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Li C, Yu H, Chen S, Song L, Yuan A, Wei F, Sun D, Wang M, Xu L, He D, Liu J, Li H, Zhao J, Shen Y, Bao X. Quantification and Molecular Analysis of Antagonism between Xylose Utilization and Acetic Acid Tolerance in Glucose/Xylose Cofermentation Saccharomyces cerevisiae Strains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:6758-6771. [PMID: 40048248 DOI: 10.1021/acs.jafc.4c12275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2025]
Abstract
For bioethanol production from lignocellulosic materials, an ideal microorganism must possess both excellent xylose utilization and a high tolerance to inhibitory compounds. However, these two traits often exhibit antagonism in recombinant xylose-utilizing Saccharomyces cerevisiae strains. In this study, we developed a quantitative metric using an aggregated parameter to evaluate the degree of this antagonism and applied it to evaluate the antagonism of three strains (LF1, LF1-6M, and 6M-15), which had been iteratively evolved in xylose and hydrolyzate environments. Transcriptomic analysis revealed that the yeast strain elevates the alert level to stresses related to DNA replication, unfolded protein, starvation, and hyperosmosis, and reduces the uptake of unimportant nutrients to have a higher acetic acid tolerance during adaptive evolution in hydrolyzate. Additionally, the Snf1p-Mig1p signaling pathway was reprogrammed, enabling the strain to utilize xylose more efficiently during adaptive evolution in xylose. We also confirmed that disruption of the glyceraldehyde-3-phosphate dehydrogenase gene TDH1 significantly shortened the time required for glucose and/or xylose cofermentation under acetic acid stress by reducing reactive oxygen species accumulation and increasing ATP production. This study offers valuable insights for developing robust and efficient S. cerevisiae strains capable of glucose/xylose cofermentation.
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Affiliation(s)
- Chenhao Li
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Hengsong Yu
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Shichao Chen
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Liyun Song
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Ai Yuan
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Fangqing Wei
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Dongming Sun
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Ming Wang
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Lili Xu
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Deyun He
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Jiao Liu
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Hongxing Li
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Jianzhi Zhao
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiaoming Bao
- College of Bioengineering, Key Laboratory of Shandong Microbial Engineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China
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Choi SY, Lee Y, Yu HE, Cho IJ, Kang M, Lee SY. Sustainable production and degradation of plastics using microbes. Nat Microbiol 2023; 8:2253-2276. [PMID: 38030909 DOI: 10.1038/s41564-023-01529-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Plastics are indispensable in everyday life and industry, but the environmental impact of plastic waste on ecosystems and human health is a huge concern. Microbial biotechnology offers sustainable routes to plastic production and waste management. Bacteria and fungi can produce plastics, as well as their constituent monomers, from renewable biomass, such as crops, agricultural residues, wood and organic waste. Bacteria and fungi can also degrade plastics. We review state-of-the-art microbial technologies for sustainable production and degradation of bio-based plastics and highlight the potential contributions of microorganisms to a circular economy for plastics.
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Affiliation(s)
- So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea
- BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea
| | - Youngjoon Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea
- BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea
| | - Hye Eun Yu
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea
| | - In Jin Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea
- BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea
| | - Minju Kang
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea.
- BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea.
- BioInformatics Research Center, KAIST, Daejeon, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, Republic of Korea.
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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: 2.8] [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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Sharma S, Arora A, Sharma P, Singh S, Nain L, Paul D. Notable mixed substrate fermentation by native Kodamaea ohmeri strains isolated from Lagenaria siceraria flowers and ethanol production on paddy straw hydrolysates. Chem Cent J 2018; 12:8. [PMID: 29404706 PMCID: PMC5799091 DOI: 10.1186/s13065-018-0375-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 01/20/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bioethanol obtained by fermenting cellulosic fraction of biomass holds promise for blending in petroleum. Cellulose hydrolysis yields glucose while hemicellulose hydrolysis predominantly yields xylose. Economic feasibility of bioethanol depends on complete utilization of biomass carbohydrates and an efficient co-fermenting organism is a prerequisite. While hexose fermentation capability of Saccharomyces cerevisiae is a boon, however, its inability to ferment pentose is a setback. RESULTS Two xylose fermenting Kodamaea ohmeri strains were isolated from Lagenaria siceraria flowers through enrichment on xylose. They showed 61% glucose fermentation efficiency in fortified medium. Medium engineering with 0.1% yeast extract and peptone, stimulated co-fermentation potential of both strains yielding maximum ethanol 0.25 g g-1 on mixed sugars with ~ 50% fermentation efficiency. Strains were tolerant to inhibitors like 5-hydroxymethyl furfural, furfural and acetic acid. Both K. ohmeri strains grew well on biologically pretreated rice straw hydrolysates and produced ethanol. CONCLUSIONS This is the first report of native Kodamaea sp. exhibiting notable mixed substrate utilization and ethanol fermentation. K. ohmeri strains showed relevant traits like utilizing and co-fermenting mixed sugars, exhibiting excellent growth, inhibitor tolerance, and ethanol production on rice straw hydrolysates.
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Affiliation(s)
- Shalley Sharma
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Anju Arora
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Pankhuri Sharma
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Surender Singh
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Lata Nain
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Debarati Paul
- Amity Institute of Biotechnology, Amity University, Noida, U.P., India
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