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Yang C, Ren Y, Zhang L, Li Y, Wang C, Hang H, Tian X, Mohsin A, Chu J, Zhuang Y. Alterations in Protein Phosphorylation and Arginine Biosynthesis Metabolism Confer β-Phenylethanol Tolerance in Saccharomyces cerevisiae. Biotechnol Bioeng 2025. [PMID: 39888015 DOI: 10.1002/bit.28936] [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: 07/04/2024] [Revised: 12/23/2024] [Accepted: 01/15/2025] [Indexed: 02/01/2025]
Abstract
The aromatic compound β-phenylethanol (2-PE) is inherently toxic and can inhibit cell activity in Saccharomyces cerevisiae, making it highly challenging to enhance strain tolerance through rational design due to the lack of reliable connections between tolerance phenotype and genetic loci. This study employed adaptive laboratory evolution strategy to investigate the tolerance characteristics of S. cerevisiae S288C under inhibitory concentrations of 2-PE. The tolerant mutant SEC4.0 was characterized through comprehensive analysis of whole genome sequence, transcriptome, and phosphoproteome. The findings revealed that the high resistance of SEC4.0 was not primarily due to large-scale transcriptional upregulation of stress response genes, but rather through alterations in the phosphorylation levels of lipid-related pathways. PKC1 mutations that affect stress signal transduction and SPT3 mutations that affect arginine biosynthesis have been shown to significantly enhance 2-PE resistance. This study also investigated the effects of exogenous amino acid addition and synergistic effects with two key mutanted genes on 2-PE resistance. This study provides a foundation for enhancing yeast tolerance to this aromatic compound through rational design strategies.
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Affiliation(s)
- Chenghan Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yilin Ren
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Li Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yina Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chunxia Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Haifeng Hang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Qingdao Innovation Institute of East China University of Science and Technology, East China University of Science and Technology, Qingdao, Shandong, China
| | - Xiwei Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Qingdao Innovation Institute of East China University of Science and Technology, East China University of Science and Technology, Qingdao, Shandong, China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Qingdao Innovation Institute of East China University of Science and Technology, East China University of Science and Technology, Qingdao, Shandong, China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Qingdao Innovation Institute of East China University of Science and Technology, East China University of Science and Technology, Qingdao, Shandong, China
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2
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Xu Z, Sha Y, Li M, Chen S, Li J, Ding B, Zhang Y, Li P, Yan K, Jin M. Adaptive evolution and mechanism elucidation for ethanol tolerant Saccharomyces cerevisiae used in starch based biorefinery. Int J Biol Macromol 2025; 284:138155. [PMID: 39613065 DOI: 10.1016/j.ijbiomac.2024.138155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 09/02/2024] [Accepted: 11/26/2024] [Indexed: 12/01/2024]
Abstract
Ethanol tolerant Saccharomyces cerevisiae is compulsory for ethanol production in starch based biorefinery, especially during high-gravity fermentation. In this study, adaptive evolution with increased initial ethanol concentrations as a driving force was harnessed for achieving ethanol tolerant S. cerevisiae. After evolution, an outstanding ethanol tolerant strain was screened, which contributed to significant improvements in glucose consumption and ethanol production in scenarios of 300 g/L initial glucose, high solid loadings (30 wt%, 33 wt%, 35 wt% and 40 wt%) of corn, and high solid loadings (30 wt% and 33 wt%) of cassava, compared with the original strain. Genome re-sequencing was applied for the evolved strain, and 504 sense mutations in 205 genes were detected, among which PAM1 gene was demonstrated related to the elevated ethanol tolerance. In sum, this study provided a practical approach for obtaining ethanol tolerant strain and the identified PAM1 gene enhanced our understanding on ethanol tolerant mechanism, as well as provided a target basis for rational metabolic engineering.
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Affiliation(s)
- Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yuanyuan Sha
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Muzi Li
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Sitong Chen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jie Li
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Boning Ding
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yuwei Zhang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Pingping Li
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Kang Yan
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China.
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3
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Kuang Z, Yan X, Yuan Y, Wang R, Zhu H, Wang Y, Li J, Ye J, Yue H, Yang X. Advances in stress-tolerance elements for microbial cell factories. Synth Syst Biotechnol 2024; 9:793-808. [PMID: 39072145 PMCID: PMC11277822 DOI: 10.1016/j.synbio.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/10/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024] Open
Abstract
Microorganisms, particularly extremophiles, have evolved multiple adaptation mechanisms to address diverse stress conditions during survival in unique environments. Their responses to environmental coercion decide not only survival in severe conditions but are also an essential factor determining bioproduction performance. The design of robust cell factories should take the balance of their growing and bioproduction into account. Thus, mining and redesigning stress-tolerance elements to optimize the performance of cell factories under various extreme conditions is necessary. Here, we reviewed several stress-tolerance elements, including acid-tolerant elements, saline-alkali-resistant elements, thermotolerant elements, antioxidant elements, and so on, providing potential materials for the construction of cell factories and the development of synthetic biology. Strategies for mining and redesigning stress-tolerance elements were also discussed. Moreover, several applications of stress-tolerance elements were provided, and perspectives and discussions for potential strategies for screening stress-tolerance elements were made.
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Affiliation(s)
- Zheyi Kuang
- School of Intelligence Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Xiaofang Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yanfei Yuan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Ruiqi Wang
- School of Intelligence Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Haifan Zhu
- School of Intelligence Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Youyang Wang
- School of Intelligence Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Jianfeng Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jianwen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Haitao Yue
- School of Intelligence Science and Technology, Xinjiang University, Urumqi, 830017, China
- Laboratory of Synthetic Biology, School of Life Science and Technology, Xinjiang University, Urumqi, 830017, China
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
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Jiang L, Shen Y, Jiang Y, Mei W, Wei L, Feng J, Wei C, Liao X, Mo Y, Pan L, Wei M, Gu Y, Zheng J. Amino acid metabolism and MAP kinase signaling pathway play opposite roles in the regulation of ethanol production during fermentation of sugarcane molasses in budding yeast. Genomics 2024; 116:110811. [PMID: 38387766 DOI: 10.1016/j.ygeno.2024.110811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Sugarcane molasses is one of the main raw materials for bioethanol production, and Saccharomyces cerevisiae is the major biofuel-producing organism. In this study, a batch fermentation model has been used to examine ethanol titers of deletion mutants for all yeast nonessential genes in this yeast genome. A total of 42 genes are identified to be involved in ethanol production during fermentation of sugarcane molasses. Deletion mutants of seventeen genes show increased ethanol titers, while deletion mutants for twenty-five genes exhibit reduced ethanol titers. Two MAP kinases Hog1 and Kss1 controlling the high osmolarity and glycerol (HOG) signaling and the filamentous growth, respectively, are negatively involved in the regulation of ethanol production. In addition, twelve genes involved in amino acid metabolism are crucial for ethanol production during fermentation. Our findings provide novel targets and strategies for genetically engineering industrial yeast strains to improve ethanol titer during fermentation of sugarcane molasses.
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Affiliation(s)
- Linghuo Jiang
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China.
| | - Yuzhi Shen
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Yongqiang Jiang
- Institute of Biology, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Weiping Mei
- Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Liudan Wei
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Jinrong Feng
- Pathogen Biology Department, Nantong University, Nantong, Jiangsu 226001, China
| | - Chunyu Wei
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Xiufan Liao
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Yiping Mo
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Lingxin Pan
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Min Wei
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Yiying Gu
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Jiashi Zheng
- Laboratory of Yeast Biology and Fermentation Technology, National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Institute of Biological Sciences and Technology, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
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5
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Albuini FM, de Castro AG, Campos VJ, Ribeiro LE, Vidigal PMP, de Oliveira Mendes TA, Fietto LG. Transcriptome profiling brings new insights into the ethanol stress responses of Spathaspora passalidarum. Appl Microbiol Biotechnol 2023; 107:6573-6589. [PMID: 37658163 DOI: 10.1007/s00253-023-12730-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/01/2023] [Accepted: 08/10/2023] [Indexed: 09/03/2023]
Abstract
Spathaspora passalidarum is a xylose-fermenting microorganism promising for the fermentation of lignocellulosic hydrolysates. This yeast is more sensitive to ethanol than Saccharomyces cerevisiae for unclear reasons. An RNA-seq experiment was performed to identify transcriptional changes in S. passalidarum in response to ethanol and gain insights into this phenotype. The results showed the upregulation of genes associated with translation and the downregulation of genes encoding proteins involved in lipid metabolism, transporters, and enzymes from glycolysis and fermentation pathways. Our results also revealed that genes encoding heat-shock proteins and involved in antioxidant response were upregulated, whereas the osmotic stress response of S. passalidarum appears impaired under ethanol stress. A pseudohyphal morphology of S. passalidarum colonies was observed in response to ethanol stress, which suggests that ethanol induces a misperception of nitrogen availability in the environment. Changes in the yeast fatty acid profile were observed only after 12 h of ethanol exposure, coinciding with the recovery of the yeast xylose consumption ability. These findings suggest that the lack of fast membrane lipid adjustments, the halt in nutrient absorption and cellular metabolism, and the failure to induce the expression of osmotic stress-responsive genes are the main aspects underlying the low ethanol tolerance of S. passalidarum. KEY POINTS: • Ethanol stress halts Spathaspora passalidarum metabolism and fermentation • Genes encoding nutrient transporters showed downregulation under ethanol stress • Ethanol induces a pseudohyphal cell shape, suggesting a misperception of nutrients.
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Affiliation(s)
- Fernanda Matias Albuini
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Alex Gazolla de Castro
- Departamento de Microbiologia, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Valquíria Júnia Campos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Lílian Emídio Ribeiro
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Tiago Antônio de Oliveira Mendes
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil
| | - Luciano Gomes Fietto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil.
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6
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Li Y, Long H, Jiang G, Gong X, Yu Z, Huang M, Guan T, Guan Y, Liu X. Analysis of the ethanol stress response mechanism in Wickerhamomyces anomalus based on transcriptomics and metabolomics approaches. BMC Microbiol 2022; 22:275. [PMCID: PMC9664796 DOI: 10.1186/s12866-022-02691-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background
Wickerhamomyces anomalus (W. anomalus) is a kind of non-Saccharomyces yeast that has a variety of unique physiological characteristics and metabolic features and is widely used in many fields, such as food preservation, biomass energy, and aquaculture feed protein production. However, the mechanism of W. anomalus response to ethanol stress is still unclear, which greatly limits its application in the production of ethanol beverages and ethanol fuels. Therefore, we checked the effects of ethanol stress on the morphology, the growth, and differentially expressed genes (DEGs) and metabolites (DEMs) of W. anomalus.
Results
High concentrations of ethanol (9% ethanol and 12% ethanol) remarkably inhibited the growth of W. anomalus. Energy metabolism, amino acid metabolism, fatty acids metabolism, and nucleic acid metabolism were significantly influenced when exposing to 9% ethanol and 12% ethanolstress, which maybe universal for W. anomalus to response to different concentrations of ethanol stressl Furthermore, extracellular addition of aspartate, glutamate, and arginine significantly abated ethanol damage and improved the survival rate of W. anomalus.
Conclusions
The results obtained in this study provide insights into the mechanisms involved in W. anomalus response to ethanol stress. Therefore, new strategies can be realized to improve the ethanol tolerance of W. anomalus through metabolic engineering.
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Lázari LC, Wolf IR, Schnepper AP, Valente GT. LncRNAs of Saccharomyces cerevisiae bypass the cell cycle arrest imposed by ethanol stress. PLoS Comput Biol 2022; 18:e1010081. [PMID: 35587936 PMCID: PMC9232138 DOI: 10.1371/journal.pcbi.1010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 06/24/2022] [Accepted: 04/05/2022] [Indexed: 11/19/2022] Open
Abstract
Ethanol alters many subsystems of Saccharomyces cerevisiae, including the cell cycle. Two ethanol-responsive lncRNAs in yeast interact with cell cycle proteins, and here, we investigated the role of these RNAs in cell cycle. Our network dynamic modeling showed that higher and lower ethanol-tolerant strains undergo cell cycle arrest in mitosis and G1 phases, respectively, during ethanol stress. The higher population rebound of the lower ethanol-tolerant phenotype after stress relief responds to the late phase arrest. We found that the lncRNA lnc9136 of SEY6210 (a lower ethanol-tolerant strain) induces cells to skip mitosis arrest. Simulating an overexpression of lnc9136 and analyzing CRISPR–Cas9 mutants lacking this lncRNA suggest that lnc9136 induces a regular cell cycle even under ethanol stress, indirectly regulating Swe1p and Clb1/2 by binding to Gin4p and Hsl1p. Notably, lnc10883 of BY4742 (a higher ethanol-tolerant strain) does not prevent G1 arrest in this strain under ethanol stress. However, lnc19883 circumvents DNA and spindle damage checkpoints, maintaining a functional cell cycle by interacting with Mec1p or Bub1p even in the presence of DNA/spindle damage. Overall, we present the first evidence of direct roles for lncRNAs in regulating yeast cell cycle proteins, the dynamics of this system in different ethanol-tolerant phenotypes, and a new yeast cell cycle model. Ethanol is a cell stressor in yeast that dampen ethanol production. LncRNAs are RNAs that control many cellular processes. Computational simulations allow us to study the dynamism of cell systems. Therefore, we built a computational model of the yeast cell cycle to investigate how cells respond to ethanol stress. Simulations showed that ethanol stress or spindle damage arrests the cell cycle. Furthermore, the performance of higher and lower ethanol-tolerant strains in poststress recovery growth seems to be related to the cell cycle phase in which cells are stalled. However, two lncRNAs maintain the activity of the cell cycle even in yeast cells under these stresses by repressing specific cell cycle proteins. Finally, this model facilitates analyses of the yeast cell cycle for applied or basic science purposes.
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Affiliation(s)
- Lucas Cardoso Lázari
- Department of Parasitology, Institute of Biomedical Sciences, Sāo Paulo University (USP), Sao Paulo, Brazil
- Department of Bioprocess and Biotechnology, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Ivan Rodrigo Wolf
- Department of Bioprocess and Biotechnology, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Amanda Piveta Schnepper
- Department of Bioprocess and Biotechnology, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Guilherme Targino Valente
- Department of Bioprocess and Biotechnology, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- * E-mail: ,
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8
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Stress modulation as a means to improve yeasts for lignocellulose bioconversion. Appl Microbiol Biotechnol 2021; 105:4899-4918. [PMID: 34097119 DOI: 10.1007/s00253-021-11383-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/20/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022]
Abstract
The second-generation (2G) fermentation environment for lignocellulose conversion presents unique challenges to the fermentative organism that do not necessarily exist in other industrial fermentations. While extreme osmotic, heat, and nutrient starvation stresses are observed in sugar- and starch-based fermentation environments, additional pre-treatment-derived inhibitor stress, potentially exacerbated by stresses such as pH and product tolerance, exist in the 2G environment. Furthermore, in a consolidated bioprocessing (CBP) context, the organism is also challenged to secrete enzymes that may themselves lead to unfolded protein response and other stresses. This review will discuss responses of the yeast Saccharomyces cerevisiae to 2G-specific stresses and stress modulation strategies that can be followed to improve yeasts for this application. We also explore published -omics data and discuss relevant rational engineering, reverse engineering, and adaptation strategies, with the view of identifying genes or alleles that will make positive contributions to the overall robustness of 2G industrial strains. KEYPOINTS: • Stress tolerance is a key driver to successful application of yeast strains in biorefineries. • A wealth of data regarding stress responses has been gained through omics studies. • Integration of this knowledge could inform engineering of fit for purpose strains.
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9
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Doughty TW, Domenzain I, Millan-Oropeza A, Montini N, de Groot PA, Pereira R, Nielsen J, Henry C, Daran JMG, Siewers V, Morrissey JP. Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts. Nat Commun 2020; 11:2144. [PMID: 32358542 PMCID: PMC7195364 DOI: 10.1038/s41467-020-16073-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 04/09/2020] [Indexed: 11/20/2022] Open
Abstract
The Saccharomycotina subphylum (budding yeasts) spans 400 million years of evolution and includes species that thrive in diverse environments. To study niche-adaptation, we identify changes in gene expression in three divergent yeasts grown in the presence of various stressors. Duplicated and non-conserved genes are significantly more likely to respond to stress than genes that are conserved as single-copy orthologs. Next, we develop a sorting method that considers evolutionary origin and duplication timing to assign an evolutionary age to each gene. Subsequent analysis reveals that genes that emerged in recent evolutionary time are enriched amongst stress-responsive genes for each species. This gene expression pattern suggests that budding yeasts share a stress adaptation mechanism, whereby selective pressure leads to functionalization of young genes to improve growth in adverse conditions. Further characterization of young genes from species that thrive in harsh environments can inform the design of more robust strains for biotechnology. Fermentation parameters of industrial processes are often not the ideal growth conditions for industrial microbes. Here, the authors reveal that young genes are more responsive to environmental stress than ancient genes using a new gene age assignment method and provide targeted genes for metabolic engineering.
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Affiliation(s)
- Tyler W Doughty
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Iván Domenzain
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Aaron Millan-Oropeza
- Plateforme d'Analyse Protéomique Paris Sud-Ouest (PAPPSO), INRAE, MICALIS Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Noemi Montini
- School of Microbiology, Environmental Research Institute and APC Microbiome Ireland, University College Cork, Cork, T12YN60, Ireland
| | - Philip A de Groot
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Rui Pereira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Céline Henry
- Plateforme d'Analyse Protéomique Paris Sud-Ouest (PAPPSO), INRAE, MICALIS Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.
| | - John P Morrissey
- School of Microbiology, Environmental Research Institute and APC Microbiome Ireland, University College Cork, Cork, T12YN60, Ireland.
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10
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Integrated transcriptomic and proteomic analysis of the ethanol stress response in Saccharomyces cerevisiae Sc131. J Proteomics 2019; 203:103377. [DOI: 10.1016/j.jprot.2019.103377] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/12/2019] [Accepted: 05/12/2019] [Indexed: 12/29/2022]
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11
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Modulation of Fatty Acid Composition of Aspergillus oryzae in Response to Ethanol Stress. Microorganisms 2019; 7:microorganisms7060158. [PMID: 31159383 PMCID: PMC6616634 DOI: 10.3390/microorganisms7060158] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 11/16/2022] Open
Abstract
The koji mold Aspergillus oryzae is widely adopted for producing rice wine, wherein koji mold saccharifies rice starch and sake yeast ferments glucose to ethanol. During rice wine brewing, the accumulating ethanol becomes a major source of stress for A. oryzae, and there is a decline in hydrolysis efficiency. However, the protective mechanisms of A. oryzae against ethanol stress are poorly understood. In the present study, we demonstrate that ethanol adversity caused a significant inhibition of mycelium growth and conidia formation in A. oryzae, and this suppressive effect increased with ethanol concentration. Transmission electron microscopy analysis revealed that ethanol uptake triggered internal cellular perturbations, such as irregular nuclei and the aggregation of scattered vacuoles in A. oryzae cells. Metabolic analysis uncovered an increase in fatty acid unsaturation under high ethanol conditions, in which a large proportion of stearic acid was converted into linoleic acid, and the expression of related fatty acid desaturases was activated. Our results therefore improve the understanding of ethanol adaptation mechanisms in A. oryzae and offer target genes for ethanol tolerance enhancement via genetic engineering.
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12
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Cheng L, Zhang X, Zheng X, Wu Z, Weng P. RNA-seq transcriptomic analysis of green tea polyphenols regulation of differently expressed genes in Saccharomyces cerevisiae under ethanol stress. World J Microbiol Biotechnol 2019; 35:59. [PMID: 30915597 DOI: 10.1007/s11274-019-2639-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 03/19/2019] [Indexed: 11/24/2022]
Abstract
Saccharomyces cerevisiae has been widely used to produce alcoholic beverages and bio-fuels; however, its performance is remarkably compromised by the increased ethanol concentration during the fermentation process. In this study, RNA-sequence analysis was used to investigate the protective effect of green tea polyphenols (GTP) on S. cerevisiae cells from ethanol-induced damage. GO and KEGG analysis showed that to deal with the stress of ethanol, large amounts of genes related to cell wall, cell membrane, basic metabolism and redox regulation were significantly differentially expressed (P < 0.05), while these undesired changes could be partly relieved by administration of GTP, suggesting its potential to enhance the ethanol tolerance of S. cerevisiae. The present study provided a global view of the transcriptomic changes of S. cerevisiae in response to the accumulation of ethanol and the treatment of GTP, which might deepen our understanding about S. cerevisiae and the fermentation process, and thus benefit the development of the bioethanol production industry.
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Affiliation(s)
- Lu Cheng
- Department of Food Science, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Xin Zhang
- Department of Food Science and Engineering, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Xiaojie Zheng
- Department of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, People's Republic of China
| | - Zufang Wu
- Department of Food Science and Engineering, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Peifang Weng
- Department of Food Science and Engineering, Ningbo University, Ningbo, 315211, People's Republic of China.
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13
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Alvim MCT, Vital CE, Barros E, Vieira NM, da Silveira FA, Balbino TR, Diniz RHS, Brito AF, Bazzolli DMS, de Oliveira Ramos HJ, da Silveira WB. Ethanol stress responses of Kluyveromyces marxianus CCT 7735 revealed by proteomic and metabolomic analyses. Antonie van Leeuwenhoek 2019; 112:827-845. [DOI: 10.1007/s10482-018-01214-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
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14
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Di Gianvito P, Tesnière C, Suzzi G, Blondin B, Tofalo R. Different genetic responses to oenological conditions between a flocculent wine yeast and its FLO5 deleted strain: Insights from the transcriptome. Food Res Int 2018; 114:178-186. [DOI: 10.1016/j.foodres.2018.07.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/06/2018] [Accepted: 07/30/2018] [Indexed: 01/26/2023]
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15
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Miao Y, Xiong G, Li R, Wu Z, Zhang X, Weng P. Transcriptome profiling of Issatchenkia orientalis under ethanol stress. AMB Express 2018. [PMID: 29536208 PMCID: PMC5849708 DOI: 10.1186/s13568-018-0568-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Issatchenkia orientalis, a non-Saccharomyces yeast that can resist a wide variety of environmental stresses, has potential use in winemaking and bioethanol production. Little is known about gene expression or the physiology of I. orientalis under ethanol stress. In this study, high-throughput RNA sequencing was used to investigate the transcriptome profile of I. orientalis in response to ethanol. 502 gene transcripts were differentially expressed, of which 451 were more abundant, and 51 less abundant, in cells subjected to 4 h of ethanol stress (10% v/v). Annotation and statistical analyses suggest that multiple genes involved in ergosterol biosynthesis, trehalose metabolism, and stress response are differentially expressed under these conditions. The up-regulation of molecular chaperones HSP90 and HSP70, and also genes associated with the ubiquitin–proteasome proteolytic pathway suggests that ethanol stress may cause aggregation of misfolded proteins. Finally, ethanol stress in I. orientalis appears to have a nitrogen starvation effect, and many genes involved in nutrient uptake were up-regulated.
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16
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Li R, Xiong G, Yuan S, Wu Z, Miao Y, Weng P. Investigating the underlying mechanism of Saccharomyces cerevisiae in response to ethanol stress employing RNA-seq analysis. World J Microbiol Biotechnol 2017; 33:206. [PMID: 29101531 DOI: 10.1007/s11274-017-2376-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 10/29/2017] [Indexed: 11/26/2022]
Abstract
Saccharomyces cerevisiae has been widely used for wine fermentation and bio-fuels production. A S. cerevisiae strain Sc131 isolated from tropical fruit shows good fermentation properties and ethanol tolerance, exhibiting significant potential in Chinese bayberry wine fermentation. In this study, RNA-sequence and RT-qPCR was used to investigate the transcriptome profile of Sc131 in response to ethanol stress. Scanning Electron Microscopy were carried out to observe surface morphology of yeast cells. Totally, 937 genes were identified differential expressed, including 587 up-regulated and 350 down-regulated genes, after 4-h ethanol stress (10% v/v). Transcriptomic analysis revealed that, most genes involved in regulating filamentous growth or pseudohyphal growth were significantly up-regulated in response to ethanol stress. The complex protein quality control machineries, Hsp90/Hsp70 and Hsp104/Hsp70/Hsp40 based chaperone system combining with ubiquitin-proteasome proteolytic pathway were both activated to recognize and degrade misfolding proteins. Genes related to biosynthesis and metabolism of two well-known stress-responsive substances trehalose and ergosterol were generally up-regulated, while genes associated with amino acids biosynthesis and metabolism processes were differentially expressed. Moreover, thiamine was also important in response to ethanol stress. This research may promote the potential applications of Sc131 in the fermentation of Chinese bayberry wine.
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Affiliation(s)
- Ruoyun Li
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Guotong Xiong
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Shukun Yuan
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Zufang Wu
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China.
| | - Yingjie Miao
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Peifang Weng
- Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China
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17
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Transcriptome analysis of the thermotolerant yeast Kluyveromyces marxianus CCT 7735 under ethanol stress. Appl Microbiol Biotechnol 2017; 101:6969-6980. [DOI: 10.1007/s00253-017-8432-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/11/2017] [Accepted: 07/19/2017] [Indexed: 12/11/2022]
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