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Wagner A, Schosserer M. The epitranscriptome in ageing and stress resistance: A systematic review. Ageing Res Rev 2022; 81:101700. [PMID: 35908668 DOI: 10.1016/j.arr.2022.101700] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 01/31/2023]
Abstract
Modifications of RNA, collectively called the "epitranscriptome", might provide novel biomarkers and innovative targets for interventions in geroscience but are just beginning to be studied in the context of ageing and stress resistance. RNA modifications modulate gene expression by affecting translation initiation and speed, miRNA binding, RNA stability, and RNA degradation. Nonetheless, the precise underlying molecular mechanisms and physiological consequences of most alterations of the epitranscriptome are still only poorly understood. We here systematically review different types of modifications of rRNA, tRNA and mRNA, the methodology to analyze them, current challenges in the field, and human disease associations. Furthermore, we compiled evidence for a connection between individual enzymes, which install RNA modifications, and lifespan in yeast, worm and fly. We also included resistance to different stressors and competitive fitness as search criteria for genes potentially relevant to ageing. Promising candidates identified by this approach include RCM1/NSUN5, RRP8, and F33A8.4/ZCCHC4 that introduce base methylations in rRNA, the methyltransferases DNMT2 and TRM9/ALKBH8, as well as factors involved in the thiolation or A to I editing in tRNA, and finally the m6A machinery for mRNA.
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Affiliation(s)
- Anja Wagner
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Schosserer
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria.
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2
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Condessa BMB, da Silva KV, da Silva JFM, de Morais PB, Leal Zimmer FMA, de Almeida AF, Niculau EDS, Nogueira KL, Santos CCADA. Performance of wild
Saccharomyces
and Non‐
Saccharomyces
yeasts as starter cultures in dough fermentation and bread making. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Paula Benevides de Morais
- Bionorte – Legal Amazon Biodiversity and Biotechnology Network Federal University of Tocantins Palmas Brazil
| | | | - Alex Fernando de Almeida
- Graduate Program in Food Science and Technology Federal University of Tocantins (UFT) Palmas Brazil
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Cabrera E, Welch LC, Robinson MR, Sturgeon CM, Crow MM, Segarra VA. Cryopreservation and the Freeze-Thaw Stress Response in Yeast. Genes (Basel) 2020; 11:genes11080835. [PMID: 32707778 PMCID: PMC7463829 DOI: 10.3390/genes11080835] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 01/31/2023] Open
Abstract
The ability of yeast to survive freezing and thawing is most frequently considered in the context of cryopreservation, a practical step in both industrial and research applications of these organisms. However, it also relates to an evolved ability to withstand freeze-thaw stress that is integrated with a larger network of survival responses. These responses vary between different strains and species of yeast according to the environments to which they are adapted, and the basis of this adaptation appears to be both conditioned and genetic in origin. This review article briefly touches upon common yeast cryopreservation methods and describes in detail what is known about the biochemical and genetic determinants of cell viability following freeze-thaw stress. While we focus on the budding yeast Saccharomyces cerevisiae, in which the freeze-thaw stress response is best understood, we also highlight the emerging diversity of yeast freeze-thaw responses as a manifestation of biodiversity among these organisms.
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Khajavi MZ, Tripathi AD, Khosravi-Darani K. Strategies of Freezing Tolerance in Yeast: Genes’ Rapid Response for Accumulation of Stress Protectants. CURRENT NUTRITION & FOOD SCIENCE 2019. [DOI: 10.2174/2210315508666181009113623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Production of frozen ready-to-bake bakery products has gained significant attention during the past few years. However, the freezing process during the production of frozen bakery products may decrease the quality especially in the case of suppression of the activity of baker yeast. Great improvements in the quality of frozen bakery products may be achieved by increasing the stability of yeast during freezing storage. Many microorganisms have different kinds of mechanisms to suppress environmental, freezing or thawing stresses. In this review paper, reported strategies which are used for rising tolerance of microorganisms, especially yeast, are reviewed. One of the introduced protective procedures is the accumulation of special intra-cellular metabolites by some microorganisms. Two main key metabolites in this regard are trehalose and proline (which act as an osmoprotectant and decrease the melting point of DNA), which are introduced in this review article. Also, cloning strategies for increasing their bioaccumulation are pointed out, and their mechanisms of action are described. Finally, overexpression of SNR84 gene as an another microbial strategy for surviving in harsh environmental conditions is (small nucleolar RNAs) mentioned, which leads to ribosomal pseudouridines (responsible for freezing tolerance and decreasing growth rate of organisms).
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Affiliation(s)
- Maryam Z. Khajavi
- Students` Research Committee, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abhishek D. Tripathi
- Centre of Food Science and Technology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi-221005, U.P, India
| | - Kianoush Khosravi-Darani
- Research Department of Food Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Nakagawa Y, Fujita R, Yamamura H, Hayakawa M. Identification of CDC25-P1306L, a novel mutant allele of CDC25, conferring tolerance to multiple stresses associated with food production on Saccharomyces cerevisiae. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2018.1559094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Youji Nakagawa
- Division of Life and Agricultural Sciences, Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Risa Fujita
- Division of Biotechnology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
| | - Hideki Yamamura
- Division of Life and Agricultural Sciences, Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Masayuki Hayakawa
- Division of Life and Agricultural Sciences, Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
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6
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Luo W, Sun DW, Zhu Z, Wang QJ. Improving freeze tolerance of yeast and dough properties for enhancing frozen dough quality - A review of effective methods. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2017.11.017] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Shi S, Choi YW, Zhao H, Tan MH, Ang EL. Discovery and engineering of a 1-butanol biosensor in Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2017; 245:1343-1351. [PMID: 28712783 DOI: 10.1016/j.biortech.2017.06.114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
The present study aimed to develop a universal methodology for the discovery of biosensors sensitive to particular stresses or metabolites by using a transcriptome analysis, in order to address the need for in vivo biosensors to drive the engineering of microbial cell factories. The method was successfully applied to the discovery of 1-butanol sensors. In particular, the genome-wide transcriptome profiling of S. cerevisiae exposed to three similar short-chain alcohols, 1-butanol, 1-propanol, and ethanol, identified genes that were differentially expressed only under the treatment of 1-butanol. From these candidates, two promoters that responded specifically to 1-butanol were characterized in a dose-dependent manner and were used to distinguish differences in production levels among different 1-butanol producer strains. This strategy opens up new opportunities for the discovery of promoter-based biosensors and can potentially be used to identify biosensors for any metabolite that causes cellular transcriptomic changes.
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Affiliation(s)
- Shuobo Shi
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore.
| | - Yook Wah Choi
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore.
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Meng How Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.
| | - Ee Lui Ang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore.
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Lin X, Yu AQ, Zhang CY, Pi L, Bai XW, Xiao DG. Functional analysis of the global repressor Tup1 for maltose metabolism in Saccharomyces cerevisiae: different roles of the functional domains. Microb Cell Fact 2017; 16:194. [PMID: 29121937 PMCID: PMC5679332 DOI: 10.1186/s12934-017-0806-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/31/2017] [Indexed: 11/15/2022] Open
Abstract
Background Tup1 is a general transcriptional repressor of diverse gene families coordinately controlled by glucose repression, mating type, and other mechanisms in Saccharomyces cerevisiae. Several functional domains of Tup1 have been identified, each of which has differing effects on transcriptional repression. In this study, we aim to investigate the role of Tup1 and its domains in maltose metabolism of industrial baker’s yeast. To this end, a battery of in-frame truncations in the TUP1 gene coding region were performed in the industrial baker’s yeasts with different genetic background, and the maltose metabolism, leavening ability, MAL gene expression levels, and growth characteristics were investigated. Results The results suggest that the TUP1 gene is essential to maltose metabolism in industrial baker’s yeast. Importantly, different domains of Tup1 play different roles in glucose repression and maltose metabolism of industrial baker’s yeast cells. The Ssn6 interaction, N-terminal repression and C-terminal repression domains might play roles in the regulation of MAL transcription by Tup1 for maltose metabolism of baker’s yeast. The WD region lacking the first repeat could influence the regulation of maltose metabolism directly, rather than indirectly through glucose repression. Conclusions These findings lay a foundation for the optimization of industrial baker’s yeast strains for accelerated maltose metabolism and facilitate future research on glucose repression in other sugar metabolism. Electronic supplementary material The online version of this article (10.1186/s12934-017-0806-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xue Lin
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.,College of Food Science and Technology, Hainan University, Haikou, 570228, China
| | - Ai-Qun Yu
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Cui-Ying Zhang
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
| | - Li Pi
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Xiao-Wen Bai
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Dong-Guang Xiao
- Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China.
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Struyf N, Van der Maelen E, Hemdane S, Verspreet J, Verstrepen KJ, Courtin CM. Bread Dough and Baker's Yeast: An Uplifting Synergy. Compr Rev Food Sci Food Saf 2017; 16:850-867. [DOI: 10.1111/1541-4337.12282] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/22/2017] [Accepted: 05/29/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Nore Struyf
- Lab. of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe); KU Leuven; Kasteelpark Arenberg 20 B-3001 Leuven Belgium
- VIB Lab. for Systems Biology & CMPG Laboratory for Genetics and Genomics; KU Leuven; Bio-Incubator, Gaston Geenslaan 1 B-3001 Leuven Belgium
| | - Eva Van der Maelen
- Lab. of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe); KU Leuven; Kasteelpark Arenberg 20 B-3001 Leuven Belgium
| | - Sami Hemdane
- Lab. of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe); KU Leuven; Kasteelpark Arenberg 20 B-3001 Leuven Belgium
| | - Joran Verspreet
- Lab. of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe); KU Leuven; Kasteelpark Arenberg 20 B-3001 Leuven Belgium
| | - Kevin J. Verstrepen
- VIB Lab. for Systems Biology & CMPG Laboratory for Genetics and Genomics; KU Leuven; Bio-Incubator, Gaston Geenslaan 1 B-3001 Leuven Belgium
| | - Christophe M. Courtin
- Lab. of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe); KU Leuven; Kasteelpark Arenberg 20 B-3001 Leuven Belgium
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Zhang CY, Bai XW, Lin X, Liu XE, Xiao DG. Effects of SNF1 on Maltose Metabolism and Leavening Ability of Baker's Yeast in Lean Dough. J Food Sci 2015; 80:M2879-85. [PMID: 26580148 DOI: 10.1111/1750-3841.13137] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/05/2015] [Indexed: 11/29/2022]
Abstract
Maltose metabolism of baker's yeast (Saccharomyces cerevisiae) in lean dough is negatively influenced by glucose repression, thereby delaying the dough fermentation. To improve maltose metabolism and leavening ability, it is necessary to alleviate glucose repression. The Snf1 protein kinase is well known to be essential for the response to glucose repression and required for transcription of glucose-repressed genes including the maltose-utilization genes (MAL). In this study, the SNF1 overexpression and deletion industrial baker's yeast strains were constructed and characterized in terms of maltose utilization, growth and fermentation characteristics, mRNA levels of MAL genes (MAL62 encoding the maltase and MAL61 encoding the maltose permease) and maltase and maltose permease activities. Our results suggest that overexpression of SNF1 was effective to glucose derepression for enhancing MAL expression levels and enzymes (maltase and maltose permease) activities. These enhancements could result in an 18% increase in maltose metabolism of industrial baker's yeast in LSMLD medium (the low sugar model liquid dough fermentation medium) containing glucose and maltose and a 15% increase in leavening ability in lean dough. These findings provide a valuable insight of breeding industrial baker's yeast for rapid fermentation.
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Affiliation(s)
- Cui-Ying Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin Univ. of Science and Technology, Tianjin, 300457, P. R. China
| | - Xiao-Wen Bai
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin Univ. of Science and Technology, Tianjin, 300457, P. R. China
| | - Xue Lin
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin Univ. of Science and Technology, Tianjin, 300457, P. R. China
| | - Xiao-Er Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin Univ. of Science and Technology, Tianjin, 300457, P. R. China
| | - Dong-Guang Xiao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin Univ. of Science and Technology, Tianjin, 300457, P. R. China
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