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Wu X, Wan X, Yu H, Liu H. Recent advances in CRISPR-Cas system for Saccharomyces cerevisiae engineering. Biotechnol Adv 2025; 81:108557. [PMID: 40081781 DOI: 10.1016/j.biotechadv.2025.108557] [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: 12/04/2024] [Revised: 02/24/2025] [Accepted: 03/06/2025] [Indexed: 03/16/2025]
Abstract
Yeast Saccharomyces cerevisiae (S. cerevisiae) is a crucial industrial platform for producing a wide range of chemicals, fuels, pharmaceuticals, and nutraceutical ingredients. It is also commonly used as a model organism for fundamental research. In recent years, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) system has become the preferred technology for genetic manipulation in S. cerevisiae owing to its high efficiency, precision, and user-friendliness. This system, along with its extensive toolbox, has significantly accelerated the construction of pathways, enzyme optimization, and metabolic engineering in S. cerevisiae. Furthermore, it has allowed researchers to accelerate phenotypic evolution and gain deeper insights into fundamental biological questions, such as genotype-phenotype relationships. In this review, we summarize the latest advancements in the CRISPR-Cas toolbox for S. cerevisiae and highlight its applications in yeast cell factory construction and optimization, enzyme and phenotypic evolution, genome-scale functional interrogation, gene drives, and the advancement of biotechnologies. Finally, we discuss the challenges and potential for further optimization and applications of the CRISPR-Cas system in S. cerevisiae.
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Affiliation(s)
- Xinxin Wu
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiaowen Wan
- State Key Laboratory of Biotherapy and Cancer Centre/Collaborative Innovation Centre for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hongbin Yu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Huayi Liu
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; State Key Laboratory of Biotherapy and Cancer Centre/Collaborative Innovation Centre for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, China.
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Yook S, Alper HS. Recent advances in genetic engineering and chemical production in yeast species. FEMS Yeast Res 2025; 25:foaf009. [PMID: 40082732 PMCID: PMC11963765 DOI: 10.1093/femsyr/foaf009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Revised: 03/07/2025] [Accepted: 03/11/2025] [Indexed: 03/16/2025] Open
Abstract
Yeasts have emerged as well-suited microbial cell factory for the sustainable production of biofuels, organic acids, terpenoids, and specialty chemicals. This ability is bolstered by advances in genetic engineering tools, including CRISPR-Cas systems and modular cloning in both conventional (Saccharomyces cerevisiae) and non-conventional (Yarrowia lipolytica, Rhodotorula toruloides, Candida krusei) yeasts. Additionally, genome-scale metabolic models and machine learning approaches have accelerated efforts to create a broad range of compounds that help reduce dependency on fossil fuels, mitigate climate change, and offer sustainable alternatives to petrochemical-derived counterparts. In this review, we highlight the cutting-edge genetic tools driving yeast metabolic engineering and then explore the diverse applications of yeast-based platforms for producing value-added products. Collectively, this review underscores the pivotal role of yeast biotechnology in efforts to build a sustainable bioeconomy.
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Affiliation(s)
- Sangdo Yook
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, United States
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, United States
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, United States
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Badarinath NM, Mondal B, Yellman CM, Holland KL, Lee HJ, Phuengkham H, Cazier AP, Son J, Smith JR, Cox JR, Kristof AJ, Haikal YA, Kwong GA, Blazeck J. A facile yeast-display approach for antibody mask discovery. Protein Eng Des Sel 2025; 38:gzaf006. [PMID: 40381213 PMCID: PMC12123510 DOI: 10.1093/protein/gzaf006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2024] [Revised: 05/03/2025] [Accepted: 05/16/2025] [Indexed: 05/20/2025] Open
Abstract
Tuning in vivo activity of protein therapeutics can improve their safety. In this vein, it is possible to add a 'mask' moiety to a protein therapeutic such that its ability to bind its target is prevented until the mask has been proteolytically removed, for instance by a tumor-associated protease. As such, new methods to isolate functional masking sequences can aid development of protein therapies. Here, we describe a yeast display-based method to discover peptide sequences that prevent binding of antibody fragments to their antigen target. Our method includes an in situ ability to screen for restoration of binding by scFvs after proteolytic mask removal, and it takes advantage of the antigenic target itself to guide mask discovery. First, we genetically linked a yeast-displayed αPSCA scFv to overlapping 'tiles' of its target. By selecting for reduced antigen binding via flow cytometry, we discovered two peptide masks that we confirmed to be linear epitopes of the PSCA antigen. We then expanded our method towards developing masks for three-dimensional epitopes by using a co-crystal structure of an αHer2 antibody in complex with its antigen to guide combinatorial mask design. In sum, our efforts show the feasibility of employing yeast-displayed, antigen-based libraries to find antibody masks.
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Affiliation(s)
- Nithya M Badarinath
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Ford Environmental Science & Technology Building, Atlanta, GA 30332, United States
- Bioengineering Program, Georgia Institute of Technology, 315 Ferst Dr NW, Atlanta, GA 30332, United States
| | - Basudeb Mondal
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Ford Environmental Science & Technology Building, Atlanta, GA 30332, United States
| | - Christopher M Yellman
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Ford Environmental Science & Technology Building, Atlanta, GA 30332, United States
| | - Kendreze L Holland
- Bioengineering Program, Georgia Institute of Technology, 315 Ferst Dr NW, Atlanta, GA 30332, United States
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive NW, Atlanta, GA 30332, United States
| | - Hee Jun Lee
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive NW, Atlanta, GA 30332, United States
| | - Hathaichanok Phuengkham
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive NW, Atlanta, GA 30332, United States
| | - Andrew P Cazier
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Ford Environmental Science & Technology Building, Atlanta, GA 30332, United States
| | - Jaewoo Son
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Ford Environmental Science & Technology Building, Atlanta, GA 30332, United States
| | - Jacob R Smith
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Ford Environmental Science & Technology Building, Atlanta, GA 30332, United States
| | - John R Cox
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Ford Environmental Science & Technology Building, Atlanta, GA 30332, United States
| | - Andrew J Kristof
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Ford Environmental Science & Technology Building, Atlanta, GA 30332, United States
| | - Yusef A Haikal
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Ford Environmental Science & Technology Building, Atlanta, GA 30332, United States
| | - Gabriel A Kwong
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive NW, Atlanta, GA 30332, United States
| | - John Blazeck
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Ford Environmental Science & Technology Building, Atlanta, GA 30332, United States
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