1
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Xiong L, Wang YT, Zhou MH, Takagi H, Qin J, Zhao XQ. Overexpression of arginase gene CAR1 renders yeast Saccharomyces cerevisiae acetic acid tolerance. Synth Syst Biotechnol 2024; 9:723-732. [PMID: 38882181 PMCID: PMC11178985 DOI: 10.1016/j.synbio.2024.05.013] [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: 02/29/2024] [Revised: 05/12/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
Acetic acid is a common inhibitor present in lignocellulose hydrolysate, which inhibits the ethanol production by yeast strains. Therefore, the cellulosic ethanol industry requires yeast strains that can tolerate acetic acid stress. Here we demonstrate that overexpressing a yeast native arginase-encoding gene, CAR1, renders Saccharomyces cerevisiae acetic acid tolerance. Specifically, ethanol yield increased by 27.3% in the CAR1-overexpressing strain compared to the control strain under 5.0 g/L acetic acid stress. The global intracellular amino acid level and compositions were further analyzed, and we found that CAR1 overexpression reduced the total amino acid content in response to acetic acid stress. Moreover, the CAR1 overexpressing strain showed increased ATP level and improved cell membrane integrity. Notably, we demonstrated that the effect of CAR1 overexpression was independent of the spermidine and proline metabolism, which indicates novel mechanisms for enhancing yeast stress tolerance. Our studies also suggest that CAR1 is a novel genetic element to be used in synthetic biology of yeast for efficient production of fuel ethanol.
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Affiliation(s)
- Liang Xiong
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Ya-Ting Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ming-Hai Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hiroshi Takagi
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Jiufu Qin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Gao S, Liao Y, He H, Yang H, Yang X, Xu S, Wang X, Chen K, Ouyang P. Advance of tolerance engineering on microbes for industrial production. Synth Syst Biotechnol 2023; 8:697-707. [PMID: 38025766 PMCID: PMC10656194 DOI: 10.1016/j.synbio.2023.10.004] [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: 08/27/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Industrial microbes have become the core of biological manufacturing, which utilized as the cell factory for production of plenty of chemicals, fuels and medicine. However, the challenge that the extreme stress conditions exist in production is unavoidable for cell factory. Consequently, to enhance robustness of the chassis cell lays the foundation for development of bio-manufacturing. Currently, the researches on cell tolerance covered various aspects, involving reshaping regulatory network, cell membrane modification and other stress response. In fact, the strategies employed to improve cell robustness could be summarized into two directions, irrational engineering and rational engineering. In this review, the metabolic engineering technologies on enhancement of microbe tolerance to industrial conditions are summarized. Meanwhile, the novel thoughts emerged with the development of biological instruments and synthetic biology are discussed.
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Affiliation(s)
- Siyuan Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Yang Liao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Hao He
- Petrochemical Research Institute of PetroChina Co. Ltd., Beijing, 102206, China
| | - Huiling Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xuewei Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
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Chen Y, Yang Y, Cai W, Zeng J, Liu N, Wan Y, Fu G. Research progress of anti-environmental factor stress mechanism and anti-stress tolerance way of Saccharomyces cerevisiae during the brewing process. Crit Rev Food Sci Nutr 2023; 63:12308-12323. [PMID: 35848108 DOI: 10.1080/10408398.2022.2101090] [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: 11/03/2022]
Abstract
Saccharomyces cerevisiae plays a decisive role in the brewing of alcohol products, and the ideal growth and fermentation characteristics can give the pure flavor of alcohol products. However, S. cerevisiae can be affected profoundly by environmental factors during the brewing process, which have negative effects on the growth and fermentation characteristics of S. cerevisiae, and seriously hindered the development of brewing industry. Therefore, we summarized the environmental stress factors (ethanol, organic acids, temperature and osmotic pressure) that affect S. cerevisiae during the brewing process. Their impact mechanisms and the metabolic adaption of S. cerevisiae in response to these stress factors. Of note, S. cerevisiae can increase the ability to resist stress factors by changing the cell membrane components, expressing transcriptional regulatory factors, activating the anti-stress metabolic pathway and enhancing ROS scavenging ability. Meantime, the strategies and methods to improve the stress- tolerant ability of S. cerevisiae during the brewing process were also introduced. Compared with the addition of exogenous anti-stress substances, mutation breeding and protoplast fusion, it appears that adaptive evolution and genetic engineering are able to generate ideal environmental stress tolerance strains of S. cerevisiae and are more in line with the needs of the current brewing industry.
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Affiliation(s)
- Yanru Chen
- State Key Laboratory of Food Science and Technology & College of Food Science and Technology & International Institute of Food Innovation, Nanchang University, Nanchang, PR China
| | - Yili Yang
- China Regional Research Centre, International Centre of Genetic Engineering & Biotechnology, Taizhou, PR China
| | - Wenqin Cai
- State Key Laboratory of Food Science and Technology & College of Food Science and Technology & International Institute of Food Innovation, Nanchang University, Nanchang, PR China
| | - Jiali Zeng
- State Key Laboratory of Food Science and Technology & College of Food Science and Technology & International Institute of Food Innovation, Nanchang University, Nanchang, PR China
| | - Na Liu
- State Key Laboratory of Food Science and Technology & College of Food Science and Technology & International Institute of Food Innovation, Nanchang University, Nanchang, PR China
| | - Yin Wan
- State Key Laboratory of Food Science and Technology & College of Food Science and Technology & International Institute of Food Innovation, Nanchang University, Nanchang, PR China
| | - Guiming Fu
- State Key Laboratory of Food Science and Technology & College of Food Science and Technology & International Institute of Food Innovation, Nanchang University, Nanchang, PR China
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Data mining of Saccharomyces cerevisiae mutants engineered for increased tolerance towards inhibitors in lignocellulosic hydrolysates. Biotechnol Adv 2022; 57:107947. [DOI: 10.1016/j.biotechadv.2022.107947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 12/15/2022]
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Metabolic changes of Issatchenkia orientalis under acetic acid stress by transcriptome profile using RNA-sequencing. Int Microbiol 2021; 25:417-426. [PMID: 34811604 DOI: 10.1007/s10123-021-00217-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/21/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022]
Abstract
Issatchenkia orientalis (I. orientalis) is tolerant to various environmental stresses especially acetic acid stress in wine making. However, limited literature is available on the transcriptome profile of I. orientalis under acetic acid stress. RNA-sequence was used to investigate the metabolic changes due to underlying I. orientalis 166 (Io 166) tolerant to acetic acid. Transcriptomic analyses showed that genes involved in ergosterol biosynthesis are differentially expressed under acetic acid stress. Genes associated with ribosome function were downregulated, while energy metabolism-related genes were upregulated. Moreover, Hsp70/Hsp90 and related molecular chaperones were upregulated to recognize and degrade misfolded proteins. Compared to Saccharomyces cerevisiae, transcriptomic changes of Io 166 showed many similarities under acetic acid stress. There were significant upregulation of genes in ergosterol biosynthesis and for the application of wine production.
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Li S, Wang L, Wang N, Cong W. Combining Genome Shuffling with Streptomycin Resistance to Improve Poly-γ-L-diaminobutanoic Acid Production in Bacillus pumilus. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0320-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Wawro A. Improvement of Acetic Acid Tolerance in Saccharomyces cerevisiae by Novel Genome Shuffling. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821020198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Cheng Y, Zhu H, Du Z, Guo X, Zhou C, Wang Z, He X. Eukaryotic translation factor eIF5A contributes to acetic acid tolerance in Saccharomyces cerevisiae via transcriptional factor Ume6p. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:38. [PMID: 33557922 PMCID: PMC7869214 DOI: 10.1186/s13068-021-01885-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/16/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Saccharomyces cerevisiae is well-known as an ideal model system for basic research and important industrial microorganism for biotechnological applications. Acetic acid is an important growth inhibitor that has deleterious effects on both the growth and fermentation performance of yeast cells. Comprehensive understanding of the mechanisms underlying S. cerevisiae adaptive response to acetic acid is always a focus and indispensable for development of robust industrial strains. eIF5A is a specific translation factor that is especially required for the formation of peptide bond between certain residues including proline regarded as poor substrates for slow peptide bond formation. Decrease of eIF5A activity resulted in temperature-sensitive phenotype of yeast, while up-regulation of eIF5A protected transgenic Arabidopsis against high temperature, oxidative or osmotic stress. However, the exact roles and functional mechanisms of eIF5A in stress response are as yet largely unknown. RESULTS In this research, we compared cell growth between the eIF5A overexpressing and the control S. cerevisiae strains under various stressed conditions. Improvement of acetic acid tolerance by enhanced eIF5A activity was observed all in spot assay, growth profiles and survival assay. eIF5A prompts the synthesis of Ume6p, a pleiotropic transcriptional factor containing polyproline motifs, mainly in a translational related way. As a consequence, BEM4, BUD21 and IME4, the direct targets of Ume6p, were up-regulated in eIF5A overexpressing strain, especially under acetic acid stress. Overexpression of UME6 results in similar profiles of cell growth and target genes transcription to eIF5A overexpression, confirming the role of Ume6p and its association between eIF5A and acetic acid tolerance. CONCLUSION Translation factor eIF5A protects yeast cells against acetic acid challenge by the eIF5A-Ume6p-Bud21p/Ime4p/Bem4p axles, which provides new insights into the molecular mechanisms underlying the adaptive response and tolerance to acetic acid in S. cerevisiae and novel targets for construction of robust industrial strains.
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Affiliation(s)
- Yanfei Cheng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhengda Du
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuena Guo
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chenyao Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaoyue Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiuping He
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Li S, Wang L, Wang N. Enhanced poly-γ-L-diaminobutanoic acid production in Bacillus pumilus by combining genome shuffling with multiple antibiotic-resistance. J Ind Microbiol Biotechnol 2020; 47:1141-1154. [PMID: 32990840 DOI: 10.1007/s10295-020-02315-2] [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: 06/09/2020] [Accepted: 09/21/2020] [Indexed: 11/26/2022]
Abstract
A breeding approach combining genome shuffling with multiple antibiotic-resistance including gentamicin, rifampin and lincomycin, was developed in this research to improve the poly-γ-L-diaminobutanoic acid (γ-PAB) production in Bacillus pumilus LS-1. By this unique strategy, recombinants from the third round of genome shuffling could tolerate higher concentration of compound antibiotics and exhibited higher γ-PAB production as 392.4 mg/L in shake-flask fermentation, tenfold over the parent. In batch fermentation, B. pumilus GS3-M7 could produce γ-PAB as high as 2316.4 mg/L in two days, 5.4-fold higher than the control, which was the highest productivity ever reported. In addition, the optimal pH in B. pumilus for γ-PAB synthesis was decreased after ARTP mutagenesis and protoplast fusion, because the lower pH environment is favorable for accumulation of intracellular ATP. Some key enzymes in GS3-M7 showed higher activities than those in the parent, suggesting a greater flux to TCA circle and DAP pathway, which was a reason for enhanced γ-PAB production.
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Affiliation(s)
- Shu Li
- Marine College, Shandong University, Weihai, 264209, Shandong, China.
| | - Liang Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Nan Wang
- Testing Center, Weihai Food and Drug Administration, Weihai, 264210, China
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10
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Applications and research advance of genome shuffling for industrial microbial strains improvement. World J Microbiol Biotechnol 2020; 36:158. [PMID: 32968940 DOI: 10.1007/s11274-020-02936-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/15/2020] [Indexed: 12/25/2022]
Abstract
Genome shuffling, an efficient and practical strain improvement technology via recursive protoplasts fusion, can break through the limits of species even genus to accelerate the directed evolution of microbial strains, without requiring the comprehensively cognized genetic background and operable genetic system. Hence this technology has been widely used for many important strains to obtain the desirable industrial phenotypes. In this review, we introduce the procedure of genome shuffling, discuss the new aid strategies of genome shuffling, summarize the applications of genome shuffling for increasing metabolite yield, improving strain tolerance, enhancing substrate utilization, and put forward the outlook to the future development of this technology.
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Sharma S, Arora A. Tracking strategic developments for conferring xylose utilization/fermentation by Saccharomyces cerevisiae. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01590-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Abstract
Purpose
Efficient ethanol production through lignocellulosic biomass hydrolysates could solve energy crisis as it is economically sustainable and ecofriendly. Saccharomyces cerevisiae is the work horse for lignocellulosic bioethanol production at industrial level. But its inability to ferment and utilize xylose limits the overall efficacy of the process.
Method
Data for the review was selected using different sources, such as Biofuels digest, Statista, International energy agency (IEA). Google scholar was used as a search engine to search literature for yeast metabolic engineering approaches. Keywords used were metabolic engineering of yeast for bioethanol production from lignocellulosic biomass.
Result
Through these approaches, interconnected pathways can be targeted randomly. Moreover, the improved strains genetic makeup can help us understand the mechanisms involved for this purpose.
Conclusion
This review discusses all possible approaches for metabolic engineering of yeast. These approaches may reveal unknown hidden mechanisms and construct ways for the researchers to produce novel and modified strains.
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Stojiljkovic M, Foulquié-Moreno MR, Thevelein JM. Polygenic analysis of very high acetic acid tolerance in the yeast Saccharomyces cerevisiae reveals a complex genetic background and several new causative alleles. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:126. [PMID: 32695222 PMCID: PMC7364526 DOI: 10.1186/s13068-020-01761-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND High acetic acid tolerance is of major importance in industrial yeast strains used for second-generation bioethanol production, because of the high acetic acid content of lignocellulose hydrolysates. It is also important in first-generation starch hydrolysates and in sourdoughs containing significant acetic acid levels. We have previously identified snf4 E269* as a causative allele in strain MS164 obtained after whole-genome (WG) transformation and selection for improved acetic acid tolerance. RESULTS We have now performed polygenic analysis with the same WG transformant MS164 to identify novel causative alleles interacting with snf4 E269* to further enhance acetic acid tolerance, from a range of 0.8-1.2% acetic acid at pH 4.7, to previously unmatched levels for Saccharomyces cerevisiae. For that purpose, we crossed the WG transformant with strain 16D, a previously identified strain displaying very high acetic acid tolerance. Quantitative trait locus (QTL) mapping with pooled-segregant whole-genome sequence analysis identified four major and two minor QTLs. In addition to confirmation of snf4 E269* in QTL1, we identified six other genes linked to very high acetic acid tolerance, TRT2, MET4, IRA2 and RTG1 and a combination of MSH2 and HAL9, some of which have never been connected previously to acetic acid tolerance. Several of these genes appear to be wild-type alleles that complement defective alleles present in the other parent strain. CONCLUSIONS The presence of several novel causative genes highlights the distinct genetic basis and the strong genetic background dependency of very high acetic acid tolerance. Our results suggest that elimination of inferior mutant alleles might be equally important for reaching very high acetic acid tolerance as introduction of rare superior alleles. The superior alleles of MET4 and RTG1 might be useful for further improvement of acetic acid tolerance in specific industrial yeast strains.
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Affiliation(s)
- Marija Stojiljkovic
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
| | - María R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
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Guan N, Liu L. Microbial response to acid stress: mechanisms and applications. Appl Microbiol Biotechnol 2020; 104:51-65. [PMID: 31773206 PMCID: PMC6942593 DOI: 10.1007/s00253-019-10226-1] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/23/2019] [Accepted: 10/27/2019] [Indexed: 02/07/2023]
Abstract
Microorganisms encounter acid stress during multiple bioprocesses. Microbial species have therefore developed a variety of resistance mechanisms. The damage caused by acidic environments is mitigated through the maintenance of pH homeostasis, cell membrane integrity and fluidity, metabolic regulation, and macromolecule repair. The acid tolerance mechanisms can be used to protect probiotics against gastric acids during the process of food intake, and can enhance the biosynthesis of organic acids. The combination of systems and synthetic biology technologies offers new and wide prospects for the industrial applications of microbial acid tolerance mechanisms. In this review, we summarize acid stress response mechanisms of microbial cells, illustrate the application of microbial acid tolerance in industry, and prospect the introduction of systems and synthetic biology to further explore the acid tolerance mechanisms and construct a microbial cell factory for valuable chemicals.
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Affiliation(s)
- Ningzi Guan
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai, 200241, China.
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
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14
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Yang H, Zong X, Xu Y, Zeng Y, Zhao H. Wheat gluten hydrolysates and their fractions improve multiple stress tolerance and ethanol fermentation performances of yeast during very high-gravity fermentation. INDUSTRIAL CROPS AND PRODUCTS 2019; 128:282-289. [DOI: 10.1016/j.indcrop.2018.11.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
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15
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Overexpression of RCK1 improves acetic acid tolerance in Saccharomyces cerevisiae. J Biotechnol 2019; 292:1-4. [PMID: 30615911 DOI: 10.1016/j.jbiotec.2018.12.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/06/2018] [Accepted: 12/26/2018] [Indexed: 11/23/2022]
Abstract
Mixed sugars derived from lignocellulosic biomass can be converted into biofuels and chemicals by engineered microorganisms, but toxic fermentation inhibitors produced from harsh depolymerization processes of lignocellulosic biomass pose a critical challenge for economic production of biofuels and chemicals. Unlike other fermentation inhibitors generated from sugar degradation, acetic acid is inevitably produced from acetylated hemicellulose, and its concentrations in cellulosic hydrolysates are substantially higher than other fermentation inhibitors. The aim of this study was to identify novel genetic perturbations for improved acetic acid tolerance in Saccharomyces cerevisiae. Through a genomic library-based approach, we identified an overexpression gene target RCK1 coding for a protein kinase involved in oxidative stress. Overexpression of RCK1 significantly improved glucose and xylose fermentation under acetic acid stress conditions. Specifically, the RCK1-overexpressing strain exhibited a two-fold higher specific ethanol productivity than the control strain in glucose fermentation under the presence of acetic acid. Interestingly, the engineered S. cerevisiae overexpressing RCK1 showed 40% lower intracellular reactive oxygen species (ROS) levels as compared to the parental strain when the strains were exposed to acetic acid, suggesting that RCK1 overexpression might play a role in reducing the oxidative stress caused by acetic acid.
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16
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Yang H, Zong X, Xu Y, Zeng Y, Zhao H. Improvement of Multiple-Stress Tolerance and Ethanol Production in Yeast during Very-High-Gravity Fermentation by Supplementation of Wheat-Gluten Hydrolysates and Their Ultrafiltration Fractions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:10233-10241. [PMID: 30203970 DOI: 10.1021/acs.jafc.8b04196] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The effects of wheat-gluten hydrolysates (WGH) and their ultrafiltration fractions on multiple-stress tolerance and ethanol production in yeast during very-high-gravity (VHG) fermentation were examined. The results showed that WGH and WHG-ultrafiltration-fraction supplementations could significantly enhance the growth and viability of yeast and further improve the tolerance of yeast to osmotic stress and ethanol stress. The addition of MW < 1 kDa fractions led to 51.08 and 21.70% enhancements in cell-membrane integrity, 30.74 and 10.43% decreases in intracellular ROS accumulation, and 34.18 and 26.16% increases in mitochondrial membrane potential (ΔΨm) in yeast under osmotic stress and ethanol stress, respectively. Moreover, WGH and WHG-ultrafiltration-fraction supplementations also improved the growth and ethanol production of yeast during VHG fermentation, and supplementation with the <1 kDa fraction resulted in a maximum biomass of 16.47 g/L dry cell and an ethanol content of 18.50% (v/v) after VHG fermentation.
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Affiliation(s)
- Huirong Yang
- School of Food Science and Engineering , South China University of Technology , Guangzhou 510640 , PR China
| | - Xuyan Zong
- School of Biotechnology , Sichuan University of Science and Engineering , Zigong 643000 , PR China
| | - Yingchao Xu
- School of Food Science and Engineering , South China University of Technology , Guangzhou 510640 , PR China
| | - Yingjie Zeng
- School of Food Science and Engineering , South China University of Technology , Guangzhou 510640 , PR China
| | - Haifeng Zhao
- School of Food Science and Engineering , South China University of Technology , Guangzhou 510640 , PR China
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17
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Inactivation of the transcription factor mig1 (YGL035C) in Saccharomyces cerevisiae improves tolerance towards monocarboxylic weak acids: acetic, formic and levulinic acid. ACTA ACUST UNITED AC 2018; 45:735-751. [DOI: 10.1007/s10295-018-2053-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
Abstract
Abstract
Toxic concentrations of monocarboxylic weak acids present in lignocellulosic hydrolyzates affect cell integrity and fermentative performance of Saccharomyces cerevisiae. In this work, we report the deletion of the general catabolite repressor Mig1p as a strategy to improve the tolerance of S. cerevisiae towards inhibitory concentrations of acetic, formic or levulinic acid. In contrast with the wt yeast, where the growth and ethanol production were ceased in presence of acetic acid 5 g/L or formic acid 1.75 g/L (initial pH not adjusted), the m9 strain (Δmig1::kan) produced 4.06 ± 0.14 and 3.87 ± 0.06 g/L of ethanol, respectively. Also, m9 strain tolerated a higher concentration of 12.5 g/L acetic acid (initial pH adjusted to 4.5) without affecting its fermentative performance. Moreover, m9 strain produced 33% less acetic acid and 50–70% less glycerol in presence of weak acids, and consumed acetate and formate as carbon sources under aerobic conditions. Our results show that the deletion of Mig1p provides a single gene deletion target for improving the acid tolerance of yeast strains significantly.
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Palma M, Guerreiro JF, Sá-Correia I. Adaptive Response and Tolerance to Acetic Acid in Saccharomyces cerevisiae and Zygosaccharomyces bailii: A Physiological Genomics Perspective. Front Microbiol 2018. [PMID: 29515554 PMCID: PMC5826360 DOI: 10.3389/fmicb.2018.00274] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Acetic acid is an important microbial growth inhibitor in the food industry; it is used as a preservative in foods and beverages and is produced during normal yeast metabolism in biotechnological processes. Acetic acid is also a major inhibitory compound present in lignocellulosic hydrolysates affecting the use of this promising carbon source for sustainable bioprocesses. Although the molecular mechanisms underlying Saccharomyces cerevisiae response and adaptation to acetic acid have been studied for years, only recently they have been examined in more detail in Zygosaccharomyces bailii. However, due to its remarkable tolerance to acetic acid and other weak acids this yeast species is a major threat in the spoilage of acidic foods and beverages and considered as an interesting alternative cell factory in Biotechnology. This review paper emphasizes genome-wide strategies that are providing global insights into the molecular targets, signaling pathways and mechanisms behind S. cerevisiae and Z. bailii tolerance to acetic acid, and extends this information to other weak acids whenever relevant. Such comprehensive perspective and the knowledge gathered in these two yeast species allowed the identification of candidate molecular targets, either for the design of effective strategies to overcome yeast spoilage in acidic foods and beverages, or for the rational genome engineering to construct more robust industrial strains. Examples of successful applications are provided.
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Affiliation(s)
- Margarida Palma
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Joana F Guerreiro
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Inokuma K, Iwamoto R, Bamba T, Hasunuma T, Kondo A. Improvement of Xylose Fermentation Ability under Heat and Acid Co-Stress in Saccharomyces cerevisiae Using Genome Shuffling Technique. Front Bioeng Biotechnol 2017; 5:81. [PMID: 29326929 PMCID: PMC5742482 DOI: 10.3389/fbioe.2017.00081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/08/2017] [Indexed: 12/26/2022] Open
Abstract
Xylose-assimilating yeasts with tolerance to both fermentation inhibitors (such as weak organic acids) and high temperature are required for cost-effective simultaneous saccharification and cofermentation (SSCF) of lignocellulosic materials. Here, we demonstrate the construction of a novel xylose-utilizing Saccharomyces cerevisiae strain with improved fermentation ability under heat and acid co-stress using the drug resistance marker-aided genome shuffling technique. The mutagenized genome pools derived from xylose-utilizing diploid yeasts with thermotolerance or acid tolerance were shuffled by sporulation and mating. The shuffled strains were then subjected to screening under co-stress conditions of heat and acids, and the hybrid strain Hyb-8 was isolated. The hybrid strain displayed enhanced xylose fermentation ability in comparison to both parental strains under co-stress conditions of heat and acids. Hyb-8 consumed 33.1 ± 0.6 g/L xylose and produced 11.1 ± 0.4 g/L ethanol after 72 h of fermentation at 38°C with 20 mM acetic acid and 15 mM formic acid. We also performed transcriptomic analysis of the hybrid strain and its parental strains to screen for key genes for multiple stress tolerances. We found that 13 genes, including 5 associated with cellular transition metal ion homeostasis, were significantly upregulated in Hyb-8 compared to levels in both parental strains under co-stress conditions. The hybrid strain Hyb-8 has strong potential for cost-effective SSCF of lignocellulosic materials. Moreover, the transcriptome data gathered in this study will be useful for understanding the mechanisms of multiple tolerance to high temperature and acids in yeast and facilitate the development of robust yeast strains for SSCF.
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Affiliation(s)
- Kentaro Inokuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Ryo Iwamoto
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Takahiro Bamba
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Biomass Engineering Program, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Japan
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Zhang M, Zhang K, Mehmood MA, Zhao ZK, Bai F, Zhao X. Deletion of acetate transporter gene ADY2 improved tolerance of Saccharomyces cerevisiae against multiple stresses and enhanced ethanol production in the presence of acetic acid. BIORESOURCE TECHNOLOGY 2017; 245:1461-1468. [PMID: 28606754 DOI: 10.1016/j.biortech.2017.05.191] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/27/2017] [Accepted: 05/29/2017] [Indexed: 05/24/2023]
Abstract
The aim of this work was to study the effects of deleting acetate transporter gene ADY2 on growth and fermentation of Saccharomyces cerevisiae in the presence of inhibitors. Comparative transcriptome analysis revealed that three genes encoding plasma membrane carboxylic acid transporters, especially ADY2, were significantly downregulated under the zinc sulfate addition condition in the presence of acetic acid stress, and the deletion of ADY2 improved growth of S. cerevisiae under acetic acid, ethanol and hydrogen peroxide stresses. Consistently, a concomitant increase in ethanol production by 14.7% in the presence of 3.6g/L acetic acid was observed in the ADY2 deletion mutant of S. cerevisiae BY4741. Decreased intracellular acetic acid, ROS accumulation, and plasma membrane permeability were observed in the ADY2 deletion mutant. These findings would be useful for developing robust yeast strains for efficient ethanol production.
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Affiliation(s)
- Mingming Zhang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Keyu Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Muhammad Aamer Mehmood
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Bioenergy Research Centre, Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Zongbao Kent Zhao
- Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fengwu Bai
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Seong YJ, Lee HJ, Lee JE, Kim S, Lee DY, Kim KH, Park YC. Physiological and Metabolomic Analysis ofIssatchenkia orientalisMTY1 With Multiple Tolerance for Cellulosic Bioethanol Production. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/23/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Yeong-Je Seong
- Department of Bio and Fermentation Convergence Technology and BK21 Plus Program, Kookmin University; Seoul 136-702 Korea
| | - Hye-Jin Lee
- Department of Bio and Fermentation Convergence Technology and BK21 Plus Program, Kookmin University; Seoul 136-702 Korea
| | - Jung-Eun Lee
- Department of Bio and Fermentation Convergence Technology and BK21 Plus Program, Kookmin University; Seoul 136-702 Korea
| | - Sooah Kim
- Department of Biotechnology, Graduate School, Korea University; Seoul 136-713 Korea
| | - Do Yup Lee
- Department of Bio and Fermentation Convergence Technology and BK21 Plus Program, Kookmin University; Seoul 136-702 Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University; Seoul 136-713 Korea
| | - Yong-Cheol Park
- Department of Bio and Fermentation Convergence Technology and BK21 Plus Program, Kookmin University; Seoul 136-702 Korea
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Deparis Q, Claes A, Foulquié-Moreno MR, Thevelein JM. Engineering tolerance to industrially relevant stress factors in yeast cell factories. FEMS Yeast Res 2017; 17:3861662. [PMID: 28586408 PMCID: PMC5812522 DOI: 10.1093/femsyr/fox036] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/04/2017] [Indexed: 01/01/2023] Open
Abstract
The main focus in development of yeast cell factories has generally been on establishing optimal activity of heterologous pathways and further metabolic engineering of the host strain to maximize product yield and titer. Adequate stress tolerance of the host strain has turned out to be another major challenge for obtaining economically viable performance in industrial production. Although general robustness is a universal requirement for industrial microorganisms, production of novel compounds using artificial metabolic pathways presents additional challenges. Many of the bio-based compounds desirable for production by cell factories are highly toxic to the host cells in the titers required for economic viability. Artificial metabolic pathways also turn out to be much more sensitive to stress factors than endogenous pathways, likely because regulation of the latter has been optimized in evolution in myriads of environmental conditions. We discuss different environmental and metabolic stress factors with high relevance for industrial utilization of yeast cell factories and the experimental approaches used to engineer higher stress tolerance. Improving stress tolerance in a predictable manner in yeast cell factories should facilitate their widespread utilization in the bio-based economy and extend the range of products successfully produced in large scale in a sustainable and economically profitable way.
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Affiliation(s)
- Quinten Deparis
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Arne Claes
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Maria R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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Nasution O, Lee YM, Kim E, Lee Y, Kim W, Choi W. Overexpression ofOLE1enhances stress tolerance and constitutively activates the MAPK HOG pathway inSaccharomyces cerevisiae. Biotechnol Bioeng 2016; 114:620-631. [DOI: 10.1002/bit.26093] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 07/26/2016] [Accepted: 08/28/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Olviyani Nasution
- Interdisciplinary Program of EcoCreative; The Graduate School; Ewha Womans University; Seoul 03766 Korea
| | - Young Mi Lee
- Department of Pharmacology; School of Medicine; Ajou University; Suwon Korea
| | - Eunjung Kim
- Department of Pharmacology; School of Medicine; Ajou University; Suwon Korea
| | - Yeji Lee
- Department of Life Sciences; College of Natural Sciences, Ewha Womans University; Seoul Korea
| | - Wankee Kim
- Department of Pharmacology; School of Medicine; Ajou University; Suwon Korea
| | - Wonja Choi
- Interdisciplinary Program of EcoCreative; The Graduate School; Ewha Womans University; Seoul 03766 Korea
- Department of Life Sciences; College of Natural Sciences, Ewha Womans University; Seoul Korea
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Lee Y, Nasution O, Lee YM, Kim E, Choi W, Kim W. Overexpression of PMA1 enhances tolerance to various types of stress and constitutively activates the SAPK pathways in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2016; 101:229-239. [PMID: 27730338 DOI: 10.1007/s00253-016-7898-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 09/10/2016] [Accepted: 09/25/2016] [Indexed: 11/26/2022]
Abstract
PMA1 encodes a transmembrane polypeptide that functions to pump protons out of the cell. Ectopic PMA1 overexpression in Saccharomyces cerevisiae enhances tolerance to weak acids, reactive oxygen species (ROS) and ethanol, and changes the following physiological properties: better proton efflux, lower membrane permeability, and lessened internal hydrogen peroxide production. The enhanced stress tolerance was dependent on the mitogen-activated protein kinase (MAPK) Hog1 of the high osmolarity glycerol (HOG) pathway, but not the MAPK Slt2 of the cell wall integrity (CWI) pathway; however, a PMA1 overexpression constitutively activated both Hog1 and Slt2. The constitutive Hog1 activation required the MAPK kinase kinase (MAP3K) Ssk2 of the HOG pathway, but not Ste11 and Ssk22, two other MAP3Ks of the same pathway. The constitutive Slt2 activation did not require Rom2 and the membrane sensors of the CWI pathway, whereas Bck1 was indispensable. The PMA1 overexpression activated the stress response element but not the cyclic AMP response element and the Rlm1 transcription factor. PMA1 overexpression may facilitate the construction of industrial strains with simultaneous tolerance to weak acids, ROS, and ethanol.
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Affiliation(s)
- Yeji Lee
- Interdisciplinary Program of EcoCreative, College of Natural Sciences, Ewha Womans University, Seoul, 03766, South Korea
| | - Olviyani Nasution
- Interdisciplinary Program of EcoCreative, College of Natural Sciences, Ewha Womans University, Seoul, 03766, South Korea
| | - Young Mi Lee
- Department of Life Sciences College of Natural Sciences, Ewha Womans University, Seoul, 03766, South Korea
| | - Eunjung Kim
- Department of Pharmacology, School of Medicine, Ajou University, Suwon, 16499, South Korea
| | - Wonja Choi
- Interdisciplinary Program of EcoCreative, College of Natural Sciences, Ewha Womans University, Seoul, 03766, South Korea.
- Department of Life Sciences College of Natural Sciences, Ewha Womans University, Seoul, 03766, South Korea.
| | - Wankee Kim
- Department of Pharmacology, School of Medicine, Ajou University, Suwon, 16499, South Korea.
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25
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Guo W, Chen Y, Wei N, Feng X. Investigate the Metabolic Reprogramming of Saccharomyces cerevisiae for Enhanced Resistance to Mixed Fermentation Inhibitors via 13C Metabolic Flux Analysis. PLoS One 2016; 11:e0161448. [PMID: 27532329 PMCID: PMC4988770 DOI: 10.1371/journal.pone.0161448] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/07/2016] [Indexed: 11/18/2022] Open
Abstract
The fermentation inhibitors from the pretreatment of lignocellulosic materials, e.g., acetic acid and furfural, are notorious due to their negative effects on the cell growth and chemical production. However, the metabolic reprogramming of the cells under these stress conditions, especially metabolic response for resistance to mixed inhibitors, has not been systematically investigated and remains mysterious. Therefore, in this study, 13C metabolic flux analysis (13C-MFA), a powerful tool to elucidate the intracellular carbon flux distributions, has been applied to two Saccharomyces cerevisiae strains with different tolerances to the inhibitors under acetic acid, furfural, and mixed (i.e., acetic acid and furfural) stress conditions to unravel the key metabolic responses. By analyzing the intracellular carbon fluxes as well as the energy and cofactor utilization under different conditions, we uncovered varied metabolic responses to different inhibitors. Under acetate stress, ATP and NADH production was slightly impaired, while NADPH tended towards overproduction. Under furfural stress, ATP and cofactors (including both NADH and NADPH) tended to be overproduced. However, under dual-stress condition, production of ATP and cofactors was severely impaired due to synergistic stress caused by the simultaneous addition of two fermentation inhibitors. Such phenomenon indicated the pivotal role of the energy and cofactor utilization in resisting the mixed inhibitors of acetic acid and furfural. Based on the discoveries, valuable insights are provided to improve the tolerance of S. cerevisiae strain and further enhance lignocellulosic fermentation.
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Affiliation(s)
- Weihua Guo
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States of America
| | - Yingying Chen
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - Na Wei
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, United States of America
- * E-mail: (NW); (XF)
| | - Xueyang Feng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States of America
- * E-mail: (NW); (XF)
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26
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Optimization of genome shuffling for high-yield production of the antitumor deacetylmycoepoxydiene in an endophytic fungus of mangrove plants. Appl Microbiol Biotechnol 2016; 100:7491-8. [DOI: 10.1007/s00253-016-7457-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/01/2016] [Accepted: 03/05/2016] [Indexed: 11/26/2022]
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Wu X, Zhang L, Jin X, Fang Y, Zhang K, Qi L, Zheng D. Deletion of JJJ1 improves acetic acid tolerance and bioethanol fermentation performance of Saccharomyces cerevisiae strains. Biotechnol Lett 2016; 38:1097-106. [PMID: 27067354 DOI: 10.1007/s10529-016-2085-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/17/2016] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To improve tolerance to acetic acid that is present in lignocellulosic hydrolysates and affects bioethanol production by Saccharomyces cerevisiae. RESULTS Saccharomyces cerevisiae strains with improved tolerance to acetic acid were obtained through deletion of the JJJ1 gene. The lag phase of the JJJ1 deletion mutant BYΔJJJ1 was ~16 h shorter than that of the parent strain, BY4741, when the fermentation medium contained 4.5 g acetic acid/l. Additionally, the specific ethanol production rate of BYΔJJJ1 was increased (0.057 g/g h) compared to that of the parent strain (0.051 g/g h). Comparative transcription and physiological analyses revealed higher long chain fatty acid, trehalose, and catalase contents might be critical factors responsible for the acetic acid resistance of JJJ1 knockout strains. CONCLUSIONS JJJ1 deletion improves acetic acid tolerance and ethanol fermentation performance of S. cerevisiae.
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Affiliation(s)
- Xuechang Wu
- College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Lijie Zhang
- College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Xinna Jin
- College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Yahong Fang
- College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Ke Zhang
- College of Life Science, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Lei Qi
- Ocean College, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Daoqiong Zheng
- Ocean College, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China.
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28
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Transcriptome analysis of acetic-acid-treated yeast cells identifies a large set of genes whose overexpression or deletion enhances acetic acid tolerance. Appl Microbiol Biotechnol 2015; 99:6391-403. [DOI: 10.1007/s00253-015-6706-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/14/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
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Snoek T, Picca Nicolino M, Van den Bremt S, Mertens S, Saels V, Verplaetse A, Steensels J, Verstrepen KJ. Large-scale robot-assisted genome shuffling yields industrial Saccharomyces cerevisiae yeasts with increased ethanol tolerance. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:32. [PMID: 25759747 PMCID: PMC4354739 DOI: 10.1186/s13068-015-0216-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 01/29/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND During the final phases of bioethanol fermentation, yeast cells face high ethanol concentrations. This stress results in slower or arrested fermentations and limits ethanol production. Novel Saccharomyces cerevisiae strains with superior ethanol tolerance may therefore allow increased yield and efficiency. Genome shuffling has emerged as a powerful approach to rapidly enhance complex traits including ethanol tolerance, yet previous efforts have mostly relied on a mutagenized pool of a single strain, which can potentially limit the effectiveness. Here, we explore novel robot-assisted strategies that allow to shuffle the genomes of multiple parental yeasts on an unprecedented scale. RESULTS Screening of 318 different yeasts for ethanol accumulation, sporulation efficiency, and genetic relatedness yielded eight heterothallic strains that served as parents for genome shuffling. In a first approach, the parental strains were subjected to multiple consecutive rounds of random genome shuffling with different selection methods, yielding several hybrids that showed increased ethanol tolerance. Interestingly, on average, hybrids from the first generation (F1) showed higher ethanol production than hybrids from the third generation (F3). In a second approach, we applied several successive rounds of robot-assisted targeted genome shuffling, yielding more than 3,000 targeted crosses. Hybrids selected for ethanol tolerance showed increased ethanol tolerance and production as compared to unselected hybrids, and F1 hybrids were on average superior to F3 hybrids. In total, 135 individual F1 and F3 hybrids were tested in small-scale very high gravity fermentations. Eight hybrids demonstrated superior fermentation performance over the commercial biofuel strain Ethanol Red, showing a 2 to 7% increase in maximal ethanol accumulation. In an 8-l pilot-scale test, the best-performing hybrid fermented medium containing 32% (w/v) glucose to dryness, yielding 18.7% (v/v) ethanol with a productivity of 0.90 g ethanol/l/h and a yield of 0.45 g ethanol/g glucose. CONCLUSIONS We report the use of several different large-scale genome shuffling strategies to obtain novel hybrids with increased ethanol tolerance and fermentation capacity. Several of the novel hybrids show best-parent heterosis and outperform the commonly used bioethanol strain Ethanol Red, making them interesting candidate strains for industrial production.
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Affiliation(s)
- Tim Snoek
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Martina Picca Nicolino
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Stefanie Van den Bremt
- />Laboratory of Enzyme, Fermentation and Brewing Technology, KU Leuven technologiecampus Ghent, Gebroeders De Smetstraat 1, 9000 Ghent, Belgium
| | - Stijn Mertens
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Veerle Saels
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Alex Verplaetse
- />Laboratory of Enzyme, Fermentation and Brewing Technology, KU Leuven technologiecampus Ghent, Gebroeders De Smetstraat 1, 9000 Ghent, Belgium
| | - Jan Steensels
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Kevin J Verstrepen
- />Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium
- />Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
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Nasution O, Lee J, Srinivasa K, Choi IG, Lee YM, Kim E, Choi W, Kim W. Loss of Dfg5 glycosylphosphatidylinositol-anchored membrane protein confers enhanced heat tolerance in Saccharomyces cerevisiae. Environ Microbiol 2015; 17:2721-34. [PMID: 25297926 DOI: 10.1111/1462-2920.12649] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 12/21/2022]
Abstract
The protein product of Saccharomyces cerevisiae DFG5 gene is a glycosylphosphatidylinositol (GPI)-anchored plasma membrane protein and a putative glycosidase/glycosyltransferase that links other GPI-anchored proteins to β-glucans in the cell wall. Upon exposure to heat (41°C), DFG5 deletion mutant dfg5Δ displayed significantly enhanced heat tolerance as well as lowered level of reactive oxygen species and decreased membrane permeability compared with those in the control (BY4741). Comparative transcriptome profiles of BY4741 and dfg5Δ revealed that 38 and 23 genes were up- and down-regulated in dfg5Δ respectively. Of the 23 down-regulated genes, 11 of 13 viable deletion mutants were identified to be tolerant to heat, suggesting that the down-regulation of those genes might have contributed to the enhanced heat tolerance in dfg5Δ. Deletion of DFG5 caused slight activation of mitogen-activated protein kinases Hog1 in the high-osmolarity glycerol pathway and Slt2 in the cell wall integrity pathway. Therefore, a model is proposed on the signal transduction pathways associated with deletion of DFG5 upon heat stress.
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Affiliation(s)
- Olviyani Nasution
- Division of Ecological Sciences, Ewha Womans University, Seoul, 120-750, Korea
| | - Jaok Lee
- Division of Ecological Sciences, Ewha Womans University, Seoul, 120-750, Korea
| | - Kavitha Srinivasa
- Division of Ecological Sciences, Ewha Womans University, Seoul, 120-750, Korea
| | - In-Geol Choi
- School of Life Sciences and Biotechnology, Korea University, Seoul, 136-713, Korea
| | - Young Mi Lee
- Microbial Resources Research Center, College of Natural Sciences, Ewha Womans University, Seoul, 120-750, Korea
| | - Eunjung Kim
- Department of Pharmacology, School of Medicine, Ajou University, Suwon, 442-749, Korea
| | - Wonja Choi
- Division of Ecological Sciences, Ewha Womans University, Seoul, 120-750, Korea.,Microbial Resources Research Center, College of Natural Sciences, Ewha Womans University, Seoul, 120-750, Korea
| | - Wankee Kim
- Department of Pharmacology, School of Medicine, Ajou University, Suwon, 442-749, Korea
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Ding S, Zhang Y, Zhang J, Zeng W, Yang Y, Guan J, Pan L, Li W. Enhanced deacidification activity in Schizosaccharomyces pombe by genome shuffling. Yeast 2014; 32:317-25. [PMID: 25377082 DOI: 10.1002/yea.3053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/24/2014] [Accepted: 10/29/2014] [Indexed: 11/07/2022] Open
Abstract
A problem frequently occurring in making some kinds of wines, particularly Vitis quinquangularis Rehd wine, is the presence of malic acid at high concentrations, which is detrimental to the quality of wines. Thus, there is a need of the ways for effectively reducing the malic acid levels in wine. This study aimed to generate shuffled fusants of Schizosaccharomyces pombe with enhanced deacidification activity for reducing the excessive malic acid content in wine. Sz. pombe CGMCC 2.1628 was used as the original strain. The starting mutant population was generated by UV treatment. The mutants with higher deacidification activity were selected and subjected to recursive protoplast fusion. The resulting fusants were screened by using the indicator of malic acid concentration of fermentation supernatants on 96-well microtitre plates, measured with bromocresol green. After three rounds of genome shuffling, the best-performing fusant, named GS3-1, was obtained. Its deacidification activity (consumed 4.78 g/l malic acid within 10 days) was increased by 225.2% as compared to that of original strain. In the Vitis quinquangularis Rehd wine fermentation test, GS3-1 consumed 4.0 g/l malic acid during the whole cycle of fermentation, providing up to 185.7% improvement in malic acid consumption compared with that of the original strain. This study shows that GS3-1 has great potential for improving the quality of Vitis quinquangularis Rehd wine.
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Affiliation(s)
- Su Ding
- Xingjian College of Science and Liberal Arts, Guangxi University, People's Republic of China; Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, Guangxi University, People's Republic of China
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Inoue H, Hashimoto S, Matsushika A, Watanabe S, Sawayama S. Breeding of a xylose-fermenting hybrid strain by mating genetically engineered haploid strains derived from industrial Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2014; 41:1773-81. [PMID: 25355632 DOI: 10.1007/s10295-014-1531-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 10/18/2014] [Indexed: 01/04/2023]
Abstract
The industrial Saccharomyces cerevisiae IR-2 is a promising host strain to genetically engineer xylose-utilizing yeasts for ethanol fermentation from lignocellulosic hydrolysates. Two IR-2-based haploid strains were selected based upon the rate of xylulose fermentation, and hybrids were obtained by mating recombinant haploid strains harboring heterogeneous xylose dehydrogenase (XDH) (wild-type NAD(+)-dependent XDH or engineered NADP(+)-dependent XDH, ARSdR), xylose reductase (XR) and xylulose kinase (XK) genes. ARSdR in the hybrids selected for growth rates on yeast extract-peptone-dextrose (YPD) agar and YP-xylose agar plates typically had a higher activity than NAD(+)-dependent XDH. Furthermore, the xylose-fermenting performance of the hybrid strain SE12 with the same level of heterogeneous XDH activity was similar to that of a recombinant strain of IR-2 harboring a single set of genes, XR/ARSdR/XK. These results suggest not only that the recombinant haploid strains retain the appropriate genetic background of IR-2 for ethanol production from xylose but also that ARSdR is preferable for xylose fermentation.
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Affiliation(s)
- Hiroyuki Inoue
- Biomass Refinery Research Center (BRRC), National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan,
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Liu X, Zhang X, Zhang Z. Point mutation of H3/H4 histones affects acetic acid tolerance in Saccharomyces cerevisiae. J Biotechnol 2014; 187:116-23. [DOI: 10.1016/j.jbiotec.2014.07.445] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 07/22/2014] [Accepted: 07/25/2014] [Indexed: 10/24/2022]
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Steensels J, Snoek T, Meersman E, Nicolino MP, Voordeckers K, Verstrepen KJ. Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol Rev 2014; 38:947-95. [PMID: 24724938 PMCID: PMC4293462 DOI: 10.1111/1574-6976.12073] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 01/31/2014] [Accepted: 04/02/2014] [Indexed: 12/23/2022] Open
Abstract
Yeasts have been used for thousands of years to make fermented foods and beverages, such as beer, wine, sake, and bread. However, the choice for a particular yeast strain or species for a specific industrial application is often based on historical, rather than scientific grounds. Moreover, new biotechnological yeast applications, such as the production of second-generation biofuels, confront yeast with environments and challenges that differ from those encountered in traditional food fermentations. Together, this implies that there are interesting opportunities to isolate or generate yeast variants that perform better than the currently used strains. Here, we discuss the different strategies of strain selection and improvement available for both conventional and nonconventional yeasts. Exploiting the existing natural diversity and using techniques such as mutagenesis, protoplast fusion, breeding, genome shuffling and directed evolution to generate artificial diversity, or the use of genetic modification strategies to alter traits in a more targeted way, have led to the selection of superior industrial yeasts. Furthermore, recent technological advances allowed the development of high-throughput techniques, such as 'global transcription machinery engineering' (gTME), to induce genetic variation, providing a new source of yeast genetic diversity.
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Affiliation(s)
- Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Tim Snoek
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Esther Meersman
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Martina Picca Nicolino
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Karin Voordeckers
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
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An J, Kwon H, Kim E, Lee YM, Ko HJ, Park H, Choi IG, Kim S, Kim KH, Kim W, Choi W. Tolerance to acetic acid is improved by mutations of the TATA-binding protein gene. Environ Microbiol 2014; 17:656-69. [DOI: 10.1111/1462-2920.12489] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/16/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Jieun An
- Division of Life and Pharmaceutical Sciences; Ewha Womans University; Seoul 120-750 Korea
| | - Hyeji Kwon
- Division of Life and Pharmaceutical Sciences; Ewha Womans University; Seoul 120-750 Korea
| | - Eunjung Kim
- Department of Pharmacology, School of Medicine; Ajou University; Suwon 442-749 Korea
| | - Young Mi Lee
- Microbial Resources Research Center; Ewha Womans University; Seoul 120-750 Korea
| | - Hyeok Jin Ko
- School of Life Sciences and Biotechnology; Korea University; Seoul 136-713 Korea
| | - Hongjae Park
- School of Life Sciences and Biotechnology; Korea University; Seoul 136-713 Korea
| | - In-Geol Choi
- School of Life Sciences and Biotechnology; Korea University; Seoul 136-713 Korea
| | - Sooah Kim
- School of Life Sciences and Biotechnology; Korea University; Seoul 136-713 Korea
| | - Kyoung Heon Kim
- School of Life Sciences and Biotechnology; Korea University; Seoul 136-713 Korea
| | - Wankee Kim
- Department of Pharmacology, School of Medicine; Ajou University; Suwon 442-749 Korea
| | - Wonja Choi
- Division of Life and Pharmaceutical Sciences; Ewha Womans University; Seoul 120-750 Korea
- Microbial Resources Research Center; Ewha Womans University; Seoul 120-750 Korea
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Genome Shuffling and Ribosome Engineering of Streptomyces actuosus for High-Yield Nosiheptide Production. Appl Biochem Biotechnol 2014; 173:1553-63. [DOI: 10.1007/s12010-014-0948-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 04/24/2014] [Indexed: 11/26/2022]
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Evolutionary engineering by genome shuffling. Appl Microbiol Biotechnol 2014; 98:3877-87. [PMID: 24595425 DOI: 10.1007/s00253-014-5616-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/11/2014] [Accepted: 02/12/2014] [Indexed: 01/28/2023]
Abstract
An upsurge in the bioeconomy drives the need for engineering microorganisms with increasingly complex phenotypes. Gains in productivity of industrial microbes depend on the development of improved strains. Classical strain improvement programmes for the generation, screening and isolation of such mutant strains have existed for several decades. An alternative to traditional strain improvement methods, genome shuffling, allows the directed evolution of whole organisms via recursive recombination at the genome level. This review deals chiefly with the technical aspects of genome shuffling. It first presents the diversity of organisms and phenotypes typically evolved using this technology and then reviews available sources of genetic diversity and recombination methodologies. Analysis of the literature reveals that genome shuffling has so far been restricted to microorganisms, both prokaryotes and eukaryotes, with an overepresentation of antibiotics- and biofuel-producing microbes. Mutagenesis is the main source of genetic diversity, with few studies adopting alternative strategies. Recombination is usually done by protoplast fusion or sexual recombination, again with few exceptions. For both diversity and recombination, prospective methods that have not yet been used are also presented. Finally, the potential of genome shuffling for gaining insight into the genetic basis of complex phenotypes is also discussed.
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Wang PM, Zheng DQ, Chi XQ, Li O, Qian CD, Liu TZ, Zhang XY, Du FG, Sun PY, Qu AM, Wu XC. Relationship of trehalose accumulation with ethanol fermentation in industrial Saccharomyces cerevisiae yeast strains. BIORESOURCE TECHNOLOGY 2013; 152:371-376. [PMID: 24316480 DOI: 10.1016/j.biortech.2013.11.033] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 11/11/2013] [Accepted: 11/13/2013] [Indexed: 06/02/2023]
Abstract
The protective effect and the mechanisms of trehalose accumulation in industrial Saccharomyces cerevisiae strains were investigated during ethanol fermentation. The engineered strains with more intercellular trehalose achieved significantly higher fermentation rates and ethanol yields than their wild strain ZS during very high gravity (VHG) fermentation, while their performances were not different during regular fermentation. The VHG fermentation performances of these strains were consistent with their growth capacity under osmotic stress and ethanol stress, the key stress factors during VHG fermentation. These results suggest that trehalose accumulation is more important for VHG fermentation of industrial yeast strains than regular one. The differences in membrane integrity and antioxidative capacity of these strains indicated the possible mechanisms of trehalose as a protectant under VHG condition. Therefore, trehalose metabolic engineering may be a useful strategy for improving the VHG fermentation performance of industrial yeast strains.
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Affiliation(s)
- Pin-Mei Wang
- Ocean College, Zhejiang University, Hangzhou 310058, Zhejiang Province, China; Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Dao-Qiong Zheng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Xiao-Qin Chi
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma, Xiamen University Affiliated Zhongshan Hospital, Xiamen 361004, Fujian Province, China
| | - Ou Li
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Chao-Dong Qian
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Tian-Zhe Liu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Xiao-Yang Zhang
- State Key Laboratory of Motor Vehicle Biofuel Technology, Nanyang 473000, Henan Province, China
| | - Feng-Guang Du
- State Key Laboratory of Motor Vehicle Biofuel Technology, Nanyang 473000, Henan Province, China
| | - Pei-Yong Sun
- State Key Laboratory of Motor Vehicle Biofuel Technology, Nanyang 473000, Henan Province, China
| | - Ai-Min Qu
- State Key Laboratory of Motor Vehicle Biofuel Technology, Nanyang 473000, Henan Province, China
| | - Xue-Chang Wu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China.
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Lindberg L, Santos AX, Riezman H, Olsson L, Bettiga M. Lipidomic profiling of Saccharomyces cerevisiae and Zygosaccharomyces bailii reveals critical changes in lipid composition in response to acetic acid stress. PLoS One 2013; 8:e73936. [PMID: 24023914 PMCID: PMC3762712 DOI: 10.1371/journal.pone.0073936] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/26/2013] [Indexed: 01/03/2023] Open
Abstract
When using microorganisms as cell factories in the production of bio-based fuels or chemicals from lignocellulosic hydrolysate, inhibitory concentrations of acetic acid, released from the biomass, reduce the production rate. The undissociated form of acetic acid enters the cell by passive diffusion across the lipid bilayer, mediating toxic effects inside the cell. In order to elucidate a possible link between lipid composition and acetic acid stress, the present study presents detailed lipidomic profiling of the major lipid species found in the plasma membrane, including glycerophospholipids, sphingolipids and sterols, in Saccharomyces cerevisiae (CEN.PK 113_7D) and Zygosaccharomyces bailii (CBS7555) cultured with acetic acid. Detailed physiological characterization of the response of the two yeasts to acetic acid has also been performed in aerobic batch cultivations using bioreactors. Physiological characterization revealed, as expected, that Z. bailii is more tolerant to acetic acid than S. cerevisiae. Z. bailii grew at acetic acid concentrations above 24 g L−1, while limited growth of S. cerevisiae was observed after 11 h when cultured with only 12 g L−1 acetic acid. Detailed lipidomic profiling using electrospray ionization, multiple-reaction-monitoring mass spectrometry (ESI-MRM-MS) showed remarkable changes in the glycerophospholipid composition of Z. bailii, including an increase in saturated glycerophospholipids and considerable increases in complex sphingolipids in both S. cerevisiae (IPC 6.2×, MIPC 9.1×, M(IP)2C 2.2×) and Z. bailii (IPC 4.9×, MIPC 2.7×, M(IP)2C 2.7×), when cultured with acetic acid. In addition, the basal level of complex sphingolipids was significantly higher in Z. bailii than in S. cerevisiae, further emphasizing the proposed link between lipid saturation, high sphingolipid levels and acetic acid tolerance. The results also suggest that acetic acid tolerance is associated with the ability of a given strain to generate large rearrangements in its lipid profile.
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Affiliation(s)
- Lina Lindberg
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
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40
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Streptomycin resistance-aided genome shuffling to improve doramectin productivity of Streptomyces avermitilis NEAU1069. ACTA ACUST UNITED AC 2013; 40:877-89. [DOI: 10.1007/s10295-013-1280-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 04/25/2013] [Indexed: 11/30/2022]
Abstract
Abstract
Genome shuffling is an efficient approach for the rapid engineering of microbial strains with desirable industrial phenotypes. In this study, a strategy of incorporating streptomycin resistance screening into genome shuffling (GS-SR) was applied for rapid improvement of doramectin production by Streptomyces avermitilis NEAU1069. The starting mutant population was generated through treatment of the spores with N-methyl-N’-nitro-N-nitrosoguanidine and ultraviolet (UV) irradiation, respectively, and five mutants with higher productivity of doramectin were selected as starting strains for GS-SR. Finally, a genetically stable strain F4-137 was obtained and characterized to be able to yield 992 ± 4.4 mg/l doramectin in a shake flask, which was 7.3-fold and 11.2-fold higher than that of the starting strain UV-45 and initial strain NEAU1069, respectively. The doramectin yield by F4-137 in a 50-l fermentor reached 930.3 ± 3.8 mg/l. Furthermore, the factors associated with the improved doramectin yield were investigated and the results suggested that mutations in ribosomal protein S12 and the enhanced production of cyclohexanecarboxylic coenzyme A may contribute to the improved performance of the shuffled strains. The random amplified polymorphic DNA analysis showed a genetic diversity among the shuffled strains, which confirmed the occurrence of genome shuffling. In conclusion, our results demonstrated that GS-SR is a powerful method for enhancing the production of secondary metabolites in Streptomyces.
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Hyland PB, Mun SLS, Mahadevan R. Prediction of Weak Acid Toxicity inSaccharomyces cerevisiaeUsing Genome-Scale Metabolic Models. Ind Biotechnol (New Rochelle N Y) 2013. [DOI: 10.1089/ind.2013.0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Patrick B Hyland
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Serene Lock-Sow Mun
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
- CO2 Management Mission Oriented Research, Universiti Teknologi PETRONAS, Tronoh, Malaysia
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
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Kim SR, Lee KS, Kong II, Lesmana A, Lee WH, Seo JH, Kweon DH, Jin YS. Construction of an efficient xylose-fermenting diploid Saccharomyces cerevisiae strain through mating of two engineered haploid strains capable of xylose assimilation. J Biotechnol 2013; 164:105-11. [PMID: 23376240 DOI: 10.1016/j.jbiotec.2012.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 12/07/2012] [Accepted: 12/27/2012] [Indexed: 12/17/2022]
Abstract
Saccharomyces cerevisiae can be engineered for xylose fermentation through introduction of wild type or mutant genes (XYL1/XYL1 (R276H), XYL2, and XYL3) coding for xylose metabolic enzymes from Scheffersomyces stipitis. The resulting engineered strains, however, often yielded undesirable phenotypes such as slow xylose assimilation and xylitol accumulation. In this study, we performed the mating of two engineered strains that exhibit suboptimal xylose-fermenting phenotypes in order to develop an improved xylose-fermenting diploid strain. Specifically, we obtained two engineered haploid strains (YSX3 and SX3). The YSX3 strain consumed xylose rapidly and produced a lot of xylitol. On the contrary, the SX3 strain consumed xylose slowly with little xylitol production. After converting the mating type of SX3 from alpha to a, the resulting strain (SX3-2) was mated with YSX3 to construct a heterozygous diploid strain (KSM). The KSM strain assimilated xylose (0.25gxyloseh(-1)gcells(-1)) as fast as YSX3 and accumulated a small amount of xylitol (0.03ggxylose(-1)) as low as SX3, resulting in an improved ethanol yield (0.27ggxylose(-1)). We found that the improvement in xylose fermentation by the KSM strain was not because of heterozygosity or genome duplication but because of the complementation of the two xylose-metabolic pathways. This result suggested that mating of suboptimal haploid strains is a promising strategy to develop engineered yeast strains with improved xylose fermenting capability.
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Affiliation(s)
- Soo Rin Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Zheng DQ, Wang PM, Chen J, Zhang K, Liu TZ, Wu XC, Li YD, Zhao YH. Genome sequencing and genetic breeding of a bioethanol Saccharomyces cerevisiae strain YJS329. BMC Genomics 2012; 13:479. [PMID: 22978491 PMCID: PMC3484046 DOI: 10.1186/1471-2164-13-479] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 08/14/2012] [Indexed: 11/16/2022] Open
Abstract
Background Environmental stresses and inhibitors encountered by Saccharomyces cerevisiae strains are the main limiting factors in bioethanol fermentation. Strains with different genetic backgrounds usually show diverse stress tolerance responses. An understanding of the mechanisms underlying these phenotypic diversities within S. cerevisiae populations could guide the construction of strains with desired traits. Results We explored the genetic characteristics of the bioethanol S. cerevisiae strain YJS329 and elucidated how genetic variations in its genome were correlated with specified traits compared to similar traits in the S288c-derived strain, BYZ1. Karyotypic electrophoresis combined with array-comparative genomic hybridization indicated that YJS329 was a diploid strain with a relatively constant genome as a result of the fewer Ty elements and lack of structural polymorphisms between homologous chromosomes that it contained. By comparing the sequence with the S288c genome, a total of 64,998 SNPs, 7,093 indels and 11 unique genes were identified in the genome of YJS329-derived haploid strain YJSH1 through whole-genome sequencing. Transcription comparison using RNA-Seq identified which of the differentially expressed genes were the main contributors to the phenotypic differences between YJS329 and BYZ1. By combining the results obtained from the genome sequences and the transcriptions, we predicted how the SNPs, indels and chromosomal copy number variations may affect the mRNA expression profiles and phenotypes of the yeast strains. Furthermore, some genetic breeding strategies to improve the adaptabilities of YJS329 were designed and experimentally verified. Conclusions Through comparative functional genomic analysis, we have provided some insights into the mechanisms underlying the specific traits of the bioenthanol strain YJS329. The work reported here has not only enriched the available genetic resources of yeast but has also indicated how functional genomic studies can be used to improve genetic breeding in yeast.
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Affiliation(s)
- Dao-Qiong Zheng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, PR China
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Li S, Li F, Chen XS, Wang L, Xu J, Tang L, Mao ZG. Genome Shuffling Enhanced ε-Poly-l-Lysine Production by Improving Glucose Tolerance of Streptomyces graminearus. Appl Biochem Biotechnol 2011; 166:414-23. [DOI: 10.1007/s12010-011-9437-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/26/2011] [Indexed: 12/01/2022]
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45
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Liu JJ, Ding WT, Zhang GC, Wang JY. Improving ethanol fermentation performance of Saccharomyces cerevisiae in very high-gravity fermentation through chemical mutagenesis and meiotic recombination. Appl Microbiol Biotechnol 2011; 91:1239-46. [DOI: 10.1007/s00253-011-3404-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Revised: 05/02/2011] [Accepted: 05/22/2011] [Indexed: 11/29/2022]
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