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Chen A. Enhancing freeze-thaw tolerance in baker's yeast: strategies and perspectives. Food Sci Biotechnol 2024; 33:2953-2969. [PMID: 39220313 PMCID: PMC11364746 DOI: 10.1007/s10068-024-01637-6] [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: 04/10/2024] [Revised: 05/21/2024] [Accepted: 06/07/2024] [Indexed: 09/04/2024] Open
Abstract
Frozen dough technology is important in modern bakery operations, facilitating the transportation of dough at low temperatures to downstream sales points. However, the freeze-thaw process imposes significant stress on baker's yeast, resulting in diminished viability and fermentation capacity. Understanding the mechanisms underlying freeze-thaw stress is essential for mitigating its adverse effects on yeast performance. This review delves into the intricate mechanisms underlying freeze-thaw stress, focusing specifically on Saccharomyces cerevisiae, the primary yeast used in baking, and presents a wide range of biotechnological approaches to enhance freeze-thaw resistance in S. cerevisiae. Strategies include manipulating intracellular metabolites, altering membrane composition, managing antioxidant defenses, mediating aquaporin expression, and employing adaptive evolutionary and breeding techniques. Addressing challenges and strategies associated with freeze-thaw stress, this review provides valuable insights for future research endeavors, aiming to enhance the freeze-thaw tolerance of baker's yeast and contribute to the advancement of bakery science.
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Affiliation(s)
- Anqi Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122 China
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2
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Yuan Z, Ge Z, Fu Q, Wang F, Wang Q, Shi X, Wang B. Investigation of cold-resistance mechanisms in cryophylactic yeast Metschnikowia pulcherrima based on comparative transcriptome analysis. Front Microbiol 2024; 15:1476087. [PMID: 39386373 PMCID: PMC11462854 DOI: 10.3389/fmicb.2024.1476087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 09/05/2024] [Indexed: 10/12/2024] Open
Abstract
Introduction Low temperature inhibits the growth of most microorganisms. However, some microbes can grow well in a low temperature, even a freezing temperature. Methods In this study, the mechanisms conferring cold resistance in the cryophylactic yeast Metschnikowia (M.) pulcherrima MS612, an isolate of the epidermis of ice grapes, were investigated based on comparative transcriptome analysis. Results A total of 6018 genes and 374 differentially expressed genes (> 2-fold, p < 0.05) were identified using RNA-Seq. The differentially expressed genes were mainly involved in carbohydrate and energy metabolism, transport mechanisms, antifreeze protection, lipid synthesis, and signal transduction. M. pulcherrima MS612 maintained normal growth at low temperature (5°C) by enhancing energy metabolism, sterol synthesis, metal ion homeostasis, amino acid and MDR transport, while increased synthesis of glycerol and proline transport to improve its resistance to the freezing temperature (-5°C). Furthermore, cAMP-PKA and ERAD signaling pathways contribute to resist the low temperature and the freezing temperature, respectively. Conclusion This study provides new insights into cold resistance in cryophylactic microorganisms for maneuvering various metabolism to resist different cold environment.
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Affiliation(s)
- Zaizhu Yuan
- Key Laboratory of Agricultural Product Processing and Quality Control of Specialty (Co-Construction by Ministry and Province), School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
| | - Zhengkai Ge
- Key Laboratory of Agricultural Product Processing and Quality Control of Specialty (Co-Construction by Ministry and Province), School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
| | - Qingquan Fu
- Key Laboratory of Agricultural Product Processing and Quality Control of Specialty (Co-Construction by Ministry and Province), School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
| | - Fangfang Wang
- Key Laboratory of Agricultural Product Processing and Quality Control of Specialty (Co-Construction by Ministry and Province), School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
| | - Qingling Wang
- Key Laboratory of Agricultural Product Processing and Quality Control of Specialty (Co-Construction by Ministry and Province), School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
| | - Xuewei Shi
- Key Laboratory of Agricultural Product Processing and Quality Control of Specialty (Co-Construction by Ministry and Province), School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
| | - Bin Wang
- Key Laboratory of Agricultural Product Processing and Quality Control of Specialty (Co-Construction by Ministry and Province), School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Key Laboratory for Food Nutrition and Safety Control of Xinjiang Production and Construction Corps, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
- Engineering Research Center of Storage and Processing of Xinjiang Characteristic Fruits and Vegetables, Ministry of Education, School of Food Science and Technology, Shihezi University, Xinjiang, Shihezi, China
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García-Ríos E, Pardo J, Su Y, Guillamón JM. Different Nitrogen Consumption Patterns in Low Temperature Fermentations in the Wine Yeast Saccharomyces cerevisiae. Foods 2024; 13:2522. [PMID: 39200449 PMCID: PMC11354071 DOI: 10.3390/foods13162522] [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: 07/17/2024] [Revised: 07/31/2024] [Accepted: 08/07/2024] [Indexed: 09/02/2024] Open
Abstract
Nowadays, the wine industry carries out fermentations at low temperatures because this oenological practice clearly improves the aromatic complexity of the final wines. In addition, nitrogen content of the must also influences the quality of the wine. In this study, we carried out a phenotypic and fermentative analysis of two industrial wine Saccharomyces cerevisiae strains (P5 and P24) at 15 and 28 °C and three nitrogen concentrations (60, 140 and 300 mg N/L) in synthetic must. Our results show that both parameters, temperature and nitrogen, are interrelated and clearly determine the competitiveness of the wine strains and their ability to adapt at low temperatures. The best adapted strain at low temperatures decreased its competitiveness at lower nitrogen concentrations. In addition, our results show that it is not only the quantity of nitrogen transported that is important but also the quality of the nitrogen source used for wine yeast adaptation at low temperatures. The presence of some amino acids, such as arginine, branched chain amino acids, and some aromatic amino acids can improve the growth and fermentation activity of wine yeasts at low temperatures. These results allow us to better understand the basis of wine yeast adaptation to fermentation conditions, providing important information for winemakers to help them select the most appropriate yeast strain, thus reducing the economic costs associated with long and sluggish fermentations. The correlation between some amino acids and better yeast fermentation performance could be used in the future to design inactive dry yeast enriched in some of these amino acids, which could be added as a nutritional supplement during low temperature fermentations.
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Affiliation(s)
- Estéfani García-Ríos
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), 46980 Paterna, Valencia, Spain; (J.P.); (J.M.G.)
| | - Judit Pardo
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), 46980 Paterna, Valencia, Spain; (J.P.); (J.M.G.)
| | - Ying Su
- College of Enology, Northwest A&F University, Xianyang 712100, China;
| | - José Manuel Guillamón
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), 46980 Paterna, Valencia, Spain; (J.P.); (J.M.G.)
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Lu Y, Luo F, Zhou A, Yi C, Chen H, Li J, Guo Y, Xie Y, Zhang W, Lin D, Yang Y, Wu Z, Zhang Y, Xu S, Hu W. Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution. Gigascience 2024; 13:giae064. [PMID: 39311763 PMCID: PMC11417965 DOI: 10.1093/gigascience/giae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/08/2024] [Accepted: 08/07/2024] [Indexed: 09/26/2024] Open
Abstract
Pomacea canaliculata, an invasive species native to South America, is recognized for its broad geographic distribution and adaptability to a variety of ecological conditions. The details concerning the evolution and adaptation of P. canaliculate remain unclear due to a lack of whole-genome resequencing data. We examined 173 P. canaliculata genomes representing 17 geographic populations in East and Southeast Asia. Interestingly, P. canaliculata showed a higher level of genetic diversity than other mollusks, and our analysis suggested that the dispersal of P. canaliculata could have been driven by climate changes and human activities. Notably, we identified a set of genes associated with low temperature adaptation, including Csde1, a cold shock protein coding gene. Further RNA sequencing analysis and reverse transcription quantitative polymerase chain reaction experiments demonstrated the gene's dynamic pattern and biological functions during cold exposure. Moreover, both positive selection and balancing selection are likely to have contributed to the rapid environmental adaptation of P. canaliculata populations. In particular, genes associated with energy metabolism and stress response were undergoing positive selection, while a large number of immune-related genes showed strong signatures of balancing selection. Our study has advanced our understanding of the evolution of P. canaliculata and has provided a valuable resource concerning an invasive species.
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Affiliation(s)
- Yan Lu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Center for Evolutionary Biology, Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200438, China
| | - Fang Luo
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - An Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Center for Evolutionary Biology, Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200438, China
| | - Cun Yi
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai 200438, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jian Li
- China Basic Medical College, Guangxi Traditional Chinese Medical University, Nanning 530005, China
| | - Yunhai Guo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Yuxiang Xie
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai 200438, China
| | - Wei Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai 200438, China
| | - Datao Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yaming Yang
- Yunnan Institute of Parasitic Diseases, Yunnan 665000, China
| | - Zhongdao Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yi Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Center for Evolutionary Biology, Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200438, China
| | - Wei Hu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
- Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai 200438, China
- College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
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Navarro L, Gil i Cortiella M, Gutiérrez-Moraga A, Calisto N, Ubeda C, Corsini G. Antarctic Soil Yeasts with Fermentative Capacity and Potential for the Wine Industry. Foods 2023; 12:4496. [PMID: 38137300 PMCID: PMC10742413 DOI: 10.3390/foods12244496] [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: 11/10/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Low fermentation temperatures are usually employed to obtain high-quality wines. This is especially interesting for white wine production since it prevents the loss of volatile compounds and a browning appearance; however, available fermentative yeasts do not usually tolerate low temperatures. Therefore, an interesting place to find new yeasts with cryotolerance is the Antarctic continent. From soil samples collected in Antarctica, 125 yeasts were isolated, of which 25 exhibited fermentative activity at 10 °C. After a fingerprinting assay, we classified the candidates into nine isotypes and sequenced internal transcribed spacer regions for their identification. These yeasts were identified as part of the Mrakia genus. Sugar and alcohol tolerance tests showed that some of these Antarctic soil yeasts were able to grow up to 9% alcohol, and 25% sugar was reached; however, they exhibited longer latency periods compared to the control Saccharomyces cerevisiae. The optimal growing temperature for the isolated Antarctic yeasts was between 10 °C and 15 °C. A comprehensive analysis of the results obtained showed that the isolates 10M3-1, 4M3-6, and 4B1-35 could be good candidates for fermentation purposes due to their alcohol, sugar tolerance, and growth features. Our results prove that it is possible to isolate fermentative yeasts from Antarctic soil with promising characteristics for their potential use in the wine production industry.
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Affiliation(s)
- Laura Navarro
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8900000, Chile; (L.N.); (A.G.-M.); (N.C.)
| | - Mariona Gil i Cortiella
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Santiago 8900000, Chile;
| | - Ana Gutiérrez-Moraga
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8900000, Chile; (L.N.); (A.G.-M.); (N.C.)
- Departamento de Producción Agropecuaria, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco 4811230, Chile
| | - Nancy Calisto
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8900000, Chile; (L.N.); (A.G.-M.); (N.C.)
- Centro de Investigación y Monitoreo Ambiental Antártico (CIMAA), Departamento de Ingeniería Química, Universidad de Magallanes, Avenida Bulnes 01855, Punta Arenas 6210427, Chile
| | - Cristina Ubeda
- Departamento de Nutrición, Bromatología, Toxicología y Medicina Legal, Facultad de Farmacia, Universidad de Sevilla, C/P. García González No 2, 41012 Sevilla, Spain
| | - Gino Corsini
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8900000, Chile; (L.N.); (A.G.-M.); (N.C.)
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6
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Nguyet VTA, Ando R, Furutani N, Izawa S. Severe ethanol stress inhibits yeast proteasome activity at moderate temperatures but not at low temperatures. Genes Cells 2023; 28:736-745. [PMID: 37550872 DOI: 10.1111/gtc.13058] [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: 05/26/2023] [Revised: 07/17/2023] [Accepted: 07/26/2023] [Indexed: 08/09/2023]
Abstract
Since yeast research under laboratory conditions is usually conducted at 25-30°C (moderate temperature range), most of the findings on yeast physiology are based on analyses in this temperature range. Due to inefficiencies in cultivation and analysis, insufficient information is available on yeast physiology in the low-temperature range, although alcoholic beverage production is often conducted at relatively low temperatures (around 15°C). Recently, we reported that severe ethanol stress (10% v/v) inhibits proteasomal proteolysis in yeast cells under laboratory conditions at 28°C. In this study, proteasomal proteolysis at a low temperature (15°C) was evaluated using cycloheximide chase analysis of a short-lived protein (Gic2-3HA), an auxin-inducible degron system (Paf1-AID*-6FLAG), and Spe1-3HA, which is degraded ubiquitin-independently by the proteasome. At 15°C, proteasomal proteolysis was not inhibited under severe ethanol stress, and sufficient proteasomal activity was maintained. These results provide novel insights into the effects of low temperature and ethanol on yeast physiology.
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Affiliation(s)
- Vo Thi Anh Nguyet
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Ryoko Ando
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Noboru Furutani
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Shingo Izawa
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
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Wang B, Zhao X, Fu T, Chen X, Guo X, Li X, Yang F. Glucose Starvation Stimulates the Promoting Strength of a Novel Evolved Suc2 Promoter. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13838-13847. [PMID: 37669532 DOI: 10.1021/acs.jafc.3c03699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Promoters are essential for designing Saccharomyces cerevisiae cell factories. Identifying novel promoters tuned to produce specific metabolites under increasingly diverse industrial stresses is required to improve the economic feasibility of whole fermentation processes. In this study, a positively evolved Suc2 promoter (SUC 2p) with promoter activity stronger than that of the wild-type Suc2 promoter (SUC 2wtp) was obtained. Quantitative real-time PCR, fluorescence analysis, Western blotting, and a β-galactosidase activity assay revealed that SUC 2p is a medium-strength promoter compared with eight reported promoters at a medium glucose concentration (2% (w/v)). Different glucose concentrations modulated the strength of SUC 2p. Low glucose concentrations (0.05 and 0.5% (w/v)) enhanced the promoter strength of SUC 2p dramatically, with promoter activity higher than that of reported strong promoters. Glucose starvation resulted in the formation of a new Msn2/4 binding site on SUC 2p. Our work should facilitate the development of promoters with novel fine-tuning properties and the construction of S. cerevisiae cell factories suitable for the industrial production of essential chemicals under glucose-deprived conditions.
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Affiliation(s)
- Biying Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xiaoya Zhao
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Tong Fu
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xiaoyi Chen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xiaoyu Guo
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
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Attfield PV. Crucial aspects of metabolism and cell biology relating to industrial production and processing of Saccharomyces biomass. Crit Rev Biotechnol 2023; 43:920-937. [PMID: 35731243 DOI: 10.1080/07388551.2022.2072268] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/27/2022] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
The multitude of applications to which Saccharomyces spp. are put makes these yeasts the most prolific of industrial microorganisms. This review considers biological aspects pertaining to the manufacture of industrial yeast biomass. It is proposed that the production of yeast biomass can be considered in two distinct but interdependent phases. Firstly, there is a cell replication phase that involves reproduction of cells by their transitions through multiple budding and metabolic cycles. Secondly, there needs to be a cell conditioning phase that enables the accrued biomass to withstand the physicochemical challenges associated with downstream processing and storage. The production of yeast biomass is not simply a case of providing sugar, nutrients, and other growth conditions to enable multiple budding cycles to occur. In the latter stages of culturing, it is important that all cells are induced to complete their current budding cycle and subsequently enter into a quiescent state engendering robustness. Both the cell replication and conditioning phases need to be optimized and considered in concert to ensure good biomass production economics, and optimum performance of industrial yeasts in food and fermentation applications. Key features of metabolism and cell biology affecting replication and conditioning of industrial Saccharomyces are presented. Alternatives for growth substrates are discussed, along with the challenges and prospects associated with defining the genetic bases of industrially important phenotypes, and the generation of new yeast strains."I must be cruel only to be kind: Thus bad begins, and worse remains behind." William Shakespeare: Hamlet, Act 3, Scene 4.
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Carreras-Villaseñor N, Martínez-Rodríguez LA, Ibarra-Laclette E, Monribot-Villanueva JL, Rodríguez-Haas B, Guerrero-Analco JA, Sánchez-Rangel D. The biological relevance of the FspTF transcription factor, homologous of Bqt4, in Fusarium sp. associated with the ambrosia beetle Xylosandrus morigerus. Front Microbiol 2023; 14:1224096. [PMID: 37520351 PMCID: PMC10375492 DOI: 10.3389/fmicb.2023.1224096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
Transcription factors in phytopathogenic fungi are key players due to their gene expression regulation leading to fungal growth and pathogenicity. The KilA-N family encompasses transcription factors unique to fungi, and the Bqt4 subfamily is included in it and is poorly understood in filamentous fungi. In this study, we evaluated the role in growth and pathogenesis of the homologous of Bqt4, FspTF, in Fusarium sp. isolated from the ambrosia beetle Xylosandrus morigerus through the characterization of a CRISPR/Cas9 edited strain in Fsptf. The phenotypic analysis revealed that TF65-6, the edited strain, modified its mycelia growth and conidia production, exhibited affectation in mycelia and culture pigmentation, and in the response to certain stress conditions. In addition, the plant infection process was compromised. Untargeted metabolomic and transcriptomic analysis, clearly showed that FspTF may regulate secondary metabolism, transmembrane transport, virulence, and diverse metabolic pathways such as lipid metabolism, and signal transduction. These data highlight for the first time the biological relevance of an orthologue of Bqt4 in Fusarium sp. associated with an ambrosia beetle.
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Affiliation(s)
- Nohemí Carreras-Villaseñor
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Luis A. Martínez-Rodríguez
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Enrique Ibarra-Laclette
- Laboratorio de Genómica y Transcriptómica, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Juan L. Monribot-Villanueva
- Laboratorio de Química de Productos Naturales, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Benjamín Rodríguez-Haas
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - José A. Guerrero-Analco
- Laboratorio de Química de Productos Naturales, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
| | - Diana Sánchez-Rangel
- Laboratorios de Biología Molecular y Fitopatología, Instituto de Ecología A.C. (INECOL), Red de Estudios Moleculares Avanzados (REMAv), Xalapa, Mexico
- Investigadora Por Mexico-CONAHCyT, Xalapa, Mexico
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Gao Y, Zhang Z, Wang S, Ma N, Wang Y. Transcriptome analysis reveals wax and phytohormone metabolism potentially involved in shooting shrivelling of apple branches overwinter. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:540-558. [PMID: 37160284 DOI: 10.1071/fp22283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/27/2023] [Indexed: 05/11/2023]
Abstract
Shoot shrivelling severely threatens growth and development of deciduous trees in the northern hemisphere, and we observed that there was a significant difference in shoot shrivelling rate between different apple varieties in practice. In this study, we investigated the anatomical and physiological characteristics of branches from different germplasm resources combined with an analysis of the transcriptome. Transcriptomes of samples treated in the initial dormancy, deep dormancy and freeze-thaw periods were generated and characterised. In three different periods, 7233 differentially expressed genes (DEGs) were identified including 3538 upregulated genes and 3695 downregulated genes. DEGs related to plant hormone signal transduction, starch and sucrose metabolism, cutin, suberin and wax biosynthesis were significantly enriched. Physiological characterisation showed that dormancy overwinter can induce the accumulation of soluble sugar and starch, shoot shrivelling rate of 'Fuji' was 2.31times that of the 'Delicious'; and the critical water content of 'Delicious' was significantly higher than 'Fuji'. Phytohormone contents and proportions varied irregularly according to the overwintering phase among two varieties. Wax content, morphology and composition also exhibited difference. In conclusion, branch microstructure, phytohormone and wax metabolism all determined the overwintering performance of trees and phytohormones can regulate wax metabolism to ensure normal overwintering of trees.
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Affiliation(s)
- Yanlong Gao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhongxing Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Shuangcheng Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Naiying Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanxiu Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
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11
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Ortiz V, Chang HX, Sang H, Jacobs J, Malvick DK, Baird R, Mathew FM, Estévez de Jensen C, Wise KA, Mosquera GM, Chilvers MI. Population genomic analysis reveals geographic structure and climatic diversification for Macrophomina phaseolina isolated from soybean and dry bean across the United States, Puerto Rico, and Colombia. Front Genet 2023; 14:1103969. [PMID: 37351341 PMCID: PMC10282554 DOI: 10.3389/fgene.2023.1103969] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/20/2023] [Indexed: 06/24/2023] Open
Abstract
Macrophomina phaseolina causes charcoal rot, which can significantly reduce yield and seed quality of soybean and dry bean resulting from primarily environmental stressors. Although charcoal rot has been recognized as a warm climate-driven disease of increasing concern under global climate change, knowledge regarding population genetics and climatic variables contributing to the genetic diversity of M. phaseolina is limited. This study conducted genome sequencing for 95 M. phaseolina isolates from soybean and dry bean across the continental United States, Puerto Rico, and Colombia. Inference on the population structure using 76,981 single nucleotide polymorphisms (SNPs) revealed that the isolates exhibited a discrete genetic clustering at the continental level and a continuous genetic differentiation regionally. A majority of isolates from the United States (96%) grouped in a clade with a predominantly clonal genetic structure, while 88% of Puerto Rican and Colombian isolates from dry bean were assigned to a separate clade with higher genetic diversity. A redundancy analysis (RDA) was used to estimate the contributions of climate and spatial structure to genomic variation (11,421 unlinked SNPs). Climate significantly contributed to genomic variation at a continental level with temperature seasonality explaining the most variation while precipitation of warmest quarter explaining the most when spatial structure was accounted for. The loci significantly associated with multivariate climate were found closely to the genes related to fungal stress responses, including transmembrane transport, glycoside hydrolase activity and a heat-shock protein, which may mediate climatic adaptation for M. phaseolina. On the contrary, limited genome-wide differentiation among populations by hosts was observed. These findings highlight the importance of population genetics and identify candidate genes of M. phaseolina that can be used to elucidate the molecular mechanisms that underly climatic adaptation to the changing climate.
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Affiliation(s)
- Viviana Ortiz
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - Janette Jacobs
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Dean K. Malvick
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Richard Baird
- BCH-EPP Department, Mississippi State University, Mississippi State, MS, United States
| | - Febina M. Mathew
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | | | - Kiersten A. Wise
- Department of Plant Pathology, College of Agriculture, Food and Environment, University of Kentucky, Princeton, KY, United States
| | - Gloria M. Mosquera
- Plant Pathology, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Palmira, Colombia
| | - Martin I. Chilvers
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, United States
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12
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Jin Z, Vighi A, Dong Y, Bureau JA, Ignea C. Engineering membrane architecture for biotechnological applications. Biotechnol Adv 2023; 64:108118. [PMID: 36773706 DOI: 10.1016/j.biotechadv.2023.108118] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Cellular membranes, predominantly described as a dynamic bilayer, are composed of different lipids, transmembrane proteins, and carbohydrates. Most research on biological membranes focuses on the identification, characterization, and mechanistic aspects of their different components. These studies provide a fundamental understanding of membrane structure, function, and dynamics, establishing a basis for the development of membrane engineering strategies. To date, approaches in this field concentrate on membrane adaptation to harsh conditions during industrial fermentation, which can be caused by temperature, osmotic, or organic solvent stress. With advances in the field of metabolic engineering and synthetic biology, recent breakthroughs include proof of concept microbial production of essential medicines, such as cannabinoids and vinblastine. However, long pathways, low yields, and host adaptation continue to pose challenges to the efficient scale up production of many important compounds. The lipid bilayer is profoundly linked to the activity of heterologous membrane-bound enzymes and transport of metabolites. Therefore, strategies for improving enzyme performance, facilitating pathway reconstruction, and enabling storage of products to increase the yields directly involve cellular membranes. At the forefront of membrane engineering research are re-emerging approaches in lipid research and synthetic biology that manipulate membrane size and composition and target lipid profiles across species. This review summarizes engineering strategies applied to cellular membranes and discusses the challenges and future perspectives, particularly with regards to their applications in host engineering and bioproduction.
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Affiliation(s)
- Zimo Jin
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Asia Vighi
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Yueming Dong
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | | | - Codruta Ignea
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada.
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So KK, Le NMT, Nguyen NL, Kim DH. Improving expression and assembly of difficult-to-express heterologous proteins in Saccharomyces cerevisiae by culturing at a sub-physiological temperature. Microb Cell Fact 2023; 22:55. [PMID: 36959657 PMCID: PMC10035479 DOI: 10.1186/s12934-023-02065-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 03/19/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Escherichia coli heat labile toxin B subunit (LTB) is one of the most popular oral vaccine adjuvants and intestine adsorption enhancers. It is often expressed as a fusion partner with target antigens to enhance their immunogenicity as well as gut absorbability. However, high expression levels of a fusion protein are critical to the outcome of immunization experiments and the success of subsequent vaccine development efforts. In order to improve the expression and functional assembly of LTB-fusion proteins using Saccharomyces cerevisiae, we compared their expression under culture conditions at a sub-physiological temperature 20 °C with their expression under a standard 30 °C. RESULTS The assembled expression of LTB-EDIII2 (LTB fused to the envelope domain III (EDIII) of Dengue virus serotype 2), which was expressed at the level of 20 µg/L in our previous study, was higher when the expression temperature was 20 °C as opposed to 30 °C. We also tested whether the expression and functional assembly of a difficult-to-express LTB fusion protein could be increased. The assembled expression of the difficult-to-express LTB-VP1 fusion protein (LTB fused to VP1 antigen of Foot-and-Mouth Disease Virus) dramatically increased, although the total amount of expressed protein was still lower than that of LTB-EDIII2. Slight but significant increase in the expression of well-known reporter protein eGFP, which has previously been shown to be increased by cultivation at 20 °C, was also observed in our expression system. As no significant changes in corresponding transcripts levels and cell growth were observed between 20 °C and 30 °C, we infer that translation and post-translational assembly are responsible for these enhancements. CONCLUSIONS The effects of lowering the expression temperature from 30 °C to 20 °C on protein expression and folding levels in S. cerevisiae, using several proteins as models, are reported. When heterologous proteins are expressed at 20 °C, a greater amount of (specially, more assembled) functional proteins accumulated than at 30 °C. Although further studies are required to understand the molecular mechanisms, our results suggest that lowering the expression temperature is a convenient strategy for improving the expression of relatively complexly structured and difficult-to-express proteins in S. cerevisiae.
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Affiliation(s)
- Kum-Kang So
- Institute for Molecular Biology and Genetics, Department of Molecular Biology, Jeonbuk National University, Jeonju, Jeollabuk-Do, 54896, Republic of Korea
| | - Ngoc My Tieu Le
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Jeollabuk-Do, 54896, Republic of Korea
| | - Ngoc-Luong Nguyen
- Department of Biology, College of Sciences, Hue University, Hue, 530000, Vietnam.
| | - Dae-Hyuk Kim
- Institute for Molecular Biology and Genetics, Department of Molecular Biology, Jeonbuk National University, Jeonju, Jeollabuk-Do, 54896, Republic of Korea.
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Jeollabuk-Do, 54896, Republic of Korea.
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Wei X, Zhang M, Chi Z, Liu GL, Chi ZM. Genome-Wide Editing Provides Insights into Role of Unsaturated fatty Acids in Low Temperature Growth of the Psychrotrophic Yeast Metschnikowia bicuspidata var. australis W7-5. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:70-82. [PMID: 36418586 DOI: 10.1007/s10126-022-10182-4] [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: 05/31/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
In order to know the function of C18:2 and C18:3 fatty acids in the cold growth of the psychrotrophic yeast M. bicuspidata var. australis W7-5, the mutant 1 without C18:2 fatty acid and the mutant 2 without C18:3 fatty acids were obtained. Only the trace amount of C18:2 fatty acid in the mutant 1 occurred while no C18:3 fatty acid in the mutant 2 was detected. The growth rate of only the mutant 1 cultured at 5 ℃ and 25 ℃ was significantly reduced compared with that of the wild-type strain W7-5. But there was no difference between the growth of the mutant 2 and that of the W7-5 strain. These meant that only C18:2 synthesized by the psychrotrophic yeast played an important role in cell growth at low temperature (5 °C) and high temperature (25 °C). Meanwhile, cell wall in the mutant 1 without C18:2 fatty acid gown at 5 and 25 °C was also negatively affected, leading to the reduced cell growth rate of the mutant 1 grown at 5 and 25 °C.
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Affiliation(s)
- Xin Wei
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China
| | - Miao Zhang
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China
| | - Zhe Chi
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Guang-Lei Liu
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Zhen-Ming Chi
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China.
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15
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Slowest possible replicative life at frigid temperatures for yeast. Nat Commun 2022; 13:7518. [PMID: 36473846 PMCID: PMC9726825 DOI: 10.1038/s41467-022-35151-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Determining whether life can progress arbitrarily slowly may reveal fundamental barriers to staying out of thermal equilibrium for living systems. By monitoring budding yeast's slowed-down life at frigid temperatures and with modeling, we establish that Reactive Oxygen Species (ROS) and a global gene-expression speed quantitatively determine yeast's pace of life and impose temperature-dependent speed limits - shortest and longest possible cell-doubling times. Increasing cells' ROS concentration increases their doubling time by elongating the cell-growth (G1-phase) duration that precedes the cell-replication (S-G2-M) phase. Gene-expression speed constrains cells' ROS-reducing rate and sets the shortest possible doubling-time. To replicate, cells require below-threshold concentrations of ROS. Thus, cells with sufficiently abundant ROS remain in G1, become unsustainably large and, consequently, burst. Therefore, at a given temperature, yeast's replicative life cannot progress arbitrarily slowly and cells with the lowest ROS-levels replicate most rapidly. Fundamental barriers may constrain the thermal slowing of other organisms' lives.
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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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17
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Turchetti B, Buzzini P, Baeza M. A genomic approach to analyze the cold adaptation of yeasts isolated from Italian Alps. Front Microbiol 2022; 13:1026102. [DOI: 10.3389/fmicb.2022.1026102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022] Open
Abstract
Microorganisms including yeasts are responsible for mineralization of organic matter in cold regions, and their characterization is critical to elucidate the ecology of such environments on Earth. Strategies developed by yeasts to survive in cold environments have been increasingly studied in the last years and applied to different biotechnological applications, but their knowledge is still limited. Microbial adaptations to cold include the synthesis of cryoprotective compounds, as well as the presence of a high number of genes encoding the synthesis of proteins/enzymes characterized by a reduced proline content and highly flexible and large catalytic active sites. This study is a comparative genomic study on the adaptations of yeasts isolated from the Italian Alps, considering their growth kinetics. The optimal temperature for growth (OTG), growth rate (Gr), and draft genome sizes considerably varied (OTG, 10°C–20°C; Gr, 0.071–0.0726; genomes, 20.7–21.5 Mpb; %GC, 50.9–61.5). A direct relationship was observed between calculated protein flexibilities and OTG, but not for Gr. Putative genes encoding for cold stress response were found, as well as high numbers of genes encoding for general, oxidative, and osmotic stresses. The cold response genes found in the studied yeasts play roles in cell membrane adaptation, compatible solute accumulation, RNA structure changes, and protein folding, i.e., dihydrolipoamide dehydrogenase, glycogen synthase, omega-6 fatty acid, stearoyl-CoA desaturase, ATP-dependent RNA helicase, and elongation of very-long-chain fatty acids. A redundancy for several putative genes was found, higher for P-loop containing nucleoside triphosphate hydrolase, alpha/beta hydrolase, armadillo repeat-containing proteins, and the major facilitator superfamily protein. Hundreds of thousands of small open reading frames (SmORFs) were found in all studied yeasts, especially in Phenoliferia glacialis. Gene clusters encoding for the synthesis of secondary metabolites such as terpene, non-ribosomal peptide, and type III polyketide were predicted in four, three, and two studied yeasts, respectively.
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18
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Metabolomics analysis of freeze-thaw tolerance enhancement mechanism of ε-poly-l-lysine on industrial yeast. Food Chem 2022; 382:132315. [PMID: 35134720 DOI: 10.1016/j.foodchem.2022.132315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/07/2022] [Accepted: 01/30/2022] [Indexed: 11/23/2022]
Abstract
Antimicrobial polycationic peptide ε-poly-l-lysine (ε-PL) enhanced the freeze-thaw tolerance of industrial yeast; the enhancement mechanism of ε-PL on yeast was studied. Results showed that a ε-PL coating was observed in ε-PL-treated yeast. After 4 times of freeze-thaw, the cell viability, glycerol content, and CO2 production of 0.6 mg/mL ε-PL-treated yeast were higher than those of untreated yeast, specifically, the cell viability of ε-PL-treated yeast was 87.6%, and that of untreated yeast was 68.5%. Metabolomic results showed that the enhancement mechanism of ε-PL on yeast was related to the promotion of cell membrane-related fatty acid synthesis pathways before freeze-thaw treatment, and the promotion of trehalose biosynthesis and glycerophospholipid metabolism pathways after freeze-thaw. Furthermore, ε-PL induced inhibition of the tricarboxylic acid cycle, resulting in a longer stationary phase at the beginning of the freeze-thaw and ultimately providing a higher level of freeze-thaw stress tolerance than untreated yeast.
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19
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Li C, Xu Y, Li Z, Cheng P, Yu G. Transcriptomic and metabolomic analysis reveals the potential mechanisms underlying the improvement of β-carotene and torulene production in Rhodosporidiobolus colostri under low temperature treatment. Food Res Int 2022; 156:111158. [DOI: 10.1016/j.foodres.2022.111158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022]
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20
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Genome-wide effect of non-optimal temperatures under anaerobic conditions on gene expression in Saccharomyces cerevisiae. Genomics 2022; 114:110386. [PMID: 35569731 DOI: 10.1016/j.ygeno.2022.110386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/28/2022] [Accepted: 05/07/2022] [Indexed: 12/29/2022]
Abstract
Understanding of thermal adaptation mechanisms in yeast is crucial to develop better-adapted strains to industrial processes, providing more economical and sustainable products. We have analyzed the transcriptomic responses of three Saccharomyces cerevisiae strains, a commercial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and a commercial bioethanol strain, Ethanol Red, grown at non-optimal temperatures under anaerobic chemostat conditions. Transcriptomic analysis of the three strains revealed a huge complexity of cellular mechanisms and responses. Overall, cold exerted a stronger transcriptional response in the three strains comparing with heat conditions, with a higher number of down-regulating genes than of up-regulating genes regardless the strain analyzed. The comparison of the transcriptome at both sub- and supra-optimal temperatures showed the presence of common genes up- or down-regulated in both conditions, but also the presence of common genes up- or down-regulated in the three studied strains. More specifically, we have identified and validated three up-regulated genes at sub-optimal temperature in the three strains, OPI3, EFM6 and YOL014W. Finally, the comparison of the transcriptomic data with a previous proteomic study with the same strains revealed a good correlation between gene activity and protein abundance, mainly at low temperature. Our work provides a global insight into the specific mechanisms involved in temperature adaptation regarding both transcriptome and proteome, which can be a step forward in the comprehension and improvement of yeast thermotolerance.
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21
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Growth response of Saccharomyces cerevisiae strains to stressors associated to the vine cycle. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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Separovich RJ, Wong MW, Bartolec TK, Hamey JJ, Wilkins MR. Site-specific phosphorylation of histone H3K36 methyltransferase Set2p and demethylase Jhd1p is required for stress responses in Saccharomyces cerevisiae. J Mol Biol 2022; 434:167500. [DOI: 10.1016/j.jmb.2022.167500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/17/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
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23
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Flores-Cotera LB, Chávez-Cabrera C, Martínez-Cárdenas A, Sánchez S, García-Flores OU. Deciphering the mechanism by which the yeast Phaffia rhodozyma responds adaptively to environmental, nutritional, and genetic cues. J Ind Microbiol Biotechnol 2021; 48:kuab048. [PMID: 34302341 PMCID: PMC8788774 DOI: 10.1093/jimb/kuab048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022]
Abstract
Phaffia rhodozyma is a basidiomycetous yeast that synthesizes astaxanthin (ASX), which is a powerful and highly valuable antioxidant carotenoid pigment. P. rhodozyma cells accrue ASX and gain an intense red-pink coloration when faced with stressful conditions such as nutrient limitations (e.g., nitrogen or copper), the presence of toxic substances (e.g., antimycin A), or are affected by mutations in the genes that are involved in nitrogen metabolism or respiration. Since cellular accrual of ASX occurs under a wide variety of conditions, this yeast represents a valuable model for studying the growth conditions that entail oxidative stress for yeast cells. Recently, we proposed that ASX synthesis can be largely induced by conditions that lead to reduction-oxidation (redox) imbalances, particularly the state of the NADH/NAD+ couple together with an oxidative environment. In this work, we review the multiple known conditions that elicit ASX synthesis expanding on the data that we formerly examined. When considered alongside the Mitchell's chemiosmotic hypothesis, the study served to rationalize the induction of ASX synthesis and other adaptive cellular processes under a much broader set of conditions. Our aim was to propose an underlying mechanism that explains how a broad range of divergent conditions converge to induce ASX synthesis in P. rhodozyma. The mechanism that links the induction of ASX synthesis with the occurrence of NADH/NAD+ imbalances may help in understanding how other organisms detect any of a broad array of stimuli or gene mutations, and then adaptively respond to activate numerous compensatory cellular processes.
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Affiliation(s)
- Luis B Flores-Cotera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Cipriano Chávez-Cabrera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Anahi Martínez-Cárdenas
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Sergio Sánchez
- Department of Molecular Biology and Biotechnology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México city 04510, México
| | - Oscar Ulises García-Flores
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
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Hyperosmolarity adversely impacts recombinant protein synthesis by Yarrowia lipolytica-molecular background revealed by quantitative proteomics. Appl Microbiol Biotechnol 2021; 106:349-367. [PMID: 34913994 PMCID: PMC8720085 DOI: 10.1007/s00253-021-11731-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 12/22/2022]
Abstract
Abstract In this research, we were interested in answering a question whether subjecting a Yarrowia lipolytica strain overproducing a recombinant secretory protein (rs-Prot) to pre-optimized stress factors may enhance synthesis of the rs-Prot. Increased osmolarity (3 Osm kg−1) was the primary stress factor implemented alone or in combination with decreased temperature (20 °C), known to promote synthesis of rs-Prots. The treatments were executed in batch bioreactor cultures, and the cellular response was studied in terms of culture progression, gene expression and global proteomics, to get insight into molecular bases underlying an awaken reaction. Primarily, we observed that hyperosmolarity executed by high sorbitol concentration does not enhance synthesis of the rs-Prot but increases its transcription. Expectedly, hyperosmolarity induced synthesis of polyols at the expense of citric acid synthesis and growth, which was severely limited. A number of stress-related proteins were upregulated, including heat-shock proteins (HSPs) and aldo–keto reductases, as observed at transcriptomics and proteomics levels. Concerted downregulation of central carbon metabolism, including glycolysis, tricarboxylic acid cycle and fatty acid synthesis, highlighted redirection of carbon fluxes. Elevated abundance of HSPs and osmolytes did not outbalance the severe limitation of protein synthesis, marked by orchestrated downregulation of translation (elongation factors, several aa-tRNA synthetases), amino acid biosynthesis and ribosome biogenesis in response to the hyperosmolarity. Altogether we settled that increased osmolarity is not beneficial for rs-Prots synthesis in Y. lipolytica, even though some elements of the response could assist this process. Insight into global changes in the yeast proteome under the treatments is provided. Key points • Temp enhances, but Osm decreases rs-Prots synthesis by Y. lipolytica. • Enhanced abundance of HSPs and osmolytes is overweighted by limited translation. • Global proteome under Osm, Temp and Osm Temp treatments was studied. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11731-y.
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Development of Korean Indigenous Low-Temperature-Tolerant Yeast for Enhancing the Flavor of Yakju. FERMENTATION 2021. [DOI: 10.3390/fermentation7040260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Yakju, a traditional fermented beverage in Korea, is prepared using various raw materials and methods, and, hence, exhibits various characteristics. Low-temperature-fermented yakju can inhibit the growth of undesirable bacteria and is known for its unique flavor and refreshing taste. To increase the production of volatile aromatic compounds in yakju, strains with strong resistance to low temperatures and excellent production of volatile aromatic compounds were screened from indigenous fruits (grape, persimmon, plum, aronia, wild grape) and nuruk in Korea. One Saccharomyces cerevisiae and three non-Saccharomyces strains were finally screened, and yakju was fermented at 15 °C through mono/co-culture. The analysis of volatile aromatic compounds showed that S. cerevisiae W153 produced 1.5 times more isoamyl alcohol than the control strain and reduced the production of 2,3-butanediol by a third. Similarly, a single culture of Pichia kudriavzevii N373 also produced 237.7 mg/L of ethyl acetate, whereas Hanseniaspora vineae G818 produced ~11 times greater levels of 2-phenethyl acetate than the control. Alternatively, Wickerhamomyces anomalus A159 produced 95.88 mg/L of ethyl hexadecanoate. During principal component analysis, we also observed that the co-culture sample exhibited characteristics of both volatile aroma compounds of the single cultured sample of each strain. Our results suggest that yakju with unique properties can be prepared using various non-Saccharomyces strains.
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Guo R, He M, Zhang X, Ji X, Wei Y, Zhang QL, Zhang Q. Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low Temperature. Front Microbiol 2021; 12:727105. [PMID: 34603256 PMCID: PMC8481953 DOI: 10.3389/fmicb.2021.727105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/26/2021] [Indexed: 12/20/2022] Open
Abstract
Rhodosporidium kratochvilovae strain YM25235 is a cold-adapted oleaginous yeast strain that can grow at 15°C. It is capable of producing polyunsaturated fatty acids. Here, we used the Nanopore Platform to first assemble the R. kratochvilovae strain YM25235 genome into a 23.71 Mb size containing 46 scaffolds and 8,472 predicted genes. To explore the molecular mechanism behind the low temperature response of R. kratochvilovae strain YM25235, we analyzed the RNA transcriptomic data from low temperature (15°C) and normal temperature (30°C) groups using the next-generation deep sequencing technology (RNA-seq). We identified 1,300 differentially expressed genes (DEGs) by comparing the cultures grown at low temperature (15°C) and normal temperature (30°C) transcriptome libraries, including 553 significantly upregulated and 747 significantly downregulated DEGs. Gene ontology and pathway enrichment analysis revealed that DEGs were primarily related to metabolic processes, cellular processes, cellular organelles, and catalytic activity, whereas the overrepresented pathways included the MAPK signaling pathway, metabolic pathways, and amino sugar and nucleotide sugar metabolism. We validated the RNA-seq results by detecting the expression of 15 DEGs using qPCR. This study provides valuable information on the low temperature response of R. kratochvilovae strain YM25235 for further research and broadens our understanding for the response of R. kratochvilovae strain YM25235 to low temperature.
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Affiliation(s)
- Rui Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Meixia He
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiaoqing Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiuling Ji
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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Wang W, Flury AG, Garrison JL, Brem RB. Cold Survival and Its Molecular Mechanisms in a Locally Adapted Nematode Population. Genome Biol Evol 2021; 13:evab188. [PMID: 34383891 PMCID: PMC8449824 DOI: 10.1093/gbe/evab188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2021] [Indexed: 11/25/2022] Open
Abstract
Since Darwin, evolutionary biologists have sought to understand the drivers and mechanisms of natural trait diversity. The field advances toward this goal with the discovery of phenotypes that vary in the wild, their relationship to ecology, and their underlying genes. Here, we established resistance to extreme low temperature in the free-living nematode Caenorhabditis briggsae as an ecological and evolutionary model system. We found that C. briggsae strains of temperate origin were strikingly more cold-resistant than those isolated from tropical localities. Transcriptional profiling revealed expression patterns unique to the resistant temperate ecotype, including dozens of genes expressed at high levels even after multiple days of cold-induced physiological slowdown. Mutational analysis validated a role in cold resistance for seven such genes. These findings highlight a candidate case of robust, genetically complex adaptation in an emerging model nematode, and shed light on the mechanisms at play.
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Affiliation(s)
- Wenke Wang
- Buck Institute for Research on Aging, Novato, California, USA
- Department of Plant and Microbial Biology, UC Berkeley, USA
| | - Anna G Flury
- Buck Institute for Research on Aging, Novato, California, USA
- Department of Plant and Microbial Biology, UC Berkeley, USA
| | - Jennifer L Garrison
- Buck Institute for Research on Aging, Novato, California, USA
- Leonard Davis School of Gerontology, University of Southern California, USA
- Department of Cellular and Molecular Pharmacology, UC San Francisco, USA
- Global Consortium for Reproductive Longevity & Equality, Novato, California, USA
| | - Rachel B Brem
- Buck Institute for Research on Aging, Novato, California, USA
- Department of Plant and Microbial Biology, UC Berkeley, USA
- Leonard Davis School of Gerontology, University of Southern California, USA
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Ferraz L, Sauer M, Sousa MJ, Branduardi P. The Plasma Membrane at the Cornerstone Between Flexibility and Adaptability: Implications for Saccharomyces cerevisiae as a Cell Factory. Front Microbiol 2021; 12:715891. [PMID: 34434179 PMCID: PMC8381377 DOI: 10.3389/fmicb.2021.715891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022] Open
Abstract
In the last decade, microbial-based biotechnological processes are paving the way toward sustainability as they implemented the use of renewable feedstocks. Nonetheless, the viability and competitiveness of these processes are often limited due to harsh conditions such as: the presence of feedstock-derived inhibitors including weak acids, non-uniform nature of the substrates, osmotic pressure, high temperature, extreme pH. These factors are detrimental for microbial cell factories as a whole, but more specifically the impact on the cell’s membrane is often overlooked. The plasma membrane is a complex system involved in major biological processes, including establishing and maintaining transmembrane gradients, controlling uptake and secretion, intercellular and intracellular communication, cell to cell recognition and cell’s physical protection. Therefore, when designing strategies for the development of versatile, robust and efficient cell factories ready to tackle the harshness of industrial processes while delivering high values of yield, titer and productivity, the plasma membrane has to be considered. Plasma membrane composition comprises diverse macromolecules and it is not constant, as cells adapt it according to the surrounding environment. Remarkably, membrane-specific traits are emerging properties of the system and therefore it is not trivial to predict which membrane composition is advantageous under certain conditions. This review includes an overview of membrane engineering strategies applied to Saccharomyces cerevisiae to enhance its fitness under industrially relevant conditions as well as strategies to increase microbial production of the metabolites of interest.
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Affiliation(s)
- Luís Ferraz
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Michael Sauer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria João Sousa
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
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Nakazawa N, Fukuda M, Ashizaki M, Shibata Y, Takahashi K. Hsp104 contributes to freeze-thaw tolerance by maintaining proteasomal activity in a spore clone isolated from Shirakami kodama yeast. J GEN APPL MICROBIOL 2021; 67:170-178. [PMID: 34148914 DOI: 10.2323/jgam.2020.11.002] [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
The supply of oven-fresh bakery products to consumers has been improved by frozen dough technology; however, freeze-thaw stress decreases the activity of yeast cells. To breed better baker's yeasts for frozen dough, it is important to understand the factors affecting freeze-thaw stress tolerance in baker's yeast. We analyzed the stress response in IB1411, a spore clone from Saccharomyces cerevisiae Shirakami kodama yeast, with an exceptionally high tolerance to freeze-thaw stress. Genes encoding trehalose-6-phosphate synthase (TPS1), catalase (CTT1), and disaggregase (HSP104) were highly expressed in IB1411 cells even under conditions of non-stress. The expression of Hsp104 protein was also higher in IB1411 cells even under non-stress conditions. Deletion of HSP104 (hsp104Δ) in IB1411 cells reduced the activity of the ubiquitin-proteasome system (UPS). By monitoring the accumulation of aggregated proteins using the ΔssCPY*-GFP fusion protein under freeze-thaw stress or treatment with proteasomal inhibitor, we found that IB1411 cells resolved aggregated proteins faster than the hsp104Δ strain. Thus, Hsp104 seems to contribute to freeze-thaw tolerance by maintaining UPS activity via the disaggregation of aggregated proteins. Lastly, we found that the IB1411 cells maintained high leavening ability in frozen dough as compared with the parental strain, Shirakami kodama yeast, and thus will be useful for making bread.
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Affiliation(s)
- Nobushige Nakazawa
- Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University
| | - Mami Fukuda
- Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University
| | - Mizuki Ashizaki
- Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University
| | - Yukari Shibata
- Department of Biotechnology, Faculty of Bioresource Science, Akita Prefectural University
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Drosou F, Anastasakou K, Tataridis P, Dourtoglou V, Oreopoulou V. Study of the Fermentation Kinetics and Secondary Metabolites of Torulaspora delbrueckii Yeasts from Different Substrates. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2021. [DOI: 10.1080/03610470.2021.1915660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Fotini Drosou
- School of Chemical Engineering, National Technical University of Athens, Zografou, Athens, Greece
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Egaleo, Athens, Greece
| | - Katerina Anastasakou
- School of Chemical Engineering, National Technical University of Athens, Zografou, Athens, Greece
| | - Panagiotis Tataridis
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Egaleo, Athens, Greece
| | - Vassilis Dourtoglou
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Egaleo, Athens, Greece
| | - Vassiliki Oreopoulou
- School of Chemical Engineering, National Technical University of Athens, Zografou, Athens, Greece
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Jung KM, Park J, Jang J, Jung SH, Lee SH, Kim SR. Characterization of Cold-Tolerant Saccharomyces cerevisiae Cheongdo Using Phenotype Microarray. Microorganisms 2021; 9:microorganisms9050982. [PMID: 33946617 PMCID: PMC8147183 DOI: 10.3390/microorganisms9050982] [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: 03/25/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 01/29/2023] Open
Abstract
The cold-tolerant yeast Saccharomyces cerevisiae is industrially useful for lager fermentation, high-quality wine, and frozen dough production. S. cerevisiae Cheongdo is a recent isolate from frozen peach samples which has a good fermentation performance at low temperatures and desirable flavor profiles. Here, phenotype microarray was used to investigate industrial potentials of S. cerevisiae Cheongdo using 192 carbon sources. Compared to commercial wine yeast S. cerevisiae EC1118, Cheongdo showed significantly different growth rates on 34 substrates. The principal component analysis of the results highlighted that the better growth of Cheongdo on galactose than on EC1118 was the most significant difference between the two strains. The intact GAL4 gene and the galactose fermentation performance at a low temperatures suggested that S. cerevisiae Cheongdo is a promising host for industrial fermentation rich in galactose, such as lactose and agarose.
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Affiliation(s)
- Kyung-Mi Jung
- Cheongdo Peach Research Institute, Gyeongsangbuk-Do Agricultural Technology Administration, Cheongdo 38315, Korea;
| | - Jongbeom Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; (J.P.); (J.J.); (S.-H.J.); (S.H.L.)
| | - Jueun Jang
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; (J.P.); (J.J.); (S.-H.J.); (S.H.L.)
| | - Seok-Hwa Jung
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; (J.P.); (J.J.); (S.-H.J.); (S.H.L.)
| | - Sang Han Lee
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; (J.P.); (J.J.); (S.-H.J.); (S.H.L.)
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; (J.P.); (J.J.); (S.-H.J.); (S.H.L.)
- Correspondence: ; Tel.: +82-(53)-950-7769
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Sukumaran L, Radhakrishnan M. Effect of frozen storage on the inhibition of microbial population, chemical and sensory characteristics of coconut neera. J Appl Microbiol 2021; 131:1830-1839. [PMID: 33721389 DOI: 10.1111/jam.15068] [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] [Received: 09/14/2020] [Revised: 01/07/2021] [Accepted: 03/09/2021] [Indexed: 11/27/2022]
Abstract
AIM In this study, the effect of frozen storage on the inhibition of microbial population in coconut neera for shelf life extension was analysed. METHODS AND RESULTS The aliquots of fresh neera were frozen at -6 and -20°C. The microbial reduction and chemical qualities were analysed during storage days, and were compared with the control. The highest reduction in microbes was obtained at -20°C for lactic acid bacteria, yeast and total viable count. Moreover, the fluorescence cell staining and cell density analysis exhibited a decline at -20°C, however it showed higher at -6°C. At the end of 28 days, neera exhibited a pH of 5·37, total soluble solid of 14·0 °Brix and total acidity of 0·82 mg l-1 at -20°C. Besides, color, viscosity, total protein and ethanol showed a less difference with control and better sensory attribute up to 21 days at -20°C. CONCLUSIONS Frozen storage at -20°C resulted in a better inhibition of lactic acid bacteria, which preserves neera from the metabolic conversion. The physicochemical qualities of neera were preserved for a longer period when stored at -20°C than at atmospheric storage. SIGNIFICANCE AND IMPACT OF THE STUDY Frozen storage reduced microbial population and preserves the chemical properties with acceptable sensory attributes and increases the shelf life of coconut neera, making it fit for consumption.
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Affiliation(s)
- L Sukumaran
- Centre of Excellence in Nonthermal Processing, Indian Institute of Food Processing Technology, Ministry of Food Processing Industries, Government of India, Thanjavur, Tamil Nadu, India.,Affiliated to Bharathidasan University, Palkalaiperur, Tiruchirappalli, Tamil Nadu, India
| | - M Radhakrishnan
- Centre of Excellence in Nonthermal Processing, Indian Institute of Food Processing Technology, Ministry of Food Processing Industries, Government of India, Thanjavur, Tamil Nadu, India
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Maza DD, Viñarta SC, García-Ríos E, Guillamón JM, Aybar MJ. Rhodotorula glutinis T13 as a potential source of microbial lipids for biodiesel generation. J Biotechnol 2021; 331:14-18. [PMID: 33711359 DOI: 10.1016/j.jbiotec.2021.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 03/01/2021] [Indexed: 11/26/2022]
Abstract
Single cell oils (SCO) are a promising source of oils that could be exploited in different industrial areas. SCO for biodiesel production circumvents the controversy food vs. fuel, does not require large land areas for culture, and is independent of climate and seasonal variations, among other advantages in comparison to vegetable oils. In this study, a red yeast isolated from a mountain water source, identified as Rhodotorula glutinis T13, showed high potential for lipid production (40% w/w) with suitable growth parameters, yields, and fatty acids profile. Yeast lipids showed a high content of unsaturated fatty acids (56.44%; C18:1, C18:2), and the fuel properties (cetane number, iodine value, density, kinematic viscosity, etc.) of yeast oil analysed were in good agreement with international biodiesel standards. The results show that R. glutinis T13 can be used in the future as a promising microorganism for the commercial production of biodiesel.
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Affiliation(s)
- D Daniela Maza
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-Universidad Nacional de Tucumán), Tucumán, Argentina
| | - Silvana C Viñarta
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina.
| | - Estéfani García-Ríos
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Paterna, Valencia, Spain
| | - José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Paterna, Valencia, Spain
| | - Manuel J Aybar
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-Universidad Nacional de Tucumán), Tucumán, Argentina; Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia de la Universidad Nacional de Tucumán, Tucumán, Argentina.
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Local Rather than Global H3K27me3 Dynamics Are Associated with Differential Gene Expression in Verticillium dahliae. mBio 2021; 13:e0356621. [PMID: 35130723 PMCID: PMC8822345 DOI: 10.1128/mbio.03566-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Differential growth conditions typically trigger global transcriptional responses in filamentous fungi. Such fungal responses to environmental cues involve epigenetic regulation, including chemical histone modifications. It has been proposed that conditionally expressed genes, such as those that encode secondary metabolites but also effectors in pathogenic species, are often associated with a specific histone modification, lysine27 methylation of H3 (H3K27me3). However, thus far, no analyses on the global H3K27me3 profiles have been reported under differential growth conditions in order to assess if H3K27me3 dynamics govern differential transcription. Using chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing data from the plant-pathogenic fungus Verticillium dahliae grown in three in vitro cultivation media, we now show that a substantial number of the identified H3K27me3 domains globally display stable profiles among these growth conditions. However, we observe local quantitative differences in H3K27me3 ChIP-seq signals that are associated with a subset of differentially transcribed genes between media. Comparing the in vitro results to expression during plant infection suggests that in planta-induced genes may require chromatin remodeling to achieve expression. Overall, our results demonstrate that some loci display H3K27me3 dynamics associated with concomitant transcriptional variation, but many differentially expressed genes are associated with stable H3K27me3 domains. Thus, we conclude that while H3K27me3 is required for transcriptional repression, it does not appear that transcriptional activation requires the global erasure of H3K27me3. We propose that the H3K27me3 domains that do not undergo dynamic methylation may contribute to transcription through other mechanisms or may serve additional genomic regulatory functions. IMPORTANCE In many organisms, including filamentous fungi, epigenetic mechanisms that involve chemical and physical modifications of DNA without changing the genetic sequence have been implicated in transcriptional responses upon developmental or environmental cues. In fungi, facultative heterochromatin that can decondense to allow transcription in response to developmental changes or environmental stimuli is characterized by the trimethylation of lysine 27 on histone H3 (H3K27me3), and H3K27me3 has been implicated in transcriptional regulation, although the precise mechanisms and functions remain enigmatic. Based on ChIP and RNA sequencing data, we show for the soilborne broad-host-range vascular wilt plant-pathogenic fungus Verticillium dahliae that although some loci display H3K27me3 dynamics that can contribute to transcriptional variation, other loci do not show such a dependence. Thus, although we recognize that H3K27me3 is required for transcriptional repression, we also conclude that this mark is not a conditionally responsive global regulator of differential transcription upon responses to environmental cues.
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Yeast Fermentation at Low Temperatures: Adaptation to Changing Environmental Conditions and Formation of Volatile Compounds. Molecules 2021; 26:molecules26041035. [PMID: 33669237 PMCID: PMC7919833 DOI: 10.3390/molecules26041035] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022] Open
Abstract
Yeast plays a key role in the production of fermented foods and beverages, such as bread, wine, and other alcoholic beverages. They are able to produce and release from the fermentation environment large numbers of volatile organic compounds (VOCs). This is the reason for the great interest in the possibility of adapting these microorganisms to fermentation at reduced temperatures. By doing this, it would be possible to obtain better sensory profiles of the final products. It can reduce the addition of artificial flavors and enhancements to food products and influence other important factors of fermented food production. Here, we reviewed the genetic and physiological mechanisms by which yeasts adapt to low temperatures. Next, we discussed the importance of VOCs for the food industry, their biosynthesis, and the most common volatiles in fermented foods and described the beneficial impact of decreased temperature as a factor that contributes to improving the composition of the sensory profiles of fermented foods.
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Thermo-adaptive evolution to generate improved Saccharomyces cerevisiae strains for cocoa pulp fermentations. Int J Food Microbiol 2021; 342:109077. [PMID: 33550155 DOI: 10.1016/j.ijfoodmicro.2021.109077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/22/2020] [Accepted: 01/09/2021] [Indexed: 11/22/2022]
Abstract
Cocoa pulp fermentation is a consequence of the succession of indigenous yeasts, lactic acid bacteria and acetic acid bacteria that not only produce a diversity of metabolites, but also cause the production of flavour precursors. However, as such spontaneous fermentations are less reproducible and contribute to produce variability, interest in a microbial starter culture is growing that could be used to inoculate cocoa pulp fermentations. This study aimed to generate robust S. cerevisiae strains by thermo-adaptive evolution that could be used in cocoa fermentation. We evolved a cocoa strain in a sugary defined medium at high temperature to improve both fermentation and growth capacity. Moreover, adaptive evolution at high temperature (40 °C) also enabled us to unveil the molecular basis underlying the improved phenotype by analysing the whole genome sequence of the evolved strain. Adaptation to high-temperature conditions occurred at different genomic levels, and promoted aneuploidies, segmental duplication, and SNVs in the evolved strain. The lipid profile analysis of the evolved strain also evidenced changes in the membrane composition that contribute to maintain an appropriate cell membrane state at high temperature. Our work demonstrates that experimental evolution is an effective approach to generate better-adapted yeast strains at high temperature for industrial processes.
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Pinheiro T, Lip KYF, García-Ríos E, Querol A, Teixeira J, van Gulik W, Guillamón JM, Domingues L. Differential proteomic analysis by SWATH-MS unravels the most dominant mechanisms underlying yeast adaptation to non-optimal temperatures under anaerobic conditions. Sci Rep 2020; 10:22329. [PMID: 33339840 PMCID: PMC7749138 DOI: 10.1038/s41598-020-77846-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/20/2020] [Indexed: 12/28/2022] Open
Abstract
Elucidation of temperature tolerance mechanisms in yeast is essential for enhancing cellular robustness of strains, providing more economically and sustainable processes. We investigated the differential responses of three distinct Saccharomyces cerevisiae strains, an industrial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and an industrial bioethanol strain, Ethanol Red, grown at sub- and supra-optimal temperatures under chemostat conditions. We employed anaerobic conditions, mimicking the industrial processes. The proteomic profile of these strains in all conditions was performed by sequential window acquisition of all theoretical spectra-mass spectrometry (SWATH-MS), allowing the quantification of 997 proteins, data available via ProteomeXchange (PXD016567). Our analysis demonstrated that temperature responses differ between the strains; however, we also found some common responsive proteins, revealing that the response to temperature involves general stress and specific mechanisms. Overall, sub-optimal temperature conditions involved a higher remodeling of the proteome. The proteomic data evidenced that the cold response involves strong repression of translation-related proteins as well as induction of amino acid metabolism, together with components related to protein folding and degradation while, the high temperature response mainly recruits amino acid metabolism. Our study provides a global and thorough insight into how growth temperature affects the yeast proteome, which can be a step forward in the comprehension and improvement of yeast thermotolerance.
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Affiliation(s)
- Tânia Pinheiro
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Ka Ying Florence Lip
- Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Estéfani García-Ríos
- Food Biotechnology Department, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Amparo Querol
- Food Biotechnology Department, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - José Teixeira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Walter van Gulik
- Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - José Manuel Guillamón
- Food Biotechnology Department, Instituto de Agroquímica Y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
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Yu L, Chen X, Wei Y, Ding Y, Wang Q, Wang S, Tang B, Wang S. Effects of long-term cadmium exposure on trehalose metabolism, growth, and development of Aedes albopictus (Diptera: Culicidae). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 204:111034. [PMID: 32758695 DOI: 10.1016/j.ecoenv.2020.111034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/10/2020] [Accepted: 07/11/2020] [Indexed: 06/11/2023]
Abstract
Trehalose is the major blood sugar in insects; it not only serves as an energy source but also plays important roles in physiological responses to adverse conditions. However, only a few studies have explored the effects of heavy metal exposure stress on trehalose metabolism in insects. Therefore, in this study, we examined the effects of cadmium stress on changes in trehalose metabolism in Aedes albopictus. Three concentrations of cadmium (0.005, 0.01, and 0.1 mg/L) were selected for evaluation of long-term stress in Ae. albopictus (from eggs to adults); Ae. albopictus in double-distilled water was used as the control group. The trehalose and glucose contents, trehalase activity, and trehalose metabolism-related gene expression were determined. The effects of long-term cadmium exposure on growth, development, and reproduction were also assessed. Trehalose contents were increased, whereas glucose contents and trehalase activity were decreased in Ae. albopictus following long-term exposure to low concentrations of cadmium compared with those in untreated individuals. Moreover, the expression of trehalose-6-phosphate synthase was upregulated, and that of trehalase was downregulated, indicating that Ae. albopictus may enhance trehalose synthesis to resist cadmium stress. Cadmium exposure also caused Ae. albopictus individuals to become smaller with a longer developmental duration, whereas both reproduction and hatching rates of the offspring were decreased compared with those in the control group. Our findings demonstrated that cadmium exposure affected the morphology, physiology, and biochemistry of Ae. albopictus. These findings also confirmed the role of trehalose in the response of Ae. albopictus to cadmium stress, providing insights into the effects of heavy metal stress on trehalose metabolism in an insect model.
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Affiliation(s)
- Lingyuan Yu
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xumin Chen
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ying Wei
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yanjuan Ding
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qiwei Wang
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Shaohua Wang
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Bin Tang
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Shigui Wang
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.
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Gorman SD, Winston DS, Sahu D, Boehr DD. Different Solvent and Conformational Entropy Contributions to the Allosteric Activation and Inhibition Mechanisms of Yeast Chorismate Mutase. Biochemistry 2020; 59:2528-2540. [DOI: 10.1021/acs.biochem.0c00277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Scott D. Gorman
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Dennis S. Winston
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Debashish Sahu
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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40
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Li G, Moore JK. Microtubule dynamics at low temperature: evidence that tubulin recycling limits assembly. Mol Biol Cell 2020; 31:1154-1166. [PMID: 32213119 PMCID: PMC7353160 DOI: 10.1091/mbc.e19-11-0634] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How temperature specifically affects microtubule dynamics and how these lead to changes in microtubule networks in cells have not been established. We investigated these questions in budding yeast, an organism found in diverse environments and therefore predicted to exhibit dynamic microtubules across a broad temperature range. We measured the dynamics of GFP-labeled microtubules in living cells and found that lowering temperature from 37°C to 10°C decreased the rates of both polymerization and depolymerization, decreased the amount of polymer assembled before catastrophes, and decreased the frequency of microtubule emergence from nucleation sites. Lowering to 4°C caused rapid loss of almost all microtubule polymer. We provide evidence that these effects on microtubule dynamics may be explained in part by changes in the cofactor-dependent conformational dynamics of tubulin proteins. Ablation of tubulin-binding cofactors (TBCs) further sensitizes cells and their microtubules to low temperatures, and we highlight a specific role for TBCB/Alf1 in microtubule maintenance at low temperatures. Finally, we show that inhibiting the maturation cycle of tubulin by using a point mutant in β-tubulin confers hyperstable microtubules at low temperatures and rescues the requirement for TBCB/Alf1 in maintaining microtubule polymer at low temperatures. Together, these results reveal an unappreciated step in the tubulin cycle.
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Affiliation(s)
- Gabriella Li
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045
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DNA Methylation Changes Induced by Cold in Psychrophilic and Psychrotolerant Naganishia Yeast Species. Microorganisms 2020; 8:microorganisms8020296. [PMID: 32093408 PMCID: PMC7074839 DOI: 10.3390/microorganisms8020296] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 12/18/2022] Open
Abstract
The involvement of DNA methylation in the response to cold stress of two different yeast species (Naganishia antarctica, psychrophilic, and Naganishia albida, psychrotolerant), exhibiting different temperature aptitudes, has been studied. Consecutive incubations at respective optimum temperatures, at 4 °C (cold stress) and at optimum temperatures again, were performed. After Methylation Sensitive Amplified Polymorphism (MSAP) fingerprints a total of 550 and 423 clear and reproducible fragments were amplified from N. antarctica and N. albida strains, respectively. The two Naganishia strains showed a different response in terms of level of DNA methylation during cold stress and recovery from cold stress. The percentage of total methylated fragments in psychrophilic N. antarctica did not show any significant change. On the contrary, the methylation of psychrotolerant N. albida exhibited a nonsignificant increase during the incubation at 4 °C and continued during the recovery step, showing a significant difference if compared with control condition, resembling an uncontrolled response to cold stress. A total of 12 polymorphic fragments were selected, cloned, and sequenced. Four fragments were associated to genes encoding for elongation factor G and for chitin synthase export chaperon. To the best of our knowledge, this is the first study on DNA methylation in the response to cold stress carried out by comparing a psychrophilic and a psychrotolerant yeast species.
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Liu M, Yu T, Singh PK, Liu Q, Liu H, Zhu Q, Xiao Z, Xu J, Peng Y, Fu S, Chen S, He H. A Comparative Transcriptome Analysis of Volvariella volvacea Identified the Candidate Genes Involved in Fast Growth at the Mycelial Growth Stage. Genes (Basel) 2020; 11:genes11020161. [PMID: 32033161 PMCID: PMC7074523 DOI: 10.3390/genes11020161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 02/01/2020] [Indexed: 01/13/2023] Open
Abstract
The edible straw mushroom, Volvariella volvacea, is one of the most important cultivated mushrooms in tropical and sub-tropical regions. Strain improvement for V. volvacea is difficult because of the unknown mechanisms involved in its growth regulation and substrate utilization. A comparative physiological and transcriptomic study was conducted between two commercially available straw mushroom strains (v9 and v26) to explore their fast-growth regulation mechanism(s). The physiological study showed that V. volvacea v9 had a shorter growth cycle and higher biological efficiency (4% higher) than that in v26. At least 14,556 unigenes were obtained from the four cDNA libraries (two replicates per strain). Among them, the expression of 1597 unigenes was up-regulated while 1352 were down-regulated. Four heat-shock proteins were highly expressed in v9, showing that v9 has the better ability to handle stresses and/or environmental changes. Moreover, up to 14 putative transporter genes were expressed at a higher level in v9 than those in v26, implying that v9 has a better ability to transport nutrients or export xenobiotics efficiently. Our report allows to identify the candidate genes involved in the fast growth requirement of V. volvacea, which represents a valuable resource for strain improvement in this commercially important edible mushroom.
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Affiliation(s)
- Ming Liu
- Vegetables Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China; (M.L.); (Z.X.); (J.X.); (Y.P.)
| | - Ting Yu
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (T.Y.); (Q.L.); (Q.Z.)
| | - Puneet Kumar Singh
- School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China; (P.K.S.); (H.L.); (S.F.)
| | - Qinjian Liu
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (T.Y.); (Q.L.); (Q.Z.)
| | - Hao Liu
- School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China; (P.K.S.); (H.L.); (S.F.)
| | - Qingfeng Zhu
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (T.Y.); (Q.L.); (Q.Z.)
| | - Zitian Xiao
- Vegetables Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China; (M.L.); (Z.X.); (J.X.); (Y.P.)
| | - Jiang Xu
- Vegetables Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China; (M.L.); (Z.X.); (J.X.); (Y.P.)
| | - Yangyang Peng
- Vegetables Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China; (M.L.); (Z.X.); (J.X.); (Y.P.)
| | - Shiyu Fu
- School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China; (P.K.S.); (H.L.); (S.F.)
| | - Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (S.C.); (H.H.); Tel.: +1-517-884-5383 (S.C.); +86-20-38469598 (H.H.); Fax: +1-517-884-5384 (S.C.); +86-20-38469598 (H.H.)
| | - Huanqing He
- Vegetables Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China; (M.L.); (Z.X.); (J.X.); (Y.P.)
- Correspondence: (S.C.); (H.H.); Tel.: +1-517-884-5383 (S.C.); +86-20-38469598 (H.H.); Fax: +1-517-884-5384 (S.C.); +86-20-38469598 (H.H.)
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McNamar R, Abu-Adas Z, Rothblum K, Knutson BA, Rothblum LI. Conditional depletion of the RNA polymerase I subunit PAF53 reveals that it is essential for mitosis and enables identification of functional domains. J Biol Chem 2019; 294:19907-19922. [PMID: 31727736 PMCID: PMC6937585 DOI: 10.1074/jbc.ra119.009902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/05/2019] [Indexed: 12/24/2022] Open
Abstract
Our knowledge of the mechanism of rDNA transcription has benefited from the combined application of genetic and biochemical techniques in yeast. Nomura's laboratory (Nogi, Y., Vu, L., and Nomura, M. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 7026-7030 and Nogi, Y., Yano, R., and Nomura, M. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 3962-3966) developed a system in yeast to identify genes essential for ribosome biogenesis. Such systems have allowed investigators to determine whether a gene was essential and to determine its function in rDNA transcription. However, there are significant differences in both the structures and components of the transcription apparatus and the patterns of regulation between mammals and yeast. Thus, there are significant deficits in our understanding of mammalian rDNA transcription. We have developed a system combining CRISPR/Cas9 and an auxin-inducible degron that enables combining a "genetics-like"approach with biochemistry to study mammalian rDNA transcription. We now show that the mammalian orthologue of yeast RPA49, PAF53, is required for rDNA transcription and mitotic growth. We have studied the domains of the protein required for activity. We have found that the C-terminal, DNA-binding domain (tandem-winged helix), the heterodimerization, and the linker domain were essential. Analysis of the linker identified a putative helix-turn-helix (HTH) DNA-binding domain. This HTH constitutes a second DNA-binding domain within PAF53. The HTH of the yeast and mammalian orthologues is essential for function. In summary, we show that an auxin-dependent degron system can be used to rapidly deplete nucleolar proteins in mammalian cells, that PAF53 is necessary for rDNA transcription and cell growth, and that all three PAF53 domains are necessary for its function.
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Affiliation(s)
- Rachel McNamar
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma 73104
| | - Zakaria Abu-Adas
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma 73104
| | - Katrina Rothblum
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma 73104
| | - Bruce A Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210
| | - Lawrence I Rothblum
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma 73104
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Smukowski Heil CS, Large CRL, Patterson K, Hickey ASM, Yeh CLC, Dunham MJ. Temperature preference can bias parental genome retention during hybrid evolution. PLoS Genet 2019; 15:e1008383. [PMID: 31525194 PMCID: PMC6762194 DOI: 10.1371/journal.pgen.1008383] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 09/26/2019] [Accepted: 08/22/2019] [Indexed: 11/18/2022] Open
Abstract
Interspecific hybridization can introduce genetic variation that aids in adaptation to new or changing environments. Here, we investigate how hybrid adaptation to temperature and nutrient limitation may alter parental genome representation over time. We evolved Saccharomyces cerevisiae x Saccharomyces uvarum hybrids in nutrient-limited continuous culture at 15°C for 200 generations. In comparison to previous evolution experiments at 30°C, we identified a number of responses only observed in the colder temperature regime, including the loss of the S. cerevisiae allele in favor of the cryotolerant S. uvarum allele for several portions of the hybrid genome. In particular, we discovered a genotype by environment interaction in the form of a loss of heterozygosity event on chromosome XIII; which species' haplotype is lost or maintained is dependent on the parental species' temperature preference and the temperature at which the hybrid was evolved. We show that a large contribution to this directionality is due to a temperature dependent fitness benefit at a single locus, the high affinity phosphate transporter gene PHO84. This work helps shape our understanding of what forces impact genome evolution after hybridization, and how environmental conditions may promote or disfavor the persistence of hybrids over time.
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Affiliation(s)
- Caiti S. Smukowski Heil
- Genome Sciences Department, University of Washington, Seattle, Washington, United States of America
| | - Christopher R. L. Large
- Genome Sciences Department, University of Washington, Seattle, Washington, United States of America
| | - Kira Patterson
- Genome Sciences Department, University of Washington, Seattle, Washington, United States of America
| | - Angela Shang-Mei Hickey
- Genome Sciences Department, University of Washington, Seattle, Washington, United States of America
| | - Chiann-Ling C. Yeh
- Genome Sciences Department, University of Washington, Seattle, Washington, United States of America
| | - Maitreya J. Dunham
- Genome Sciences Department, University of Washington, Seattle, Washington, United States of America
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The Ustilago maydis null mutant strains of the RNA-binding protein UmRrm75 accumulate hydrogen peroxide and melanin. Sci Rep 2019; 9:10813. [PMID: 31346214 PMCID: PMC6658566 DOI: 10.1038/s41598-019-47133-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 05/09/2019] [Indexed: 01/24/2023] Open
Abstract
Ustilago maydis is a dimorphic fungus that has emerged as a model organism for the study of fungal phytopathogenicity and RNA biology. In a previous study, we isolated the U. maydis UmRrm75 gene. The deletion of the UmRrm75 gene affected morphogenesis and pathogenicity. UmRrm75 gene encodes a protein containing three RNA recognition motifs. Here we determined that UmRrm75 has chaperone activity in Escherichia coli using the transcription anti-termination assay. Subsequently, we analyzed the growth of ΔUmRrm75 mutants at 15 °C and 37 °C, observing that mutant strains had reduced growth in comparison to parental strains. UmRrm75 gene expression was induced under these non-optimal temperatures. ΔUmRrm75 mutant colonies displayed a dark-brown color at 28 °C, which was confirmed to be melanin based on spectroscopic analysis and spectrometric data. Furthermore, ΔUmRrm75 mutant strains showed the presence of peroxisomes, and increased H2O2 levels, even at 28 °C. The ΔUmRrm75 mutant strains displayed a higher expression of redox-sensor UmYap1 gene and increased catalase activity than the parental strains. Our data show that deletion of the UmRrm75 gene results in higher levels of H2O2, increased melanin content, and abiotic stress sensitivity.
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Somani A, Box WG, Smart KA, Powell CD. Physiological and transcriptomic response of Saccharomyces pastorianus to cold storage. FEMS Yeast Res 2019; 19:5420514. [PMID: 31073596 DOI: 10.1093/femsyr/foz025] [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: 11/22/2018] [Accepted: 03/22/2019] [Indexed: 11/13/2022] Open
Abstract
Removal of yeast biomass at the end of fermentation, followed by a period of storage before re-inoculation into a subsequent fermentation, is common in the brewing industry. Storage is typically conducted at cold temperatures to preserve yeast quality, a practice which has unfavourable cost and environmental implications. To determine the potential for alleviating these effects, the transcriptomic and physiological response of Saccharomyces pastorianus strain W34/70 to standard (4°C) and elevated (10°C) storage temperatures was explored. Higher temperatures resulted in increased expression of genes associated with the production and mobilisation of intracellular glycogen, trehalose, glycerol and fatty acids, although these observations were limited to early stages of storage. Intracellular trehalose and glycerol concentrations were higher at 4°C than at 10°C, as a consequence of the cellular response to cold stress. However, significant changes in glycogen degradation or cellular fatty acid composition did not occur between the two sets of populations, ensuring that cell viability remained consistent. It is anticipated that this data may lead to changes in standard practice for handling yeast cultures, without compromising yeast quality. This work has significance not only for the brewing industry, but also for food and biofuel sectors requiring short-term storage of liquid yeast.
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Affiliation(s)
- Abhishek Somani
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom.,Institute of Biological, Environmental and Rural Sciences, Gogerddan Campus, University of Aberystwyth, Aberystwyth, Ceredigion, SY23 3EB, United Kingdom
| | - Wendy G Box
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Katherine A Smart
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom.,Department of Chemical Engineering and Biotechnology, University of Cambridge, Phillipa Fawcet Drive, Cambridge, Cambridgeshire, CB3 0AS, United Kingdom
| | - Chris D Powell
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
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47
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Sun ZG, Wang MQ, Wang YP, Xing S, Hong KQ, Chen YF, Guo XW, Xiao DG. Identification by comparative transcriptomics of core regulatory genes for higher alcohol production in a top-fermenting yeast at different temperatures in beer fermentation. Appl Microbiol Biotechnol 2019; 103:4917-4929. [DOI: 10.1007/s00253-019-09807-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 11/29/2022]
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48
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Aroma production and fermentation performance of S. cerevisiae × S. kudriavzevii natural hybrids under cold oenological conditions. Int J Food Microbiol 2019; 297:51-59. [DOI: 10.1016/j.ijfoodmicro.2019.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 02/04/2019] [Accepted: 03/10/2019] [Indexed: 12/30/2022]
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49
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García-Ríos E, Nuévalos M, Barrio E, Puig S, Guillamón JM. A new chromosomal rearrangement improves the adaptation of wine yeasts to sulfite. Environ Microbiol 2019; 21:1771-1781. [PMID: 30859719 DOI: 10.1111/1462-2920.14586] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/05/2019] [Accepted: 03/06/2019] [Indexed: 11/27/2022]
Abstract
Sulfite-generating compounds are widely used during winemaking as preservatives because of its antimicrobial and antioxidant properties. Thus, wine yeast strains have developed different genetic strategies to increase its sulfite resistance. The most efficient sulfite detoxification mechanism in Saccharomyces cerevisiae uses a plasma membrane protein called Ssu1 to efflux sulfite. In wine yeast strains, two chromosomal translocations (VIIItXVI and XVtXVI) involving the SSU1 promoter region have been shown to upregulate SSU1 expression and, as a result, increase sulfite tolerance. In this study, we have identified a novel chromosomal rearrangement that triggers wine yeast sulfite adaptation. An inversion in chromosome XVI (inv-XVI) probably due to sequence microhomology, which involves SSU1 and GCR1 regulatory regions, increases the expression of SSU1 and the sulfite resistance of a commercial wine yeast strain. A detailed dissection of this chimeric SSU1 promoter indicates that both the removed SSU1 promoter sequence and the relocated GCR1 sequence contribute to SSU1 upregulation and sulfite tolerance. However, no relevant function has been attributed to the SSU1-promoter-binding transcription factor Fzf1. These results unveil a new genomic event that confers an evolutive advantage to wine yeast strains.
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Affiliation(s)
- Estéfani García-Ríos
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - Marcos Nuévalos
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain.,Departament de Genètica, Universitat de València, Doctor Moliner 50, E-46100, Burjassot, Valencia, Spain
| | - Sergi Puig
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
| | - José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Agustín Escardino 7, E-46980, Paterna, Valencia, Spain
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50
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Hanya A. The Effect of Cold Incubation before Mass Spectrometry Identification on Different <i>Saccharomyces cerevisiae </i>Strains. J JPN SOC FOOD SCI 2019. [DOI: 10.3136/nskkk.66.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Akira Hanya
- Aichi Center for Industry and Science Technology
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