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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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2
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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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3
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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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4
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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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5
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Watanabe D, Kawashima M, Yoshioka N, Sugimoto Y, Takagi H. Rational design of alcoholic fermentation targeting extracellular carbon. NPJ Sci Food 2023; 7:37. [PMID: 37479699 PMCID: PMC10361962 DOI: 10.1038/s41538-023-00215-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Breeding yeast strains for industrial alcoholic fermentation requires laborious screening due to the lack of in vivo modification strategies. Here we show that quiescence-specific cell wall thickening via synthesis of a major component, 1,3-β-glucan, critically antagonizes cellular fermentation ability by sequestering the available cytoplasmic carbon sources. This study provides insights into glycolytic control and reports an effective and reliable rational fermentation design.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
| | - Mikiya Kawashima
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Naoya Yoshioka
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Yukiko Sugimoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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Kleijn IT, Martínez-Segura A, Bertaux F, Saint M, Kramer H, Shahrezaei V, Marguerat S. Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast. Life Sci Alliance 2022; 5:5/5/e202101223. [PMID: 35228260 PMCID: PMC8886410 DOI: 10.26508/lsa.202101223] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 12/20/2022] Open
Abstract
Cellular resources are limited and their relative allocation to gene expression programmes determines physiological states and global properties such as the growth rate. Here, we determined the importance of the growth rate in explaining relative changes in protein and mRNA levels in the simple eukaryote Schizosaccharomyces pombe grown on non-limiting nitrogen sources. Although expression of half of fission yeast genes was significantly correlated with the growth rate, this came alongside wide-spread nutrient-specific regulation. Proteome and transcriptome often showed coordinated regulation but with notable exceptions, such as metabolic enzymes. Genes positively correlated with growth rate participated in every level of protein production apart from RNA polymerase II-dependent transcription. Negatively correlated genes belonged mainly to the environmental stress response programme. Critically, metabolic enzymes, which represent ∼55-70% of the proteome by mass, showed mostly condition-specific regulation. In summary, we provide a rich account of resource allocation to gene expression in a simple eukaryote, advancing our basic understanding of the interplay between growth-rate-dependent and nutrient-specific gene expression.
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Affiliation(s)
- Istvan T Kleijn
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK,Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Amalia Martínez-Segura
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - François Bertaux
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK,Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Malika Saint
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Holger Kramer
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Vahid Shahrezaei
- Department of Mathematics, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Samuel Marguerat
- Medical Research Council London Institute of Medical Sciences (MRC LMS), London, UK .,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
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7
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Yatabe F, Okahashi N, Seike T, Matsuda F. Comparative 13 C-metabolic flux analysis indicates elevation of ATP regeneration, carbon dioxide, and heat production in industrial Saccharomyces cerevisiae strains. Biotechnol J 2021; 17:e2000438. [PMID: 33983677 DOI: 10.1002/biot.202000438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND Various industrial Saccharomyces cerevisiae strains are used for specific processes, such as sake, wine brewing and bread making. Understanding mechanisms underlying the fermentation performance of these strains would be useful for further engineering of the S. cerevisiae metabolism. However, the relationship between the fermentation performance, intra-cellular metabolic states, and other phenotypic characteristics of industrial yeasts is still unclear. In this study, 13 C-metabolic flux analysis of four diploid yeast strains-laboratory, sake, bread, and wine yeasts-was conducted. RESULTS While the Crabtree effect was observed for all strains, the metabolic flux level of glycolysis was elevated in bread and sake yeast. Furthermore, increased flux levels of the TCA cycle were commonly observed in the three industrial strains. The specific rates of CO2 production, net ATP regeneration, and metabolic heat generation estimated from the metabolic flux distribution were two to three times greater than those of the laboratory strain. The elevation in metabolic heat generation was correlated with the tolerance to low-temperature stress. CONCLUSION These results indicate that the metabolic flux distribution of sake and bread yeast strains contributes to faster production of ethanol and CO2 . It is also suggested that the generation of metabolic heat is preferable under the actual industrial fermentation conditions.
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Affiliation(s)
- Futa Yatabe
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Taisuke Seike
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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8
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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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9
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Songdech P, Ruchala J, Semkiv MV, Jensen LT, Sibirny A, Ratanakhanokchai K, Soontorngun N. Overexpression of Transcription Factor ZNF1 of Glycolysis Improves Bioethanol Productivity under High Glucose Concentration and Enhances Acetic Acid Tolerance of Saccharomyces cerevisiae. Biotechnol J 2020; 15:e1900492. [PMID: 32196937 DOI: 10.1002/biot.201900492] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/01/2020] [Indexed: 12/28/2022]
Abstract
Saccharomyces cerevisiae offers an attractive platform for synthesis of biofuels and biochemical; however, robust strains that can withstand high substrate concentration and fermentation conditions are required. To improve the yield and productivity of bioethanol, modification of glucose metabolism and cellular stress adaptation is investigated. Specifically, the role of Znf1 transcription factor in metabolic regulation of glucose is characterized. Here, Znf1 is first shown to activate key genes in glycolysis, pyruvate metabolism, and alcoholic fermentation when glucose is provided as the sole carbon source. Under conditions of high glucose (20 g L-1 ), overexpression of ZNF1 accelerated glucose consumption with only 0.67-0.80% of glucose remaining after 24 or 36 h of fermentation. Importantly, ZNF1 overexpression increases ethanol concentrations by 14-24% and achieves a maximum ethanol concentration of 76.12-88.60 g L-1 . Ethanol productivity is increased 3.17-3.69 in strains overexpressing ZNF1 compared to 2.42-3.35 and 2.94-3.50 for the znf1Δ and wild-type strains, respectively. Moreover, strains overexpressing ZNF1 also display enhanced tolerance to osmotic and weak-acid stresses, important trait in alcoholic fermentation. Overexpresssion of key transcriptional activators of genes in glycolysis and stress responses appears to be an effective strategy to improve bioethanol productivity and enhance strain robustness.
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Affiliation(s)
- Pattanan Songdech
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Justyna Ruchala
- Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszow, 35-601, Poland
| | - Marta V Semkiv
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, Lviv, 79005, Ukraine
| | - Laran T Jensen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Andriy Sibirny
- Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszow, 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, Lviv, 79005, Ukraine
| | - Khanok Ratanakhanokchai
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Nitnipa Soontorngun
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
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10
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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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11
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Lin L, Wang S, Li X, He Q, Benz JP, Tian C. STK-12 acts as a transcriptional brake to control the expression of cellulase-encoding genes in Neurospora crassa. PLoS Genet 2019; 15:e1008510. [PMID: 31765390 PMCID: PMC6901240 DOI: 10.1371/journal.pgen.1008510] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/09/2019] [Accepted: 11/05/2019] [Indexed: 12/21/2022] Open
Abstract
Cellulolytic fungi have evolved a complex regulatory network to maintain the precise balance of nutrients required for growth and hydrolytic enzyme production. When fungi are exposed to cellulose, the transcript levels of cellulase genes rapidly increase and then decline. However, the mechanisms underlying this bell-shaped expression pattern are unclear. We systematically screened a protein kinase deletion set in the filamentous fungus Neurospora crassa to search for mutants exhibiting aberrant expression patterns of cellulase genes. We observed that the loss of stk-12 (NCU07378) caused a dramatic increase in cellulase production and an extended period of high transcript abundance of major cellulase genes. These results suggested that stk-12 plays a critical role as a brake to turn down the transcription of cellulase genes to repress the overexpression of hydrolytic enzymes and prevent energy wastage. Transcriptional profiling analyses revealed that cellulase gene expression levels were maintained at high levels for 56 h in the Δstk-12 mutant, compared to only 8 h in the wild-type (WT) strain. After growth on cellulose for 3 days, the transcript levels of cellulase genes in the Δstk-12 mutant were 3.3-fold over WT, and clr-2 (encoding a transcriptional activator) was up-regulated in Δstk-12 while res-1 and rca-1 (encoding two cellulase repressors) were down-regulated. Consequently, total cellulase production in the Δstk-12 mutant was 7-fold higher than in the WT. These results strongly suggest that stk-12 deletion results in dysregulation of the cellulase expression machinery. Further analyses showed that STK-12 directly targets IGO-1 to regulate cellulase production. The TORC1 pathway promoted cellulase production, at least partly, by inhibiting STK-12 function, and STK-12 and CRE-1 functioned in parallel pathways to repress cellulase gene expression. Our results clarify how cellulase genes are repressed at the transcriptional level during cellulose induction, and highlight a new strategy to improve industrial fungal strains.
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Affiliation(s)
- Liangcai Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Shanshan Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiaolin Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qun He
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - J. Philipp Benz
- Technical University of Munich, TUM School of Life Sciences Weihenstephan, Hans-Carl-von-Carlowitz-Platz, Freising, Germany
- Technical University of Munich, Institute for Advanced Study, Lichtenbergstr, Garching, Germany
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- * E-mail:
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12
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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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13
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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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