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Zuo F, Wu Y, Sun Y, Xie C, Tang Y. Mechanism of enhanced salt tolerance in Saccharomyces cerevisiae by CRZ1 overexpression. Sci Rep 2024; 14:22875. [PMID: 39358483 PMCID: PMC11447063 DOI: 10.1038/s41598-024-74174-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024] Open
Abstract
Achieving high-gravity fermentation in the industrial production of fuel ethanol, and enhancing the fermentation efficiency of high-salt raw materials, such as waste molasses, can significantly reduce wastewater output and process costs. Therefore, the development of hyperosmotic-tolerant industrial Saccharomyces cerevisiae strains, capable of resisting high-salt stress, offers both environmental and economic benefits. Our previous study highlighted the potential of CRZ1 overexpression as a strategy to improve the yeast strain's resistance to high-salt stress, however, the underlying molecular mechanisms remain unexplored. The fermentation capabilities of the CRZ1-overexpressing strain, KCR3, and its parental strain, KF7, were evaluated under condition of 1.25 M NaCl at 35 °C. Compared to KF7, KCR3 showed an 81% increase in glucose consumption (129.25 ± 0.83 g/L) and a 105% increase in ethanol production (47.59 ± 0.93 g/L), with a yield of 0.37 g/g. Comparative transcriptomic analysis showed that under high-salt stress, KCR3 exhibited significantly upregulated expression of genes associated with ion transport, stress response, gluconeogenesis, and the utilization of alternative carbon sources, while genes related to glycolysis and the biosynthesis of ribosomes, amino acids, and fatty acids were notably downregulated compared to KF7. Crz1 likely expands its influence by regulating the expression of numerous transcription factors, thereby impacting genes involved in multiple aspects of cellular function. The study revealed the regulatory mechanism of Crz1 under high-salt stress, thereby providing guidance for the construction of salt-tolerant strains.
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Affiliation(s)
- Furong Zuo
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, 610065, Sichuan, China
| | - Yajing Wu
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, 610065, Sichuan, China
| | - Yanqiu Sun
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, 610065, Sichuan, China
| | - Caiyun Xie
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China.
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, 610065, Sichuan, China.
- Engineering Research Center of Alternative Energy Materials and Devices, Ministry of Education, Chengdu, 610065, Sichuan, China.
| | - Yueqin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, 610065, Sichuan, China
- Engineering Research Center of Alternative Energy Materials and Devices, Ministry of Education, Chengdu, 610065, Sichuan, China
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Yuan B, Wang WB, Wang YT, Zhao XQ. Regulatory mechanisms underlying yeast chemical stress response and development of robust strains for bioproduction. Curr Opin Biotechnol 2024; 86:103072. [PMID: 38330874 DOI: 10.1016/j.copbio.2024.103072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/10/2024]
Abstract
Yeast is widely studied in producing biofuels and biochemicals using renewable biomass. Among various yeasts, Saccharomyces cerevisiae has been particularly recognized as an important yeast cell factory. However, economic bioproduction using S. cerevisiae is challenged by harsh environments during fermentation, among which inhibitory chemicals in the culture media or toxic products are common experiences. Understanding the stress-responsive mechanisms is conducive to developing robust yeast strains. Here, we review recent progress in mechanisms underlying yeast stress response, including regulation of cell wall integrity, membrane transport, antioxidative system, and gene transcription. We highlight epigenetic regulation of stress response and summarize manipulation of yeast stress tolerance for improved bioproduction. Prospects in the application of machine learning to improve production efficiency are also discussed.
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Affiliation(s)
- Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ya-Ting Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Liang Y, Gao S, Qi X, Valentovich LN, An Y. Progress in Gene Editing and Metabolic Regulation of Saccharomyces cerevisiae with CRISPR/Cas9 Tools. ACS Synth Biol 2024; 13:428-448. [PMID: 38326929 DOI: 10.1021/acssynbio.3c00685] [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] [Indexed: 02/09/2024]
Abstract
The CRISPR/Cas9 systems have been developed as tools for genetic engineering and metabolic engineering in various organisms. In this review, various aspects of CRISPR/Cas9 in Saccharomyces cerevisiae, from basic principles to practical applications, have been summarized. First, a comprehensive review has been conducted on the history of CRISPR/Cas9, successful cases of gene disruptions, and efficiencies of multiple DNA fragment insertions. Such advanced systems have accelerated the development of microbial engineering by reducing time and labor, and have enhanced the understanding of molecular genetics. Furthermore, the research progress of the CRISPR/Cas9-based systems in the production of high-value-added chemicals and the improvement of stress tolerance in S. cerevisiae have been summarized, which should have an important reference value for genetic and synthetic biology studies based on S. cerevisiae.
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Affiliation(s)
- Yaokun Liang
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
| | - Song Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
| | - Xianghui Qi
- School of Life Sciences, Guangzhou University, Guangdong 511370, China
| | - Leonid N Valentovich
- Institute of Microbiology, National Academy of Sciences of Belarus, Minsk 220072, Belarus
| | - Yingfeng An
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
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Wei Y, Qiu J, Han Z, Wang X, Zhang H, Hou X, Lv X, Mao X. Antifungal bio-coating of endotracheal tube built by overexpressing the MCP1 gene of Saccharomyces boulardii and employing hydrogel as a "house" to antagonize Candida albicans. Biomater Res 2023; 27:97. [PMID: 37798667 PMCID: PMC10557164 DOI: 10.1186/s40824-023-00443-1] [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: 06/21/2023] [Accepted: 10/01/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND For some ICU patients, an artificial airway must be established with an endotracheal tube, but Candida albicans can easily adhere to the tube surface and form a biofilm, leading to potentially life threatening fungal infections. Therefore, it is urgent to prevent and reduce C. albicans infections introduced by the endotracheal tube. However, there are few antifungal drugs effective against C. albicans, and each of these drugs may have adverse effects on human cells. Saccharomyces boulardii is regarded as an alternative strategy to inhibit the adhesion of C. albicans, but it is affected by environmental stress. We hypothesized that it is feasible to strengthen the antagonistic ability of S. boulardii via encapsulating and genetically modification. METHODS In this study, a bioactive material carrying the overexpressed MCP1 gene of Saccharomyces boulardii was constructed based on one-step photo-crosslinking. This material achieved spatial growth control of S. boulardii by encapsulating each S. boulardii cell within a hydrogel pore. The bioactive material was coated on an endotracheal tube and tested for its ability to inhibit the adhesion of C. albicans. Additionally, the material's antagonistic activity towards C. albicans was evaluated by detecting intracellular Adenosine-triphosphate content, reactive oxygen species level and the activity of antioxidative enzymes. Tissue invasion experiment was executed to further evaluate the anti-adhesion ability of S. boulardii bio-coating. RESULTS Encapsulating the overexpression of MCP1 by S. boulardii in hydrogel pores enhanced the viability of probiotics in the presence of high salt and oxidation stress. When used as the coating of an endotracheal tube, the S. boulardii bioactive material efficiently inhibited the adhesion of C. albicans by impairing the activities of superoxide dismutase and catalase and disturbing mitochondrial functions. In vivo, the S. boulardii bioactive material coating displayed good biocompatibility and reduced the host tissue invasion and virulence of C. albicans. CONCLUSIONS The integration of genetic modification and immobilization model breaks the bottleneck of previous application of microorganisms, and provides a new way to prevent fungal infections introduced by endotracheal tubes.
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Affiliation(s)
- Yunyun Wei
- School of Radiology, The Second Affiliated Hospital of Shandong First Medical University, Tai'an, 271016, China
- School of Radiology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, 271000, China
| | - Jianfeng Qiu
- School of Radiology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, 271000, China
- Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Ziqiang Han
- School of Laboratory Animal & Shandong Laboratory Animal Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250000, China
| | - Xuanyi Wang
- Department of Clinical Medicine, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Hui Zhang
- School of Laboratory Animal & Shandong Laboratory Animal Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250000, China
| | - Xinya Hou
- Department of Clinical Medicine, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Xiangwei Lv
- Department of Clinical Medicine, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Xiaolong Mao
- School of Laboratory Animal & Shandong Laboratory Animal Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250000, China.
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Huanca-Juarez J, Nascimento-Silva EA, Silva NH, Silva-Rocha R, Guazzaroni ME. Identification and functional analysis of novel protein-encoding sequences related to stress-resistance. Front Microbiol 2023; 14:1268315. [PMID: 37840709 PMCID: PMC10568318 DOI: 10.3389/fmicb.2023.1268315] [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: 07/27/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
Currently, industrial bioproducts are less competitive than chemically produced goods due to the shortcomings of conventional microbial hosts. Thus, is essential developing robust bacteria for improved cell tolerance to process-specific parameters. In this context, metagenomic approaches from extreme environments can provide useful biological parts to improve bacterial robustness. Here, in order to build genetic constructs that increase bacterial resistance to diverse stress conditions, we recovered novel protein-encoding sequences related to stress-resistance from metagenomic databases using an in silico approach based on Hidden-Markov-Model profiles. For this purpose, we used metagenomic shotgun sequencing data from microbial communities of extreme environments to identify genes encoding chaperones and other proteins that confer resistance to stress conditions. We identified and characterized 10 novel protein-encoding sequences related to the DNA-binding protein HU, the ATP-dependent protease ClpP, and the chaperone protein DnaJ. By expressing these genes in Escherichia coli under several stress conditions (including high temperature, acidity, oxidative and osmotic stress, and UV radiation), we identified five genes conferring resistance to at least two stress conditions when expressed in E. coli. Moreover, one of the identified HU coding-genes which was retrieved from an acidic soil metagenome increased E. coli tolerance to four different stress conditions, implying its suitability for the construction of a synthetic circuit directed to expand broad bacterial resistance.
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Affiliation(s)
- Joshelin Huanca-Juarez
- Department of Cell and Molecular Biology, Ribeirão Preto School of Medicine (FMRP) – University of São Paulo (USP), São Paulo, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP) – University of São Paulo (USP), São Paulo, Brazil
| | - Edson Alexandre Nascimento-Silva
- Department of Cell and Molecular Biology, Ribeirão Preto School of Medicine (FMRP) – University of São Paulo (USP), São Paulo, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP) – University of São Paulo (USP), São Paulo, Brazil
| | - Ninna Hirata Silva
- Department of Cell and Molecular Biology, Ribeirão Preto School of Medicine (FMRP) – University of São Paulo (USP), São Paulo, Brazil
| | | | - María-Eugenia Guazzaroni
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP) – University of São Paulo (USP), São Paulo, Brazil
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Wang M, Qiao J, Sheng Y, Wei J, Cui H, Li X, Yue G. Bioconversion of corn fiber to bioethanol: Status and perspectives. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 157:256-268. [PMID: 36577277 DOI: 10.1016/j.wasman.2022.12.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/17/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Due to the rising demand for green energy, bioethanol has attracted increasing attention from academia and industry. Limited by the bottleneck of bioethanol yield in traditional corn starch dry milling processes, an increasing number of studies focus on fully utilizing all corn ingredients, especially kernel fiber, to further improve the bioethanol yield. This mini-review addresses the technological challenges and opportunities on the way to achieving the efficient conversion of corn fiber. Significant advances during the review period include the detailed characterization of different forms of corn kernel fiber and the development of off-line and in-situ conversion strategies. Lessons from cellulosic ethanol technologies offer new ways to utilize corn fiber in traditional processes. However, the commercialization of corn kernel fiber conversion may be hampered by enzyme cost, conversion efficiency, and overall process economics. Thus, future studies should address these technical limitations.
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Affiliation(s)
- Minghui Wang
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
| | - Jie Qiao
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
| | - Yijie Sheng
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
| | - Junnan Wei
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China
| | - Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Xiujuan Li
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China.
| | - Guojun Yue
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210009, People's Republic of China; SDIC Biotech Investment Co., Ltd., Beijing 100034, China
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Tadioto V, Deoti JR, Müller C, de Souza BR, Fogolari O, Purificação M, Giehl A, Deoti L, Lucaroni AC, Matsushika A, Treichel H, Stambuk BU, Alves Junior SL. Prospecting and engineering yeasts for ethanol production under inhibitory conditions: an experimental design analysis. Bioprocess Biosyst Eng 2022:10.1007/s00449-022-02812-x. [DOI: 10.1007/s00449-022-02812-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/09/2022] [Indexed: 11/25/2022]
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