1
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Watanabe T, Kimura Y, Umeno D. Systematic promoter design for plasmid-encoded S-adenosylmethionine sensing systems. J GEN APPL MICROBIOL 2024; 70:n/a. [PMID: 38281753 DOI: 10.2323/jgam.2024.01.002] [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: 01/30/2024]
Abstract
S-adenosylmethionine (SAM) is an important biomolecule that mainly acts as a methyl donor and plays many roles in a variety of biological functions. SAM is also required for the biosynthesis of valuable methylated compounds, but its supply is a bottleneck for these biosynthetic pathways. To overcome this bottleneck and to reconfigure SAM homeostasis, a high-throughput sensing system for changes in intracellular SAM availability is required. We constructed a plasmid that can detect the factors that can alter SAM availability using minimal components. It does so by placing a fluorescent protein under a promoter controlled by endogenous MetJ, a transcription factor that represses its own regulons upon binding with SAM. Next, to validate SAM-responsive behavior, we systematically reconstructed 10 synthetic promoters with different positions and with different number of metbox sites. We found that a position between the -35 box and the -10 box was the most effective for repression and that this setup was suitable for detecting the genetic or environmental factors that can deplete and recover the intracellular SAM availability. Overall, the response patterns of the synthetic MetJ-regulated promoters characterized in this study may be useful for the development of better SAM biosensing systems.
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Affiliation(s)
- Taro Watanabe
- Department of Applied Chemistry, Faculty of Science, and Engineering, Waseda University
- Kirin Central Research Institute, Kirin Holdings Company, Limited
| | - Yuki Kimura
- Department of Applied Chemistry, Faculty of Science, and Engineering, Waseda University
| | - Daisuke Umeno
- Department of Applied Chemistry, Faculty of Science, and Engineering, Waseda University
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2
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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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3
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Tian Z, Shao D, Tang L, Li Z, Chen Q, Song Y, Li T, Simmel FC, Song J. Circular single-stranded DNA as a programmable vector for gene regulation in cell-free protein expression systems. Nat Commun 2024; 15:4635. [PMID: 38821953 PMCID: PMC11143192 DOI: 10.1038/s41467-024-49021-6] [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: 10/12/2023] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
Cell-free protein expression (CFE) systems have emerged as a critical platform for synthetic biology research. The vectors for protein expression in CFE systems mainly rely on double-stranded DNA and single-stranded RNA for transcription and translation processing. Here, we introduce a programmable vector - circular single-stranded DNA (CssDNA), which is shown to be processed by DNA and RNA polymerases for gene expression in a yeast-based CFE system. CssDNA is already widely employed in DNA nanotechnology due to its addressability and programmability. To apply above methods in the context of synthetic biology, CssDNA can not only be engineered for gene regulation via the different pathways of sense CssDNA and antisense CssDNA, but also be constructed into several gene regulatory logic gates in CFE systems. Our findings advance the understanding of how CssDNA can be utilized in gene expression and gene regulation, and thus enrich the synthetic biology toolbox.
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Affiliation(s)
- Zhijin Tian
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Dandan Shao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhen Li
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Chen
- College of Forestry, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Yongxiu Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Ningbo institute of Dalian University of Technology, Ningbo, 315016, China
| | - Tao Li
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
| | - Friedrich C Simmel
- Department of Bioscience, School of Natural Sciences, Technische Universität München, Garching, Germany
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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4
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Choi S, Park YS, Lee KW, Park YJ, Jang HJ, Kim DM, Yoo TH. Sensitive Methods to Detect Single-Stranded Nucleic Acids of Food Pathogens Based on Cell-Free Protein Synthesis and Retroreflection Signal Detection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3783-3792. [PMID: 38346351 DOI: 10.1021/acs.jafc.3c07785] [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: 02/22/2024]
Abstract
Cell-free protein synthesis (CFPS) has recently gained considerable attention as a new platform for developing methods to detect various molecules, ranging from small chemicals to biological macromolecules. Retroreflection has been used as an alternative signal to develop analytical methods because it can be detected by using a simple instrument comprising a white light source and a camera. Here, we report a novel reporter protein that couples the capability of CFPS and the simplicity of retroreflection signal detection. The design of the reporter was based on two pairs of protein-peptide interactions, SpyCatcher003-SpyTag003 and MDM2-PMI(N8A). MDM2-MDM2-SpyCatcher003 was decided as the reporter protein, and the two peptides, SpyTag003 and PMI(N8A), were immobilized on the surfaces of retroreflective Janus particles and microfluidic chips, respectively. The developed retroreflection signal detection system was combined with a previously reported CFPS reaction that can transduce the presence of a single-stranded nucleic acid into protein synthesis. The resulting methods were applied to detect 16S rRNAs of several foodborne pathogens. Concentration-dependent relationships were observed over a range of 10° fM to 102 pM, with the limits of detection being single-digit femtomolar concentrations. Considering the designability of the CFPS system for other targets, the retroreflection signal detection method will enable the development of novel methods to detect various molecules.
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Affiliation(s)
- Sunjoo Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Ye Seop Park
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Kyung Won Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Yu Jin Park
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Korea
| | - Hee Ju Jang
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Korea
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5
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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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6
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Jung JK, Rasor BJ, Rybnicky GA, Silverman AD, Standeven J, Kuhn R, Granito T, Ekas HM, Wang BM, Karim AS, Lucks JB, Jewett MC. At-Home, Cell-Free Synthetic Biology Education Modules for Transcriptional Regulation and Environmental Water Quality Monitoring. ACS Synth Biol 2023; 12:2909-2921. [PMID: 37699423 DOI: 10.1021/acssynbio.3c00223] [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: 09/14/2023]
Abstract
As the field of synthetic biology expands, the need to grow and train science, technology, engineering, and math (STEM) practitioners is essential. However, the lack of access to hands-on demonstrations has led to inequalities of opportunity and practice. In addition, there is a gap in providing content that enables students to make their own bioengineered systems. To address these challenges, we develop four shelf-stable cell-free biosensing educational modules that work by simply adding water and DNA to freeze-dried crude extracts of non-pathogenic Escherichia coli. We introduce activities and supporting curricula to teach the structure and function of the lac operon, dose-responsive behavior, considerations for biosensor outputs, and a "build-your-own" activity for monitoring environmental contaminants in water. We piloted these modules with K-12 teachers and 130 high-school students in their classrooms─and at home─without professional laboratory equipment. This work promises to catalyze access to interactive synthetic biology education opportunities.
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Affiliation(s)
- Jaeyoung K Jung
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, United States
| | - Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Grant A Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Adam D Silverman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, United States
| | | | - Robert Kuhn
- Centennial High School, Roswell, Georgia 30076, United States
- Innovation Academy STEM High School, Alpharetta, Georgia 30009, United States
| | - Teresa Granito
- Evanston Township High School, Evanston, Illinois 60201, United States
| | - Holly M Ekas
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Brenda M Wang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States
- Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
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7
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Li W, Xu Y, Zhang Y, Li P, Zhu X, Feng C. Cell-Free Biosensing Genetic Circuit Coupled with Ribozyme Cleavage Reaction for Rapid and Sensitive Detection of Small Molecules. ACS Synth Biol 2023; 12:1657-1666. [PMID: 37196142 DOI: 10.1021/acssynbio.3c00003] [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: 05/19/2023]
Abstract
Synthetic biological systems have been utilized to develop a wide range of genetic circuits and components that enhance the performance of biosensing systems. Among them, cell-free systems are emerging as important platforms for synthetic biology applications. Genetic circuits play an essential role in cell-free systems, mainly consisting of sensing modules, regulation modules, and signal output modules. Currently, fluorescent proteins and aptamers are commonly used as signal outputs. However, these signal output modes cannot simultaneously achieve faster signal output, more accurate and reliable performance, and signal amplification. Ribozyme is a highly structured and catalytic RNA molecule that can specifically recognize and cut specific substrate sequences. Here, by adopting ribozyme as the signal output, we developed a cell-free biosensing genetic circuit coupled with the ribozyme cleavage reaction, enabling rapid and sensitive detection of small molecules. More importantly, we have also successfully constructed a 3D-printed sensor array and thereby achieved high-throughput analysis of an inhibitory drug. Furthermore, our method will help expand the application range of ribozyme in the field of synthetic biology and also optimize the signal output system of cell-free biosensing, thus promoting the development of cell-free synthetic biology in biomedical research, clinical diagnosis, environmental monitoring, and food inspection.
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Affiliation(s)
- Wenxing Li
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Yiming Xu
- Department of Applied Biology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yue Zhang
- Department of Applied Biology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Pengfei Li
- Department of Applied Biology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
- Shaoxing Institute of Shanghai University, Shaoxing 312071, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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8
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Wagner L, Jules M, Borkowski O. What remains from living cells in bacterial lysate-based cell-free systems. Comput Struct Biotechnol J 2023; 21:3173-3182. [PMID: 37333859 PMCID: PMC10275740 DOI: 10.1016/j.csbj.2023.05.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023] Open
Abstract
Because they mimic cells while offering an accessible and controllable environment, lysate-based cell-free systems (CFS) have emerged as valuable biotechnology tools for synthetic biology. Historically used to uncover fundamental mechanisms of life, CFS are nowadays used for a multitude of purposes, including protein production and prototyping of synthetic circuits. Despite the conservation of fundamental functions in CFS like transcription and translation, RNAs and certain membrane-embedded or membrane-bound proteins of the host cell are lost when preparing the lysate. As a result, CFS largely lack some essential properties of living cells, such as the ability to adapt to changing conditions, to maintain homeostasis and spatial organization. Regardless of the application, shedding light on the black-box of the bacterial lysate is necessary to fully exploit the potential of CFS. Most measurements of the activity of synthetic circuits in CFS and in vivo show significant correlations because these only require processes that are preserved in CFS, like transcription and translation. However, prototyping circuits of higher complexity that require functions that are lost in CFS (cell adaptation, homeostasis, spatial organization) will not show such a good correlation with in vivo conditions. Both for prototyping circuits of higher complexity and for building artificial cells, the cell-free community has developed devices to reconstruct cellular functions. This mini-review compares bacterial CFS to living cells, focusing on functional and cellular process differences and the latest developments in restoring lost functions through complementation of the lysate or device engineering.
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9
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Jung KJ, Rasor BJ, Rybnicky GA, Silverman AD, Standeven J, Kuhn R, Granito T, Ekas HM, Wang BM, Karim AS, Lucks JB, Jewett MC. At-home, cell-free synthetic biology education modules for transcriptional regulation and environmental water quality monitoring. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523248. [PMID: 36711593 PMCID: PMC9881948 DOI: 10.1101/2023.01.09.523248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
As the field of synthetic biology expands, the need to grow and train science, technology, engineering, and math (STEM) practitioners is essential. However, the lack of access to hands-on demonstrations has led to inequalities of opportunity and practice. In addition, there is a gap in providing content that enables students to make their own bioengineered systems. To address these challenges, we develop four shelf-stable cell-free biosensing educational modules that work by just-adding-water and DNA to freeze-dried crude extracts of Escherichia coli . We introduce activities and supporting curricula to teach the structure and function of the lac operon, dose-responsive behavior, considerations for biosensor outputs, and a 'build-your-own' activity for monitoring environmental contaminants in water. We piloted these modules with K-12 teachers and 130 high school students in their classrooms - and at home - without professional laboratory equipment or researcher oversight. This work promises to catalyze access to interactive synthetic biology education opportunities.
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Affiliation(s)
- Kirsten J. Jung
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Center for Water Research, Northwestern University, Evanston, IL 60208, USA
| | - Blake J. Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Grant A. Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, 60208, USA
| | - Adam D. Silverman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Center for Water Research, Northwestern University, Evanston, IL 60208, USA
| | | | - Robert Kuhn
- Centennial High School, Roswell, GA 30076, USA
- Fulton County Schools Innovation Academy, Alpharetta, GA 30009, USA
| | | | - Holly M. Ekas
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Brenda M. Wang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Ashty S. Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Center for Water Research, Northwestern University, Evanston, IL 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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10
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Sánchez-Costa M, López-Gallego F. Solid-Phase Cell-Free Protein Synthesis and Its Applications in Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:21-46. [PMID: 37306703 DOI: 10.1007/10_2023_226] [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: 06/13/2023]
Abstract
Cell-free systems for the in vitro production of proteins have revolutionized the synthetic biology field. In the last decade, this technology is gaining momentum in molecular biology, biotechnology, biomedicine and even education. Materials science has burst into the field of in vitro protein synthesis to empower the value of existing tools and expand its applications. In this sense, the combination of solid materials (normally functionalized with different biomacromolecules) together with cell-free components has made this technology more versatile and robust. In this chapter, we discuss the combination of solid materials with DNA and transcription-translation machinery to synthesize proteins within compartments, to immobilize and purify in situ the nascent protein, to transcribe and transduce DNAs immobilized on solid surfaces, and the combination of all or some of these strategies.
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Affiliation(s)
- Mercedes Sánchez-Costa
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain.
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11
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Copeland CE, Kim J, Copeland PL, Heitmeier CJ, Kwon YC. Characterizing a New Fluorescent Protein for a Low Limit of Detection Sensing in the Cell-Free System. ACS Synth Biol 2022; 11:2800-2810. [PMID: 35850511 PMCID: PMC9396652 DOI: 10.1021/acssynbio.2c00180] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell-free protein synthesis-based biosensors have been developed as highly accurate, low-cost biosensors. However, since most biomarkers exist at low concentrations in various types of biopsies, the biosensor's dynamic range must be increased in the system to achieve low limits of detection necessary while deciphering from higher background signals. Many attempts to increase the dynamic range have relied on amplifying the input signal from the analyte, which can lead to complications of false positives. In this study, we aimed to increase the protein synthesis capability of the cell-free protein synthesis system and the output signal of the reporter protein to achieve a lower limit of detection. We utilized a new fluorescent protein, mNeonGreen, which produces a higher output than those commonly used in cell-free biosensors. Optimizations of DNA sequence and the subsequent cell-free protein synthesis reaction conditions allowed characterizing protein expression variability by given DNA template types, reaction environment, and storage additives that cause the greatest time constraint on designing the cell-free biosensor. Finally, we characterized the fluorescence kinetics of mNeonGreen compared to the commonly used reporter protein, superfolder green fluorescent protein. We expect that this finely tuned cell-free protein synthesis platform with the new reporter protein can be used with sophisticated synthetic gene circuitry networks to increase the dynamic range of a cell-free biosensor to reach lower detection limits and reduce the false-positive proportion.
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Affiliation(s)
- Caroline E Copeland
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Jeehye Kim
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Pearce L Copeland
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Chloe J Heitmeier
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Yong-Chan Kwon
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Louisiana State University Agricultural Center, Baton Rouge, Louisiana 70803, United States
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12
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Yang J, Wang C, Lu Y. A Temperature-Controlled Cell-Free Expression System by Dynamic Repressor. ACS Synth Biol 2022; 11:1408-1416. [PMID: 35319196 DOI: 10.1021/acssynbio.1c00641] [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: 11/30/2022]
Abstract
The cell-free protein synthesis (CFPS) system is a typical protein production platform in the field of synthetic biology. However, there are limitations in controlling protein synthesis in the CFPS system. Compared with the traditional method of adding chemicals, temperature is an ideal control switch to achieve precise spatiotemporal control with few side effects. Hence, the design of a temperature-controlled cell-free protein synthesis (tcCFPS) system based on E. coli was carried out with the repressor cI protein in this study. The corresponding tcCFPS achieved a 143-fold dynamic protein expression level at 37 °C than that at 30 °C. Besides, the artificial cell controlled by temperature was constructed to expand the applications of tcCFPS. This study provides a new effective method for active protein synthesis in a cell-free system and a potential means of drug synthesis and delivery.
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Affiliation(s)
- Junzhu Yang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Chen Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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13
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Dupin A, Aufinger L, Styazhkin I, Rothfischer F, Kaufmann BK, Schwarz S, Galensowske N, Clausen-Schaumann H, Simmel FC. Synthetic cell-based materials extract positional information from morphogen gradients. SCIENCE ADVANCES 2022; 8:eabl9228. [PMID: 35394842 PMCID: PMC8993112 DOI: 10.1126/sciadv.abl9228] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/17/2022] [Indexed: 05/19/2023]
Abstract
Biomaterials composed of synthetic cells have the potential to adapt and differentiate guided by physicochemical environmental cues. Inspired by biological systems in development, which extract positional information (PI) from morphogen gradients in the presence of uncertainties, we here investigate how well synthetic cells can determine their position within a multicellular structure. To calculate PI, we created and analyzed a large number of synthetic cellular assemblies composed of emulsion droplets connected via lipid bilayer membranes. These droplets contained cell-free feedback gene circuits that responded to gradients of a genetic inducer acting as a morphogen. PI is found to be limited by gene expression noise and affected by the temporal evolution of the morphogen gradient and the cell-free expression system itself. The generation of PI can be rationalized by computational modeling of the system. We scale our approach using three-dimensional printing and demonstrate morphogen-based differentiation in larger tissue-like assemblies.
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Affiliation(s)
- Aurore Dupin
- Physics Department (E14), TU Munich, 85748 Garching, Germany
| | - Lukas Aufinger
- Physics Department (E14), TU Munich, 85748 Garching, Germany
| | - Igor Styazhkin
- Physics Department (E14), TU Munich, 85748 Garching, Germany
| | | | - Benedikt K. Kaufmann
- Center for NanoScience (CeNS), Schellingstraße 4, 80799 Munich, Germany
- Center for Applied Tissue Engineering and Regenerative Medicine-CANTER, Munich University of Applied Sciences, Lothstrasse 34, 80335 Munich, Germany
- Heinz-Nixdorf-Chair of Biomedical Electronics, TranslaTUM, TU Munich, 81675 Munich, Germany
| | - Sascha Schwarz
- Center for NanoScience (CeNS), Schellingstraße 4, 80799 Munich, Germany
- Center for Applied Tissue Engineering and Regenerative Medicine-CANTER, Munich University of Applied Sciences, Lothstrasse 34, 80335 Munich, Germany
| | | | - Hauke Clausen-Schaumann
- Center for NanoScience (CeNS), Schellingstraße 4, 80799 Munich, Germany
- Center for Applied Tissue Engineering and Regenerative Medicine-CANTER, Munich University of Applied Sciences, Lothstrasse 34, 80335 Munich, Germany
| | - Friedrich C. Simmel
- Physics Department (E14), TU Munich, 85748 Garching, Germany
- Corresponding author.
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14
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Yang J, Lu Y. Optical Sensing in Cell-Free Expression. Methods Mol Biol 2022; 2433:343-349. [PMID: 34985755 DOI: 10.1007/978-1-0716-1998-8_21] [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: 06/14/2023]
Abstract
Light can be used as a control switch for gene expression with potential advantages, avoiding the defects induced by chemical substances. By transplanting components capable of emitting light at a specific wavelength from cells into a cell-free synthesis system, controlled gene expression can be achieved in vitro. Here, we describe an effective method to achieve optical sensing in cell-free protein synthesis (CFPS) based on Escherichia coli crude extract containing the two-component system (TCSs) YF1/FixJ, which was able to respond to blue light. Plasmids capable of interacting with the photosensitive components were constructed, and the fluorescent protein mCherry was used as a reporter. This protocol provides a detailed procedure guiding how to construct the blue-light sensing system in CFPS.
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Affiliation(s)
- Junzhu Yang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China.
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15
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Tran TM, Kim SC, Modavi C, Abate AR. Robotic automation of droplet microfluidics. BIOMICROFLUIDICS 2022; 16:014102. [PMID: 35145570 PMCID: PMC8816516 DOI: 10.1063/5.0064265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Droplet microfluidics enables powerful analytic capabilities but often requires workflows involving macro- and microfluidic processing steps that are cumbersome to perform manually. Here, we demonstrate the automation of droplet microfluidics with commercial fluid-handling robotics. The workflows incorporate common microfluidic devices including droplet generators, mergers, and sorters and utilize the robot's native capabilities for thermal control, incubation, and plate scanning. The ability to automate microfluidic devices using commercial fluid handling will speed up the integration of these methods into biological workflows.
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Affiliation(s)
- Tuan M. Tran
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Samuel C. Kim
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
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16
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Amalfitano E, Karlikow M, Norouzi M, Jaenes K, Cicek S, Masum F, Sadat Mousavi P, Guo Y, Tang L, Sydor A, Ma D, Pearson JD, Trcka D, Pinette M, Ambagala A, Babiuk S, Pickering B, Wrana J, Bremner R, Mazzulli T, Sinton D, Brumell JH, Green AA, Pardee K. A glucose meter interface for point-of-care gene circuit-based diagnostics. Nat Commun 2021; 12:724. [PMID: 33526784 PMCID: PMC7851131 DOI: 10.1038/s41467-020-20639-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 12/01/2020] [Indexed: 01/24/2023] Open
Abstract
Recent advances in cell-free synthetic biology have given rise to gene circuit-based sensors with the potential to provide decentralized and low-cost molecular diagnostics. However, it remains a challenge to deliver this sensing capacity into the hands of users in a practical manner. Here, we leverage the glucose meter, one of the most widely available point-of-care sensing devices, to serve as a universal reader for these decentralized diagnostics. We describe a molecular translator that can convert the activation of conventional gene circuit-based sensors into a glucose output that can be read by off-the-shelf glucose meters. We show the development of new glucogenic reporter systems, multiplexed reporter outputs and detection of nucleic acid targets down to the low attomolar range. Using this glucose-meter interface, we demonstrate the detection of a small-molecule analyte; sample-to-result diagnostics for typhoid, paratyphoid A/B; and show the potential for pandemic response with nucleic acid sensors for SARS-CoV-2. Getting synthetic biology circuit-based sensors into field applications is still a challenge. Here the authors combine a circuit sensor with a glucose meter for small analyte and nucleic acid detection.
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Affiliation(s)
- Evan Amalfitano
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Margot Karlikow
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Masoud Norouzi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Katariina Jaenes
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Seray Cicek
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Fahim Masum
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | | | - Yuxiu Guo
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Laura Tang
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Andrew Sydor
- Program in Cell Biology, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, Toronto, ON, M5G 0A4, Canada
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and the School of Molecular Sciences, Arizona State University, AZ, 85287, USA
| | - Joel D Pearson
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, M5G 1X5, ON, Canada.,Department of Ophthalmology and Vision Science, University of Toronto, Toronto, M5T 3A9, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Daniel Trcka
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, M5G 1X5, ON, Canada
| | - Mathieu Pinette
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, R3E 3M4, MB, Canada
| | - Aruna Ambagala
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, R3E 3M4, MB, Canada
| | - Shawn Babiuk
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, R3E 3M4, MB, Canada
| | - Bradley Pickering
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, R3E 3M4, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, Faculty of Medicine, University of Manitoba, Winnipeg, R3E 0J9, MB, Canada.,Iowa State University, College of Veterinary Medicine, Department of Veterinary Microbiology and Preventive Medicine, Ames, IA, 50011, USA
| | - Jeff Wrana
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, M5G 1X5, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Rod Bremner
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, M5G 1X5, ON, Canada.,Department of Ophthalmology and Vision Science, University of Toronto, Toronto, M5T 3A9, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Tony Mazzulli
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Department of Microbiology, Sinai Health System/University Health Network, Toronto, M5G 1X5, ON, Canada
| | - David Sinton
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, M5S 3G8, ON, Canada
| | - John H Brumell
- Program in Cell Biology, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, M5S 1A8, ON, Canada.,SickKids IBD Centre, Hospital for Sick Children, Toronto, M5G 1X8, ON, Canada
| | - Alexander A Green
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and the School of Molecular Sciences, Arizona State University, AZ, 85287, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada. .,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, M5S 3G8, ON, Canada.
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17
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Wang X, Zhu K, Chen D, Wang J, Wang X, Xu A, Wu L, Li L, Chen S. Monitoring arsenic using genetically encoded biosensors in vitro: The role of evolved regulatory genes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111273. [PMID: 32916524 DOI: 10.1016/j.ecoenv.2020.111273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Toxic pollutant (TP) detection in situ using analytical instruments or whole-cell biosensors is inconvenient. Designing and developing genetically coded biosensors in vitro for real-world TP detection is a promising alternative. However, because the bioactivity and stability of some key biomolecules are weakened in vitro, the response and regulation of reporter protein become difficult. Here, we established a genetically encoded biosensor in vitro with an arsenical resistance operon repressor (ArsR) and GFP reporter gene. Given that the wildtype ArsR did not respond to arsenic and activate GFP expression in vitro, we found, after screening, an evolved ArsR mutant ep3 could respond to arsenic and exhibited an approximately 3.4-fold fluorescence increase. Arsenic induced expression of both wildtype ArsR and ep3 mutant in vitro, however, only ep3 mutant regulated the expression of reporter gene. Furthermore, the effects of cell extracts, temperature, pH, incubation, and equilibrium time were investigated, and the equilibration of reaction mixtures for 30 min at 37 °C was found to be essential for in vitro arsenic detection prior to treatment with arsenic. Based on our data, we established a standard procedure for arsenic detection in vitro. Our results will facilitate the practical application of genetically encoded biosensors in TP monitoring.
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Affiliation(s)
- Xuanyu Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Kaili Zhu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Dongdong Chen
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Juan Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Xiaofei Wang
- School of Biology, Food and Environment, Hefei University, Hefei, Anhui, 230601, China
| | - An Xu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Lijun Wu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China; Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Luzhi Li
- School of Biology, Food and Environment, Hefei University, Hefei, Anhui, 230601, China
| | - Shaopeng Chen
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China.
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18
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Yang J, Lu Y. Physical stimuli-responsive cell-free protein synthesis. Synth Syst Biotechnol 2020; 5:363-368. [PMID: 33294650 PMCID: PMC7695910 DOI: 10.1016/j.synbio.2020.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 11/18/2022] Open
Abstract
Cell-free protein synthesis has been developed as a critical platform in synthetic biology. Unlike the cell-based synthesis system, cell-free system activates transcriptional and translational mechanisms in vitro, and can control protein synthesis by artificially adding components or chemicals. However, the control method puts forward higher requirements in terms of accurate and non-toxic control, which cannot be achieved by chemical substances. For cell-free system, physical signal is a kind of ideal spatiotemporal control approach to replace chemical substances, realizing high accuracy with little side effect. Here we review the methods of using physical signals to control gene expression in cell-free systems, including studies based on light, temperature, electric field, and magnetic force. The transfer of these switches into cell-free system further expands the flexibility and controllability of the system, thus further expanding the application capability of cell-free systems. Finally, existing problems such as signal source and signal transmission are discussed, and future applications in pharmaceutical production, delivery and industrial production are further looked into.
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Affiliation(s)
- Junzhu Yang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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19
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Mohr B, Giannone RJ, Hettich RL, Doktycz MJ. Targeted Growth Medium Dropouts Promote Aromatic Compound Synthesis in Crude E. coli Cell-Free Systems. ACS Synth Biol 2020; 9:2986-2997. [PMID: 33044063 DOI: 10.1021/acssynbio.9b00524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Progress in cell-free protein synthesis (CFPS) has spurred resurgent interest in engineering complex biological metabolism outside of the cell. Unlike purified enzyme systems, crude cell-free systems can be prepared for a fraction of the cost and contain endogenous cellular pathways that can be activated for biosynthesis. Endogenous activity performs essential functions in cell-free systems including substrate biosynthesis and energy regeneration; however, use of crude cell-free systems for bioproduction has been hampered by the under-described complexity of the metabolic networks inherent to a crude lysate. Physical and chemical cultivation parameters influence the endogenous activity of the resulting lysate, but targeted efforts to engineer this activity by manipulation of these nongenetic factors has been limited. Here growth medium composition was manipulated to improve the one-pot in vitro biosynthesis of phenol from glucose via the expression of Pasteurella multocida phenol-tyrosine lyase in crude E. coli lysates. Crude cell lysate metabolic activity was focused toward the limiting precursor tyrosine by targeted growth medium dropouts guided by proteomics. The result is the activation of a 25-step enzymatic reaction cascade involving at least three endogenous E. coli metabolic pathways. Additional modification of this system, through CFPS of feedback intolerant AroG improves yield. This effort demonstrates the ability to activate a long, complex pathway in vitro and provides a framework for harnessing the metabolic potential of diverse organisms for cell-free metabolic engineering. The more than 6-fold increase in phenol yield with limited genetic manipulation demonstrates the benefits of optimizing growth medium for crude cell-free extract production and illustrates the advantages of a systems approach to cell-free metabolic engineering.
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Affiliation(s)
- Benjamin Mohr
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Richard J. Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Robert L. Hettich
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Mitchel J. Doktycz
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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20
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Liu D, Yang Z, Zhang L, Wei M, Lu Y. Cell-free biology using remote-controlled digital microfluidics for individual droplet control. RSC Adv 2020; 10:26972-26981. [PMID: 35515808 PMCID: PMC9055536 DOI: 10.1039/d0ra04588h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/02/2020] [Indexed: 12/26/2022] Open
Abstract
Cell-free biology for diverse protein expression and biodetection in vitro has developed rapidly in recent years because of its more open and controllable reaction environment. However, complex liquid handling schemes are troublesome, especially when scaling up to perform multiple different reactions simultaneously. Digital microfluidic (DMF) technology can operate a single droplet by controlling its movement, mixing, separation, and some other actions, and is a suitable scaffold for cell-free reactions with higher efficiency. In this paper, a commercial DMF board, OpenDrop, was used, and DMF technology via remote real-time control inspired by the Internet of Things (IoT) was developed for detecting glucose enzyme catalytic cell-free reactions and verifying the feasibility of programmed cell-free protein expression. A cell-free biological reaction process which can be remote-controlled visually with excellent interactivity, controllability and flexibility was achieved. As proof-of-concept research, this work proposed a new control interface for single-drop cell-free biological reactions. It is much like the "droplet operation desktop" concept, used for remote-controllable operations and distributions of cell-free biology for efficient biological screening and protein synthesis in complex reaction networks, with expanded operability and less artificial interference.
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Affiliation(s)
- Dong Liu
- Department of Chemical Engineering, Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University Beijing 100084 China
| | - Zhenghuan Yang
- Department of Chemical Engineering, Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University Beijing 100084 China
| | - Luyang Zhang
- Department of Chemical Engineering, Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University Beijing 100084 China
| | - Minglun Wei
- Department of Chemical Engineering, Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University Beijing 100084 China
| | - Yuan Lu
- Department of Chemical Engineering, Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University Beijing 100084 China
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21
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Abstract
Cell-free systems are a widely used research tool in systems and synthetic biology and a promising platform for manufacturing of proteins and chemicals. In the past, cell-free biology was primarily used to better understand fundamental biochemical processes. Notably, E. coli cell-free extracts were used in the 1960s to decipher the sequencing of the genetic code. Since then, the transcription and translation capabilities of cell-free systems have been repeatedly optimized to improve energy efficiency and product yield. Today, cell-free systems, in combination with the rise of synthetic biology, have taken on a new role as a promising technology for just-in-time manufacturing of therapeutically important biologics and high-value small molecules. They have also been implemented at an industrial scale for the production of antibodies and cytokines. In this review, we discuss the evolution of cell-free technologies, in particular advancements in extract preparation, cell-free protein synthesis, and cell-free metabolic engineering applications. We then conclude with a discussion of the mathematical modeling of cell-free systems. Mathematical modeling of cell-free processes could be critical to addressing performance bottlenecks and estimating the costs of cell-free manufactured products.
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22
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Silverman AD, Akova U, Alam KK, Jewett MC, Lucks JB. Design and Optimization of a Cell-Free Atrazine Biosensor. ACS Synth Biol 2020; 9:671-677. [PMID: 32078765 DOI: 10.1021/acssynbio.9b00388] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent advances in cell-free synthetic biology have spurred the development of in vitro molecular diagnostics that serve as effective alternatives to whole-cell biosensors. However, cell-free sensors for detecting manmade organic water contaminants such as pesticides are sparse, partially because few characterized natural biological sensors can directly detect such pollutants. Here, we present a platform for the cell-free detection of one critical water contaminant, atrazine, by combining a previously characterized cyanuric acid biosensor with a reconstituted atrazine-to-cyanuric acid metabolic pathway composed of several protein-enriched bacterial extracts mixed in a one pot reaction. Our cell-free sensor detects atrazine within an hour of incubation at an activation ratio superior to previously reported whole-cell atrazine sensors. We also show that the response characteristics of the atrazine sensor can be tuned by manipulating the ratios of enriched extracts in the cell-free reaction mixture. Our approach of utilizing multiple metabolic steps, encoded in protein-enriched cell-free extracts, to convert a target of interest into a molecule that can be sensed by a transcription factor is modular. Our work thus serves as an effective proof-of-concept for a scheme of "metabolic biosensing", which should enable rapid, field-deployable detection of complex organic water contaminants.
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Affiliation(s)
| | | | | | - Michael C. Jewett
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Julius B. Lucks
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, United States
- Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, Illinois 60208, United States
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23
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Silverman AD, Akova U, Alam KK, Jewett MC, Lucks JB. Design and Optimization of a Cell-Free Atrazine Biosensor. ACS Synth Biol 2020. [PMID: 32078765 DOI: 10.1101/779827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Recent advances in cell-free synthetic biology have spurred the development of in vitro molecular diagnostics that serve as effective alternatives to whole-cell biosensors. However, cell-free sensors for detecting manmade organic water contaminants such as pesticides are sparse, partially because few characterized natural biological sensors can directly detect such pollutants. Here, we present a platform for the cell-free detection of one critical water contaminant, atrazine, by combining a previously characterized cyanuric acid biosensor with a reconstituted atrazine-to-cyanuric acid metabolic pathway composed of several protein-enriched bacterial extracts mixed in a one pot reaction. Our cell-free sensor detects atrazine within an hour of incubation at an activation ratio superior to previously reported whole-cell atrazine sensors. We also show that the response characteristics of the atrazine sensor can be tuned by manipulating the ratios of enriched extracts in the cell-free reaction mixture. Our approach of utilizing multiple metabolic steps, encoded in protein-enriched cell-free extracts, to convert a target of interest into a molecule that can be sensed by a transcription factor is modular. Our work thus serves as an effective proof-of-concept for a scheme of "metabolic biosensing", which should enable rapid, field-deployable detection of complex organic water contaminants.
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Affiliation(s)
| | | | | | - Michael C Jewett
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Julius B Lucks
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, United States
- Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, Illinois 60208, United States
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24
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Libicher K, Hornberger R, Heymann M, Mutschler H. In vitro self-replication and multicistronic expression of large synthetic genomes. Nat Commun 2020; 11:904. [PMID: 32060271 PMCID: PMC7021806 DOI: 10.1038/s41467-020-14694-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/27/2020] [Indexed: 11/25/2022] Open
Abstract
The generation of a chemical system capable of replication and evolution is a key objective of synthetic biology. This could be achieved by in vitro reconstitution of a minimal self-sustaining central dogma consisting of DNA replication, transcription and translation. Here, we present an in vitro translation system, which enables self-encoded replication and expression of large DNA genomes under well-defined, cell-free conditions. In particular, we demonstrate self-replication of a multipartite genome of more than 116 kb encompassing the full set of Escherichia coli translation factors, all three ribosomal RNAs, an energy regeneration system, as well as RNA and DNA polymerases. Parallel to DNA replication, our system enables synthesis of at least 30 encoded translation factors, half of which are expressed in amounts equal to or greater than their respective input levels. Our optimized cell-free expression platform could provide a chassis for the generation of a partially self-replicating in vitro translation system.
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Affiliation(s)
- K Libicher
- Biomimetic Systems, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - R Hornberger
- Biomimetic Systems, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - M Heymann
- Intelligent Biointegrative Systems Group, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - H Mutschler
- Biomimetic Systems, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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25
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Liu X, Silverman AD, Alam KK, Iverson E, Lucks JB, Jewett MC, Raman S. Design of a Transcriptional Biosensor for the Portable, On-Demand Detection of Cyanuric Acid. ACS Synth Biol 2020; 9:84-94. [PMID: 31825601 PMCID: PMC7372534 DOI: 10.1021/acssynbio.9b00348] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rapid molecular biosensing is an emerging application area for synthetic biology. Here, we engineer a portable biosensor for cyanuric acid (CYA), an analyte of interest for human and environmental health, using a LysR-type transcription regulator (LTTR) from Pseudomonas within the context of Escherichia coli gene expression machinery. To overcome cross-host portability challenges of LTTRs, we rationally engineered hybrid Pseudomonas-E. coli promoters by integrating DNA elements required for transcriptional activity and ligand-dependent regulation from both hosts, which enabled E. coli to function as a whole-cell biosensor for CYA. To alleviate challenges of whole-cell biosensing, we adapted these promoter designs to function within a freeze-dried E. coli cell-free system to sense CYA. This portable, on-demand system robustly detects CYA within an hour from laboratory and real-world samples and works with both fluorescent and colorimetric reporters. This work elucidates general principles to facilitate the engineering of a wider array of LTTR-based environmental sensors.
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Affiliation(s)
- Xiangyang Liu
- Biophysics Graduate Program, University of Wisconsin, Madison, WI, USA
| | - Adam D. Silverman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Khalid K. Alam
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Erik Iverson
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
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26
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Thavarajah W, Verosloff MS, Jung JK, Alam KK, Miller JD, Jewett MC, Young SL, Lucks JB. A Primer on Emerging Field-Deployable Synthetic Biology Tools for Global Water Quality Monitoring. NPJ CLEAN WATER 2020; 3:18. [PMID: 34267944 PMCID: PMC8279131 DOI: 10.1038/s41545-020-0064-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/09/2020] [Indexed: 05/22/2023]
Abstract
Tracking progress towards Target 6.1 of the United Nations Sustainable Development Goals, "achieving universal and equitable access to safe and affordable drinking water for all", necessitates the development of simple, inexpensive tools to monitor water quality. The rapidly growing field of synthetic biology has the potential to address this need by taking DNA-encoded sensing elements from nature and reassembling them to create field-deployable 'biosensors' that can detect pathogenic or chemical water contaminants. Here we describe water quality monitoring strategies enabled by synthetic biology and compare them to previous approaches used to detect three priority water contaminants: fecal pathogens, arsenic, and fluoride in order to explain the potential for engineered biosensors to simplify and decentralize water quality monitoring. We also briefly discuss expanding biosensors to detect emerging contaminants including metals and pharmaceuticals. We conclude with an outlook on the future of biosensor development, in which we discuss adaptability to emerging contaminants, outline current limitations, and propose steps to overcome the field's outstanding challenges to facilitate global water quality monitoring.
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Affiliation(s)
- Walter Thavarajah
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Matthew S. Verosloff
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, 2204 Tech Drive, Evanston, IL, 60208, USA
| | - Jaeyoung K. Jung
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Khalid K. Alam
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Joshua D. Miller
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Department of Anthropology, Northwestern University, 1810 Hinman Ave., Evanston, IL, 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Sera L. Young
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Department of Anthropology, Northwestern University, 1810 Hinman Ave., Evanston, IL, 60208, USA
- Institute for Policy Research, Northwestern University, 2040 Sheridan Rd, Evanston, IL, 60208 USA
- To whom correspondence should be addressed, ,
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, 2145, Sheridan Rd, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Water Research, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- Center for Engineering, Sustainability and Resilience, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
- To whom correspondence should be addressed, ,
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27
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Silverman AD, Karim AS, Jewett MC. Cell-free gene expression: an expanded repertoire of applications. Nat Rev Genet 2019; 21:151-170. [DOI: 10.1038/s41576-019-0186-3] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/24/2022]
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28
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Sadat Mousavi P, Smith SJ, Chen JB, Karlikow M, Tinafar A, Robinson C, Liu W, Ma D, Green AA, Kelley SO, Pardee K. A multiplexed, electrochemical interface for gene-circuit-based sensors. Nat Chem 2019; 12:48-55. [PMID: 31767994 PMCID: PMC7700015 DOI: 10.1038/s41557-019-0366-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/30/2019] [Indexed: 12/23/2022]
Abstract
The field of synthetic biology has used the engineered assembly of synthetic gene networks to create a wide range of function in biological systems. As part of this work, gene circuit-based sensors have primarily used optical proteins (e.g. fluorescent, colorimetric) as reporter outputs, which has limited the potential to measure multiple distinct signals. Here we present an electrochemical interface that permits expanded multiplexed reporting for cell-free gene circuit-based sensors. We have engineered a scalable system of reporter enzymes that cleave specific DNA sequences in solution, which results in an electrochemical signal when these newly liberated strands are captured at the surface of a nanostructured microelectrode. We describe the development of this interface and show its utility using a ligand-inducible gene circuit and toehold switch-based sensors, including the detection of multiple antibiotic resistance genes in parallel. This technology has the potential to expand the field of synthetic biology by providing an interface with materials, hardware and software.
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Affiliation(s)
| | - Sarah J Smith
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.,Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | - Jenise B Chen
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Margot Karlikow
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Aidan Tinafar
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Clare Robinson
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Wenhan Liu
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and the School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Alexander A Green
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and the School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Shana O Kelley
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada. .,Department of Chemistry, University of Toronto, Toronto, Ontario, Canada. .,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.
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29
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Guo X, Li F, Bai L, Yu W, Zhang X, Zhu Y, Yang D. Gene Circuit Compartment on Nanointerface Facilitatating Cascade Gene Expression. J Am Chem Soc 2019; 141:19171-19177. [PMID: 31721571 DOI: 10.1021/jacs.9b11407] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular genes that are functionally related to each other are usually confined in specialized subcellular compartments for efficient biochemical reactions. Construction of spatially controlled biosynthetic systems will facilitate the study of biological design principles. Herein, we fabricated a gene circuit compartment by coanchoring two function-related genes on surface of gold nanoparticles and investigated the compartment effect on cascade gene expression in a cell-free system. The gene circuit consisted of a T7 RNA polymerase (T7 RNAP) expression cassette as regulatory gene and a fluorescent protein expression cassette as regulated reporter gene. Both the expression cassettes were attached on a Y-shaped DNA nanostructure whose other two branches were mercapto-modified in order to steadily anchor the gene expression cassettes on the surface of gold nanoparticles. Experimental results demonstrated that both the yield and initial expression rate of the fluorescent reporter protein in the gene circuit compartment system were enhanced compared with those in free gene circuit system. Mechanism investigation revealed that the gene circuit compartment on nanoparticle made the regulatory gene and regulated reporter gene spatially proximal at nanoscale, thus effectively improving the transfer efficiency of the regulatory proteins (T7 RNAP) from regulatory genes to the regulated reporter genes in the compartments, and consequently, the biochemical reaction efficiency was significantly increased. This work not only provided a simplified model for rational molecular programming of genes circuit compartments on nanointerface but also presented implications for the cellular structure-function relationship.
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Affiliation(s)
- Xiaocui Guo
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology , Tianjin University , Tianjin , 300350 , P.R. China
| | - Feng Li
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology , Tianjin University , Tianjin , 300350 , P.R. China
| | - Lihui Bai
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology , Tianjin University , Tianjin , 300350 , P.R. China
| | - Wenting Yu
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology , Tianjin University , Tianjin , 300350 , P.R. China
| | - Xue Zhang
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology , Tianjin University , Tianjin , 300350 , P.R. China
| | - Yi Zhu
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology , Tianjin University , Tianjin , 300350 , P.R. China
| | - Dayong Yang
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology , Tianjin University , Tianjin , 300350 , P.R. China
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30
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Pandi A, Koch M, Voyvodic PL, Soudier P, Bonnet J, Kushwaha M, Faulon JL. Metabolic perceptrons for neural computing in biological systems. Nat Commun 2019; 10:3880. [PMID: 31462649 PMCID: PMC6713752 DOI: 10.1038/s41467-019-11889-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/08/2019] [Indexed: 12/30/2022] Open
Abstract
Synthetic biological circuits are promising tools for developing sophisticated systems for medical, industrial, and environmental applications. So far, circuit implementations commonly rely on gene expression regulation for information processing using digital logic. Here, we present a different approach for biological computation through metabolic circuits designed by computer-aided tools, implemented in both whole-cell and cell-free systems. We first combine metabolic transducers to build an analog adder, a device that sums up the concentrations of multiple input metabolites. Next, we build a weighted adder where the contributions of the different metabolites to the sum can be adjusted. Using a computational model fitted on experimental data, we finally implement two four-input perceptrons for desired binary classification of metabolite combinations by applying model-predicted weights to the metabolic perceptron. The perceptron-mediated neural computing introduced here lays the groundwork for more advanced metabolic circuits for rapid and scalable multiplex sensing.
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Affiliation(s)
- Amir Pandi
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Mathilde Koch
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Peter L Voyvodic
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, University of Montpellier, Montpellier, France
| | - Paul Soudier
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jerome Bonnet
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, University of Montpellier, Montpellier, France
| | - Manish Kushwaha
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
- iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
- SYNBIOCHEM Center, School of Chemistry, University of Manchester, Manchester, UK.
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31
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McManus JB, Emanuel PA, Murray RM, Lux MW. A method for cost-effective and rapid characterization of engineered T7-based transcription factors by cell-free protein synthesis reveals insights into the regulation of T7 RNA polymerase-driven expression. Arch Biochem Biophys 2019; 674:108045. [PMID: 31326518 DOI: 10.1016/j.abb.2019.07.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/26/2019] [Accepted: 07/13/2019] [Indexed: 12/20/2022]
Abstract
The T7 bacteriophage RNA polymerase (T7 RNAP) serves as a model for understanding RNA synthesis, as a tool for protein expression, and as an actuator for synthetic gene circuit design in bacterial cells and cell-free extract. T7 RNAP is an attractive tool for orthogonal protein expression in bacteria owing to its compact single subunit structure and orthogonal promoter specificity. Understanding the mechanisms underlying T7 RNAP regulation is important to the design of engineered T7-based transcription factors, which can be used in gene circuit design. To explore regulatory mechanisms for T7 RNAP-driven expression, we developed a rapid and cost-effective method to characterize engineered T7-based transcription factors using cell-free protein synthesis and an acoustic liquid handler. Using this method, we investigated the effects of the tetracycline operator's proximity to the T7 promoter on the regulation of T7 RNAP-driven expression. Our results reveal a mechanism for regulation that functions by interfering with the transition of T7 RNAP from initiation to elongation and validates the use of the method described here to engineer future T7-based transcription factors.
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Affiliation(s)
- John B McManus
- Army Research Laboratory - West Campus, California Institute of Technology, 1200 East California Blvd, Pasadena, CA, 91125, USA
| | - Peter A Emanuel
- US Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Rd, APG, MD, 21010, USA
| | - Richard M Murray
- California Institute of Technology, Biology and Biological Engineering, 1200 East California Blvd, Pasadena, CA, 91125, USA
| | - Matthew W Lux
- US Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Rd, APG, MD, 21010, USA.
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32
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Halter W, Murray RM, Allgöwer F. Analysis of primitive genetic interactions for the design of a genetic signal differentiator. Synth Biol (Oxf) 2019; 4:ysz015. [PMID: 32995540 PMCID: PMC7445770 DOI: 10.1093/synbio/ysz015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/01/2019] [Accepted: 05/28/2019] [Indexed: 11/28/2022] Open
Abstract
We study the dynamic and static input-output behavior of several primitive genetic interactions and their effect on the performance of a genetic signal differentiator. In a simplified design, several requirements for the linearity and time-scales of processes like transcription, translation and competitive promoter binding were introduced. By experimentally probing simple genetic constructs in a cell-free experimental environment and fitting semi-mechanistic models to these data, we show that some of these requirements can be verified, while others are only met with reservations in certain operational regimes. Analyzing the linearized model of the resulting genetic network, we conclude that it approximates a differentiator with relative degree one. Taking also the discovered nonlinearities into account and using a describing function approach, we further determine the particular frequency and amplitude ranges where the genetic differentiator can be expected to behave as such.
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Affiliation(s)
- Wolfgang Halter
- Institute for Systems Theory and Automatic Control, University of Stuttgart, Stuttgart, Germany
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, CA, USA
| | - Frank Allgöwer
- Institute for Systems Theory and Automatic Control, University of Stuttgart, Stuttgart, Germany
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33
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Yue K, Zhu Y, Kai L. Cell-Free Protein Synthesis: Chassis toward the Minimal Cell. Cells 2019; 8:cells8040315. [PMID: 30959805 PMCID: PMC6523147 DOI: 10.3390/cells8040315] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 11/16/2022] Open
Abstract
The quest for a minimal cell not only sheds light on the fundamental principles of life but also brings great advances in related applied fields such as general biotechnology. Minimal cell projects came from the study of a plausible route to the origin of life. Later on, research extended and also referred to the construction of artificial cells, or even more broadly, as in vitro synthetic biology. The cell-free protein synthesis (CFPS) techniques harness the central cellular activity of transcription/translation in an open environment, providing the framework for multiple cellular processes assembling. Therefore, CFPS systems have become the first choice in the construction of the minimal cell. In this review, we focus on the recent advances in the quantitative analysis of CFPS and on its advantage for addressing the bottom-up assembly of a minimal cell and illustrate the importance of systemic chassis behavior, such as stochasticity under a compartmentalized micro-environment.
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Affiliation(s)
- Ke Yue
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Shanghai Road 101, Xuzhou 221116, China.
| | - Yiyong Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China.
| | - Lei Kai
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Shanghai Road 101, Xuzhou 221116, China.
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany.
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34
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Gräwe A, Dreyer A, Vornholt T, Barteczko U, Buchholz L, Drews G, Ho UL, Jackowski ME, Kracht M, Lüders J, Bleckwehl T, Rositzka L, Ruwe M, Wittchen M, Lutter P, Müller K, Kalinowski J. A paper-based, cell-free biosensor system for the detection of heavy metals and date rape drugs. PLoS One 2019; 14:e0210940. [PMID: 30840628 PMCID: PMC6402643 DOI: 10.1371/journal.pone.0210940] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 11/22/2018] [Indexed: 11/18/2022] Open
Abstract
Biosensors have emerged as a valuable tool with high specificity and sensitivity for fast and reliable detection of hazardous substances in drinking water. Numerous substances have been addressed using synthetic biology approaches. However, many proposed biosensors are based on living, genetically modified organisms and are therefore limited in shelf life, usability and biosafety. We addressed these issues by the construction of an extensible, cell-free biosensor. Storage is possible through freeze drying on paper. Following the addition of an aqueous sample, a highly efficient cell-free protein synthesis (CFPS) reaction is initiated. Specific allosteric transcription factors modulate the expression of ‘superfolder’ green fluorescent protein (sfGFP) depending on the presence of the substance of interest. The resulting fluorescence intensities are analyzed with a conventional smartphone accompanied by simple and cheap light filters. An ordinary differential equitation (ODE) model of the biosensors was developed, which enabled prediction and optimization of performance. With an optimized cell-free biosensor based on the Shigella flexneri MerR transcriptional activator, detection of 6 μg/L Hg(II) ions in water was achieved. Furthermore, a completely new biosensor for the detection of gamma-hydroxybutyrate (GHB), a substance used as date-rape drug, was established by employing the naturally occurring transcriptional repressor BlcR from Agrobacterium tumefaciens.
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Affiliation(s)
- Alexander Gräwe
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Anna Dreyer
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tobias Vornholt
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Ursela Barteczko
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Luzia Buchholz
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Gila Drews
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Uyen Linh Ho
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marta Eva Jackowski
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Melissa Kracht
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Janina Lüders
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tore Bleckwehl
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Lukas Rositzka
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Matthias Ruwe
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Manuel Wittchen
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Petra Lutter
- Faculty of Biology, Mathematical Methods in Systems Biology, Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Kristian Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology, Bielefeld University, Bielefeld, Germany
- * E-mail:
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Dudley QM, Nash CJ, Jewett MC. Cell-free biosynthesis of limonene using enzyme-enriched Escherichia coli lysates. Synth Biol (Oxf) 2019; 4:ysz003. [PMID: 30873438 PMCID: PMC6407499 DOI: 10.1093/synbio/ysz003] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/18/2018] [Accepted: 12/23/2018] [Indexed: 11/25/2022] Open
Abstract
Isoprenoids are an attractive class of metabolites for enzymatic synthesis from renewable substrates. However, metabolic engineering of microorganisms for monoterpenoid production is limited by the need for time-consuming, and often non-intuitive, combinatorial tuning of biosynthetic pathway variations to meet design criteria. Towards alleviating this limitation, the goal of this work was to build a modular, cell-free platform for construction and testing of monoterpenoid pathways, using the fragrance and flavoring molecule limonene as a model. In this platform, multiple Escherichia coli lysates, each enriched with a single overexpressed pathway enzyme, are mixed to construct the full biosynthetic pathway. First, we show the ability to synthesize limonene from six enriched lysates with mevalonate substrate, an adenosine triphosphate (ATP) source, and cofactors. Next, we extend the pathway to use glucose as a substrate, which relies on native metabolism in the extract to convert glucose to acetyl-CoA along with three additional enzymes to convert acetyl-CoA to mevalonate. We find that the native E. coli farnesyl diphosphate synthase (IspA) is active in the lysate and diverts flux from the pathway intermediate geranyl pyrophospahte to farnesyl pyrophsophate and the byproduct farnesol. By adjusting the relative levels of cofactors NAD+, ATP and CoA, the system can synthesize 0.66 mM (90.2 mg l-1) limonene over 24 h, a productivity of 3.8 mg l-1 h-1. Our results highlight the flexibility of crude lysates to sustain complex metabolism and, by activating a glucose-to-limonene pathway with 9 heterologous enzymes encompassing 20 biosynthetic steps, expands an approach of using enzyme-enriched lysates for constructing, characterizing and prototyping enzymatic pathways.
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Affiliation(s)
- Quentin M Dudley
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Connor J Nash
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute Northwestern University, Chicago, IL, USA
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36
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Dopp BJL, Tamiev DD, Reuel NF. Cell-free supplement mixtures: Elucidating the history and biochemical utility of additives used to support in vitro protein synthesis in E. coli extract. Biotechnol Adv 2019; 37:246-258. [DOI: 10.1016/j.biotechadv.2018.12.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/06/2018] [Accepted: 12/15/2018] [Indexed: 12/18/2022]
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37
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Wang W, Li Y, Wang Y, Shi C, Li C, Li Q, Linhardt RJ. Bacteriophage T7 transcription system: an enabling tool in synthetic biology. Biotechnol Adv 2018; 36:2129-2137. [DOI: 10.1016/j.biotechadv.2018.10.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 10/28/2022]
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38
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Xiang Y, Dalchau N, Wang B. Scaling up genetic circuit design for cellular computing: advances and prospects. NATURAL COMPUTING 2018; 17:833-853. [PMID: 30524216 PMCID: PMC6244767 DOI: 10.1007/s11047-018-9715-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Synthetic biology aims to engineer and redesign biological systems for useful real-world applications in biomanufacturing, biosensing and biotherapy following a typical design-build-test cycle. Inspired from computer science and electronics, synthetic gene circuits have been designed to exhibit control over the flow of information in biological systems. Two types are Boolean logic inspired TRUE or FALSE digital logic and graded analog computation. Key principles for gene circuit engineering include modularity, orthogonality, predictability and reliability. Initial circuits in the field were small and hampered by a lack of modular and orthogonal components, however in recent years the library of available parts has increased vastly. New tools for high throughput DNA assembly and characterization have been developed enabling rapid prototyping, systematic in situ characterization, as well as automated design and assembly of circuits. Recently implemented computing paradigms in circuit memory and distributed computing using cell consortia will also be discussed. Finally, we will examine existing challenges in building predictable large-scale circuits including modularity, context dependency and metabolic burden as well as tools and methods used to resolve them. These new trends and techniques have the potential to accelerate design of larger gene circuits and result in an increase in our basic understanding of circuit and host behaviour.
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Affiliation(s)
- Yiyu Xiang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR UK
| | | | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR UK
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Senoussi A, Lee Tin Wah J, Shimizu Y, Robert J, Jaramillo A, Findeiss S, Axmann IM, Estevez-Torres A. Quantitative Characterization of Translational Riboregulators Using an in Vitro Transcription-Translation System. ACS Synth Biol 2018; 7:1269-1278. [PMID: 29617125 DOI: 10.1021/acssynbio.7b00387] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Riboregulators are short RNA sequences that, upon binding to a ligand, change their secondary structure and influence the expression rate of a downstream gene. They constitute an attractive alternative to transcription factors for building synthetic gene regulatory networks because they can be engineered de novo. However, riboregulators are generally designed in silico and tested in vivo, which provides little quantitative information about their performances, thus hindering the improvement of design algorithms. Here we show that a cell-free transcription-translation (TX-TL) system provides valuable information about the performances of in silico designed riboregulators. We first propose a simple model that provides a quantitative definition of the dynamic range of a riboregulator. We further characterize two types of translational riboregulators composed of a cis-repressed (cr) and a trans-activating (ta) strand. At the DNA level we demonstrate that high concentrations of taDNA poisoned the activator until total shut off, in agreement with our model, and that relative dynamic ranges of riboregulators determined in vitro are in agreement with published in vivo data. At the RNA level, we show that this approach provides a fast and simple way to measure dissociation constants of functional riboregulators, in contrast to standard mobility-shift assays. Our method opens the route for using cell-free TX-TL systems for the quantitative characterization of functional riboregulators in order to improve their design in silico.
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Affiliation(s)
- Anis Senoussi
- Sorbonne Université and CNRS, Laboratoire Jean Perrin, F-75005, Paris, France
| | | | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Quantitative Biology Center, Osaka 565-0874, Japan
| | - Jérôme Robert
- Sorbonne Université and CNRS, Laboratoire Jean Perrin, F-75005, Paris, France
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, CV4 7AL, Coventry, U.K
- CNRS Laboratoire iSSB, Université Paris-Saclay, Université d’ Évry and CEA, DRF, IG, Genoscope, F-91000 Évry, France
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain
| | - Sven Findeiss
- Dept. Computer Science and ICB, University Leipzig, D-04107 Leipzig, Germany
- University of Vienna, Faculties of Computer Science and Chemistry, Dept. of Theoretical Chemistry, A-1090 Vienna, Austria
| | - Ilka M. Axmann
- Institute for Synthetic Microbiology and CEPLAS, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
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40
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Jayaraman P, Yeoh JW, Jayaraman S, Teh AY, Zhang J, Poh CL. Cell-Free Optogenetic Gene Expression System. ACS Synth Biol 2018; 7:986-994. [PMID: 29596741 DOI: 10.1021/acssynbio.7b00422] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Optogenetic tools provide a new and efficient way to dynamically program gene expression with unmatched spatiotemporal precision. To date, their vast potential remains untapped in the field of cell-free synthetic biology, largely due to the lack of simple and efficient light-switchable systems. Here, to bridge the gap between cell-free systems and optogenetics, we studied our previously engineered one component-based blue light-inducible Escherichia coli promoter in a cell-free environment through experimental characterization and mathematical modeling. We achieved >10-fold dynamic expression and demonstrated rapid and reversible activation of the target gene to generate oscillatory response. The deterministic model developed was able to recapitulate the system behavior and helped to provide quantitative insights to optimize dynamic response. This in vitro optogenetic approach could be a powerful new high-throughput screening technology for rapid prototyping of complex biological networks in both space and time without the need for chemical induction.
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41
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Borkowski O, Bricio C, Murgiano M, Rothschild-Mancinelli B, Stan GB, Ellis T. Cell-free prediction of protein expression costs for growing cells. Nat Commun 2018; 9:1457. [PMID: 29654285 PMCID: PMC5899134 DOI: 10.1038/s41467-018-03970-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 03/26/2018] [Indexed: 01/12/2023] Open
Abstract
Translating heterologous proteins places significant burden on host cells, consuming expression resources leading to slower cell growth and productivity. Yet predicting the cost of protein production for any given gene is a major challenge, as multiple processes and factors combine to determine translation efficiency. To enable prediction of the cost of gene expression in bacteria, we describe here a standard cell-free lysate assay that provides a relative measure of resource consumption when a protein coding sequence is expressed. These lysate measurements can then be used with a computational model of translation to predict the in vivo burden placed on growing E. coli cells for a variety of proteins of different functions and lengths. Using this approach, we can predict the burden of expressing multigene operons of different designs and differentiate between the fraction of burden related to gene expression compared to action of a metabolic pathway.
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Affiliation(s)
- Olivier Borkowski
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Carlos Bricio
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Michela Murgiano
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Brooke Rothschild-Mancinelli
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Guy-Bart Stan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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42
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Schoborg JA, Jewett MC. Cell-Free Protein Synthesis: An Emerging Technology for Understanding, Harnessing, and Expanding the Capabilities of Biological Systems. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Jennifer A. Schoborg
- Department of Chemical and Biological Engineering; Northwestern University, 2145 Sheridan Road, Evanston, IL; 60208-3120 USA
- Chemistry of Life Processes Institute; 2170 Campus Drive, Evanston, IL; 60208-3120 USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering; Northwestern University, 2145 Sheridan Road, Evanston, IL; 60208-3120 USA
- Chemistry of Life Processes Institute; 2170 Campus Drive, Evanston, IL; 60208-3120 USA
- Robert H. Lurie Comprehensive Cancer Center; Northwestern University, 676 N. St Clair St; Suite 1200 Chicago IL 60611-3068 USA
- Simpson Querrey Institute; Northwestern University; 303 E. Superior St; Suite 11-131, Chicago IL 60611-2875 USA
- Center for Synthetic Biology; Northwestern University, 2145 Sheridan Road; Evanston IL 60208-3120 USA
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43
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Karig DK, Bessling S, Thielen P, Zhang S, Wolfe J. Preservation of protein expression systems at elevated temperatures for portable therapeutic production. J R Soc Interface 2018; 14:rsif.2016.1039. [PMID: 28446704 PMCID: PMC5414909 DOI: 10.1098/rsif.2016.1039] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/04/2017] [Indexed: 12/23/2022] Open
Abstract
Many biotechnology capabilities are limited by stringent storage needs of reagents, largely prohibiting use outside of specialized laboratories. Focusing on a large class of protein-based biotechnology applications, we address this issue by developing a method for preserving cell-free protein expression systems for months above room temperature. Our approach realizes unprecedented long-term stability at elevated temperatures by leveraging the sugar alcohol trehalose, a simple, low-cost, open-air drying step, and strategic separation of reaction components during drying. The resulting preservation capacity enables efficient production of a wide range of on-demand proteins under adverse conditions, for instance during emergency outbreaks or in remote locations. To demonstrate application potential, we use cell-free reagents subjected to months of exposure at 37°C and atmospheric conditions to produce sufficient concentrations of a pyocin protein to kill Pseudomonas aeruginosa, a troublesome pathogen for traumatic and burn wound injuries. Our work makes possible new biotechnology applications that demand ruggedness and scalability.
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Affiliation(s)
- David K Karig
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA .,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Seneca Bessling
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA
| | - Peter Thielen
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA
| | - Sherry Zhang
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA
| | - Joshua Wolfe
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA
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44
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A plasmid-based Escherichia coli gene expression system with cell-to-cell variation below the extrinsic noise limit. PLoS One 2017; 12:e0187259. [PMID: 29084263 PMCID: PMC5662224 DOI: 10.1371/journal.pone.0187259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 10/17/2017] [Indexed: 11/19/2022] Open
Abstract
Experiments in synthetic biology and microbiology can benefit from protein expression systems with low cell-to-cell variability (noise) and expression levels precisely tunable across a useful dynamic range. Despite advances in understanding the molecular biology of microbial gene regulation, many experiments employ protein-expression systems exhibiting high noise and nearly all-or-none responses to induction. I present an expression system that incorporates elements known to reduce gene expression noise: negative autoregulation and bicistronic transcription. I show by stochastic simulation that while negative autoregulation can produce a more gradual response to induction, bicistronic expression of a repressor and gene of interest can be necessary to reduce noise below the extrinsic limit. I synthesized a plasmid-based system incorporating these principles and studied its properties in Escherichia coli cells, using flow cytometry and fluorescence microscopy to characterize induction dose-response, induction/repression kinetics and gene expression noise. By varying ribosome binding site strengths, expression levels from 55–10,740 molecules/cell were achieved with noise below the extrinsic limit. Individual strains are inducible across a dynamic range greater than 20-fold. Experimental comparison of different regulatory networks confirmed that bicistronic autoregulation reduces noise, and revealed unexpectedly high noise for a conventional expression system with a constitutively expressed transcriptional repressor. I suggest a hybrid, low-noise expression system to increase the dynamic range.
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45
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Hurst GB, Asano KG, Doktycz CJ, Consoli EJ, Doktycz WL, Foster CM, Morrell-Falvey JL, Standaert RF, Doktycz MJ. Proteomics-Based Tools for Evaluation of Cell-Free Protein Synthesis. Anal Chem 2017; 89:11443-11451. [DOI: 10.1021/acs.analchem.7b02555] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Robert F. Standaert
- University of Tennessee, Department of Biochemistry & Cellular and Molecular Biology, Knoxville, Tennessee 37996, United States
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46
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Ogawa A, Masuoka H, Ota T. Artificial OFF-Riboswitches That Downregulate Internal Ribosome Entry without Hybridization Switches in a Eukaryotic Cell-Free Translation System. ACS Synth Biol 2017; 6:1656-1662. [PMID: 28613837 DOI: 10.1021/acssynbio.7b00124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We constructed novel artificial riboswitches that function in a eukaryotic translation system (wheat germ extract), by rationally implanting an in vitro-selected aptamer into the intergenic internal ribosome entry site (IRES) of Plautia stali intestine virus. These eukaryotic OFF-riboswitches (OFF-eRSs) ligand-dose-dependently downregulate IRES-mediated translation without hybridization switches, which typical riboswitches utilize for gene regulation. The hybridization-switch-free mechanism not only allows for easy design but also requires less energy for regulation, resulting in a higher switching efficiency than hybridization-switch-based OFF-eRSs provide. In addition, even a small ligand such as theophylline can induce satisfactory repression, in contrast to other types of OFF-eRSs that modulate the 5' cap-dependent canonical translation. Because our proposed hybridization-switch-free OFF-eRSs are based on a versatile IRES that functions well in many types of eukaryotic translation systems, they would be widely usable elements for synthetic gene circuits in both cell-free and cell-based synthetic biology.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3
Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hiroki Masuoka
- Proteo-Science Center, Ehime University, 3
Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Tsubasa Ota
- Proteo-Science Center, Ehime University, 3
Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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47
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Rampley CPN, Davison PA, Qian P, Preston GM, Hunter CN, Thompson IP, Wu LJ, Huang WE. Development of SimCells as a novel chassis for functional biosensors. Sci Rep 2017; 7:7261. [PMID: 28775370 PMCID: PMC5543166 DOI: 10.1038/s41598-017-07391-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/28/2017] [Indexed: 01/31/2023] Open
Abstract
This work serves as a proof-of-concept for bacterially derived SimCells (Simple Cells), which contain the cell machinery from bacteria and designed DNA (or potentially a simplified genome) to instruct the cell to carry out novel, specific tasks. SimCells represent a reprogrammable chassis without a native chromosome, which can host designed DNA to perform defined functions. In this paper, the use of Escherichia coli MC1000 ∆minD minicells as a non-reproducing chassis for SimCells was explored, as demonstrated by their ability to act as sensitive biosensors for small molecules. Highly purified minicells derived from E. coli strains containing gene circuits for biosensing were able to transduce the input signals from several small molecules (glucarate, acrylate and arabinose) into the production of green fluorescent protein (GFP). A mathematical model was developed to fit the experimental data for induction of gene expression in SimCells. The intracellular ATP level was shown to be important for SimCell function. A purification and storage protocol was developed to prepare SimCells which could retain their functions for an extended period of time. This study demonstrates that SimCells are able to perform as ‘smart bioparticles’ controlled by designed gene circuits.
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Affiliation(s)
- Cordelia P N Rampley
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Paul A Davison
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, Oxford, United Kingdom
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Ling Juan Wu
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom.
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48
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Moore SJ, MacDonald JT, Freemont PS. Cell-free synthetic biology for in vitro prototype engineering. Biochem Soc Trans 2017; 45:785-791. [PMID: 28620040 PMCID: PMC5473021 DOI: 10.1042/bst20170011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 03/24/2017] [Accepted: 03/31/2017] [Indexed: 12/21/2022]
Abstract
Cell-free transcription-translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells.
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Affiliation(s)
- Simon J Moore
- Department of Medicine, Centre for Synthetic Biology and Innovation, South Kensington Campus, London, U.K
| | - James T MacDonald
- Department of Medicine, Centre for Synthetic Biology and Innovation, South Kensington Campus, London, U.K
| | - Paul S Freemont
- Department of Medicine, Centre for Synthetic Biology and Innovation, South Kensington Campus, London, U.K.
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A real-time control system of gene expression using ligand-bound nucleic acid aptamer for metabolic engineering. Metab Eng 2017; 42:85-97. [PMID: 28603040 DOI: 10.1016/j.ymben.2017.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/18/2017] [Accepted: 06/05/2017] [Indexed: 11/23/2022]
Abstract
Artificial control of bio-functions through regulating gene expression is one of the most important and attractive technologies to build novel living systems that are useful in the areas of chemical synthesis, nanotechnology, pharmacology, cell biology. Here, we present a novel real-time control system of gene regulation that includes an enhancement element by introducing duplex DNA aptamers upstream promoter and a repression element by introducing a RNA aptamer upstream ribosome binding site. With the presence of ligands corresponding to the DNA aptamers, the expression of the target gene can be potentially enhanced at the transcriptional level by strengthening the recognition capability of RNAP to the recognition region and speeding up the separation efficiency of the unwinding region due to the induced DNA bubble around the thrombin-bound aptamers; while with the presence of RNA aptamer ligand, the gene expression can be repressed at the translational level by weakening the recognition capability of ribosome to RBS due to the shielding of RBS by the formed aptamer-ligand complex upstream RBS. The effectiveness and potential utility of the developed gene regulation system were demonstrated by regulating the expression of ecaA gene in the cell-free systems. The realistic metabolic engineering application of the system has also tested by regulating the expression of mgtC gene and thrombin cDNA in Escherichia coli JD1021 for controlling metabolic flux and improving thrombin production, verifying that the real-time control system of gene regulation is able to realize the dynamic regulation of gene expression with potential applications in bacterial physiology studies and metabolic engineering.
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Karig DK. Cell-free synthetic biology for environmental sensing and remediation. Curr Opin Biotechnol 2017; 45:69-75. [DOI: 10.1016/j.copbio.2017.01.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/24/2017] [Indexed: 01/15/2023]
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