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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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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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3
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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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Cell Cycle Progression Influences Biofilm Formation in Saccharomyces cerevisiae 1308. Microbiol Spectr 2022; 10:e0276521. [PMID: 35670600 PMCID: PMC9241733 DOI: 10.1128/spectrum.02765-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilm-immobilized continuous fermentation is a novel fermentation strategy that has been utilized in ethanol fermentation. Continuous fermentation contributes to the self-proliferation of Saccharomyces cerevisiae biofilms. Previously, we successfully described the cell cycle differences between biofilm-immobilized fermentation and calcium alginate-immobilized fermentation. In the present study, we investigated the relationship between biofilm formation and the cell cycle. We knocked down CLN3, SIC1, and ACE2 and found that Δcln3 and Δsic1 exhibited a predominance of G2/M phase cells, increased biofilm formation, and significantly increased extracellular polysaccharide formation and expression of genes in the FLO gene family during immobilisation fermentation. Δace2 exhibited a contrasting performance. These findings suggest that the increase in the proportion of cells in the G2/M phase of the cell cycle facilitates biofilm formation and that the cell cycle influences biofilm formation by regulating cell adhesion and polysaccharide formation. This opens new avenues for basic research and may also help to provide new ideas for biofilm prevention and optimization. IMPORTANCE Immobilised fermentation can be achieved using biofilm resistance, resulting in improved fermentation efficiency and yield. The link between the cell cycle and biofilms deserves further study since reports are lacking in this area. This study showed that the ability of Saccharomyces cerevisiae to produce biofilm differed when cell cycle progression was altered. Further studies suggested that cell cycle regulatory genes influenced biofilm formation by regulating cell adhesion and polysaccharide formation. Findings related to cell cycle regulation of biofilm formation set the stage for biofilm in Saccharomyces cerevisiae and provide a theoretical basis for the development of a new method to improve biofilm-based industrial fermentation.
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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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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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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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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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Oomuro M, Motoyama Y, Watanabe T. Isolation of a lager yeast with an increased copy number of theYCK1gene and high fermentation performance. JOURNAL OF THE INSTITUTE OF BREWING 2018. [DOI: 10.1002/jib.543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Mayu Oomuro
- Department of Fermentation and Microbiology Technology; Asahi Breweries Ltd; 1-1-21 Midori Moriya Ibaraki 302-0106 Japan
| | - Yasuo Motoyama
- Department of Fermentation and Microbiology Technology; Asahi Breweries Ltd; 1-1-21 Midori Moriya Ibaraki 302-0106 Japan
| | - Tetsuya Watanabe
- Department of Fermentation and Microbiology Technology; Asahi Breweries Ltd; 1-1-21 Midori Moriya Ibaraki 302-0106 Japan
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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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Interactions between carbon and nitrogen sources depend on RIM15 and determine fermentative or respiratory growth in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2018; 102:4535-4548. [DOI: 10.1007/s00253-018-8951-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/06/2018] [Accepted: 03/14/2018] [Indexed: 12/29/2022]
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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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