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Paulk AM, Williams RL, Liu CC. Rapidly Inducible Yeast Surface Display for Antibody Evolution with OrthoRep. ACS Synth Biol 2024. [PMID: 39052526 DOI: 10.1021/acssynbio.4c00370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
We recently developed "autonomous hypermutation yeast surface display" (AHEAD), a technology that enables the rapid generation of potent and specific antibodies in yeast. AHEAD pairs yeast surface display with an error-prone orthogonal DNA replication system (OrthoRep) to continuously and rapidly mutate surface-displayed antibodies, thereby enabling enrichment for stronger binding variants through repeated rounds of cell growth and fluorescence-activated cell sorting. AHEAD currently utilizes a standard galactose induction system to drive the selective display of antibodies on the yeast surface. However, achieving maximal display levels can require up to 48 h of induction. Here we report an updated version of the AHEAD platform that utilizes a synthetic β-estradiol-induced gene expression system to regulate the surface display of antibodies and find that induction is notably faster in achieving surface display for both our AHEAD system and traditional yeast surface display from nuclear plasmids that do not hypermutate. The updated AHEAD platform was fully functional in repeated rounds of evolution to drive the rapid evolution of antibodies.
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Affiliation(s)
- Alexandra M Paulk
- Program in Mathematical, Computational and Systems Biology, University of California, Irvine, California 92697, United States
- Department of Biomedical Engineering, University of California, Irvine, California 92697, United States
- Center for Synthetic Biology, University of California, Irvine, California 92697, United States
| | - Rory L Williams
- Department of Biomedical Engineering, University of California, Irvine, California 92697, United States
- Center for Synthetic Biology, University of California, Irvine, California 92697, United States
| | - Chang C Liu
- Department of Biomedical Engineering, University of California, Irvine, California 92697, United States
- Center for Synthetic Biology, University of California, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States
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Paulk AM, Williams RL, Liu CC. Rapidly inducible yeast surface display for antibody evolution with OrthoRep. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595666. [PMID: 38826191 PMCID: PMC11142247 DOI: 10.1101/2024.05.24.595666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
We recently developed 'autonomous hypermutation yeast surface display' (AHEAD), a technology that enables the rapid generation of potent and specific antibodies in yeast. AHEAD pairs yeast surface display with an error-prone orthogonal DNA replication system (OrthoRep) to continuously and rapidly mutate surface-displayed antibodies, thereby enabling enrichment for stronger binding variants through repeated rounds of cell growth and fluorescence activated cell sorting (FACS). AHEAD currently utilizes a standard galactose induction system to drive the selective display of antibodies on the yeast surface. However, achieving maximal display levels can require up to 48 hours of induction. Here, we report an updated version of the AHEAD platform that utilizes a synthetic β-estradiol induced gene expression system to regulate the surface display of antibodies and find that induction is notably faster in achieving surface display for both our AHEAD system as well as traditional yeast surface display from nuclear plasmids that do not hypermutate. The updated AHEAD platform was fully functional in repeated rounds of evolution to drive the rapid evolution of antibodies.
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Ma XY, Coleman B, Prabhu P, Yang M, Wen F. Engineering Compositionally Uniform Yeast Whole-Cell Biocatalysts with Maximized Surface Enzyme Density for Cellulosic Biofuel Production. ACS Synth Biol 2024; 13:1225-1236. [PMID: 38551819 DOI: 10.1021/acssynbio.3c00669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
In recent decades, whole-cell biocatalysis has played an increasingly important role in the food, pharmaceutical, and energy sector. One promising application is the use of ethanologenic yeast displaying minicellulosomes on the cell surface to combine cellulose hydrolysis and fermentation into a single step for consolidated bioprocessing. However, cellulosic ethanol production using existing yeast whole-cell biocatalysts (yWCBs) has not reached industrial feasibility due to their inefficient cellulose hydrolysis. As prior studies have demonstrated enzyme density on the yWCB surface to be one of the most important parameters for enhancing cellulose hydrolysis, we sought to maximize this parameter at both the population and single-cell levels in yWCBs displaying tetrafunctional minicellulosomes. At the population level, enzyme density is limited by the presence of a nondisplay population constituting 25-50% of all cells. In this study, we identified the cause to be plasmid loss and successfully eliminated the nondisplay population to generate compositionally uniform yWCBs. At the single-cell level, we demonstrate that enzyme density is limited by molecular crowding, which hinders minicellulosome assembly. By adjusting the integrated gene copy number, we obtained yWCBs of tunable enzyme display levels. This tunability allowed us to avoid the crowding-limited regime and achieve a maximum enzyme density per cell. As a result, the best strain showed a cellulose-to-ethanol yield of 4.92 g/g, corresponding to 96% of the theoretical maximum and near-complete conversion (∼96%) of the starting cellulose (1% PASC). Our holistic engineering strategy that combines a population and single-cell level approach is broadly applicable to enhance the WCB performance in other biocatalytic cascade schemes.
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Affiliation(s)
- Xiao Yin Ma
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bryan Coleman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ponnandy Prabhu
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Margaret Yang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
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Zhang C, Chen H, Zhu Y, Zhang Y, Li X, Wang F. Saccharomyces cerevisiae cell surface display technology: Strategies for improvement and applications. Front Bioeng Biotechnol 2022; 10:1056804. [PMID: 36568309 PMCID: PMC9767963 DOI: 10.3389/fbioe.2022.1056804] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Microbial cell surface display technology provides a powerful platform for engineering proteins/peptides with enhanced properties. Compared to the classical intracellular and extracellular expression (secretion) systems, this technology avoids enzyme purification, substrate transport processes, and is an effective solution to enzyme instability. Saccharomyces cerevisiae is well suited to cell surface display as a common cell factory for the production of various fuels and chemicals, with the advantages of large cell size, being a Generally Regarded As Safe (GRAS) organism, and post-translational processing of secreted proteins. In this review, we describe various strategies for constructing modified S. cerevisiae using cell surface display technology and outline various applications of this technology in industrial processes, such as biofuels and chemical products, environmental pollution treatment, and immunization processes. The approaches for enhancing the efficiency of cell surface display are also discussed.
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Affiliation(s)
- Chenmeng Zhang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Hongyu Chen
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Yiping Zhu
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Yu Zhang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Xun Li
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China
| | - Fei Wang
- Jiangsu Co Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China,Jiangsu Provincial Key Lab for Chemistry and Utilization of Agro Forest Biomass, Jiangsu Key Lab of Biomass Based Green Fuels and Chemicals, Nanjing, China,International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing, China,*Correspondence: Fei Wang,
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