1
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Cardiff RAL, Carothers JM, Zalatan JG, Sauro HM. Systems-Level Modeling for CRISPR-Based Metabolic Engineering. ACS Synth Biol 2024; 13:2643-2652. [PMID: 39119666 DOI: 10.1021/acssynbio.4c00053] [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: 08/10/2024]
Abstract
The CRISPR-Cas system has enabled the development of sophisticated, multigene metabolic engineering programs through the use of guide RNA-directed activation or repression of target genes. To optimize biosynthetic pathways in microbial systems, we need improved models to inform design and implementation of transcriptional programs. Recent progress has resulted in new modeling approaches for identifying gene targets and predicting the efficacy of guide RNA targeting. Genome-scale and flux balance models have successfully been applied to identify targets for improving biosynthetic production yields using combinatorial CRISPR-interference (CRISPRi) programs. The advent of new approaches for tunable and dynamic CRISPR activation (CRISPRa) promises to further advance these engineering capabilities. Once appropriate targets are identified, guide RNA prediction models can lead to increased efficacy in gene targeting. Developing improved models and incorporating approaches from machine learning may be able to overcome current limitations and greatly expand the capabilities of CRISPR-Cas9 tools for metabolic engineering.
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Affiliation(s)
- Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - James M Carothers
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jesse G Zalatan
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Herbert M Sauro
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
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2
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Yurchenko A, Özkul G, van Riel NAW, van Hest JCM, de Greef TFA. Mechanism-based and data-driven modeling in cell-free synthetic biology. Chem Commun (Camb) 2024; 60:6466-6475. [PMID: 38847387 DOI: 10.1039/d4cc01289e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Cell-free systems have emerged as a versatile platform in synthetic biology, finding applications in various areas such as prototyping synthetic circuits, biosensor development, and biomanufacturing. To streamline the prototyping process, cell-free systems often incorporate a modeling step that predicts the outcomes of various experimental scenarios, providing a deeper insight into the underlying mechanisms and functions. There are two recognized approaches for modeling these systems: mechanism-based modeling, which models the underlying reaction mechanisms; and data-driven modeling, which makes predictions based on data without preconceived interactions between system components. In this highlight, we focus on the latest advancements in both modeling approaches for cell-free systems, exploring their potential for the design and optimization of synthetic genetic circuits.
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Affiliation(s)
- Angelina Yurchenko
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Synthetic Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Gökçe Özkul
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Synthetic Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Natal A W van Riel
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Eindhoven MedTech Innovation Center, 5612 AX Eindhoven, The Netherlands
- Department of Vascular Medicine, Amsterdam UMC, Amsterdam, The Netherlands
| | - Jan C M van Hest
- Bio-Organic Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
- Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Synthetic Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, 3584 CB Utrecht, The Netherlands
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3
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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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4
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Paulino NMG, Foo M, de Greef TFA, Kim J, Bates DG. A Theoretical Framework for Implementable Nucleic Acids Feedback Systems. Bioengineering (Basel) 2023; 10:466. [PMID: 37106653 PMCID: PMC10136085 DOI: 10.3390/bioengineering10040466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Chemical reaction networks can be utilised as basic components for nucleic acid feedback control systems' design for Synthetic Biology application. DNA hybridisation and programmed strand-displacement reactions are effective primitives for implementation. However, the experimental validation and scale-up of nucleic acid control systems are still considerably falling behind their theoretical designs. To aid with the progress heading into experimental implementations, we provide here chemical reaction networks that represent two fundamental classes of linear controllers: integral and static negative state feedback. We reduced the complexity of the networks by finding designs with fewer reactions and chemical species, to take account of the limits of current experimental capabilities and mitigate issues pertaining to crosstalk and leakage, along with toehold sequence design. The supplied control circuits are quintessential candidates for the first experimental validations of nucleic acid controllers, since they have a number of parameters, species, and reactions small enough for viable experimentation with current technical capabilities, but still represent challenging feedback control systems. They are also well suited to further theoretical analysis to verify results on the stability, performance, and robustness of this important new class of control systems.
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Affiliation(s)
| | - Mathias Foo
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK
| | - Tom F. A. de Greef
- Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Gyeongbuk, Republic of Korea
| | - Declan G. Bates
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK
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5
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Kardynska M, Kogut D, Pacholczyk M, Smieja J. Mathematical modeling of regulatory networks of intracellular processes - Aims and selected methods. Comput Struct Biotechnol J 2023; 21:1523-1532. [PMID: 36851915 PMCID: PMC9958294 DOI: 10.1016/j.csbj.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/03/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Regulatory networks structure and signaling pathways dynamics are uncovered in time- and resource consuming experimental work. However, it is increasingly supported by modeling, analytical and computational techniques as well as discrete mathematics and artificial intelligence applied to to extract knowledge from existing databases. This review is focused on mathematical modeling used to analyze dynamics and robustness of these networks. This paper presents a review of selected modeling methods that facilitate advances in molecular biology.
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Affiliation(s)
- Malgorzata Kardynska
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland
| | - Daria Kogut
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland.,Dept. of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Marcin Pacholczyk
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland.,Dept. of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Jaroslaw Smieja
- Dept. of Biosensors and Processing of Biomedical Signals, Silesian University of Technology, Gliwice, Poland.,Dept. of Systems Biology and Engineering, Silesian University of Technology, Gliwice, Poland
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6
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Kim KJ, Lee SJ, Kim DM. The Use of Cell-free Protein Synthesis to Push the Boundaries of Synthetic Biology. BIOTECHNOL BIOPROC E 2023; 28:1-7. [PMID: 36687336 PMCID: PMC9840425 DOI: 10.1007/s12257-022-0279-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/10/2022] [Accepted: 10/23/2022] [Indexed: 01/15/2023]
Abstract
Cell-free protein synthesis is emerging as a powerful tool to accelerate the progress of synthetic biology. Notably, cell-free systems that harness extracted synthetic machinery of cells can address many of the issues associated with the complexity and variability of living systems. In particular, cell-free systems can be programmed with various configurations of genetic information, providing great flexibility and accessibility to the field of synthetic biology. Empowered by recent progress, cell-free systems are now evolving into artificial biological systems that can be tailored for various applications, including on-demand biomanufacturing, diagnostics, and new materials design. Here, we review the key developments related to cell-free protein synthesis systems, and discuss the future directions of these promising technologies.
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Affiliation(s)
- Kyu Jae Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134 Korea
| | - So-Jeong Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134 Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134 Korea
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7
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Expanding luciferase reporter systems for cell-free protein expression. Sci Rep 2022; 12:11489. [PMID: 35798760 PMCID: PMC9263134 DOI: 10.1038/s41598-022-15624-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/27/2022] [Indexed: 11/08/2022] Open
Abstract
Luciferases are often used as a sensitive, versatile reporter in cell-free transcription-translation (TXTL) systems, for research and practical applications such as engineering genetic parts, validating genetic circuits, and biosensor outputs. Currently, only two luciferases (Firefly and Renilla) are commonly used without substrate cross-talk. Here we demonstrate the expansion of the cell-free luciferase reporter system, with two orthogonal luciferase reporters: N. nambi luciferase (Luz) and LuxAB. These luciferases do not have cross-reactivity with the Firefly and Renilla substrates. We also demonstrate a substrate regeneration pathway for one of the new luciferases, enabling long-term time courses of protein expression monitoring in the cell-free system. Furthermore, we reduced the number of genes required in TXTL expression, by engineering a cell extract containing part of the luciferase enzymes. Our findings lead to an expanded platform with multiple orthogonal luminescence translation readouts for in vitro protein expression.
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8
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Sato W, Sharon J, Deich C, Gaut N, Cash B, Engelhart AE, Adamala KP. Akaby-Cell-free protein expression system for linear templates. PLoS One 2022; 17:e0266272. [PMID: 35390057 PMCID: PMC8989226 DOI: 10.1371/journal.pone.0266272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/17/2022] [Indexed: 12/01/2022] Open
Abstract
Cell-free protein expression is increasingly becoming popular for biotechnology, biomedical and research applications. Among cell-free systems, the most popular one is based on Escherichia coli (E. coli). Endogenous nucleases in E. coli cell-free transcription-translation (TXTL) degrade the free ends of DNA, resulting in inefficient protein expression from linear DNA templates. RecBCD is a nuclease complex that plays a major role in nuclease activity in E. coli, with the RecB subunit possessing the actual nuclease activity. We created a RecB knockout of an E. coli strain optimized for cell-free expression. We named this new strain Akaby. We demonstrated that Akaby TXTL successfully reduced linear DNA degradations, rescuing the protein expression efficiency from the linear DNA templates. The practicality of Akaby for TXTL is an efficient, simple alternative for linear template expression in cell-free reactions. We also use this work as a model protocol for modifying the TXTL source E. coli strain, enabling the creation of TXTL systems with other custom modifications.
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Affiliation(s)
- Wakana Sato
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States of America
| | - Judee Sharon
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States of America
| | - Christopher Deich
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States of America
| | - Nathaniel Gaut
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States of America
| | - Brock Cash
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States of America
| | - Aaron E. Engelhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States of America
| | - Katarzyna P. Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States of America
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9
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Brookwell A, Oza JP, Caschera F. Biotechnology Applications of Cell-Free Expression Systems. Life (Basel) 2021; 11:life11121367. [PMID: 34947898 PMCID: PMC8705439 DOI: 10.3390/life11121367] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Cell-free systems are a rapidly expanding platform technology with an important role in the engineering of biological systems. The key advantages that drive their broad adoption are increased efficiency, versatility, and low cost compared to in vivo systems. Traditionally, in vivo platforms have been used to synthesize novel and industrially relevant proteins and serve as a testbed for prototyping numerous biotechnologies such as genetic circuits and biosensors. Although in vivo platforms currently have many applications within biotechnology, they are hindered by time-constraining growth cycles, homeostatic considerations, and limited adaptability in production. Conversely, cell-free platforms are not hindered by constraints for supporting life and are therefore highly adaptable to a broad range of production and testing schemes. The advantages of cell-free platforms are being leveraged more commonly by the biotechnology community, and cell-free applications are expected to grow exponentially in the next decade. In this study, new and emerging applications of cell-free platforms, with a specific focus on cell-free protein synthesis (CFPS), will be examined. The current and near-future role of CFPS within metabolic engineering, prototyping, and biomanufacturing will be investigated as well as how the integration of machine learning is beneficial to these applications.
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Affiliation(s)
- August Brookwell
- Department of Chemistry & Biochemistry, College of Science & Mathematics, California Polytechnic State University, San Luis Obispo, CA 93407, USA;
| | - Javin P. Oza
- Department of Chemistry & Biochemistry, College of Science & Mathematics, California Polytechnic State University, San Luis Obispo, CA 93407, USA;
- Correspondence: (J.P.O.); (F.C.)
| | - Filippo Caschera
- Nuclera Nucleics Ltd., Cambridge CB4 0GD, UK
- Correspondence: (J.P.O.); (F.C.)
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10
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11
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Daley SK, Cordell GA. Natural Products, the Fourth Industrial Revolution, and the Quintuple Helix. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211003029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The profound interconnectedness of the sciences and technologies embodied in the Fourth Industrial Revolution is discussed in terms of the global role of natural products, and how that interplays with the development of sustainable and climate-conscious practices of cyberecoethnopharmacolomics within the Quintuple Helix for the promotion of a healthier planet and society.
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Affiliation(s)
| | - Geoffrey A. Cordell
- Natural Products Inc., Evanston, IL, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, USA
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12
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Kitagawa T, Nishio T, Yoshikawa Y, Umezawa N, Higuchi T, Shew CY, Kenmotsu T, Yoshikawa K. Effects of Structural Isomers of Spermine on the Higher-Order Structure of DNA and Gene Expression. Int J Mol Sci 2021; 22:ijms22052355. [PMID: 33652986 PMCID: PMC7956460 DOI: 10.3390/ijms22052355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 11/16/2022] Open
Abstract
Polyamines are involved in various biological functions, including cell proliferation, differentiation, gene regulation, etc. Recently, it was found that polyamines exhibit biphasic effects on gene expression: promotion and inhibition at low and high concentrations, respectively. Here, we compared the effects of three naturally occurring tetravalent polyamines, spermine (SPM), thermospermine (TSPM), and N4-aminopropylspermidine (BSPD). Based on the single DNA observation with fluorescence microscopy together with measurements by atomic force microscopy revealed that these polyamines induce shrinkage and then compaction of DNA molecules, at low and high concentrations, respectively. We also performed the observation to evaluate the effects of these polyamine isomers on the activity of gene expression by adapting a cell-free luciferase assay. Interestingly, the potency of their effects on the DNA conformation and also on the inhibition of gene expression activity indicates the highest for TSPM among spermine isomers. A numerical evaluation of the strength of the interaction of these polyamines with negatively charged double-strand DNA revealed that this ordering of the potency corresponds to the order of the strength of the attractive interaction between phosphate groups of DNA and positively charged amino groups of the polyamines.
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Affiliation(s)
- Tomoki Kitagawa
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
| | - Takashi Nishio
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
| | - Yuko Yoshikawa
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan; (N.U.); (T.H.)
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan; (N.U.); (T.H.)
| | - Chwen-Yang Shew
- Doctoral Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA;
- Department of Chemistry, College of Staten Island, Staten Island, New York, NY 10314, USA
| | - Takahiro Kenmotsu
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
- Correspondence: (T.K.); (K.Y.)
| | - Kenichi Yoshikawa
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto 606-8501, Japan
- Correspondence: (T.K.); (K.Y.)
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13
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Verbič A, Praznik A, Jerala R. A guide to the design of synthetic gene networks in mammalian cells. FEBS J 2020; 288:5265-5288. [PMID: 33289352 DOI: 10.1111/febs.15652] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/06/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
Synthetic biology aims to harness natural and synthetic biological parts and engineering them in new combinations and systems, producing novel therapies, diagnostics, bioproduction systems, and providing information on the mechanism of function of biological systems. Engineering cell function requires the rewiring or de novo construction of cell information processing networks. Using natural and synthetic signal processing elements, researchers have demonstrated a wide array of signal sensing, processing and propagation modules, using transcription, translation, or post-translational modification to program new function. The toolbox for synthetic network design is ever-advancing and has still ample room to grow. Here, we review the diversity of synthetic gene networks, types of building modules, techniques of regulation, and their applications.
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Affiliation(s)
- Anže Verbič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
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14
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Müller J, Siemann-Herzberg M, Takors R. Modeling Cell-Free Protein Synthesis Systems-Approaches and Applications. Front Bioeng Biotechnol 2020; 8:584178. [PMID: 33195146 PMCID: PMC7655533 DOI: 10.3389/fbioe.2020.584178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/29/2020] [Indexed: 01/03/2023] Open
Abstract
In vitro systems are ideal setups to investigate the basic principles of biochemical reactions and subsequently the bricks of life. Cell-free protein synthesis (CFPS) systems mimic the transcription and translation processes of whole cells in a controlled environment and allow the detailed study of single components and reaction networks. In silico studies of CFPS systems help us to understand interactions and to identify limitations and bottlenecks in those systems. Black-box models laid the foundation for understanding the production and degradation dynamics of macromolecule components such as mRNA, ribosomes, and proteins. Subsequently, more sophisticated models revealed shortages in steps such as translation initiation and tRNA supply and helped to partially overcome these limitations. Currently, the scope of CFPS modeling has broadened to various applications, ranging from the screening of kinetic parameters to the stochastic analysis of liposome-encapsulated CFPS systems and the assessment of energy supply properties in combination with flux balance analysis (FBA).
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Affiliation(s)
| | | | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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15
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Marucci L, Barberis M, Karr J, Ray O, Race PR, de Souza Andrade M, Grierson C, Hoffmann SA, Landon S, Rech E, Rees-Garbutt J, Seabrook R, Shaw W, Woods C. Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. Front Bioeng Biotechnol 2020; 8:942. [PMID: 32850764 PMCID: PMC7426639 DOI: 10.3389/fbioe.2020.00942] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/21/2020] [Indexed: 01/03/2023] Open
Abstract
Computer-aided design (CAD) for synthetic biology promises to accelerate the rational and robust engineering of biological systems. It requires both detailed and quantitative mathematical and experimental models of the processes to (re)design biology, and software and tools for genetic engineering and DNA assembly. Ultimately, the increased precision in the design phase will have a dramatic impact on the production of designer cells and organisms with bespoke functions and increased modularity. CAD strategies require quantitative models of cells that can capture multiscale processes and link genotypes to phenotypes. Here, we present a perspective on how whole-cell, multiscale models could transform design-build-test-learn cycles in synthetic biology. We show how these models could significantly aid in the design and learn phases while reducing experimental testing by presenting case studies spanning from genome minimization to cell-free systems. We also discuss several challenges for the realization of our vision. The possibility to describe and build whole-cells in silico offers an opportunity to develop increasingly automatized, precise and accessible CAD tools and strategies.
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Affiliation(s)
- Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom.,School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom.,Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom
| | - Matteo Barberis
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom.,Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, United Kingdom.,Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Jonathan Karr
- Icahn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Oliver Ray
- Department of Computer Science, University of Bristol, Bristol, United Kingdom
| | - Paul R Race
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Miguel de Souza Andrade
- Brazilian Agricultural Research Corporation/National Institute of Science and Technology - Synthetic Biology, Brasília, Brazil.,Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Claire Grierson
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Stefan Andreas Hoffmann
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Sophie Landon
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom.,Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom
| | - Elibio Rech
- Brazilian Agricultural Research Corporation/National Institute of Science and Technology - Synthetic Biology, Brasília, Brazil
| | - Joshua Rees-Garbutt
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Richard Seabrook
- Elizabeth Blackwell Institute for Health Research (EBI), University of Bristol, Bristol, United Kingdom
| | - William Shaw
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Christopher Woods
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Chemistry, University of Bristol, Bristol, United Kingdom
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16
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Liu JL, Zabetakis D, Breger JC, Anderson GP, Goldman ER. Multi-Enzyme Assembly on T4 Phage Scaffold. Front Bioeng Biotechnol 2020; 8:571. [PMID: 32671028 PMCID: PMC7327620 DOI: 10.3389/fbioe.2020.00571] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 01/11/2023] Open
Abstract
Over the past two decades, various scaffolds have been designed and synthesized to organize enzyme cascades spatially for enhanced enzyme activity based on the concepts of substrate channeling and enhanced stability. The most bio-compatible synthetic scaffolds known for enzyme immobilization are protein and DNA nanostructures. Herein, we examined the utility of the T4 phage capsid to serve as a naturally occurring protein scaffold for the immobilization of a three-enzyme cascade: Amylase, Maltase, and Glucokinase. Covalent constructs between each of the enzymes and the outer capsid protein Hoc were prepared through SpyTag-SpyCatcher pairing and assembled onto phage capsids in vitro with an estimated average of 90 copies per capsid. The capsid-immobilized Maltase has a fourfold higher initial rate relative to Maltase free in solution. Kinetic analysis also revealed that the immobilized three-enzyme cascade has an 18-fold higher converted number of NAD+ to NADH relative to the mixtures in solution. Our results demonstrate that the T4 phage capsid can act as a naturally occurring scaffold with substantial potential to enhance enzyme activity by spatially organizing enzymes on the capsid Hoc.
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Affiliation(s)
- Jinny L Liu
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
| | - Daniel Zabetakis
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
| | - Joyce C Breger
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
| | - George P Anderson
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
| | - Ellen R Goldman
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States
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17
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Laohakunakorn N, Grasemann L, Lavickova B, Michielin G, Shahein A, Swank Z, Maerkl SJ. Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:213. [PMID: 32266240 PMCID: PMC7105575 DOI: 10.3389/fbioe.2020.00213] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-free systems offer a promising approach to engineer biology since their open nature allows for well-controlled and characterized reaction conditions. In this review, we discuss the history and recent developments in engineering recombinant and crude extract systems, as well as breakthroughs in enabling technologies, that have facilitated increased throughput, compartmentalization, and spatial control of cell-free protein synthesis reactions. Combined with a deeper understanding of the cell-free systems themselves, these advances improve our ability to address a range of scientific questions. By mastering control of the cell-free platform, we will be in a position to construct increasingly complex biomolecular systems, and approach natural biological complexity in a bottom-up manner.
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Affiliation(s)
- Nadanai Laohakunakorn
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura Grasemann
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbora Lavickova
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Grégoire Michielin
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Amir Shahein
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zoe Swank
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J. Maerkl
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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18
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Klein WP, Thomsen RP, Turner KB, Walper SA, Vranish J, Kjems J, Ancona MG, Medintz IL. Enhanced Catalysis from Multienzyme Cascades Assembled on a DNA Origami Triangle. ACS NANO 2019; 13:13677-13689. [PMID: 31751123 DOI: 10.1021/acsnano.9b05746] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Developing reliable methods of constructing cell-free multienzyme biocatalytic systems is a milestone goal of synthetic biology. It would enable overcoming the limitations of current cell-based systems, which suffer from the presence of competing pathways, toxicity, and inefficient access to extracellular reactants and removal of products. DNA nanostructures have been suggested as ideal scaffolds for assembling sequential enzymatic cascades in close enough proximity to potentially allow for exploiting of channeling effects; however, initial demonstrations have provided somewhat contradictory results toward confirming this phenomenon. In this work, a three-enzyme sequential cascade was realized by site-specifically immobilizing DNA-conjugated amylase, maltase, and glucokinase on a self-assembled DNA origami triangle. The kinetics of seven different enzyme configurations were evaluated experimentally and compared to simulations of optimized activity. A 30-fold increase in the pathway's kinetic activity was observed for enzymes assembled to the DNA. Detailed kinetic analysis suggests that this catalytic enhancement originated from increased enzyme stability and a localized DNA surface affinity or hydration layer effect and not from a directed enzyme-to-enzyme channeling mechanism. Nevertheless, the approach used to construct this pathway still shows promise toward improving other more elaborate multienzymatic cascades and could potentially allow for the custom synthesis of complex (bio)molecules that cannot be realized with conventional organic chemistry approaches.
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Affiliation(s)
- William P Klein
- National Research Council , Washington , D.C. 20001 , United States
| | - Rasmus P Thomsen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics , Aarhus University , 8000 Aarhus , Denmark
| | | | - Scott A Walper
- National Research Council , Washington , D.C. 20001 , United States
| | - James Vranish
- Ave Maria University , Ave Maria , Florida 34142 , United States
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics , Aarhus University , 8000 Aarhus , Denmark
| | | | - Igor L Medintz
- National Research Council , Washington , D.C. 20001 , United States
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19
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Khambhati K, Bhattacharjee G, Gohil N, Braddick D, Kulkarni V, Singh V. Exploring the Potential of Cell-Free Protein Synthesis for Extending the Abilities of Biological Systems. Front Bioeng Biotechnol 2019; 7:248. [PMID: 31681738 PMCID: PMC6797904 DOI: 10.3389/fbioe.2019.00248] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/16/2019] [Indexed: 12/19/2022] Open
Abstract
Cell-free protein synthesis (CFPS) system is a simple, rapid, and sensitive tool that is devoid of membrane-bound barriers, yet contains all the mandatory substrates, biomolecules, and machineries required for the synthesis of the desired proteins. It has the potential to overcome loopholes in the current in vivo production systems and is a promising tool in both basic and applied scientific research. It facilitates a simplified organization of desired experiments with a variety of reaction conditions, making CFPS a powerful tool in biological research. It has been used for the expansion of genetic code, assembly of viruses, and in metabolic engineering for production of toxic and complex proteins. Subsequently, CFPS systems have emerged as potent technology for high-throughput production of membrane proteins, enzymes, and therapeutics. The present review highlights the recent advances and uses of CFPS systems in biomedical, therapeutic, and biotechnological applications. Additionally, we highlight possible solutions to the potential biosafety issues that may be encountered while using CFPS technology.
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Affiliation(s)
- Khushal Khambhati
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | - Gargi Bhattacharjee
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | - Nisarg Gohil
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | | | - Vishwesh Kulkarni
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Vijai Singh
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
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20
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Pseudomonas putida in the quest of programmable chemistry. Curr Opin Biotechnol 2019; 59:111-121. [DOI: 10.1016/j.copbio.2019.03.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/15/2019] [Accepted: 03/12/2019] [Indexed: 11/19/2022]
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21
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Gabant P, Borrero J. PARAGEN 1.0: A Standardized Synthetic Gene Library for Fast Cell-Free Bacteriocin Synthesis. Front Bioeng Biotechnol 2019; 7:213. [PMID: 31552239 PMCID: PMC6743375 DOI: 10.3389/fbioe.2019.00213] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/22/2019] [Indexed: 02/06/2023] Open
Abstract
The continuous emergence of microbial resistance to our antibiotic arsenal is widely becoming recognized as an imminent threat to global human health. Bacteriocins are antimicrobial peptides currently under consideration as real alternatives or complements to common antibiotics. These peptides have been much studied, novel bacteriocins are regularly reported and several genomic databases on these peptides are currently updated. Despite this, to our knowledge, a physical collection of bacteriocins that would allow testing and comparing them for different applications does not exist. Rapid advances in synthetic biology in combination with cell-free protein synthesis technologies offer great potential for fast protein production. Based on the amino acid sequences of the mature peptide available in different databases, we have built a bacteriocin gene library, called PARAGEN 1.0, containing all the genetic elements required for in vitro cell-free peptide synthesis. Using PARAGEN 1.0 and a commercial kit for cell-free protein synthesis we have produced 164 different bacteriocins. Of the bacteriocins synthesized, 54% have shown antimicrobial activity against at least one of the indicator strains tested, including Gram-positive and Gram-negative bacteria representing commonly used lab strains, industrially relevant microorganisms, and known pathogens. This bacteriocin collection represents a streamlined pipeline for selection, production, and screening of bacteriocins as well as a reservoir of ready-to-use antimicrobials against virtually any class of relevant bacteria.
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22
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El Karoui M, Hoyos-Flight M, Fletcher L. Future Trends in Synthetic Biology-A Report. Front Bioeng Biotechnol 2019; 7:175. [PMID: 31448268 PMCID: PMC6692427 DOI: 10.3389/fbioe.2019.00175] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/08/2019] [Indexed: 11/20/2022] Open
Abstract
Leading researchers working on synthetic biology and its applications gathered at the University of Edinburgh in May 2018 to discuss the latest challenges and opportunities in the field. In addition to the potential socio-economic benefits of synthetic biology, they also examined the ethics and security risks arising from the development of these technologies. Speakers from industry, academia and not-for-profit organizations presented their vision for the future of the field and provided guidance to funding and regulatory bodies to ensure that synthetic biology research is carried out responsibly and can realize its full potential. This report aims to capture the collective views and recommendations that emerged from the discussions that took place. The meeting was held under the Chatham House Rule (i.e., a private invite-only meeting where comments can be freely used but not attributed) to promote open discussion; the findings and quotes included in the report are therefore not attributed to individuals. The goal of the meeting was to identify research priorities and bottlenecks. It also provided the opportunity to discuss how best to manage risk and earn public acceptance of this emerging and disruptive technology.
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Affiliation(s)
- Meriem El Karoui
- SynthSys-Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Monica Hoyos-Flight
- Innogen Institute, School of Social and Political Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Liz Fletcher
- SynthSys-Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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