1
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Ushiyama Y, Nishida I, Tomiyama S, Tanaka H, Kume K, Hirata D. Search for protein kinase(s) related to cell growth or viability maintenance in the presence of ethanol in budding and fission yeasts. Biosci Biotechnol Biochem 2024; 88:804-815. [PMID: 38592956 DOI: 10.1093/bbb/zbae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Alcohol fermentation comprises two phases: phase 1, alcohol fermentation occurs while yeast cells proliferate; phase 2, growth stops and alcohol fermentation continues. We categorized genes related to proliferation in low ethanol (phase 1) and viability in high ethanol (phase 2) as Alcohol Growth Ability (AGA) and Alcohol Viability (ALV), respectively. Although genes required for phase 1 are examined in budding yeast, those for phase 2 are unknown. We set conditions for ALV screening, searched for protein kinases (PKs) related to ALV in budding yeast, and expanded two screenings to fission yeast. Bub1 kinase was important for proliferation in low ethanol but not for viability in high ethanol, suggesting that the important PKs differ between the two phases. It was indeed the case. Further, 3 common PKs were identified as AGA in both yeasts, suggesting that the important cellular mechanism in phase 1 is conserved in both yeasts, at least partially.
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Affiliation(s)
- Yuto Ushiyama
- Sakeology Course, Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
| | - Ikuhisa Nishida
- Sakeology Center, Niigata University, Ikarashi, Niigata, Japan
| | - Saki Tomiyama
- Sakeology Course, Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
| | - Hitomi Tanaka
- Sakeology Course, Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
| | - Kazunori Kume
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Dai Hirata
- Sakeology Course, Graduate School of Science and Technology, Niigata University, Ikarashi, Niigata, Japan
- Sakeology Center, Niigata University, Ikarashi, Niigata, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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2
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Nakagawa T, Yoshimura A, Sawai Y, Hisamatsu K, Akao T, Masaki K. Japanese sake making using wild yeasts isolated from natural environments. Biosci Biotechnol Biochem 2024; 88:231-236. [PMID: 38364793 DOI: 10.1093/bbb/zbae003] [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: 09/29/2023] [Accepted: 01/04/2024] [Indexed: 02/18/2024]
Abstract
Saccharomyces cerevisiae is one of the most important microorganisms for the food industry, including Japanese sake, beer, wine, bread, and other products. For sake making, Kyokai sake yeast strains are considered one of the best sake yeast strains because these strains possess fermentation properties that are suitable for the quality of sake required. In recent years, the momentum for the development of unique sake, which is distinct from conventional sake, has grown, and there is now a demand to develop unique sake yeasts that have different sake making properties than Kyokai sake yeast strains. In this minireview, we focus on "wild yeasts," which inhabit natural environments, and introduce basic research on the wild yeasts for sake making, such as their genetic and sake fermentation aspects. Finally, we also discuss the molecular breeding of wild yeast strains for sake fermentation and the possibility for sake making using wild yeasts.
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Affiliation(s)
- Tomoyuki Nakagawa
- The Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | | | - Yoshinori Sawai
- Gifu Prefectural Research Institute for Food Sciences, Gifu, Japan
| | | | - Takeshi Akao
- National Research Institute of Brewing, Higashihiroshima, Hiroshima, Japan
| | - Kazuo Masaki
- National Research Institute of Brewing, Higashihiroshima, Hiroshima, Japan
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3
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Watanabe D. Sake yeast symbiosis with lactic acid bacteria and alcoholic fermentation. Biosci Biotechnol Biochem 2024; 88:237-241. [PMID: 38006236 DOI: 10.1093/bbb/zbad167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
The yeast Saccharomyces cerevisiae plays a pivotal role in the production of fermented foods by converting sugars in ingredients into ethanol through alcoholic fermentation. However, how accurate is our understanding of its biological significance? Although yeast is essential to produce alcoholic beverages and bioethanol, yeast does not yield ethanol for humankind. Yeast obtains energy in the form of ATP for its own vital processes through alcoholic fermentation, which generates ethanol as a byproduct. The production of ethanol may have more significance for yeast, since many other organisms do not produce ethanol, a highly toxic substance, to obtain energy. The key to address this issue has not been found using conventional microbiology, where yeasts are isolated and cultured in pure form. This review focuses on a possible novel role of yeast alcohol fermentation, which is revealed through our recent studies of microbial interactions.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
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4
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Watanabe D, Kumano M, Sugimoto Y, Takagi H. Spontaneous Attenuation of Alcoholic Fermentation via the Dysfunction of Cyc8p in Saccharomyces cerevisiae. Int J Mol Sci 2023; 25:304. [PMID: 38203474 PMCID: PMC10778621 DOI: 10.3390/ijms25010304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/19/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
A cell population characterized by the release of glucose repression and known as [GAR+] emerges spontaneously in the yeast Saccharomyces cerevisiae. This study revealed that the [GAR+] variants exhibit retarded alcoholic fermentation when glucose is the sole carbon source. To identify the key to the altered glucose response, the gene expression profile of [GAR+] cells was examined. Based on RNA-seq data, the [GAR+] status was linked to impaired function of the Cyc8p-Tup1p complex. Loss of Cyc8p led to a decrease in the initial rate of alcoholic fermentation under glucose-rich conditions via the inactivation of pyruvate decarboxylase, an enzyme unique to alcoholic fermentation. These results suggest that Cyc8p can become inactive to attenuate alcoholic fermentation. These findings may contribute to the elucidation of the mechanism of non-genetic heterogeneity in yeast alcoholic fermentation.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
| | - Maika Kumano
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
| | - Yukiko Sugimoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan
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5
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Sugimura M, Seike T, Okahashi N, Izumi Y, Bamba T, Ishii J, Matsuda F. Improved 2,3-Butanediol Production Rate of Metabolically Engineered Saccharomyces cerevisiae by Deletion of RIM15 and Activation of Pyruvate Consumption Pathway. Int J Mol Sci 2023; 24:16378. [PMID: 38003568 PMCID: PMC10671664 DOI: 10.3390/ijms242216378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/31/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Saccharomyces cerevisiae is a promising host for the bioproduction of higher alcohols, such as 2,3-butanediol (2,3-BDO). Metabolically engineered S. cerevisiae strains that produce 2,3-BDO via glycolysis have been constructed. However, the specific 2,3-BDO production rates of engineered strains must be improved. To identify approaches to improving the 2,3-BDO production rate, we investigated the factors contributing to higher ethanol production rates in certain industrial strains of S. cerevisiae compared to laboratory strains. Sequence analysis of 11 industrial strains revealed the accumulation of many nonsynonymous substitutions in RIM15, a negative regulator of high fermentation capability. Comparative metabolome analysis suggested a positive correlation between the rate of ethanol production and the activity of the pyruvate-consuming pathway. Based on these findings, RIM15 was deleted, and the pyruvate-consuming pathway was activated in YHI030, a metabolically engineered S. cerevisiae strain that produces 2,3-BDO. The titer, specific production rate, and yield of 2,3-BDO in the test tube-scale culture using the YMS106 strain reached 66.4 ± 4.4 mM, 1.17 ± 0.017 mmol (g dry cell weight h)-1, and 0.70 ± 0.03 mol (mol glucose consumed)-1. These values were 2.14-, 2.92-, and 1.81-fold higher than those of the vector control, respectively. These results suggest that bioalcohol production via glycolysis can be enhanced in a metabolically engineered S. cerevisiae strain by deleting RIM15 and activating the pyruvate-consuming pathway.
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Affiliation(s)
- Masahiko Sugimura
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Taisuke Seike
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Fukuoka, Japan
| | - Takeshi Bamba
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Fukuoka, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan
| | - Fumio Matsuda
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita 565-0871, Osaka, Japan
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6
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Hou D, Xu X, Wang J, Liu C, Niu C, Zheng F, Li Q. Effect of environmental stresses during fermentation on brewing yeast and exploration on the novel flocculation-associated function of RIM15 gene. BIORESOURCE TECHNOLOGY 2023; 379:129004. [PMID: 37004888 DOI: 10.1016/j.biortech.2023.129004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
Flocculation of brewer's yeast is an environment-friendly and cost-effective way to separate yeast cells from fermentation broth for subsequent production. Diverse genetic background and complex fermentation environment cause difficulty to explore flocculation mechanism and regulate yeast flocculation. In this study, comparative transcriptome analysis was carried out between an industrial brewing yeast and its flocculation-enhanced mutant strain, unveiling the differentially-expressed genes were enriched in response to stresses. The expression level of Lg-FLO1 was the highest among all FLO genes. Environmental stresses of fermentation were simulated to stimulated yeast cells and it was found that nitrogen and amino acid starvation promoted the process of flocculation. It is the first time to reveal the nutrient-responsive gene RIM15 has a novel genetic function regulating flocculation. The study provides novel direction and strategies to manage yeast flocculation and achieve effective cell utilization in fermentation.
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Affiliation(s)
- Dan Hou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Xin Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Jinjing Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Feiyun Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China; Laboratory of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China.
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7
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Opalek M, Tutaj H, Pirog A, Smug BJ, Rutkowska J, Wloch-Salamon D. A Systematic Review on Quiescent State Research Approaches in S. cerevisiae. Cells 2023; 12:1608. [PMID: 37371078 DOI: 10.3390/cells12121608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Quiescence, the temporary and reversible arrest of cell growth, is a fundamental biological process. However, the lack of standardization in terms of reporting the experimental details of quiescent cells and populations can cause confusion and hinder knowledge transfer. We employ the systematic review methodology to comprehensively analyze the diversity of approaches used to study the quiescent state, focusing on all published research addressing the budding yeast Saccharomyces cerevisiae. We group research articles into those that consider all cells comprising the stationary-phase (SP) population as quiescent and those that recognize heterogeneity within the SP by distinguishing phenotypically distinct subpopulations. Furthermore, we investigate the chronological age of the quiescent populations under study and the methods used to induce the quiescent state, such as gradual starvation or abrupt environmental change. We also assess whether the strains used in research are prototrophic or auxotrophic. By combining the above features, we identify 48 possible experimental setups that can be used to study quiescence, which can be misleading when drawing general conclusions. We therefore summarize our review by proposing guidelines and recommendations pertaining to the information included in research articles. We believe that more rigorous reporting on the features of quiescent populations will facilitate knowledge transfer within and between disciplines, thereby stimulating valuable scientific discussion.
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Affiliation(s)
- Monika Opalek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Hanna Tutaj
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Adrian Pirog
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Bogna J Smug
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Joanna Rutkowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Dominika Wloch-Salamon
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
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8
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Negoro H, Ishida H. Development of sake yeast breeding and analysis of genes related to its various phenotypes. FEMS Yeast Res 2022; 22:6825454. [PMID: 36370450 DOI: 10.1093/femsyr/foac057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/21/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022] Open
Abstract
Sake is a traditional Japanese alcoholic beverage made from rice and water, fermented by the filamentous fungi Aspergillus oryzae and the yeast Saccharomyces cerevisiae. Yeast strains, also called sake yeasts, with high alcohol yield and the ability to produce desired flavor compounds in the sake, have been isolated from the environment for more than a century. Furthermore, numerous methods to breed sake yeasts without genetic modification have been developed. The objectives of breeding include increasing the efficiency of production, improving the aroma and taste, enhancing safety, imparting functional properties, and altering the appearance of sake. With the recent development of molecular biology, the suitable sake brewing characteristics in sake yeasts, and the causes of acquisition of additional phenotypes in bred yeasts have been elucidated genetically. This mini-review summarizes the history and lineage of sake yeasts, their genetic characteristics, the major breeding methods used, and molecular biological analysis of the acquired strains. The data in this review on the metabolic mechanisms of sake yeasts and their genetic profiles will enable the development of future strains with superior phenotypes.
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Affiliation(s)
- Hiroaki Negoro
- Research Institute, Gekkeikan Sake Co. Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
| | - Hiroki Ishida
- Research Institute, Gekkeikan Sake Co. Ltd., 101 Shimotoba-koyanagi-cho, Fushimi-ku, Kyoto 612-8385, Japan
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9
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Kato T, Takahashi T. Studies on the Genetic Characteristics of the Brewing Yeasts Saccharomyces: A Review. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2022. [DOI: 10.1080/03610470.2022.2134972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Taku Kato
- Brewing Science Laboratories, Asahi Quality and Innovations Ltd, Moriya, Japan
| | - Tomoko Takahashi
- Core Technology Laboratories, Asahi Quality and Innovations Ltd, Moriya, Japan
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10
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Predicted Functional and Structural Diversity of Receiver Domains in Fungal Two-Component Regulatory Systems. mSphere 2021; 6:e0072221. [PMID: 34612676 PMCID: PMC8510515 DOI: 10.1128/msphere.00722-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Fungal two-component regulatory systems incorporate receiver domains into hybrid histidine kinases (HHKs) and response regulators. We constructed a nonredundant database of 670 fungal receiver domain sequences from 51 species sampled from nine fungal phyla. A much greater proportion (21%) of predicted fungal response regulators did not belong to known groups than previously appreciated. Receiver domains in Rim15 response regulators from Ascomycota and other phyla are very different from one another, as are the duplicate receiver domains in group XII HHKs. Fungal receiver domains from five known types of response regulators and 20 known types of HHKs exhibit distinct patterns of amino acids at conserved and variable positions known to be structurally and functionally important in bacterial receiver domains. We inferred structure/activity relationships from the patterns and propose multiple experimentally testable hypotheses about the mechanisms of signal transduction mediated by fungal receiver domains.
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11
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Yuzawa T, Shirai T, Orishimo R, Kawai K, Kondo A, Hirasawa T. 13C-metabolic flux analysis in glycerol-assimilating strains of Saccharomyces cerevisiae. J GEN APPL MICROBIOL 2021; 67:142-149. [PMID: 33967166 DOI: 10.2323/jgam.2020.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Glycerol is an attractive raw material for the production of useful chemicals using microbial cells. We previously identified metabolic engineering targets for the improvement of glycerol assimilation ability in Saccharomyces cerevisiae based on adaptive laboratory evolution (ALE) and transcriptome analysis of the evolved cells. We also successfully improved glycerol assimilation ability by the disruption of the RIM15 gene encoding a Greatwall protein kinase together with overexpression of the STL1 gene encoding the glycerol/H+ symporter. To understand glycerol assimilation metabolism in the evolved glycerol-assimilating strains and STL1-overexpressing RIM15 disruptant, we performed metabolic flux analysis using 13C-labeled glycerol. Significant differences in metabolic flux distributions between the strains obtained from the culture after 35 and 85 generations in ALE were not found, indicating that metabolic flux changes might occur in the early phase of ALE (i.e., before 35 generations at least). Similarly, metabolic flux distribution was not significantly changed by RIM15 gene disruption. However, fluxes for the lower part of glycolysis and the TCA cycle were larger and, as a result, flux for the pentose phosphate pathway was smaller in the STL1-overexpressing RIM15 disruptant than in the strain obtained from the culture after 85 generations in ALE. It could be effective to increase flux for the pentose phosphate pathway to improve the glycerol assimilation ability in S. cerevisiae.
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Affiliation(s)
- Taiji Yuzawa
- School of Life Science and Technology, Tokyo Institute of Technology
| | | | | | - Kazuki Kawai
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN.,Graduate School of Science, Technology and Innovation, Kobe University
| | - Takashi Hirasawa
- School of Life Science and Technology, Tokyo Institute of Technology
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12
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Bourret RB, Kennedy EN, Foster CA, Sepúlveda VE, Goldman WE. A Radical Reimagining of Fungal Two-Component Regulatory Systems. Trends Microbiol 2021; 29:883-893. [PMID: 33853736 DOI: 10.1016/j.tim.2021.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 11/17/2022]
Abstract
Bacterial two-component regulatory systems (TCSs) mediate signal transduction by transferring phosphoryl groups between sensor kinase and response regulator proteins, sometimes using intermediary histidine-phosphotransferase (Hpt) domains to form multistep phosphorelays. Because (i) almost all known fungal sensor kinases exhibit a domain architecture characteristic of bacterial TCS phosphorelays, (ii) all known fungal Hpts are stand-alone proteins suited to shuttle between cytoplasm and nucleus, and (iii) the best-characterized fungal TCS is a canonical phosphorelay, it is widely assumed that most or all fungal TCSs function via phosphorelays. However, fungi generally encode more sensor kinases than Hpts or response regulators, leading to a disparity between putative phosphorelay inputs and outputs. The simplest resolution of this paradox is to hypothesize that most fungal sensor kinases do not participate in phosphorelays. Reimagining how fungal TCSs might function leads to multiple testable predictions.
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Affiliation(s)
- Robert B Bourret
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA.
| | - Emily N Kennedy
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
| | - Clay A Foster
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
| | - Victoria E Sepúlveda
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
| | - William E Goldman
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC 27599-7290, USA
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13
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Acquired Resistance to Severe Ethanol Stress in Saccharomyces cerevisiae Protein Quality Control. Appl Environ Microbiol 2021; 87:AEM.02353-20. [PMID: 33361368 DOI: 10.1128/aem.02353-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Acute severe ethanol stress (10% [vol/vol]) damages proteins and causes the intracellular accumulation of insoluble proteins in Saccharomyces cerevisiae On the other hand, a pretreatment with mild stress increases tolerance to subsequent severe stress, which is called acquired stress resistance. It currently remains unclear whether the accumulation of insoluble proteins under severe ethanol stress may be mitigated by increasing protein quality control (PQC) activity in cells pretreated with mild stress. In the present study, we examined the induction of resistance to severe ethanol stress in PQC and confirmed that a pretreatment with 6% (vol/vol) ethanol or mild thermal stress at 37°C significantly reduced insoluble protein levels and the aggregation of Lsg1, which is prone to denaturation and aggregation by stress, in yeast cells under 10% (vol/vol) ethanol stress. The induction of this stress resistance required the new synthesis of proteins; the expression of proteins comprising the bichaperone system (Hsp104, Ssa3, and Fes1), Sis1, and Hsp42 was upregulated during the pretreatment and maintained under subsequent severe ethanol stress. Since the pretreated cells of deficient mutants in the bichaperone system (fes1Δ hsp104Δ and ssa2Δ ssa3Δ ssa4Δ) failed to sufficiently reduce insoluble protein levels and Lsg1 aggregation, the enhanced activity of the bichaperone system appears to be important for the induction of adequate stress resistance. In contrast, the importance of proteasomes and aggregases (Btn2 and Hsp42) in the induction of stress resistance has not been confirmed. These results provide further insights into the PQC activity of yeast cells under severe ethanol stress, including the brewing process.IMPORTANCE Although the budding yeast S. cerevisiae, which is used in the production of alcoholic beverages and bioethanol, is highly tolerant of ethanol, high concentrations of ethanol are also stressful to the yeast and cause various adverse effects, including protein denaturation. A pretreatment with mild stress improves the ethanol tolerance of yeast cells; however, it currently remains unclear whether it increases PQC activity and reduces the levels of denatured proteins. In the present study, we found that a pretreatment with mild ethanol upregulated the expression of proteins involved in PQC and mitigated the accumulation of insoluble proteins, even under severe ethanol stress. These results provide novel insights into ethanol tolerance and the adaptive capacity of yeast. They may also contribute to research on the physiology of yeast cells during the brewing process, in which the concentration of ethanol gradually increases.
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14
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Crossbreeding of Yeasts Domesticated for Fermentation: Infertility Challenges. Int J Mol Sci 2020; 21:ijms21217985. [PMID: 33121129 PMCID: PMC7662550 DOI: 10.3390/ijms21217985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 01/07/2023] Open
Abstract
Sexual reproduction is almost a universal feature of eukaryotic organisms, which allows the reproduction of new organisms by combining the genetic information from two individuals of different sexes. Based on the mechanism of sexual reproduction, crossbreeding provides an attractive opportunity to improve the traits of animals, plants, and fungi. The budding yeast Saccharomyces cerevisiae has been widely utilized in fermentative production since ancient times. Currently it is still used for many essential biotechnological processes including the production of beer, wine, and biofuels. It is surprising that many yeast strains used in the industry exhibit low rates of sporulation resulting in limited crossbreeding efficiency. Here, I provide an overview of the recent findings about infertility challenges of yeasts domesticated for fermentation along with the progress in crossbreeding technologies. The aim of this review is to create an opportunity for future crossbreeding of yeasts used for fermentation.
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15
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Ogata T, Ayuzawa R, Yamada R. Tetrad analysis of sake yeast and identification of an RFLP marker for the absence of phenolic off-flavour production. J GEN APPL MICROBIOL 2020; 66:175-180. [PMID: 31495807 DOI: 10.2323/jgam.2019.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mating is a promising breeding method for industrial yeast. Although sake yeast has a low spore-formation ability, segregants exhibiting a mating type have been isolated from sake yeast K7. Here, we constructed zygotes from a cross between those segregants and a laboratory yeast strain. Because most sake and brewing yeast strains are prototrophs, we developed a PCR-based method to confirm that mating had taken place based on genome sequencing data and differences in nucleotide sequences between the two parental strains. The mated strain, termed S. cerevisiae MITOY123, showed restored spore-formation ability, unlike most sake and brewing yeast strains. By using the mated yeast strain MITOY123, it was possible to carry out tetrad analysis for the trait of the absence of off-flavour due to phenolic products such as 4-vinylguiacol (4-VG) in sake yeast K7. This tetrad analysis indicated that a single genetic region around the gene PAD1 is responsible for the absence of phenolic off-flavour in sake yeast K7. In order to aid the breeding of sake and brewing yeast strains by mating, we also identified a restriction fragment length polymorphism (RFLP) marker for the absence of phenolic off-flavour production in strains derived from sake yeast K7. Collectively, our data show that it is possible to breed new sake and brewing yeast strains by mating and to test for the absence of phenolic off-flavour production in resultant strains easily by RFLP analysis.
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Affiliation(s)
- Tomoo Ogata
- Department of Biotechnology, Maebashi Institute of Technology
| | - Ryo Ayuzawa
- Department of Biotechnology, Maebashi Institute of Technology
| | - Ryusuke Yamada
- Department of Biotechnology, Maebashi Institute of Technology
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16
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Liang C, Ding S, Sun W, Liu L, Zhao W, Zhang D, Ying H, Liu D, Chen Y. Biofilm-based fermentation: a novel immobilisation strategy for Saccharomyces cerevisiae cell cycle progression during ethanol production. Appl Microbiol Biotechnol 2020; 104:7495-7505. [PMID: 32666184 DOI: 10.1007/s00253-020-10770-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 06/07/2020] [Accepted: 07/02/2020] [Indexed: 12/11/2022]
Abstract
Biofilm-based fermentation, as a new immobilisation strategy, is beneficial for industrial fermentation due to its excellent environmental resistance, high productivity and continuous fermentation relative to calcium alginate-immobilised fermentation. These two techniques differ mainly regarding cell stages. Here, we describe the cell phenotype of Saccharomyces cerevisiae biofilm-based fermentation and compare cell cycle stages with those during immobilisation in calcium alginate. Most cells in the biofilm-based fermentation adhered to the cotton-fibre carrier of the biofilm and were in the G2/M phase whereas alginate-embedded cells were in the G1/G0 phase. Deletion of the RIM15 gene, which regulates cell cycle progression according to nutritional status, hampered the cell cycle arrest observed in alginate-embedded cells, enhanced biofilm formation and improved fermentation ability. The improved biofilm formation shown by the rim15△ strain could be attributed to an increase in the expression level of the adhesion protein FLO11 and synthesis of trehalose. These findings suggest that the extracellular environment is mainly responsible for the difference between biofilm-based fermentation and alginate-embedded fermentation, and that RIM15 plays an essential role in cell cycle progression. KEY POINTS: • In the biofilm, S. cerevisiae cell populations were mostly in the G2/M phase while alginate-embedded cells were arrested in the G1/G0 phase. • The RIM15 gene partially influenced the cell cycle progression observed during ethanol fermentation. • Biofilm-based cells were actively adsorbed on the physical carrier. • Biofilm immobilisation could maintain cell division activity explaining its fermentation efficiency.
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Affiliation(s)
- Caice Liang
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Sai Ding
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Wenjun Sun
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Li Liu
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Wei Zhao
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Deli Zhang
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Hanjie Ying
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, 450000, China
| | - Dong Liu
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, 450000, China
| | - Yong Chen
- National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China. .,State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.
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17
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Shimoi H, Kawamura N, Yamada M. Cloning of the SPO11 gene that complements a meiotic recombination defect in sake yeast. J Biosci Bioeng 2020; 130:367-373. [PMID: 32646632 DOI: 10.1016/j.jbiosc.2020.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 02/04/2023]
Abstract
Cross hybridization breeding of sake yeasts is hampered by difficulty in acquisition of haploid cells through sporulation. We previously demonstrated that typical sake yeast strains were defective in meiotic chromosome recombination, which caused poor sporulation and loss of spore viability. In this study, we screened a single copy plasmid genomic DNA library of the laboratory Saccharomyces cerevisiae GRF88 for genes that might complement the meiotic recombination defect of UTCAH-3, a strain derived from the sake yeast Kyokai no. 7 (K7). We identified the SPO11 gene of the laboratory strain (ScSPO11), encoding a meiosis-specific endonuclease that catalyzes DNA double-strand breaks required for meiotic recombination, as a gene that restored meiotic recombination and spore viability of UTCAH-3. K7SPO11 could not restore sporulation efficiency and spore viability of UTCAH-3 and a laboratory strain BY4743 spo11Δ/spo11Δ, indicating that K7SPO11 is not functional. Sequence analysis of the SPO11 genes of various Kyokai sake yeasts (K1, and K3-K10) revealed that the K7 group of sake yeasts (K6, K7, K9, and K10) had a mutual missense mutation (C73T) in addition to other three common mutations present in all Kyokai yeasts tested. ScSPO11C73T created through in vitro mutagenesis could not restore spore viability of BY4743 spo11Δ/spo11Δ. On the other hand, K8SPO11, which have the three common mutations except for C73T could restore spore viability of BY4743 spo11Δ/spo11Δ. These results suggest that C73T might be a causative mutation of recombination defect in K7SPO11. Moreover, we found that the introduction of ScRIM15 restored sporulation efficiency but not spore viability.
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Affiliation(s)
- Hitoshi Shimoi
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan; Brewing Society of Japan, 2-6-30, Takinogawa, Kita-ku, Tokyo 114-0023, Japan.
| | - Natsuki Kawamura
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Miwa Yamada
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
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18
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Kim HS. Disruption of RIM15 confers an increased tolerance to heavy metals in Saccharomyces cerevisiae. Biotechnol Lett 2020; 42:1193-1202. [PMID: 32248397 DOI: 10.1007/s10529-020-02884-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/02/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The aim of this study was to identify genes related to a heavy metal tolerance and to elucidate the tolerance mechanism in a eukaryote model using Saccharomyces cerevisiae. RESULTS In this study, one strain tolerant to up to 50 μM Pb(NO3)2 and 30 μM CdCl2 was isolated by screening a transposon-mediated mutant library and the disrupted gene was determined to be RIM15. In addition, this gene's characteristics related to heavy metals-tolerance was proved by deletion and overexpressing of this corresponding gene. The transposon mutant grew faster than the control strain and showed an obvious reduction in the intracellular level of reactive oxygen species (ROS) with activation of MSN4 and CTT1 in YPD medium containing 50 μM Pb(NO3)2 and 30 μM CdCl2 respectively. CONCLUSIONS Disruption of RIM15 in S. cerevisiae results in increased tolerance to heavy metal stress.
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Affiliation(s)
- Hyun-Soo Kim
- Department of Food Science and Technology, Jungwon University, 85, Munmu-ro, Goesan-eup, Goesan-gun, Chungbuk, 367-805, Republic of Korea.
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19
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Yamasaki R, Goshima T, Oba K, Kanai M, Ohdoi R, Hirata D, Akao T. Development of sake yeast haploid set with diverse brewing properties using sake yeast strain Hiroshima no. 6 exhibiting sexual reproduction. J Biosci Bioeng 2020; 129:706-714. [PMID: 32085973 DOI: 10.1016/j.jbiosc.2020.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 10/25/2022]
Abstract
Among sake yeast strains, Kyokai no. 7 (K7) and its closely related strains (K7 group) are predominantly used because of their excellent brewing properties. In the sake industrial sector, the need for various types of yeast strains is high. Although crossbreeding is an effective method for generating genetic diversity that should result in diverse characteristics, most K7 group strains lack normal sporulation ability, including the ability to undergo meiotic chromosomal recombination, which leads to difficulties in crossbreeding. Accordingly, the improvement of sake yeast strains primarily depends on mutagenesis and suitable selection in a stepwise manner. Our recent study revealed that the long-preserved sake yeast strain Hiroshima no. 6 (H6) does not belong to the K7 group despite genetically being extremely similar. In addition, H6 exhibited normal sporulation. Thus, we isolated haploid cells from H6 and mated them with previously isolated haploid cells of K7 group strains. The crossbred diploid strains had normal sporulation ability; hence, we performed tetrad analysis. The brewing characteristics of the obtained haploid set were extremely diverse. Principal component analysis based on the volatile and organic acid components measured using small-scale sake brewing tests revealed that the haploid strains derived from each diploid strain displayed a characteristic distribution. Thus, we demonstrated the availability of genetic crossbreeding using H6 with sporulation ability to facilitate both the development of novel sake yeast strains with many desirable characteristics and analyses of the function of sake yeast.
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Affiliation(s)
- Risa Yamasaki
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046, Japan; Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, 12-70 Hijiyamahonmachi, Minami-Ku, Hiroshima 732-0816, Japan
| | - Tetsuya Goshima
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
| | - Kenji Oba
- Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, 12-70 Hijiyamahonmachi, Minami-Ku, Hiroshima 732-0816, Japan
| | - Muneyoshi Kanai
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
| | - Ritsushi Ohdoi
- Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, 12-70 Hijiyamahonmachi, Minami-Ku, Hiroshima 732-0816, Japan
| | - Dai Hirata
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan; Sakeology Center, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan; Sake Research Center, Asahi Sake Brewing Co., Ltd., 880-1 Asahi, Nagaoka, Niigata 949-5494, Japan
| | - Takeshi Akao
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046, Japan; Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan.
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20
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Yamasaki R, Goshima T, Oba K, Isogai A, Ohdoi R, Hirata D, Akao T. Characteristic analysis of the fermentation and sporulation properties of the traditional sake yeast strain Hiroshima no.6. Biosci Biotechnol Biochem 2019; 84:842-853. [PMID: 31868109 DOI: 10.1080/09168451.2019.1706441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
General sake yeasts (e.g., Kyokai no.7, K7) show high fermentation ability and low sporulation frequency. Former is related to stress-response defect due to the loss-of-function of MSN4 and RIM15. Later is mainly caused by low IME1 expression, leading to difficulty in breeding and genetic analysis. Sake yeast Hiroshima no.6 (H6), which had been applied for sake fermentation, has sporulation ability. However, its detailed properties have not been unveiled. Here we present that the fermentation ability of H6 is suitable for sake brewing, and the precursor of dimethyl trisulfide in sake from H6 is low. MSN4 but not RIM15 of H6 has the same mutation as K7. Our phylogenetic analysis indicated that H6 is closely related to the K7 group. Unlike K7, H6 showed normal sporulation frequency in a partially RIM15-dependent manner, and IME1 in H6 was expressed. H6 possesses excellent properties as a partner strain for breeding by crossing.
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Affiliation(s)
- Risa Yamasaki
- National Research Institute of Brewing, Higashi-Hiroshima, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, Hiroshima, Japan
| | - Tetsuya Goshima
- National Research Institute of Brewing, Higashi-Hiroshima, Japan
| | - Kenji Oba
- Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, Hiroshima, Japan
| | - Atsuko Isogai
- National Research Institute of Brewing, Higashi-Hiroshima, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Ritsushi Ohdoi
- Food Technology Research Center, Hiroshima Prefectural Technology Research Institute, Hiroshima, Japan
| | - Dai Hirata
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Sake Research Center, Asahi Sake Brewing Co., Niigata, Japan.,Sakeology Center, Niigata University, Niigata, Japan
| | - Takeshi Akao
- National Research Institute of Brewing, Higashi-Hiroshima, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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21
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García-Blanco N, Vázquez-Bolado A, Moreno S. Greatwall-Endosulfine: A Molecular Switch that Regulates PP2A/B55 Protein Phosphatase Activity in Dividing and Quiescent Cells. Int J Mol Sci 2019; 20:ijms20246228. [PMID: 31835586 PMCID: PMC6941129 DOI: 10.3390/ijms20246228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 12/13/2022] Open
Abstract
During the cell cycle, hundreds of proteins become phosphorylated and dephosphorylated, indicating that protein kinases and protein phosphatases play a central role in its regulation. It has been widely recognized that oscillation in cyclin-dependent kinase (CDK) activity promotes DNA replication, during S-phase, and chromosome segregation, during mitosis. Each CDK substrate phosphorylation status is defined by the balance between CDKs and CDK-counteracting phosphatases. In fission yeast and animal cells, PP2A/B55 is the main protein phosphatase that counteracts CDK activity. PP2A/B55 plays a key role in mitotic entry and mitotic exit, and it is regulated by the Greatwall-Endosulfine (ENSA) molecular switch that inactivates PP2A/B55 at the onset of mitosis, allowing maximal CDK activity at metaphase. The Greatwall-ENSA-PP2A/B55 pathway is highly conserved from yeast to animal cells. In yeasts, Greatwall is negatively regulated by nutrients through TORC1 and S6 kinase, and couples cell growth, regulated by TORC1, to cell cycle progression, driven by CDK activity. In animal cells, Greatwall is phosphorylated and activated by Cdk1 at G2/M, generating a bistable molecular switch that results in full activation of Cdk1/CyclinB. Here we review the current knowledge of the Greatwall-ENSA-PP2A/B55 pathway and discuss its role in cell cycle progression and as an integrator of nutritional cues.
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22
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Watanabe D, Tashiro S, Shintani D, Sugimoto Y, Iwami A, Kajiwara Y, Takashita H, Takagi H. Loss of Rim15p in shochu yeast alters carbon utilization during barley shochu fermentation. Biosci Biotechnol Biochem 2019; 83:1594-1597. [DOI: 10.1080/09168451.2019.1594679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
ABSTRACT
Rim15p of the yeast Saccharomyces cerevisiae is a Greatwall-family protein kinase that inhibits alcoholic fermentation during sake brewing. To elucidate the roles of Rim15p in barley shochu fermentation, RIM15 was deleted in shochu yeast. The disruptant did not improve ethanol yield, but altered sugar and glycerol contents in the mash, suggesting that Rim15p has a novel function in carbon utilization.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Satoshi Tashiro
- Research & Development Laboratory, Sanwa Shurui Co. Ltd., Oita, Japan
| | - Dai Shintani
- Research & Development Laboratory, Sanwa Shurui Co. Ltd., Oita, Japan
| | - Yukiko Sugimoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Akihiko Iwami
- Research & Development Laboratory, Sanwa Shurui Co. Ltd., Oita, Japan
| | - Yasuhiro Kajiwara
- Research & Development Laboratory, Sanwa Shurui Co. Ltd., Oita, Japan
| | | | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
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23
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Peltier E, Friedrich A, Schacherer J, Marullo P. Quantitative Trait Nucleotides Impacting the Technological Performances of Industrial Saccharomyces cerevisiae Strains. Front Genet 2019; 10:683. [PMID: 31396264 PMCID: PMC6664092 DOI: 10.3389/fgene.2019.00683] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/01/2019] [Indexed: 11/13/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae is certainly the prime industrial microorganism and is related to many biotechnological applications including food fermentations, biofuel production, green chemistry, and drug production. A noteworthy characteristic of this species is the existence of subgroups well adapted to specific processes with some individuals showing optimal technological traits. In the last 20 years, many studies have established a link between quantitative traits and single-nucleotide polymorphisms found in hundreds of genes. These natural variations constitute a pool of QTNs (quantitative trait nucleotides) that modulate yeast traits of economic interest for industry. By selecting a subset of genes functionally validated, a total of 284 QTNs were inventoried. Their distribution across pan and core genome and their frequency within the 1,011 Saccharomyces cerevisiae genomes were analyzed. We found that 150 of the 284 QTNs have a frequency lower than 5%, meaning that these variants would be undetectable by genome-wide association studies (GWAS). This analysis also suggests that most of the functional variants are private to a subpopulation, possibly due to their adaptive role to specific industrial environment. In this review, we provide a literature survey of their phenotypic impact and discuss the opportunities and the limits of their use for industrial strain selection.
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Affiliation(s)
- Emilien Peltier
- Department Sciences du vivant et de la sante, Université de Bordeaux, UR Œnologie EA 4577, Bordeaux, France
- Biolaffort, Bordeaux, France
| | - Anne Friedrich
- Department Micro-organismes, Génomes, Environnement, Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Department Micro-organismes, Génomes, Environnement, Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Philippe Marullo
- Department Sciences du vivant et de la sante, Université de Bordeaux, UR Œnologie EA 4577, Bordeaux, France
- Biolaffort, Bordeaux, France
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24
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Abstract
The AGC signaling pathway represents a conserved distinct signaling pathway in regulation of fungal differentiation and virulence, while it has not been identified or characterized in the sugarcane smut fungus Sporisorium scitamineum. In this study, we identified a PAS domain-containing AGC kinase, SsAgc1, in S. scitamineum. Functional analysis revealed that SsAgc1 plays a regulatory role on the fungal dimorphic switch. Sporisorium scitamineum is the fungal pathogen causing severe sugarcane smut disease that leads to massive economic losses globally. S. scitamineum invades host cane by dikaryotic hyphae, formed after sexual mating of two haploid sporidia of opposite mating type. Therefore, mating/filamentation is critical for S. scitamineum pathogenicity, while its molecular mechanisms remain largely unknown. The AGC (cyclic AMP [cAMP]-dependent protein kinase 1 [protein kinase A {PKA}], cGMP-dependent protein kinase [PKG], and protein kinase C [PKC]) kinase family is a group of serine/threonine (Ser/Thr) protein kinases conserved among eukaryotic genomes, serving a variety of physiological functions, including cell growth, metabolism, differentiation, and cell death. In this study, we identified an AGC kinase, named SsAgc1 (for S. scitamineum Agc1), and characterized its function by reverse genetics. Our results showed that SsAgc1 is critical for S. scitamineum mating/filamentation and pathogenicity, and oxidative stress tolerance under some circumstances. Transcriptional profiling revealed that the SsAgc1 signaling pathway may control expression of the genes governing fungal mating/filamentation and tryptophan metabolism, especially for tryptophol production. We showed that tryptophan and tryptophol could at least partially restore ssagc1Δ mating/filamentation. Overall, our work revealed a signaling pathway mediated by AGC protein kinases to regulate fungal mating/filamentation, possibly through sensing and responding to tryptophol as signal molecules. IMPORTANCE The AGC signaling pathway represents a conserved distinct signaling pathway in regulation of fungal differentiation and virulence, while it has not been identified or characterized in the sugarcane smut fungus Sporisorium scitamineum. In this study, we identified a PAS domain-containing AGC kinase, SsAgc1, in S. scitamineum. Functional analysis revealed that SsAgc1 plays a regulatory role on the fungal dimorphic switch.
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25
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Abstract
Yeasts are very important microorganisms for food production. The high fermentative capacity, mainly of the species of the genus Saccharomyces, is a key factor for their biotechnological use, particularly to produce alcoholic beverages. As viability and vitality are essential to ensure their correct performance in industry, this review addresses the main aspects related to the cellular aging of these fungi as their senescence impacts their proper functioning. Laboratory strains of S. cerevisiae have proven a very successful model for elucidating the molecular mechanisms that control life span. Those mechanisms are shared by all eukaryotic cells. S. cerevisiae has two models of aging, replicative and chronological. Replicative life span is measured by the number of daughter cells a mother can produce. This kind of aging is relevant when the yeast biomass is reused, as in the case of beer fermentations. Chronological life span is measured by the time cells are viable in the stationary phase, and this is relevant for batch fermentations when cells are most of the time in a non-dividing state, such as wine fermentations. The molecular causes and pathways regulating both types of aging are explained in this review.
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26
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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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27
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Shimoi H, Hanazumi Y, Kawamura N, Yamada M, Shimizu S, Suzuki T, Watanabe D, Akao T. Meiotic chromosomal recombination defect in sake yeasts. J Biosci Bioeng 2019; 127:190-196. [DOI: 10.1016/j.jbiosc.2018.07.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 07/19/2018] [Accepted: 07/29/2018] [Indexed: 10/28/2022]
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28
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Nutrient Signaling via the TORC1-Greatwall-PP2A B55δ Pathway Is Responsible for the High Initial Rates of Alcoholic Fermentation in Sake Yeast Strains of Saccharomyces cerevisiae. Appl Environ Microbiol 2018; 85:AEM.02083-18. [PMID: 30341081 DOI: 10.1128/aem.02083-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/13/2018] [Indexed: 01/14/2023] Open
Abstract
Saccharomyces cerevisiae sake yeast strain Kyokai no. 7 (K7) and its relatives carry a homozygous loss-of-function mutation in the RIM15 gene, which encodes a Greatwall family protein kinase. Disruption of RIM15 in nonsake yeast strains leads to improved alcoholic fermentation, indicating that the defect in Rim15p is associated with the enhanced fermentation performance of sake yeast cells. In order to understand how Rim15p mediates fermentation control, we here focused on target-of-rapamycin protein kinase complex 1 (TORC1) and protein phosphatase 2A with the B55δ regulatory subunit (PP2AB55δ), complexes that are known to act upstream and downstream of Rim15p, respectively. Several lines of evidence, including our previous transcriptomic analysis data, suggested enhanced TORC1 signaling in sake yeast cells during sake fermentation. Fermentation tests of the TORC1-related mutants using a laboratory strain revealed that TORC1 signaling positively regulates the initial fermentation rate in a Rim15p-dependent manner. Deletion of the CDC55 gene, encoding B55δ, abolished the high fermentation performance of Rim15p-deficient laboratory yeast and sake yeast cells, indicating that PP2AB55δ mediates the fermentation control by TORC1 and Rim15p. The TORC1-Greatwall-PP2AB55δ pathway similarly affected the fermentation rate in the fission yeast Schizosaccharomyces pombe, strongly suggesting that the evolutionarily conserved pathway governs alcoholic fermentation in yeasts. It is likely that elevated PP2AB55δ activity accounts for the high fermentation performance of sake yeast cells. Heterozygous loss-of-function mutations in CDC55 found in K7-related sake strains may indicate that the Rim15p-deficient phenotypes are disadvantageous to cell survival.IMPORTANCE The biochemical processes and enzymes responsible for glycolysis and alcoholic fermentation by the yeast S. cerevisiae have long been the subject of scientific research. Nevertheless, the factors determining fermentation performance in vivo are not fully understood. As a result, the industrial breeding of yeast strains has required empirical characterization of fermentation by screening numerous mutants through laborious fermentation tests. To establish a rational and efficient breeding strategy, key regulators of alcoholic fermentation need to be identified. In the present study, we focused on how sake yeast strains of S. cerevisiae have acquired high alcoholic fermentation performance. Our findings provide a rational molecular basis to design yeast strains with optimal fermentation performance for production of alcoholic beverages and bioethanol. In addition, as the evolutionarily conserved TORC1-Greatwall-PP2AB55δ pathway plays a major role in the glycolytic control, our work may contribute to research on carbohydrate metabolism in higher eukaryotes.
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Accumulation of intracellular S-adenosylmethionine increases the fermentation rate of bottom-fermenting brewer's yeast during high-gravity brewing. J Biosci Bioeng 2018; 126:736-741. [DOI: 10.1016/j.jbiosc.2018.05.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/31/2018] [Accepted: 05/31/2018] [Indexed: 01/05/2023]
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Metabolic switching of sake yeast by kimoto lactic acid bacteria through the [GAR] non-genetic element. J Biosci Bioeng 2018; 126:624-629. [DOI: 10.1016/j.jbiosc.2018.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/08/2018] [Accepted: 05/15/2018] [Indexed: 12/11/2022]
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Takao Y, Takahashi T, Yamada T, Goshima T, Isogai A, Sueno K, Fujii T, Akao T. Characteristic features of the unique house sake yeast strain Saccharomyces cerevisiae Km67 used for industrial sake brewing. J Biosci Bioeng 2018; 126:617-623. [DOI: 10.1016/j.jbiosc.2018.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/02/2018] [Accepted: 05/08/2018] [Indexed: 11/24/2022]
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Tomimoto K, Akao T, Fukuda H. Histone deacetylases in sake yeast affect fermentation characteristics. Biosci Biotechnol Biochem 2018; 83:1498-1505. [PMID: 30355069 DOI: 10.1080/09168451.2018.1536514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Yeast histone deacetylases (HDAC) affect the production of alcoholic beverages. In this study, we evaluated the sake fermentation characteristics when using HDAC gene-disrupted yeast strain Kyokai No. 701. Flavor components of the sake product were significantly changed. RPD3 or HDA1 disruption increased twofold the amount of isoamyl acetate, and isoamyl alcohol levels also increased in the rpd3Δ strain. To determine the contribution of Rpd3L and Rpd3S complexes to sake characteristics, a gene responsible for Rpd3L and/or Rpd3S formation was also disrupted. Disruption of DEP1 or SDS3 that is an essential component of Rpd3L led to increased isoamyl alcohol production similar to that of the rpd3Δ strain, but the efficiency of isoamyl alcohol esterification was not affected. In addition, Rpd3 and Hda1 may regulate the responsiveness to oxygen in isoamyl acetate production. We conclude that HDAC genes regulate the production of flavor components during sake fermentation. Abbreviations: HDAC: Histone deacetylase; HAT: histone acetyltransferase; K701: sake yeast Kyokai No. 701; PCR: polymerase chain reaction; HPLC: high performance liquid chromatography; E/A: Ester/Alcohol; BCAA: branched chain-amino acid; Atf: alcohol acetyltransferase.
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Affiliation(s)
- Kazuya Tomimoto
- a Brewing Microbiology Division , National Research Institute of Brewing, Higashi-hiroshima , Higashi-hiroshima , Japan
| | - Takeshi Akao
- a Brewing Microbiology Division , National Research Institute of Brewing, Higashi-hiroshima , Higashi-hiroshima , Japan
| | - Hisashi Fukuda
- b Planning and Management Division , National Research Institute of Brewing Higashi-hiroshima , Higashi-hiroshima , Japan
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Comparative analysis of fermentation and enzyme expression profiles among industrial Saccharomyces cerevisiae strains. Appl Microbiol Biotechnol 2018; 102:7071-7081. [DOI: 10.1007/s00253-018-9128-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 01/09/2023]
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Importance of Proteasome Gene Expression during Model Dough Fermentation after Preservation of Baker's Yeast Cells by Freezing. Appl Environ Microbiol 2018; 84:AEM.00406-18. [PMID: 29625985 DOI: 10.1128/aem.00406-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 03/30/2018] [Indexed: 11/20/2022] Open
Abstract
Freeze-thaw stress causes various types of cellular damage, survival and/or proliferation defects, and metabolic alterations. However, the mechanisms underlying how cells cope with freeze-thaw stress are poorly understood. Here, model dough fermentations using two baker's yeast strains, 45 and YF, of Saccharomyces cerevisiae were compared after 2 weeks of cell preservation in a refrigerator or freezer. YF exhibited slow fermentation after exposure to freeze-thaw stress due to low cell viability. A DNA microarray analysis of the YF cells during fermentation revealed that the genes involved in oxidative phosphorylation were relatively strongly expressed, suggesting a decrease in the glycolytic capacity. Furthermore, we found that mRNA levels of the genes that encode the components of the proteasome complex were commonly low, and ubiquitinated proteins were accumulated by freeze-thaw stress in the YF strain. In the cells with a laboratory strain background, treatment with the proteasome inhibitor MG132 or the deletion of each transcriptional activator gene for the proteasome genes (RPN4, PDR1, or PDR3) led to marked impairment of model dough fermentation using the frozen cells. Based on these data, proteasomal degradation of freeze-thaw-damaged proteins may guarantee high cell viability and fermentation performance. We also found that the freeze-thaw stress-sensitive YF strain was heterozygous at the PDR3 locus, and one of the alleles (A148T/A229V/H336R/L541P) was shown to possess a dominant negative phenotype of slow fermentation. Removal of such responsible mutations could improve the freeze-thaw stress tolerance and the fermentation performance of baker's yeast strains, as well as other industrial S. cerevisiae strains.IMPORTANCE The development of freezing technology has enabled the long-term preservation and long-distance transport of foods and other agricultural products. Fresh yeast, however, is usually not frozen because the fermentation performance and/or the viability of individual cells is severely affected after thawing. Here, we demonstrate that proteasomal degradation of ubiquitinated proteins is an essential process in the freeze-thaw stress responses of S. cerevisiae Upstream transcriptional activator genes for the proteasome components are responsible for the fermentation performance after freezing preservation. Thus, this study provides a potential linkage between freeze-thaw stress inputs and the transcriptional regulatory network that might be functionally conserved in higher eukaryotes. Elucidation of the molecular targets of freeze-thaw stress will contribute to advances in cryobiology, such as freezing preservation of human cells, tissues, and embryos for medical purposes and breeding of industrial microorganisms and agricultural crops that adapt well to low temperatures.
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Genomic Sequence of Saccharomyces cerevisiae BAW-6, a Yeast Strain Optimal for Brewing Barley Shochu. GENOME ANNOUNCEMENTS 2018; 6:6/14/e00228-18. [PMID: 29622617 PMCID: PMC5887032 DOI: 10.1128/genomea.00228-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Here, we report the draft genome sequence of Saccharomyces cerevisiae strain BAW-6, which is used for the production of barley shochu, a traditional Japanese spirit. This genomic information can be used to elucidate the genetic basis underlying the high alcohol production capacity and citric acid tolerance of shochu yeast.
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Jung PP, Zhang Z, Paczia N, Jaeger C, Ignac T, May P, Linster CL. Natural variation of chronological aging in the Saccharomyces cerevisiae species reveals diet-dependent mechanisms of life span control. NPJ Aging Mech Dis 2018; 4:3. [PMID: 29560271 PMCID: PMC5845861 DOI: 10.1038/s41514-018-0022-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/30/2018] [Accepted: 02/08/2018] [Indexed: 02/07/2023] Open
Abstract
Aging is a complex trait of broad scientific interest, especially because of its intrinsic link with common human diseases. Pioneering work on aging-related mechanisms has been made in Saccharomyces cerevisiae, mainly through the use of deletion collections isogenic to the S288c reference strain. In this study, using a recently published high-throughput approach, we quantified chronological life span (CLS) within a collection of 58 natural strains across seven different conditions. We observed a broad aging variability suggesting the implication of diverse genetic and environmental factors in chronological aging control. Two major Quantitative Trait Loci (QTLs) were identified within a biparental population obtained by crossing two natural isolates with contrasting aging behavior. Detection of these QTLs was dependent upon the nature and concentration of the carbon sources available for growth. In the first QTL, the RIM15 gene was identified as major regulator of aging under low glucose condition, lending further support to the importance of nutrient-sensing pathways in longevity control under calorie restriction. In the second QTL, we could show that the SER1 gene, encoding a conserved aminotransferase of the serine synthesis pathway not previously linked to aging, is causally associated with CLS regulation, especially under high glucose condition. These findings hint toward a new mechanism of life span control involving a trade-off between serine synthesis and aging, most likely through modulation of acetate and trehalose metabolism. More generally it shows that genetic linkage studies across natural strains represent a promising strategy to further unravel the molecular basis of aging. A Sake yeast strain deficient in producing the protein building block serine lives longer than other yeast strains, especially when exposed to high glucose. A team led by Carole Linster at the University of Luxembourg found a broad variability of lifespan when analyzing more than fifty Saccharomyces cerevisiae strains isolated from around the world. Combining hundreds of lifespan measurements with genotype data from a progeny obtained by crossing the long-lived Sake strain and a short-lived collection strain, they identified two genes playing a pivotal role in causing the contrasting aging behavior of the parents: RIM15, when glucose was limiting and SER1, when glucose was plenty. RIM15 is part of a signaling cascade also regulating aging in mammals; SER1 revealed that a blockage in serine synthesis reprograms metabolism to favor glucose storage and long life.
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Affiliation(s)
- Paul P Jung
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Zhi Zhang
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Nicole Paczia
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Christian Jaeger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Tomasz Ignac
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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Genome Sequence of Saccharomyces cerevisiae Strain Kagoshima No. 2, Used for Brewing the Japanese Distilled Spirit Shōchū. GENOME ANNOUNCEMENTS 2017; 5:5/41/e01126-17. [PMID: 29025949 PMCID: PMC5637509 DOI: 10.1128/genomea.01126-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Here, we report a draft genome sequence of Saccharomyces cerevisiae strain Kagoshima no. 2, which is used for brewing shōchū, a traditional distilled spirit in Japan. The genome data will facilitate an understanding of the evolutional traits and genetic background related to the characteristic features of strain Kagoshima no. 2.
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Watanabe D, Takagi H. Pleiotropic functions of the yeast Greatwall-family protein kinase Rim15p: a novel target for the control of alcoholic fermentation. Biosci Biotechnol Biochem 2017; 81:1061-1068. [DOI: 10.1080/09168451.2017.1295805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract
Rim15p, a Greatwall-family protein kinase in yeast Saccharomyces cerevisiae, is required for cellular nutrient responses, such as the entry into quiescence and the induction of meiosis and sporulation. In higher eukaryotes, the orthologous gene products are commonly involved in the cell cycle G2/M transition. How are these pleiotropic functions generated from a single family of protein kinases? Recent advances in both research fields have identified the conserved Greatwall-mediated signaling pathway and a variety of downstream target molecules. In addition, our studies of S. cerevisiae sake yeast strains revealed that Rim15p also plays a significant role in the control of alcoholic fermentation. Despite an extensive history of research on glycolysis and alcoholic fermentation, there has been no critical clue to artificial modification of fermentation performance of yeast cells. Our finding of an in vivo metabolic regulatory mechanism is expected to provide a major breakthrough in yeast breeding technologies for fermentation applications.
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Affiliation(s)
- Daisuke Watanabe
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Hiroshi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
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Watanabe D, Kaneko A, Sugimoto Y, Ohnuki S, Takagi H, Ohya Y. Promoter engineering of the Saccharomyces cerevisiae RIM15 gene for improvement of alcoholic fermentation rates under stress conditions. J Biosci Bioeng 2017; 123:183-189. [DOI: 10.1016/j.jbiosc.2016.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/14/2016] [Accepted: 08/12/2016] [Indexed: 01/05/2023]
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Oomuro M, Kato T, Zhou Y, Watanabe D, Motoyama Y, Yamagishi H, Akao T, Aizawa M. Defective quiescence entry promotes the fermentation performance of bottom-fermenting brewer's yeast. J Biosci Bioeng 2016; 122:577-582. [PMID: 27212268 DOI: 10.1016/j.jbiosc.2016.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 04/04/2016] [Accepted: 04/25/2016] [Indexed: 10/21/2022]
Abstract
One of the key processes in making beer is fermentation. In the fermentation process, brewer's yeast plays an essential role in both the production of ethanol and the flavor profile of beer. Therefore, the mechanism of ethanol fermentation by of brewer's yeast is attracting much attention. The high ethanol productivity of sake yeast has provided a good basis from which to investigate the factors that regulate the fermentation rates of brewer's yeast. Recent studies found that the elevated fermentation rate of sake Saccharomyces cerevisiae species is closely related to a defective transition from vegetative growth to the quiescent (G0) state. In the present study, to clarify the relationship between the fermentation rate of brewer's yeast and entry into G0, we constructed two types of mutant of the bottom-fermenting brewer's yeast Saccharomyces pastorianus Weihenstephan 34/70: a RIM15 gene disruptant that was defective in entry into G0; and a CLN3ΔPEST mutant, in which the G1 cyclin Cln3p accumulated at high levels. Both strains exhibited higher fermentation rates under high-maltose medium or high-gravity wort conditions (20° Plato) as compared with the wild-type strain. Furthermore, G1 arrest and/or G0 entry were defective in both the RIM15 disruptant and the CLN3ΔPEST mutant as compared with the wild-type strain. Taken together, these results indicate that regulation of the G0/G1 transition might govern the fermentation rate of bottom-fermenting brewer's yeast in high-gravity wort.
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Affiliation(s)
- Mayu Oomuro
- Department of Brewing Microbiology, Asahi Breweries Ltd., 1-1-21 Midori, Moriya, Ibaraki 302-0106, Japan.
| | - Taku Kato
- Department of Brewing Microbiology, Asahi Breweries Ltd., 1-1-21 Midori, Moriya, Ibaraki 302-0106, Japan
| | - Yan Zhou
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Daisuke Watanabe
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Yasuo Motoyama
- Department of Brewing Microbiology, Asahi Breweries Ltd., 1-1-21 Midori, Moriya, Ibaraki 302-0106, Japan
| | - Hiromi Yamagishi
- Quality Control Center, Asahi Breweries Ltd., 1-1-21 Midori, Moriya, Ibaraki 302-0106, Japan
| | - Takeshi Akao
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Masayuki Aizawa
- Department of Brewing Microbiology, Asahi Breweries Ltd., 1-1-21 Midori, Moriya, Ibaraki 302-0106, Japan
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Kessi-Pérez EI, Araos S, García V, Salinas F, Abarca V, Larrondo LF, Martínez C, Cubillos FA. RIM15 antagonistic pleiotropy is responsible for differences in fermentation and stress response kinetics in budding yeast. FEMS Yeast Res 2016; 16:fow021. [PMID: 26945894 DOI: 10.1093/femsyr/fow021] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 12/23/2022] Open
Abstract
Different natural yeast populations have faced dissimilar selective pressures due to the heterogeneous fermentation substrates available around the world; this increases the genetic and phenotypic diversity in Saccharomyces cerevisiae In this context, we expect prominent differences between isolates when exposed to a particular condition, such as wine or sake musts. To better comprehend the mechanisms underlying niche adaptation between two S. cerevisiae isolates obtained from wine and sake fermentation processes, we evaluated fermentative and fungicide resistance phenotypes and identify the molecular origin of such adaptive variation. Multiple regions were associated with fermentation rate under different nitrogen conditions and fungicide resistance, with a single QTL co-localizing in all traits. Analysis around this region identified RIM15 as the causative locus driving fungicide sensitivity, together with efficient nitrogen utilization and glycerol production in the wine strain. A null RIM15 variant confers a greater fermentation rate through the utilization of available glucose instead of its storage. However, this variant has a detrimental effect on fungicide resistance since complex sugars are not synthesized and transported into the membrane. Together, our results reveal the antagonist pleiotropic nature of a RIM15 null variant, positively affecting a series of fermentation related phenotypes, but apparently detrimental in the wild.
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Affiliation(s)
- Eduardo I Kessi-Pérez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Sebastián Araos
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Verónica García
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Francisco Salinas
- Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago 8331150, Chile
| | - Valentina Abarca
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Luis F Larrondo
- Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago 8331150, Chile
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Francisco A Cubillos
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170201, Chile Millennium Nucleus for Fungal Integrative and Synthetic Biology (MN-FISB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago 8331150, Chile
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Watanabe D, Zhou Y, Hirata A, Sugimoto Y, Takagi K, Akao T, Ohya Y, Takagi H, Shimoi H. 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; 82:340-51. [PMID: 26497456 PMCID: PMC4702617 DOI: 10.1128/aem.02977-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/20/2015] [Indexed: 11/20/2022] Open
Abstract
The high fermentation rate of Saccharomyces cerevisiae sake yeast strains is attributable to a loss-of-function mutation in the RIM15 gene, which encodes a Greatwall-family protein kinase that is conserved among eukaryotes. In the present study, we performed intracellular metabolic profiling analysis and revealed that deletion of the RIM15 gene in a laboratory strain impaired glucose-anabolic pathways through the synthesis of UDP-glucose (UDPG). Although Rim15p is required for the synthesis of trehalose and glycogen from UDPG upon entry of cells into the quiescent state, we found that Rim15p is also essential for the accumulation of cell wall β-glucans, which are also anabolic products of UDPG. Furthermore, the impairment of UDPG or 1,3-β-glucan synthesis contributed to an increase in the fermentation rate. Transcriptional induction of PGM2 (phosphoglucomutase) and UGP1 (UDPG pyrophosphorylase) was impaired in Rim15p-deficient cells in the early stage of fermentation. These findings demonstrate that the decreased anabolism of glucose into UDPG and 1,3-β-glucan triggered by a defect in the Rim15p-mediated upregulation of PGM2 and UGP1 redirects the glucose flux into glycolysis. Consistent with this, sake yeast strains with defective Rim15p exhibited impaired expression of PGM2 and UGP1 and decreased levels of β-glucans, trehalose, and glycogen during sake fermentation. We also identified a sake yeast-specific mutation in the glycogen synthesis-associated glycogenin gene GLG2, supporting the conclusion that the glucose-anabolic pathway is impaired in sake yeast. These findings demonstrate that downregulation of the UDPG synthesis pathway is a key mechanism accelerating alcoholic fermentation in industrially utilized S. cerevisiae sake strains.
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Affiliation(s)
- Daisuke Watanabe
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan National Research Institute of Brewing, Higashihiroshima, Hiroshima, Japan
| | - Yan Zhou
- National Research Institute of Brewing, Higashihiroshima, Hiroshima, Japan
| | - Aiko Hirata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Yukiko Sugimoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Kenichi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Takeshi Akao
- National Research Institute of Brewing, Higashihiroshima, Hiroshima, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiroshi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Hitoshi Shimoi
- National Research Institute of Brewing, Higashihiroshima, Hiroshima, Japan Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
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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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Nakamura H, Kikuma T, Jin FJ, Maruyama JI, Kitamoto K. AoRim15 is involved in conidial stress tolerance, conidiation and sclerotia formation in the filamentous fungus Aspergillus oryzae. J Biosci Bioeng 2015; 121:365-71. [PMID: 26467693 DOI: 10.1016/j.jbiosc.2015.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 08/12/2015] [Accepted: 08/18/2015] [Indexed: 12/11/2022]
Abstract
The serine-threonine kinase Rim15p is a master regulator of stress signaling and is required for stress tolerance and sexual sporulation in the yeast Saccharomyces cerevisiae. However, in filamentous fungi that reproduce asexually via conidiation, the physiological function of Rim15p homologs has not been extensively analyzed. Here, we functionally characterized the protein homolog of Rim15p in the filamentous fungus Aspergillus oryzae, by deleting and overexpressing the corresponding Aorim15 gene and examining the role of this protein in stress tolerance and development. Deletion of Aorim15 resulted in an increase in the sensitivity of conidia to oxidative and heat stresses, whereas conidia of the Aorim15 overexpressing strain were more resistant to these stresses. These results indicated that AoRim15 functions in stress tolerance, similar to S. cerevisiae Rim15p. Phenotypic analysis revealed that conidiation was markedly reduced by overexpression of Aorim15 in A. oryzae, and was completely abolished in the deletion strain. In addition, the formation of sclerotia, which is another type of developmental structure in filamentous fungi, was decreased by the deletion of Aorim15, whereas Aorim15 overexpression increased the number of sclerotia. These results indicated that AoRim15 is a positive regulator of sclerotia formation and that overexpression of AoRim15 shifts the developmental balance from conidiation towards sclerotia formation. Collectively, we demonstrated that AoRim15 is involved in the stress tolerance of conidia and differentially regulates between the two developmental fates of conidiation and sclerotia formation.
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Affiliation(s)
- Hidetoshi Nakamura
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takashi Kikuma
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Feng Jie Jin
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jun-ichi Maruyama
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Katsuhiko Kitamoto
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Tamura H, Okada H, Kume K, Koyano T, Goshima T, Nakamura R, Akao T, Shimoi H, Mizunuma M, Ohya Y, Hirata D. Isolation of a spontaneous cerulenin-resistant sake yeast with both high ethyl caproate-producing ability and normal checkpoint integrity. Biosci Biotechnol Biochem 2015; 79:1191-9. [PMID: 25787154 DOI: 10.1080/09168451.2015.1020756] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In the brewing of high-quality sake such as Daiginjo-shu, the cerulenin-resistant sake yeast strains with high producing ability to the flavor component ethyl caproate have been used widely. Genetic stability of sake yeast would be important for the maintenance of both fermentation properties of yeast and quality of sake. In eukaryotes, checkpoint mechanisms ensure genetic stability. However, the integrity of these mechanisms in sake yeast has not been examined yet. Here, we investigated the checkpoint integrity of sake yeasts, and the results suggested that a currently used cerulenin-resistant sake yeast had a defect in spindle assembly checkpoint (SAC). We also isolated a spontaneous cerulenin-resistant sake yeast FAS2-G1250S mutant, G9CR, which showed both high ethyl caproate-producing ability and integrity/intactness of the checkpoint mechanisms. Further, morphological phenotypic robustness analysis by use of CalMorph supported the genetic stability of G9CR. Finally, we confirmed the high quality of sake from G9CR in an industrial sake brewing setting.
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Affiliation(s)
- Hiroyasu Tamura
- a Research and Development Department , Asahi Sake Brewing Co., Ltd. , Nagaoka , Japan
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46
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Transcriptional response of Saccharomyces cerevisiae to low temperature during wine fermentation. Antonie van Leeuwenhoek 2015; 107:1029-48. [DOI: 10.1007/s10482-015-0395-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/22/2015] [Indexed: 01/31/2023]
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47
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Development of industrial yeast strain with improved acid- and thermo-tolerance through evolution under continuous fermentation conditions followed by haploidization and mating. J Biosci Bioeng 2014; 118:689-95. [PMID: 24958128 DOI: 10.1016/j.jbiosc.2014.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 05/14/2014] [Accepted: 05/18/2014] [Indexed: 11/20/2022]
Abstract
Continuous fermentation using the industrial Saccharomyces cerevisiae diploid strain WW was carried out under acidic or high-temperature conditions to achieve acid- or thermo-tolerant mutants. Mutants isolated at pH 2.5 and 41°C showed improved growth and fermentation ability under acidic and elevated temperature conditions. Haploid strains WW17A1 and WW17A4 obtained from the mutated diploid strain WW17A showed better growth and 4.5-6.5% higher ethanol yields at pH 2.7 than the original strains. Haploid strain WW12T4 obtained from mutated diploid strain WW12T showed 1.25-1.50 times and 2.8-4.7 times higher total cell number and cell viability, respectively, than the original strains at 42°C. Strain AT, which had significantly improved acid- and thermo-tolerance, was developed by mating strain WW17A1 with WW12T4. Batch fermentation at 41°C and pH 3.5 showed that the ethanol concentration and yield achieved during fermentation by strain AT were 55.4 g/L and 72.5%, respectively, which were 10 g/L and 13.4% higher than that of the original strain WW. The present study demonstrates that continuous cultivation followed by haploidization and mating is a powerful approach for enhancing the tolerance of industrial strains.
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48
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Brice C, Sanchez I, Bigey F, Legras JL, Blondin B. A genetic approach of wine yeast fermentation capacity in nitrogen-starvation reveals the key role of nitrogen signaling. BMC Genomics 2014; 15:495. [PMID: 24947828 PMCID: PMC4073503 DOI: 10.1186/1471-2164-15-495] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/10/2014] [Indexed: 11/16/2022] Open
Abstract
Background In conditions of nitrogen limitation, Saccharomyces cerevisiae strains differ in their fermentation capacities, due to differences in their nitrogen requirements. The mechanisms ensuring the maintenance of glycolytic flux in these conditions are unknown. We investigated the genetic basis of these differences, by studying quantitative trait loci (QTL) in a population of 133 individuals from the F2 segregant population generated from a cross between two strains with different nitrogen requirements for efficient fermentation. Results By comparing two bulks of segregants with low and high nitrogen requirements, we detected four regions making a quantitative contribution to these traits. We identified four polymorphic genes, in three of these four regions, for which involvement in the phenotype was validated by hemizygote comparison. The functions of the four validated genes, GCN1, MDS3, ARG81 and BIO3, relate to key roles in nitrogen metabolism and signaling, helping to maintain fermentation performance. Conclusions This study reveals that differences in nitrogen requirement between yeast strains results from a complex allelic combination. The identification of three genes involved in sensing and signaling nitrogen and specially one from the TOR pathway as affecting nitrogen requirements suggests a role for this pathway in regulating the fermentation rate in starvation through unknown mechanisms linking nitrogen signaling to glycolytic flux. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-495) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Bruno Blondin
- INRA, UMR1083 Science pour l'Œnologie, 2 Place Viala, F-34060 Montpellier, France.
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49
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Nishibori N, Sasaki K, Okimori Y, Kanai M, Isogai A, Yamada O, Fujii T, Goto-Yamamoto N. Yeast cell lysis enhances dimethyl trisulfide formation in sake. J Biosci Bioeng 2014; 118:526-8. [PMID: 24932967 DOI: 10.1016/j.jbiosc.2014.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/26/2014] [Accepted: 04/16/2014] [Indexed: 11/27/2022]
Abstract
The present study showed that the lysis of yeast cells and subsequent release of cell contents in sake mash accelerated dimethyl trisulfide (DMTS) formation. Among these, heat unstable and relatively high molecular weight compounds were assumed to be enzymes; thus, enzymatic reactions probably contribute to DMTS formation.
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Affiliation(s)
- Nahoko Nishibori
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima 739-0046, Japan
| | - Kei Sasaki
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4, Kagamiyama, Higashi-hiroshima 739-8528, Japan
| | - Yuta Okimori
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4, Kagamiyama, Higashi-hiroshima 739-8528, Japan
| | - Muneyoshi Kanai
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima 739-0046, Japan
| | - Atsuko Isogai
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima 739-0046, Japan
| | - Osamu Yamada
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima 739-0046, Japan
| | - Tsutomu Fujii
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima 739-0046, Japan; Graduate School of Biosphere Science, Hiroshima University, 1-4-4, Kagamiyama, Higashi-hiroshima 739-8528, Japan.
| | - Nami Goto-Yamamoto
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-hiroshima 739-0046, Japan; Graduate School of Biosphere Science, Hiroshima University, 1-4-4, Kagamiyama, Higashi-hiroshima 739-8528, Japan
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50
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Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G. A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol 2014; 31:872-88. [PMID: 24425782 PMCID: PMC3969562 DOI: 10.1093/molbev/msu037] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies.
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Affiliation(s)
- Anders Bergström
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
| | | | - Francisco Salinas
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
| | - Benjamin Barré
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
| | - Leopold Parts
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Amin Zia
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine
| | - Alex N. Nguyen Ba
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Alan M. Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Edward J. Louis
- Centre of Genetic Architecture of Complex Traits, University of Leicester, Leicester, United Kingdom
| | - Ville Mustonen
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Richard Durbin
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Gianni Liti
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
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