saccharomyces cerevisiae strains from industrial and natural geographical environments are reported to show great variation in copy number of chromosomal regions. Such variation contributes to the mechanisms underlying adaptation to different environments. Here, we created and phenotypically analyzed segmentally haploidized strains, each harboring a deletion of one copy of approximately 100-300 kb of the left or right terminal region of 16 chromosomes in a diploid strain by using a PCR-mediated chromosomal deletion method. No haploidized strain of the 158-kb deleted right terminal region of chromosome III or the 172-kb deleted right terminal region of chromosome VI was produced; however, segmentally haploidized strains of the remaining 30 terminal regions were obtained. Among these 30 strains, two exhibited higher lactic acid resistance and two displayed higher thermo-tolerance at 41°C versus the host diploid strain. By contrast, four and two segmentally haploidized strains showed sensitivity to 6% lactic acid and low temperature at 13°C, respectively. The effect of the decreased copy number of the chromosomal terminal regions on ethanol production was analyzed. As compared with the host diploid strain, a 3.8% and 4.3% improvement in ethanol production in 10% glucose medium was observed for two strains in which one of two copies of the 197-kb left terminal region of chromosome V and one of two copies of the 195-kb left terminal region of chromosome X was deleted, respectively. These results indicate that artificial segmental haploidization might contribute to improvement of industrially important phenotypes and provide a new approach to breeding superior yeast strains.
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Affiliation(s)
- Saeed Kaboli
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Miyamoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keisuke Sunada
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yu Sasano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Minetaka Sugiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Satoshi Harashima
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Yamaoka C, Kurita O, Kubo T. Improved ethanol tolerance of Saccharomyces cerevisiae in mixed cultures with Kluyveromyces lactis on high-sugar fermentation. Microbiol Res 2014; 169:907-14. [DOI: 10.1016/j.micres.2014.04.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 03/29/2014] [Accepted: 04/14/2014] [Indexed: 10/25/2022]
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Akao T, Yashiro I, Hosoyama A, Kitagaki H, Horikawa H, Watanabe D, Akada R, Ando Y, Harashima S, Inoue T, Inoue Y, Kajiwara S, Kitamoto K, Kitamoto N, Kobayashi O, Kuhara S, Masubuchi T, Mizoguchi H, Nakao Y, Nakazato A, Namise M, Oba T, Ogata T, Ohta A, Sato M, Shibasaki S, Takatsume Y, Tanimoto S, Tsuboi H, Nishimura A, Yoda K, Ishikawa T, Iwashita K, Fujita N, Shimoi H. Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7. DNA Res 2011; 18:423-34. [PMID: 21900213 PMCID: PMC3223075 DOI: 10.1093/dnares/dsr029] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The term ‘sake yeast’ is generally used to indicate the Saccharomyces cerevisiae strains that possess characteristics distinct from others including the laboratory strain S288C and are well suited for sake brewery. Here, we report the draft whole-genome shotgun sequence of a commonly used diploid sake yeast strain, Kyokai no. 7 (K7). The assembled sequence of K7 was nearly identical to that of the S288C, except for several subtelomeric polymorphisms and two large inversions in K7. A survey of heterozygous bases between the homologous chromosomes revealed the presence of mosaic-like uneven distribution of heterozygosity in K7. The distribution patterns appeared to have resulted from repeated losses of heterozygosity in the ancestral lineage of K7. Analysis of genes revealed the presence of both K7-acquired and K7-lost genes, in addition to numerous others with segmentations and terminal discrepancies in comparison with those of S288C. The distribution of Ty element also largely differed in the two strains. Interestingly, two regions in chromosomes I and VII of S288C have apparently been replaced by Ty elements in K7. Sequence comparisons suggest that these gene conversions were caused by cDNA-mediated recombination of Ty elements. The present study advances our understanding of the functional and evolutionary genomics of the sake yeast.
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Affiliation(s)
- Takeshi Akao
- National Research Institute of Brewing, Higashi-hiroshima, Japan
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Urbanczyk H, Noguchi C, Wu H, Watanabe D, Akao T, Takagi H, Shimoi H. Sake yeast strains have difficulty in entering a quiescent state after cell growth cessation. J Biosci Bioeng 2011; 112:44-8. [PMID: 21459038 DOI: 10.1016/j.jbiosc.2011.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/07/2011] [Accepted: 03/07/2011] [Indexed: 11/27/2022]
Abstract
Sake yeast strains produce a high concentration of ethanol during sake brewing compared to laboratory yeast strains. As ethanol fermentation by yeast cells continues even after cell growth stops, analysis of the physiological state of the stationary phase cells is very important for understanding the mechanism of producing higher concentrations of ethanol. We compared the physiological characteristics of stationary phase cells of both sake and laboratory yeast strains in an aerobic batch culture and under sake brewing conditions. We unexpectedly found that sake yeast cells in the stationary phase had a lower buoyant density and stress tolerance than did the laboratory yeast cells under both experimental conditions. These results suggest that it is difficult for sake yeast cells to enter a quiescent state after cell growth has stopped, which may be one reason for the higher fermentation rate of sake yeast compared to laboratory yeast strains.
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Affiliation(s)
- Henryk Urbanczyk
- National Research Institute of Brewing, Higashi-Hiroshima 739-0046, Japan
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Enhancement of the initial rate of ethanol fermentation due to dysfunction of yeast stress response components Msn2p and/or Msn4p. Appl Environ Microbiol 2010; 77:934-41. [PMID: 21131516 DOI: 10.1128/aem.01869-10] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sake yeasts (strains of Saccharomyces cerevisiae) produce high concentrations of ethanol in sake fermentation. To investigate the molecular mechanisms underlying this brewing property, we compared gene expression of sake and laboratory yeasts in sake mash. DNA microarray and reporter gene analyses revealed defects of sake yeasts in environmental stress responses mediated by transcription factors Msn2p and/or Msn4p (Msn2/4p) and stress response elements (STRE). Furthermore, we found that dysfunction of MSN2 and/or MSN4 contributes to the higher initial rate of ethanol fermentation in both sake and laboratory yeasts. These results provide novel insights into yeast stress responses as major impediments of effective ethanol fermentation.
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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