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Sword TT, Dinglasan JLN, Abbas GSK, Barker JW, Spradley ME, Greene ER, Gooden DS, Emrich SJ, Gilchrist MA, Doktycz MJ, Bailey CB. Profiling expression strategies for a type III polyketide synthase in a lysate-based, cell-free system. Sci Rep 2024; 14:12983. [PMID: 38839808 PMCID: PMC11153635 DOI: 10.1038/s41598-024-61376-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/06/2024] [Indexed: 06/07/2024] Open
Abstract
Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli often results in a myriad of unpredictable issues with regard to protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as a valuable expression platform as a testbed for rapid prototyping expression parameters. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We applied a library of constructs with different combinations of promoters and rppA coding sequences to investigate the synergies between promoter and codon usage. Subsequently, we assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. More importantly, the choice of coding sequences and promoters impact protein expression synergistically, which should be considered for future efforts to use CFE for high-yield protein expression. The promoter strategy when applied to RppA was not completely correlated with that observed with GFP, indicating that different promoter strategies should be applied for different proteins. In vivo experiments suggest that there is correlation, but not complete alignment between expressing in cell free and in vivo. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs, which advances CFE as a tool for natural product research.
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Affiliation(s)
- Tien T Sword
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Jaime Lorenzo N Dinglasan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Ghaeath S K Abbas
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
- School of Chemistry, University of Sydney, Sydney, NSW, Australia
| | - J William Barker
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Madeline E Spradley
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Elijah R Greene
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Damian S Gooden
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Scott J Emrich
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
- Department of Electrical Engineering and Computer Science, University of Tennessee-Knoxville, Knoxville, TN, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Michael A Gilchrist
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA.
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA.
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA.
- School of Chemistry, University of Sydney, Sydney, NSW, Australia.
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Sword TT, Dinglasan JLN, Abbas GS, William Barker J, Spradley ME, Greene ER, Gooden DS, Emrich SJ, Gilchrist MA, Doktycz MJ, Bailey CB. Profiling Expression Strategies for a Type III Polyketide Synthase in a Lysate-Based, Cell-free System. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569483. [PMID: 38077034 PMCID: PMC10705458 DOI: 10.1101/2023.11.30.569483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli frequently results in a myriad of unpredictable issues with protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts, such as BGC refactoring, can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as 1) a valuable expression platform for enzymes that are challenging to synthesize in vivo, and as 2) a testbed for rapid prototyping that can improve cellular expression. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We synergistically tune promoter and codon usage to improve flaviolin production from cell-free expressed RppA. We then assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs. By showing the coordinators between CFE versus in vivo expression, this work advances CFE as a tool for natural product research.
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Affiliation(s)
- Tien T. Sword
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Jaime Lorenzo N. Dinglasan
- Biosciences Division, Oak Ridge National Laboratory (Oak Ridge, TN USA)
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
| | - Ghaeath S.K. Abbas
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
- University of Sydney, School of Chemistry (Sydney, NSW, Australia)
| | - J. William Barker
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Madeline E. Spradley
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Elijah R. Greene
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Damian S. Gooden
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Scott J. Emrich
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
- Department of Electrical Engineering and Computer Science, University of Tennessee-Knoxville (Knoxville, TN USA)
- Department of Ecology & Evolutionary Biology, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Michael A. Gilchrist
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
- Department of Ecology & Evolutionary Biology, University of Tennessee-Knoxville (Knoxville, TN USA)
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory (Oak Ridge, TN USA)
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
| | - Constance B. Bailey
- Department of Chemistry, University of Tennessee-Knoxville (Knoxville, TN USA)
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville Knoxville (Knoxville, TN USA)
- University of Sydney, School of Chemistry (Sydney, NSW, Australia)
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Yue K, Chen J, Li Y, Kai L. Advancing synthetic biology through cell-free protein synthesis. Comput Struct Biotechnol J 2023; 21:2899-2908. [PMID: 37216017 PMCID: PMC10196276 DOI: 10.1016/j.csbj.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Junyu Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
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