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Peng A, Yin G, Zuo W, Zhang L, Du G, Chen J, Wang Y, Kang Z. Regulatory RNAs in Bacillus subtilis: A review on regulatory mechanism and applications in synthetic biology. Synth Syst Biotechnol 2024; 9:223-233. [PMID: 38385150 PMCID: PMC10877136 DOI: 10.1016/j.synbio.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Bacteria exhibit a rich repertoire of RNA molecules that intricately regulate gene expression at multiple hierarchical levels, including small RNAs (sRNAs), riboswitches, and antisense RNAs. Notably, the majority of these regulatory RNAs lack or have limited protein-coding capacity but play pivotal roles in orchestrating gene expression by modulating transcription, post-transcription or translation processes. Leveraging and redesigning these regulatory RNA elements have emerged as pivotal strategies in the domains of metabolic engineering and synthetic biology. While previous investigations predominantly focused on delineating the roles of regulatory RNA in Gram-negative bacterial models such as Escherichia coli and Salmonella enterica, this review aims to summarize the mechanisms and functionalities of endogenous regulatory RNAs inherent to typical Gram-positive bacteria, notably Bacillus subtilis. Furthermore, we explore the engineering and practical applications of these regulatory RNA elements in the arena of synthetic biology, employing B. subtilis as a foundational chassis.
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Affiliation(s)
- Anqi Peng
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guobin Yin
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Wenjie Zuo
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Luyao Zhang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yang Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zhen Kang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
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2
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Liu B, Samaniego CC, Bennett MR, Franco E, Chappell J. A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria. Nat Commun 2023; 14:5268. [PMID: 37644054 PMCID: PMC10465534 DOI: 10.1038/s41467-023-40785-x] [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: 02/24/2023] [Accepted: 08/10/2023] [Indexed: 08/31/2023] Open
Abstract
A lack of composable and tunable gene regulators has hindered efforts to engineer non-model bacteria and consortia. Toward addressing this, we explore the broad-host potential of small transcription activating RNA (STAR) and propose a design strategy to achieve tunable gene control. First, we demonstrate that STARs optimized for E. coli function across different Gram-negative species and can actuate using phage RNA polymerase, suggesting that RNA systems acting at the level of transcription are portable. Second, we explore an RNA design strategy that uses arrays of tandem and transcriptionally fused RNA regulators to precisely alter regulator concentration from 1 to 8 copies. This provides a simple means to predictably tune output gain across species and does not require access to large regulatory part libraries. Finally, we show RNA arrays can be used to achieve tunable cascading and multiplexing circuits across species, analogous to the motifs used in artificial neural networks.
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Affiliation(s)
- Baiyang Liu
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Christian Cuba Samaniego
- Department of Mechanical and Aerospace Engineering, Bioengineering, Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, Bioengineering, Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - James Chappell
- Department of Biosciences, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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3
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Liu B, Samaniego CC, Bennett MR, Franco E, Chappell J. A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529951. [PMID: 36865180 PMCID: PMC9980294 DOI: 10.1101/2023.02.24.529951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
A lack of composable and tunable gene regulators has hindered efforts to engineer non-model bacteria and consortia. To address this, we explore the broad-host potential of small transcription activating RNA (STAR) and propose a novel design strategy to achieve tunable gene control. First, we demonstrate that STARs optimized for E. coli function across different Gram-negative species and can actuate using phage RNA polymerase, suggesting that RNA systems acting at the level of transcription are portable. Second, we explore a novel RNA design strategy that uses arrays of tandem and transcriptionally fused RNA regulators to precisely alter regulator concentration from 1 to 8 copies. This provides a simple means to predictably tune output gain across species and does not require access to large regulatory part libraries. Finally, we show RNA arrays can be used to achieve tunable cascading and multiplexing circuits across species, analogous to the motifs used in artificial neural networks.
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Affiliation(s)
- Baiyang Liu
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Christian Cuba Samaniego
- Department of Mechanical and Aerospace Engineering, Bioengineering, and Molecular Biology Institute, University of California at Los Angeles, CA, USA
| | - Matthew R. Bennett
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, Bioengineering, and Molecular Biology Institute, University of California at Los Angeles, CA, USA
| | - James Chappell
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
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4
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Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria. J Mol Biol 2022; 434:167689. [PMID: 35717997 DOI: 10.1016/j.jmb.2022.167689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 01/24/2023]
Abstract
RNA switches are versatile tools in synthetic biology for sensing and regulation applications. The discoveries of RNA-mediated translational and transcriptional control have facilitated the development of complexde novodesigns of RNA switches. Specifically, RNA toehold-mediated switches, in which binding to the toehold sensing domain controls the transition between switch states via strand displacement, have been extensively adapted for coupling systems responses to specifictrans-RNA inputs. This review highlights some of the challenges associated with applying these switches for native RNA detectionin vivo, including transferability between organisms. The applicability and design considerations of toehold-mediated switches are discussed by highlighting twelve recently developed switch designs. This review finishes with future perspectives to address current gaps in the field, particularly regarding the power of structural prediction algorithms for improved in vivo functionality of RNA switches.
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5
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Liu B, Cuba Samaniego C, Bennett M, Chappell J, Franco E. RNA Compensation: A Positive Feedback Insulation Strategy for RNA-Based Transcription Networks. ACS Synth Biol 2022; 11:1240-1250. [PMID: 35244392 DOI: 10.1021/acssynbio.1c00540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The lack of signaling modularity of biomolecular systems poses major challenges toward engineering complex networks. Directional signaling between an upstream and a downstream circuit requires the presence of binding events, which result in the consumption of regulatory molecules and can compromise the operation of the upstream circuit. This issue has been previously addressed by introducing insulation strategies that include high-gain negative feedback and activation-deactivation reaction cycles. In this paper, we focus on RNA-based circuits and propose a new positive-feedback strategy to mitigate signal consumption that we propose occurs for each regulatory event due to irreversible binding of the RNA input to the RNA target. To mitigate this, an extra RNA input is added in tandem with transcription output to compensate the RNA consumption, leading to concentration robustness of the input RNA molecule regardless of the amount of downstream modules. We term this strategy RNA compensation, and it can be applied to systems that have a stringent input-output gain, such as Small Transcription Activating RNAs (STARs). Our theoretical analysis shows that RNA compensation not only eliminates the signaling consumption in individual STAR-based regulators, but also improves the composability of STAR cascades and the modularity of RNA bistable systems.
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Affiliation(s)
- Baiyang Liu
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Christian Cuba Samaniego
- Department of Mechanical and Aerospace Engineering, Bioengineering, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Matthew Bennett
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - James Chappell
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, Bioengineering, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
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6
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Liu B, Chappell J. Computational Design of Small Transcription Activating RNAs (STARs). Methods Mol Biol 2022; 2518:87-97. [PMID: 35666440 DOI: 10.1007/978-1-0716-2421-0_5] [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: 06/15/2023]
Abstract
A major goal of synthetic biology has been to develop libraries of versatile genetic regulators that enable the precise control of gene expression. In recent years, the creation of novel RNA design motifs has allowed for the bottom-up, computational design of large libraries of high-performing and orthogonal RNA regulator systems. One example of this is Small Transcription Activating RNAs (STARs), which function through the conditional formation of terminator hairpins to activate the transcription of targeted genes. STARs have found broad utility for creating synthetic gene circuits, engineering metabolic pathways, and creating new types of diagnostics. Here we describe the method to computationally design, build, and characterize STAR regulators.
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Affiliation(s)
- Baiyang Liu
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - James Chappell
- Department of BioSciences, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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7
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Methods for the Development of Recombinant Microorganisms for the Production of Natural Products. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2396:1-17. [PMID: 34786671 DOI: 10.1007/978-1-0716-1822-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Metabolic engineering strives to develop microbial strains that are capable of producing a target chemical in a biological organism. There are still many challenges to overcome in order to achieve titers, yields, and productivities necessary for industrial production. The use of recombinant microorganisms to meet these needs is the next step for metabolic engineers. In this chapter, we aim to provide insight on both the applications of metabolic engineering for natural product biosynthesis as well as optimization methods.
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Lins MRDCR, Amorim LADS, Corrêa GG, Picão BW, Mack M, Cerri MO, Pedrolli DB. Targeting riboswitches with synthetic small RNAs for metabolic engineering. Metab Eng 2021; 68:59-67. [PMID: 34517126 DOI: 10.1016/j.ymben.2021.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/25/2021] [Accepted: 09/08/2021] [Indexed: 11/29/2022]
Abstract
Our growing knowledge of the diversity of non-coding RNAs in natural systems and our deepening knowledge of RNA folding and function have fomented the rational design of RNA regulators. Based on that knowledge, we designed and implemented a small RNA tool to target bacterial riboswitches and activate gene expression (rtRNA). The synthetic rtRNA is suitable for regulation of gene expression both in cell-free and in cellular systems. It targets riboswitches to promote the antitermination folding regardless the cognate metabolite concentration. Therefore, it prevents transcription termination increasing gene expression up to 103-fold. We successfully used small RNA arrays for multiplex targeting of riboswitches. Finally, we used the synthetic rtRNAs to engineer an improved riboflavin producer strain. The easiness to design and construct, and the fact that the rtRNA works as a single genome copy, make it an attractive tool for engineering industrial metabolite-producing strains.
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Affiliation(s)
- Milca Rachel da Costa Ribeiro Lins
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau Km1, 14800-903, Araraquara, Brazil
| | - Laura Araujo da Silva Amorim
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau Km1, 14800-903, Araraquara, Brazil
| | - Graciely Gomes Corrêa
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau Km1, 14800-903, Araraquara, Brazil
| | - Bruno Willian Picão
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau Km1, 14800-903, Araraquara, Brazil
| | - Matthias Mack
- Mannheim University of Applied Sciences, Institute for Technical Microbiology, Paul-Wittsack-Str. 10, 68163, Mannheim, Germany
| | - Marcel Otávio Cerri
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau Km1, 14800-903, Araraquara, Brazil
| | - Danielle Biscaro Pedrolli
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau Km1, 14800-903, Araraquara, Brazil.
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9
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Recent advances in tuning the expression and regulation of genes for constructing microbial cell factories. Biotechnol Adv 2021; 50:107767. [PMID: 33974979 DOI: 10.1016/j.biotechadv.2021.107767] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022]
Abstract
To overcome environmental problems caused by the use of fossil resources, microbial cell factories have become a promising technique for the sustainable and eco-friendly development of valuable products from renewable resources. Constructing microbial cell factories with high titers, yields, and productivity requires a balance between growth and production; to this end, tuning gene expression and regulation is necessary to optimise and precisely control complicated metabolic fluxes. In this article, we review the current trends and advances in tuning gene expression and regulation and consider their engineering at each of the three stages of gene regulation: genomic, mRNA, and protein. In particular, the technological approaches utilised in a diverse range of genetic-engineering-based tools for the construction of microbial cell factories are reviewed and representative applications of these strategies are presented. Finally, the prospects for strategies and systems for tuning gene expression and regulation are discussed.
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10
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Lakin MR, Phillips A. Domain-Specific Programming Languages for Computational Nucleic Acid Systems. ACS Synth Biol 2020; 9:1499-1513. [PMID: 32589838 DOI: 10.1021/acssynbio.0c00050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The construction of models of system behavior is of great importance throughout science and engineering. In bioengineering and bionanotechnology, these often take the form of dynamic models that specify the evolution of different species over time. To ensure that scientific observations and conclusions are consistent and that systems can be reliably engineered on the basis of model predictions, it is important that models of biomolecular systems can be constructed in a reliable, principled, and efficient manner. This review focuses on efforts to address this need by using domain-specific programming languages as the basis for custom design tools for researchers working on computational nucleic acid devices, where a domain-specific language is simply a programming language tailored to a particular application domain. The underlying thesis of our review is that there is a continuum of practical implementation strategies for computational nucleic acid systems, which can all benefit from appropriate domain-specific languages and software design tools. We emphasize the need for specialized yet flexible tools that can be realized using domain-specific languages that compile to more general-purpose representations.
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Affiliation(s)
- Matthew R. Lakin
- Department of Computer Science, University of New Mexico, Albuquerque, New Mexico 87131, United States
- Department of Chemical & Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
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11
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RNA nanotechnology in synthetic biology. Curr Opin Biotechnol 2020; 63:135-141. [PMID: 32035339 DOI: 10.1016/j.copbio.2019.12.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 12/16/2019] [Indexed: 01/04/2023]
Abstract
We review recent advances in the design and expression of synthetic RNA sequences inside cells, to regulate gene expression and to achieve spatial localization of components. We focus on approaches that exploit the programmability of the secondary and tertiary structure of RNA to build scalable and modular devices that fold spontaneously and have the capacity to respond to environmental inputs.
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12
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Kim J, Zhou Y, Carlson PD, Teichmann M, Chaudhary S, Simmel FC, Silver PA, Collins JJ, Lucks JB, Yin P, Green AA. De novo-designed translation-repressing riboregulators for multi-input cellular logic. Nat Chem Biol 2019; 15:1173-1182. [PMID: 31686032 PMCID: PMC6864284 DOI: 10.1038/s41589-019-0388-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 09/10/2019] [Indexed: 01/24/2023]
Abstract
Efforts to construct synthetic biological circuits with more complex functions have often been hindered by the idiosyncratic behavior, limited dynamic range, and crosstalk of commonly utilized parts. Here, we employ de novo RNA design to develop two high-performance translational repressors with sensing and logic capabilities. These synthetic riboregulators, termed toehold repressors and three-way junction (3WJ) repressors, detect transcripts with nearly arbitrary sequences, repress gene expression by up to 300-fold, and yield orthogonal sets of up to 15 devices. Automated forward engineering is used to improve toehold repressor dynamic range and SHAPE-Seq is applied to confirm the designed switching mechanism of 3WJ repressors in living cells. We integrate the modular repressors into biological circuits that execute universal NAND and NOR logic and evaluate the four-input expression NOT ((A1 AND A2) OR (B1 AND B2)) in Escherichia coli. These capabilities make toehold and 3WJ repressors valuable new tools for biotechnological applications.
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Affiliation(s)
- Jongmin Kim
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Yu Zhou
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Paul D Carlson
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Mario Teichmann
- Physics Department E14 and ZNN/WSI, Technische Universität München, Garching, Germany
| | - Soma Chaudhary
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Friedrich C Simmel
- Physics Department E14 and ZNN/WSI, Technische Universität München, Garching, Germany.,Nanosystems Initiative Munich, Munich, Germany
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julius B Lucks
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.,Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. .,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Alexander A Green
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.
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13
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Lehr FX, Hanst M, Vogel M, Kremer J, Göringer HU, Suess B, Koeppl H. Cell-Free Prototyping of AND-Logic Gates Based on Heterogeneous RNA Activators. ACS Synth Biol 2019; 8:2163-2173. [PMID: 31393707 DOI: 10.1021/acssynbio.9b00238] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
RNA-based devices controlling gene expression bear great promise for synthetic biology, as they offer many advantages such as short response times and light metabolic burden compared to protein-circuits. However, little work has been done regarding their integration to multilevel regulated circuits. In this work, we combined a variety of small transcriptional activator RNAs (STARs) and toehold switches to build highly effective AND-gates. To characterize the components and their dynamic range, we used an Escherichia coli (E. coli) cell-free transcription-translation (TX-TL) system dispensed via nanoliter droplets. We analyzed a prototype gate in vitro as well as in silico, employing parametrized ordinary differential equations (ODEs), for which parameters were inferred via parallel tempering, a Markov chain Monte Carlo (MCMC) method. On the basis of this analysis, we created nine additional AND-gates and tested them in vitro. The functionality of the gates was found to be highly dependent on the concentration of the activating RNA for either the STAR or the toehold switch. All gates were successfully implemented in vivo, offering a dynamic range comparable to the level of protein circuits. This study shows the potential of a rapid prototyping approach for RNA circuit design, using cell-free systems in combination with a model prediction.
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Affiliation(s)
- François-Xavier Lehr
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Maleen Hanst
- Department of Electrical Engineering, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Marc Vogel
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Jennifer Kremer
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - H. Ulrich Göringer
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Heinz Koeppl
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
- Department of Electrical Engineering, Technische Universität Darmstadt, 64283 Darmstadt, Germany
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14
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Advances in engineered trans-acting regulatory RNAs and their application in bacterial genome engineering. J Ind Microbiol Biotechnol 2019; 46:819-830. [PMID: 30887255 DOI: 10.1007/s10295-019-02160-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 03/05/2019] [Indexed: 12/15/2022]
Abstract
Small noncoding RNAs, a large class of ancient posttranscriptional regulators, are increasingly recognized and utilized as key modulators of gene expression in a broad range of microorganisms. Owing to their small molecular size and the central role of Watson-Crick base pairing in defining their interactions, structure and function, numerous diverse types of trans-acting RNA regulators that are functional at the DNA, mRNA and protein levels have been experimentally characterized. It has become increasingly clear that most small RNAs play critical regulatory roles in many processes and are, therefore, considered to be powerful tools for genetic engineering and synthetic biology. The trans-acting regulatory RNAs accelerate this ability to establish potential framework for genetic engineering and genome-scale engineering, which allows RNA structure characterization, easier to design and model compared to DNA or protein-based systems. In this review, we summarize recent advances in engineered trans-acting regulatory RNAs that are used in bacterial genome-scale engineering and in novel cellular capabilities as well as their implementation in wide range of biotechnological, biological and medical applications.
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15
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Shaver ZM, Bent SS, Bilby SR, Brown M, Buser A, Cuellar IG, Davis AJ, Doolan L, Enriquez FC, Estrada A, Herner S, Herron JC, Hunn AM, Hunter M, Johnston H, Koucky O, Mackley CC, Maghini D, Mattoon D, McDonald HT, Sinks H, Sprague AJ, Sullivan D, Tutar A, Umphreys A, Watson C, Zweerink D, Heyer LJ, Poet JL, Eckdahl TT, Campbell AM. Attempted use of PACE for riboswitch discovery generates three new translational theophylline riboswitch side products. BMC Res Notes 2018; 11:861. [PMID: 30518404 PMCID: PMC6280357 DOI: 10.1186/s13104-018-3965-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 11/29/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The purpose of this project was to use an in vivo method to discover riboswitches that are activated by new ligands. We employed phage-assisted continuous evolution (PACE) to evolve new riboswitches in vivo. We started with one translational riboswitch and one transcriptional riboswitch, both of which were activated by theophylline. We used xanthine as the new target ligand during positive selection followed by negative selection using theophylline. The goal was to generate very large M13 phage populations that contained unknown mutations, some of which would result in new aptamer specificity. We discovered side products of three new theophylline translational riboswitches with different levels of protein production. RESULTS We used next generation sequencing to identify M13 phage that carried riboswitch mutations. We cloned and characterized the most abundant riboswitch mutants and discovered three variants that produce different levels of translational output while retaining their theophylline specificity. Although we were unable to demonstrate evolution of new riboswitch ligand specificity using PACE, we recommend careful design of recombinant M13 phage to avoid evolution of "cheaters" that short circuit the intended selection pressure.
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Affiliation(s)
| | | | - Steven R Bilby
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | - Michael Brown
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Anna Buser
- Department of Biology, Davidson College, Davidson, USA
| | | | - Athena J Davis
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | - Lindsay Doolan
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | | | - Autumn Estrada
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Shelby Herner
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | - J Cody Herron
- Department of Biology, Davidson College, Davidson, USA
| | - Andrew M Hunn
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | | | | | - Owen Koucky
- Department of Biology, Davidson College, Davidson, USA
| | | | - Dylan Maghini
- Department of Biology, Davidson College, Davidson, USA.,Department of Math and Computer Science, Davidson College, Davidson, USA
| | - Devin Mattoon
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Haden T McDonald
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Hannah Sinks
- Department of Biology, Davidson College, Davidson, USA.,Department of Math and Computer Science, Davidson College, Davidson, USA
| | - Austin J Sprague
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - David Sullivan
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Altan Tutar
- Department of Math and Computer Science, Davidson College, Davidson, USA
| | - Avery Umphreys
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | - Chris Watson
- Department of Biology, Missouri Western State University, Saint Joseph, USA
| | - Daniel Zweerink
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Laurie J Heyer
- Department of Math and Computer Science, Davidson College, Davidson, USA
| | - Jeffrey L Poet
- Department of Computer Science, Math, and Physics, Missouri Western State University, Saint Joseph, USA
| | - Todd T Eckdahl
- Department of Biology, Missouri Western State University, Saint Joseph, USA
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16
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Peters G, Maertens J, Lammertyn J, De Mey M. Exploring of the feature space of de novo developed post-transcriptional riboregulators. PLoS Comput Biol 2018; 14:e1006170. [PMID: 30118473 PMCID: PMC6114898 DOI: 10.1371/journal.pcbi.1006170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 08/29/2018] [Accepted: 04/30/2018] [Indexed: 11/23/2022] Open
Abstract
Metabolic engineering increasingly depends upon RNA technology to customly rewire the metabolism to maximize production. To this end, pure riboregulators allow dynamic gene repression without the need of a potentially burdensome coexpressed protein like typical Hfq binding small RNAs and clustered regularly interspaced short palindromic repeats technology. Despite this clear advantage, no clear general design principles are available to de novo develop repressing riboregulators, limiting the availability and the reliable development of these type of riboregulators. Here, to overcome this lack of knowledge on the functionality of repressing riboregulators, translation inhibiting RNAs are developed from scratch. These de novo developed riboregulators explore features related to thermodynamical and structural factors previously attributed to translation initiation modulation. In total, 12 structural and thermodynamic features were defined of which six features were retained after removing correlations from an in silico generated riboregulator library. From this translation inhibiting RNA library, 18 riboregulators were selected using a experimental design and subsequently constructed and co-expressed with two target untranslated regions to link the translation inhibiting RNA features to functionality. The pure riboregulators in the design of experiments showed repression down to 6% of the original protein expression levels, which could only be partially explained by a ordinary least squares regression model. To allow reliable forward engineering, a partial least squares regression model was constructed and validated to link the properties of translation inhibiting RNA riboregulators to gene repression. In this model both structural and thermodynamic features were important for efficient gene repression by pure riboregulators. This approach enables a more reliable de novo forward engineering of effective pure riboregulators, which further expands the RNA toolbox for gene expression modulation. To allow reliable forward engineering of microbial cell factories, various metabolic engineering efforts rely on RNA-based technology. As such, programmable riboregulators allow dynamic control over gene expression. However, no clear design principles exist for de novo developed repressing riboregulators, which limits their applicability. Here, various engineering principles are identified and computationally explored. Subsequently, various design criteria are used in an experimental design, which were explored in an in vivo study. This resulted in a regression model that enables a more reliable computational design of repression small RNAs.
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Affiliation(s)
- Gert Peters
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
| | | | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
- * E-mail:
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17
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Lee YJ, Kim SJ, Moon TS. Multilevel Regulation of Bacterial Gene Expression with the Combined STAR and Antisense RNA System. ACS Synth Biol 2018; 7:853-865. [PMID: 29429328 DOI: 10.1021/acssynbio.7b00322] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Synthetic small RNA regulators have emerged as a versatile tool to predictably control bacterial gene expression. Owing to their simple design principles, small size, and highly orthogonal behavior, these engineered genetic parts have been incorporated into genetic circuits. However, efforts to achieve more sophisticated cellular functions using RNA regulators have been hindered by our limited ability to integrate different RNA regulators into complex circuits. Here, we present a combined RNA regulatory system in Escherichia coli that uses small transcription activating RNA (STAR) and antisense RNA (asRNA) to activate or deactivate target gene expression in a programmable manner. Specifically, we demonstrated that the activated target output by the STAR system can be deactivated by expressing two different types of asRNAs: one binds to and sequesters the STAR regulator, affecting the transcription process, while the other binds to the target mRNA, affecting the translation process. We improved deactivation efficiencies (up to 96%) by optimizing each type of asRNA and then integrating the two optimized asRNAs into a single circuit. Furthermore, we demonstrated that the combined STAR and asRNA system can control gene expression in a reversible way and can regulate expression of a gene in the genome. Lastly, we constructed and simultaneously tested two A AND NOT B logic gates in the same cell to show sophisticated multigene regulation by the combined system. Our approach establishes a methodology for integrating multiple RNA regulators to rationally control multiple genes.
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Affiliation(s)
- Young Je Lee
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Soo-Jung Kim
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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18
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Roßmanith J, Weskamp M, Narberhaus F. Design of a Temperature-Responsive Transcription Terminator. ACS Synth Biol 2018; 7:613-621. [PMID: 29191010 DOI: 10.1021/acssynbio.7b00356] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA structures regulate various steps in gene expression. Transcription in bacteria is typically terminated by stable hairpin structures. Translation initiation can be modulated by metabolite- or temperature-sensitive RNA structures, called riboswitches or RNA thermometers (RNATs), respectively. RNATs control translation initiation by occlusion of the ribosome binding site at low temperatures. Increasing temperatures destabilize the RNA structure and facilitate ribosome access. In this study, we exploited temperature-responsive RNAT structures to design regulatory elements that control transcription termination instead of translation initiation in Escherichia coli. In order to mimic the structure of factor-independent intrinsic terminators, naturally occurring RNAT hairpins were genetically engineered to be followed by a U-stretch. Functional temperature-responsive terminators (thermoterms) prevented mRNA synthesis at low temperatures but resumed transcription after a temperature upshift. The successful design of temperature-controlled terminators highlights the potential of RNA structures as versatile gene expression control elements.
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Affiliation(s)
| | - Mareen Weskamp
- Microbial Biology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, 44780 Bochum, Germany
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19
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Chappell J, Westbrook A, Verosloff M, Lucks JB. Computational design of small transcription activating RNAs for versatile and dynamic gene regulation. Nat Commun 2017; 8:1051. [PMID: 29051490 PMCID: PMC5648800 DOI: 10.1038/s41467-017-01082-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/17/2017] [Indexed: 01/04/2023] Open
Abstract
A longstanding goal of synthetic biology has been the programmable control of cellular functions. Central to this is the creation of versatile regulatory toolsets that allow for programmable control of gene expression. Of the many regulatory molecules available, RNA regulators offer the intriguing possibility of de novo design-allowing for the bottom-up molecular-level design of genetic control systems. Here we present a computational design approach for the creation of a bacterial regulator called Small Transcription Activating RNAs (STARs) and create a library of high-performing and orthogonal STARs that achieve up to ~ 9000-fold gene activation. We demonstrate the versatility of these STARs-from acting synergistically with existing constitutive and inducible regulators, to reprogramming cellular phenotypes and controlling multigene metabolic pathway expression. Finally, we combine these new STARs with themselves and CRISPRi transcriptional repressors to deliver new types of RNA-based genetic circuitry that allow for sophisticated and temporal control of gene expression.
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Affiliation(s)
- James Chappell
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA
| | - Alexandra Westbrook
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 113 Ho Plaza, Ithaca, NY, 14583, USA
| | - Matthew Verosloff
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, 2204 Tech Drive, Evanston, IL, 60208, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA. .,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, 2204 Tech Drive, Evanston, IL, 60208, USA.
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20
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Martínez-García E, de Lorenzo V. Molecular tools and emerging strategies for deep genetic/genomic refactoring of Pseudomonas. Curr Opin Biotechnol 2017; 47:120-132. [DOI: 10.1016/j.copbio.2017.06.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/19/2017] [Indexed: 11/26/2022]
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21
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Findeiß S, Etzel M, Will S, Mörl M, Stadler PF. Design of Artificial Riboswitches as Biosensors. SENSORS 2017; 17:s17091990. [PMID: 28867802 PMCID: PMC5621056 DOI: 10.3390/s17091990] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/23/2017] [Accepted: 08/25/2017] [Indexed: 12/11/2022]
Abstract
RNA aptamers readily recognize small organic molecules, polypeptides, as well as other nucleic acids in a highly specific manner. Many such aptamers have evolved as parts of regulatory systems in nature. Experimental selection techniques such as SELEX have been very successful in finding artificial aptamers for a wide variety of natural and synthetic ligands. Changes in structure and/or stability of aptamers upon ligand binding can propagate through larger RNA constructs and cause specific structural changes at distal positions. In turn, these may affect transcription, translation, splicing, or binding events. The RNA secondary structure model realistically describes both thermodynamic and kinetic aspects of RNA structure formation and refolding at a single, consistent level of modelling. Thus, this framework allows studying the function of natural riboswitches in silico. Moreover, it enables rationally designing artificial switches, combining essentially arbitrary sensors with a broad choice of read-out systems. Eventually, this approach sets the stage for constructing versatile biosensors.
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Affiliation(s)
- Sven Findeiß
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.
- Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, University of Vienna, Währingerstraße 29, A-1090 Vienna, Austria.
- Faculty of Chemistry, Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria.
| | - Maja Etzel
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Sebastian Will
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.
- Faculty of Chemistry, Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria.
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.
- Faculty of Chemistry, Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany.
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany.
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, 04103 Leipzig, Germany.
- Center for RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg , Denmark.
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA.
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22
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Domin G, Findeiß S, Wachsmuth M, Will S, Stadler PF, Mörl M. Applicability of a computational design approach for synthetic riboswitches. Nucleic Acids Res 2017; 45:4108-4119. [PMID: 27994029 PMCID: PMC5397205 DOI: 10.1093/nar/gkw1267] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/06/2016] [Indexed: 02/07/2023] Open
Abstract
Riboswitches have gained attention as tools for synthetic biology, since they enable researchers to reprogram cells to sense and respond to exogenous molecules. In vitro evolutionary approaches produced numerous RNA aptamers that bind such small ligands, but their conversion into functional riboswitches remains difficult. We previously developed a computational approach for the design of synthetic theophylline riboswitches based on secondary structure prediction. These riboswitches have been constructed to regulate ligand-dependent transcription termination in Escherichia coli. Here, we test the usability of this design strategy by applying the approach to tetracycline and streptomycin aptamers. The resulting tetracycline riboswitches exhibit robust regulatory properties in vivo. Tandem fusions of these riboswitches with theophylline riboswitches represent logic gates responding to two different input signals. In contrast, the conversion of the streptomycin aptamer into functional riboswitches appears to be difficult. Investigations of the underlying aptamer secondary structure revealed differences between in silico prediction and structure probing. We conclude that only aptamers adopting the minimal free energy (MFE) structure are suitable targets for construction of synthetic riboswitches with design approaches based on equilibrium thermodynamics of RNA structures. Further improvements in the design strategy are required to implement aptamer structures not corresponding to the calculated MFE state.
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Affiliation(s)
- Gesine Domin
- Leipzig University, Institute for Biochemistry, 04103 Leipzig, Germany
| | - Sven Findeiß
- University of Vienna, Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, A-1090 Vienna, Austria.,University of Vienna, Institute for Theoretical Chemistry, A-1090 Vienna, Austria
| | - Manja Wachsmuth
- Leipzig University, Institute for Biochemistry, 04103 Leipzig, Germany
| | - Sebastian Will
- Leipzig University, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, 04107 Leipzig, Germany
| | - Peter F Stadler
- University of Vienna, Institute for Theoretical Chemistry, A-1090 Vienna, Austria.,Leipzig University, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Science, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.,Santa Fe Institute, Santa Fe NM 87501, USA
| | - Mario Mörl
- Leipzig University, Institute for Biochemistry, 04103 Leipzig, Germany
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23
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Ausländer S, Ausländer D, Fussenegger M. Synthetische Biologie - die Synthese der Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - David Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
- Faculty of Science; Universität Basel; Mattenstrasse 26 4058 Basel Schweiz
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24
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Ausländer S, Ausländer D, Fussenegger M. Synthetic Biology-The Synthesis of Biology. Angew Chem Int Ed Engl 2017; 56:6396-6419. [PMID: 27943572 DOI: 10.1002/anie.201609229] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/17/2016] [Indexed: 01/01/2023]
Abstract
Synthetic biology concerns the engineering of man-made living biomachines from standardized components that can perform predefined functions in a (self-)controlled manner. Different research strategies and interdisciplinary efforts are pursued to implement engineering principles to biology. The "top-down" strategy exploits nature's incredible diversity of existing, natural parts to construct synthetic compositions of genetic, metabolic, or signaling networks with predictable and controllable properties. This mainly application-driven approach results in living factories that produce drugs, biofuels, biomaterials, and fine chemicals, and results in living pills that are based on engineered cells with the capacity to autonomously detect and treat disease states in vivo. In contrast, the "bottom-up" strategy seeks to be independent of existing living systems by designing biological systems from scratch and synthesizing artificial biological entities not found in nature. This more knowledge-driven approach investigates the reconstruction of minimal biological systems that are capable of performing basic biological phenomena, such as self-organization, self-replication, and self-sustainability. Moreover, the syntheses of artificial biological units, such as synthetic nucleotides or amino acids, and their implementation into polymers inside living cells currently set the boundaries between natural and artificial biological systems. In particular, the in vitro design, synthesis, and transfer of complete genomes into host cells point to the future of synthetic biology: the creation of designer cells with tailored desirable properties for biomedicine and biotechnology.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - David Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
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25
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Harris EA, Buzina A, Moffat J, McMillen DR. Design and Experimental Validation of Small Activating RNAs Targeting an Exogenous Promoter in Human Cells. ACS Synth Biol 2017; 6:628-637. [PMID: 28033709 DOI: 10.1021/acssynbio.6b00125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
It is increasingly practical to co-opt many native cellular components into use as elements of synthetic biological systems. We present the design and experimental investigation of the first exogenous genetic construct to be successfully targeted by RNA activation, a phenomenon whereby small double-stranded RNAs increase gene expression from sequence-similar promoters by a mechanism thought to be related to that of RNA interference. Our selection of activating RNA candidates was informed by a custom-written computer program designed to choose target sites in the promoter of interest according to a set of empirical optimality criteria drawn from prior research. Activating RNA candidates were assessed for activity against two exogenously derived target promoters, with successful candidates being subjected to further rounds of validation as a precaution against potential off-target effects. A genetic platform was assembled that allowed activating RNA candidates to be simultaneously screened both for positive activity on the target reporter gene and for possible nonspecific effects on cell metabolism. Several candidate sequences were tested to appraise the utility of this platform, with the most successful achieving a moderate activation level with minimal off-target effects.
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Affiliation(s)
- Edouard A. Harris
- Department
of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 1A7, Canada
- Department
of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
- Impact
Centre, University of Toronto, 112 College Street, Toronto, Ontario M5G 1A7, Canada
| | - Alla Buzina
- Banting
and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5E 3E1, Canada
| | - Jason Moffat
- Department
of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - David R. McMillen
- Department
of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 1A7, Canada
- Department
of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
- Impact
Centre, University of Toronto, 112 College Street, Toronto, Ontario M5G 1A7, Canada
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26
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Bradley RW, Buck M, Wang B. Recognizing and engineering digital-like logic gates and switches in gene regulatory networks. Curr Opin Microbiol 2016; 33:74-82. [DOI: 10.1016/j.mib.2016.07.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/14/2016] [Accepted: 07/06/2016] [Indexed: 02/08/2023]
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27
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Kushwaha M, Rostain W, Prakash S, Duncan JN, Jaramillo A. Using RNA as Molecular Code for Programming Cellular Function. ACS Synth Biol 2016; 5:795-809. [PMID: 26999422 DOI: 10.1021/acssynbio.5b00297] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA is involved in a wide-range of important molecular processes in the cell, serving diverse functions: regulatory, enzymatic, and structural. Together with its ease and predictability of design, these properties can lead RNA to become a useful handle for biological engineers with which to control the cellular machinery. By modifying the many RNA links in cellular processes, it is possible to reprogram cells toward specific design goals. We propose that RNA can be viewed as a molecular programming language that, together with protein-based execution platforms, can be used to rewrite wide ranging aspects of cellular function. In this review, we catalogue developments in the use of RNA parts, methods, and associated computational models that have contributed to the programmability of biology. We discuss how RNA part repertoires have been combined to build complex genetic circuits, and review recent applications of RNA-based parts and circuitry. We explore the future potential of RNA engineering and posit that RNA programmability is an important resource for firmly establishing an era of rationally designed synthetic biology.
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Affiliation(s)
- Manish Kushwaha
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - William Rostain
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
| | - Satya Prakash
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - John N. Duncan
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - Alfonso Jaramillo
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
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28
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Becker J, Gießelmann G, Hoffmann SL, Wittmann C. Corynebacterium glutamicum for Sustainable Bioproduction: From Metabolic Physiology to Systems Metabolic Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:217-263. [DOI: 10.1007/10_2016_21] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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