1
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Ortega AD. Real-Time Assessment of Intracellular Metabolites in Single Cells through RNA-Based Sensors. Biomolecules 2023; 13:biom13050765. [PMID: 37238635 DOI: 10.3390/biom13050765] [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: 03/24/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Quantification of the concentration of particular cellular metabolites reports on the actual utilization of metabolic pathways in physiological and pathological conditions. Metabolite concentration also constitutes the readout for screening cell factories in metabolic engineering. However, there are no direct approaches that allow for real-time assessment of the levels of intracellular metabolites in single cells. In recent years, the modular architecture of natural bacterial RNA riboswitches has inspired the design of genetically encoded synthetic RNA devices that convert the intracellular concentration of a metabolite into a quantitative fluorescent signal. These so-called RNA-based sensors are composed of a metabolite-binding RNA aptamer as the sensor domain, connected through an actuator segment to a signal-generating reporter domain. However, at present, the variety of available RNA-based sensors for intracellular metabolites is still very limited. Here, we go through natural mechanisms for metabolite sensing and regulation in cells across all kingdoms, focusing on those mediated by riboswitches. We review the design principles underlying currently developed RNA-based sensors and discuss the challenges that hindered the development of novel sensors and recent strategies to address them. We finish by introducing the current and potential applicability of synthetic RNA-based sensors for intracellular metabolites.
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Affiliation(s)
- Alvaro Darío Ortega
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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2
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Spirov AV, Myasnikova EM. Heuristic algorithms in evolutionary computation and modular organization of biological macromolecules: Applications to in vitro evolution. PLoS One 2022; 17:e0260497. [PMID: 35085255 PMCID: PMC8794168 DOI: 10.1371/journal.pone.0260497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Evolutionary computing (EC) is an area of computer sciences and applied mathematics covering heuristic optimization algorithms inspired by evolution in Nature. EC extensively study all the variety of methods which were originally based on the principles of selectionism. As a result, many new algorithms and approaches, significantly more efficient than classical selectionist schemes, were found. This is especially true for some families of special problems. There are strong arguments to believe that EC approaches are quite suitable for modeling and numerical analysis of those methods of synthetic biology and biotechnology that are known as in vitro evolution. Therefore, it is natural to expect that the new algorithms and approaches developed in EC can be effectively applied in experiments on the directed evolution of biological macromolecules. According to the John Holland's Schema theorem, the effective evolutionary search in genetic algorithms (GA) is provided by identifying short schemata of high fitness which in the further search recombine into the larger building blocks (BBs) with higher and higher fitness. The multimodularity of functional biological macromolecules and the preservation of already found modules in the evolutionary search have a clear analogy with the BBs in EC. It seems reasonable to try to transfer and introduce the methods of EC, preserving BBs and essentially accelerating the search, into experiments on in vitro evolution. We extend the key instrument of the Holland's theory, the Royal Roads fitness function, to problems of the in vitro evolution (Biological Royal Staircase, BioRS, functions). The specific version of BioRS developed in this publication arises from the realities of experimental evolutionary search for (DNA-) RNA-devices (aptazymes). Our numerical tests showed that for problems with the BioRS functions, simple heuristic algorithms, which turned out to be very effective for preserving BBs in GA, can be very effective in in vitro evolution approaches. We are convinced that such algorithms can be implemented in modern methods of in vitro evolution to achieve significant savings in time and resources and a significant increase in the efficiency of evolutionary search.
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Affiliation(s)
- Alexander V. Spirov
- I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences, St. Petersburg, Russia
- The Institute of Scientific Information for Social Sciences RAS, Moscow, Russia
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3
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McCarthy J. Engineering and standardization of posttranscriptional biocircuitry in Saccharomyces cerevisiae. Integr Biol (Camb) 2021; 13:210-220. [PMID: 34270725 DOI: 10.1093/intbio/zyab013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/14/2022]
Abstract
This short review considers to what extent posttranscriptional steps of gene expression can provide the basis for novel control mechanisms and procedures in synthetic biology and biotechnology. The term biocircuitry is used here to refer to functionally connected components comprising DNA, RNA or proteins. The review begins with an overview of the diversity of devices being developed and then considers the challenges presented by trying to engineer more scaled-up systems. While the engineering of RNA-based and protein-based circuitry poses new challenges, the resulting 'toolsets' of components and novel mechanisms of operation will open up multiple new opportunities for synthetic biology. However, agreed procedures for standardization will need to be placed at the heart of this expanding field if the full potential benefits are to be realized.
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Affiliation(s)
- John McCarthy
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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4
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Aptamers, Riboswitches, and Ribozymes in S. cerevisiae Synthetic Biology. Life (Basel) 2021; 11:life11030248. [PMID: 33802772 PMCID: PMC8002509 DOI: 10.3390/life11030248] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 01/09/2023] Open
Abstract
Among noncoding RNA sequences, riboswitches and ribozymes have attracted the attention of the synthetic biology community as circuit components for translation regulation. When fused to aptamer sequences, ribozymes and riboswitches are enabled to interact with chemicals. Therefore, protein synthesis can be controlled at the mRNA level without the need for transcription factors. Potentially, the use of chemical-responsive ribozymes/riboswitches would drastically simplify the design of genetic circuits. In this review, we describe synthetic RNA structures that have been used so far in the yeast Saccharomyces cerevisiae. We present their interaction mode with different chemicals (e.g., theophylline and antibiotics) or proteins (such as the RNase III) and their recent employment into clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9 (CRISPR-Cas) systems. Particular attention is paid, throughout the whole paper, to their usage and performance into synthetic gene circuits.
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5
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Ender A, Etzel M, Hammer S, Findeiß S, Stadler P, Mörl M. Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch. Nucleic Acids Res 2021; 49:1784-1800. [PMID: 33469651 PMCID: PMC7897497 DOI: 10.1093/nar/gkaa1282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 11/29/2022] Open
Abstract
We describe a synthetic riboswitch element that implements a regulatory principle which directly addresses an essential tRNA maturation step. Constructed using a rational in silico design approach, this riboswitch regulates RNase P-catalyzed tRNA 5′-processing by either sequestering or exposing the single-stranded 5′-leader region of the tRNA precursor in response to a ligand. A single base pair in the 5′-leader defines the regulatory potential of the riboswitch both in vitro and in vivo. Our data provide proof for prior postulates on the importance of the structure of the leader region for tRNA maturation. We demonstrate that computational predictions of ligand-dependent structural rearrangements can address individual maturation steps of stable non-coding RNAs, thus making them amenable as promising target for regulatory devices that can be used as functional building blocks in synthetic biology.
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Affiliation(s)
- Anna Ender
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Maja Etzel
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Stefan Hammer
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Sven Findeiß
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Peter Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstr. 16-18, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Science, Inselstr. 22, 04103 Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, Währingerstr. 17, A-1090 Vienna, Austria.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
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6
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Mc Cafferty S, De Temmerman J, Kitada T, Becraft JR, Weiss R, Irvine DJ, Devreese M, De Baere S, Combes F, Sanders NN. In Vivo Validation of a Reversible Small Molecule-Based Switch for Synthetic Self-Amplifying mRNA Regulation. Mol Ther 2020; 29:1164-1173. [PMID: 33186690 DOI: 10.1016/j.ymthe.2020.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/03/2020] [Accepted: 11/05/2020] [Indexed: 12/01/2022] Open
Abstract
Synthetic mRNA therapeutics have the potential to revolutionize healthcare, as they enable patients to produce therapeutic proteins inside their own bodies. However, convenient methods that allow external control over the timing and magnitude of protein production after in vivo delivery of synthetic mRNA are lacking. In this study, we validate the in vivo utility of a synthetic self-amplifying mRNA (RNA replicon) whose expression can be turned off using a genetic switch that responds to oral administration of trimethoprim (TMP), a US Food and Drug Administration (FDA)-approved small-molecule drug. After intramuscular electroporation, the engineered RNA replicon exhibited dose-dependent and reversible expression of its encoded protein upon TMP administration. The TMP serum level needed for maximal downregulation of protein translation was approximately 45-fold below that used in humans for therapeutic purposes. To demonstrate the therapeutic potential of the technology, we injected mice with a TMP-responsive RNA replicon encoding erythropoietin (EPO) and successfully controlled the timing and magnitude of EPO production as well as changes in hematocrit. This work demonstrates the feasibility of controlling mRNA kinetics in vivo, thereby broadly expanding the clinical versatility of mRNA therapeutics.
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Affiliation(s)
- Sean Mc Cafferty
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium
| | - Joyca De Temmerman
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; Department of Pathology, Bacteriology and Poultry diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | | | | | - Ron Weiss
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Darrell J Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Mathias Devreese
- Laboratory of Pharmacology and Toxicology, Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Siegrid De Baere
- Laboratory of Pharmacology and Toxicology, Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Francis Combes
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium
| | - Niek N Sanders
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium.
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7
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Wrist A, Sun W, Summers RM. The Theophylline Aptamer: 25 Years as an Important Tool in Cellular Engineering Research. ACS Synth Biol 2020; 9:682-697. [PMID: 32142605 DOI: 10.1021/acssynbio.9b00475] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The theophylline aptamer was isolated from an oligonucleotide library in 1994. Since that time, the aptamer has found wide utility, particularly in synthetic biology, cellular engineering, and diagnostic applications. The primary application of the theophylline aptamer is in the construction and characterization of synthetic riboswitches for regulation of gene expression. These riboswitches have been used to control cellular motility, regulate carbon metabolism, construct logic gates, screen for mutant enzymes, and control apoptosis. Other applications of the theophylline aptamer in cellular engineering include regulation of RNA interference and genome editing through CRISPR systems. Here we describe the uses of the theophylline aptamer for cellular engineering over the past 25 years. In so doing, we also highlight important synthetic biology applications to control gene expression in a ligand-dependent manner.
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Affiliation(s)
- Alexandra Wrist
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Wanqi Sun
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Ryan M. Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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8
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Endoh T, Sugimoto N. Co-Transcriptional Molecular Assembly Results in a Kinetically Controlled Irreversible RNA Conformational Switch. Anal Chem 2018; 90:11193-11197. [DOI: 10.1021/acs.analchem.8b03427] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi,
Chuo-ku, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi,
Chuo-ku, Kobe, 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
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9
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Kobori S, Yokobayashi Y. Analyzing and Tuning Ribozyme Activity by Deep Sequencing To Modulate Gene Expression Level in Mammalian Cells. ACS Synth Biol 2018; 7:371-376. [PMID: 29343061 DOI: 10.1021/acssynbio.7b00367] [Citation(s) in RCA: 15] [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
Self-cleaving ribozymes, in combination with aptamers and various classes of RNAs, have been heavily engineered to create RNA devices to control gene expression. Although understanding of sequence-function relationships of ribozymes is critical for such efforts, our current knowledge of self-cleaving ribozymes is mostly limited to the results from small scale mutational studies performed under different conditions, or qualitative results of mutate-and-select experiments that may contain experimental biases. Here, we applied our strategy based on deep sequencing to comprehensively assay a large number of mutants to systematically examine the effect of the P4 stem sequence on the activity of an HDV-like ribozyme. We discovered that the ribozyme activity is highly sensitive to the sequence and the apparent stability of the varied positions. Furthermore, we demonstrated that the collection of the ribozyme variants with different activities can be used as a convenient device to fine-tune the level of gene expression in mammalian cells.
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Affiliation(s)
- Shungo Kobori
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
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10
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Etzel M, Mörl M. Synthetic Riboswitches: From Plug and Pray toward Plug and Play. Biochemistry 2017; 56:1181-1198. [PMID: 28206750 DOI: 10.1021/acs.biochem.6b01218] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In synthetic biology, metabolic engineering, and gene therapy, there is a strong demand for orthogonal or externally controlled regulation of gene expression. Here, RNA-based regulatory devices represent a promising emerging alternative to proteins, allowing a fast and direct control of gene expression, as no synthesis of regulatory proteins is required. Besides programmable ribozyme elements controlling mRNA stability, regulatory RNA structures in untranslated regions are highly interesting for engineering approaches. Riboswitches are especially well suited, as they show a modular composition of sensor and response elements, allowing a free combination of different modules in a plug-and-play-like mode. The sensor or aptamer domain specifically interacts with a trigger molecule as a ligand, modulating the activity of the adjacent response domain that controls the expression of the genes located downstream, in most cases at the level of transcription or translation. In this review, we discuss the recent advances and strategies for designing such synthetic riboswitches based on natural or artificial components and readout systems, from trial-and-error approaches to rational design strategies. As the past several years have shown dramatic development in this fascinating field of research, we can give only a limited overview of the basic riboswitch design principles that is far from complete, and we apologize for not being able to consider every successful and interesting approach described in the literature.
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Affiliation(s)
- Maja Etzel
- Institute for Biochemistry, Leipzig University , Brüderstrasse 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University , Brüderstrasse 34, 04103 Leipzig, Germany
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11
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Peters G, Coussement P, Maertens J, Lammertyn J, De Mey M. Putting RNA to work: Translating RNA fundamentals into biotechnological engineering practice. Biotechnol Adv 2015; 33:1829-44. [PMID: 26514597 DOI: 10.1016/j.biotechadv.2015.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/13/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022]
Abstract
Synthetic biology, in close concert with systems biology, is revolutionizing the field of metabolic engineering by providing novel tools and technologies to rationally, in a standardized way, reroute metabolism with a view to optimally converting renewable resources into a broad range of bio-products, bio-materials and bio-energy. Increasingly, these novel synthetic biology tools are exploiting the extensive programmable nature of RNA, vis-à-vis DNA- and protein-based devices, to rationally design standardized, composable, and orthogonal parts, which can be scaled and tuned promptly and at will. This review gives an extensive overview of the recently developed parts and tools for i) modulating gene expression ii) building genetic circuits iii) detecting molecules, iv) reporting cellular processes and v) building RNA nanostructures. These parts and tools are becoming necessary armamentarium for contemporary metabolic engineering. Furthermore, the design criteria, technological challenges, and recent metabolic engineering success stories of the use of RNA devices are highlighted. Finally, the future trends in transforming metabolism through RNA engineering are critically evaluated and summarized.
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Affiliation(s)
- Gert Peters
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Pieter Coussement
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jo Maertens
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jeroen Lammertyn
- BIOSYST-MeBioS, KU Leuven, Willem de Croylaan 42, 3001 Louvain, Belgium
| | - Marjan De Mey
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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12
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Liu D, Evans T, Zhang F. Applications and advances of metabolite biosensors for metabolic engineering. Metab Eng 2015; 31:35-43. [DOI: 10.1016/j.ymben.2015.06.008] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 06/23/2015] [Accepted: 06/23/2015] [Indexed: 01/01/2023]
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13
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Endoh T, Sugimoto N. Rational Design and Tuning of Functional RNA Switch to Control an Allosteric Intermolecular Interaction. Anal Chem 2015; 87:7628-35. [DOI: 10.1021/acs.analchem.5b00765] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tamaki Endoh
- Frontier
Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojimaminamimachi, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier
Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojimaminamimachi, Kobe, 650-0047, Japan
- Graduate
School of Frontiers of Innovative
Research in Science and Technology (FIRST), Konan University, 7-1-20
Minatojimaminamimachi, Kobe, 650-0047, Japan
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14
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Redden H, Morse N, Alper HS. The synthetic biology toolbox for tuning gene expression in yeast. FEMS Yeast Res 2014; 15:1-10. [DOI: 10.1111/1567-1364.12188] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/28/2014] [Accepted: 07/15/2014] [Indexed: 02/04/2023] Open
Affiliation(s)
- Heidi Redden
- Department for Molecular Biosciences; The University of Texas at Austin; Austin TX USA
| | - Nicholas Morse
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
| | - Hal S. Alper
- Department for Molecular Biosciences; The University of Texas at Austin; Austin TX USA
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
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15
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Kröner C, Thunemann M, Vollmer S, Kinzer M, Feil R, Richert C. Endless: a purine-binding RNA motif that can be expressed in cells. Angew Chem Int Ed Engl 2014; 53:9198-202. [PMID: 25045108 DOI: 10.1002/anie.201403579] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 04/29/2014] [Indexed: 01/16/2023]
Abstract
It is becoming increasingly clear that nature uses RNAs extensively for regulating vital functions of the cell, and short sequences are frequently used to suppress gene expression. However, controlling the concentration of small molecules intracellularly through designed RNA sequences that fold into ligand-binding structures is difficult. The development of "endless", a triplex-based folding motif that can be expressed in mammalian cells and binds the second messenger 3',5'-cyclic guanosine monophosphate (cGMP), is described. In vitro, DNA or RNA versions of endless show low micromolar to nanomolar dissociation constants for cGMP. To test its functionality in vivo, four endless RNA motifs arranged in tandem were co-expressed with a fluorescent cGMP sensor protein in murine vascular smooth muscle cells. Nitric oxide induced endogenous cGMP signals were suppressed in endless-expressing cells compared to cells expressing a control motif, which suggests that endless can act as a genetically encoded cGMP sink to modulate signal transduction in cells.
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Affiliation(s)
- Christoph Kröner
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
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16
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Kröner C, Thunemann M, Vollmer S, Kinzer M, Feil R, Richert C. Endless: A Purine-Binding RNA Motif that Can Be Expressed in Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Ang J, Harris E, Hussey BJ, Kil R, McMillen DR. Tuning response curves for synthetic biology. ACS Synth Biol 2013; 2:547-67. [PMID: 23905721 PMCID: PMC3805330 DOI: 10.1021/sb4000564] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Indexed: 01/07/2023]
Abstract
Synthetic biology may be viewed as an effort to establish, formalize, and develop an engineering discipline in the context of biological systems. The ability to tune the properties of individual components is central to the process of system design in all fields of engineering, and synthetic biology is no exception. A large and growing number of approaches have been developed for tuning the responses of cellular systems, and here we address specifically the issue of tuning the rate of response of a system: given a system where an input affects the rate of change of an output, how can the shape of the response curve be altered experimentally? This affects a system's dynamics as well as its steady-state properties, both of which are critical in the design of systems in synthetic biology, particularly those with multiple components. We begin by reviewing a mathematical formulation that captures a broad class of biological response curves and use this to define a standard set of varieties of tuning: vertical shifting, horizontal scaling, and the like. We then survey the experimental literature, classifying the results into our defined categories, and organizing them by regulatory level: transcriptional, post-transcriptional, and post-translational.
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Affiliation(s)
- Jordan Ang
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Edouard Harris
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Brendan J. Hussey
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - Richard Kil
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
| | - David R. McMillen
- Department of Chemical and Physical Sciences and Institute
for Optical Sciences, University of Toronto, Mississauga, Ontario, Canada L5L 1C6
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18
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Nicholson AW. Ribonuclease III mechanisms of double-stranded RNA cleavage. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:31-48. [PMID: 24124076 PMCID: PMC3867540 DOI: 10.1002/wrna.1195] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/09/2013] [Accepted: 08/10/2013] [Indexed: 12/22/2022]
Abstract
Double-stranded(ds) RNA has diverse roles in gene expression and regulation, host defense, and genome surveillance in bacterial and eukaryotic cells. A central aspect of dsRNA function is its selective recognition and cleavage by members of the ribonuclease III (RNase III) family of divalent-metal-ion-dependent phosphodiesterases. The processing of dsRNA by RNase III family members is an essential step in the maturation and decay of coding and noncoding RNAs, including miRNAs and siRNAs. RNase III, as first purified from Escherichia coli, has served as a biochemically well-characterized prototype, and other bacterial orthologs provided the first structural information. RNase III family members share a unique fold (RNase III domain) that can dimerize to form a structure that binds dsRNA and cleaves phosphodiesters on each strand, providing the characteristic 2 nt, 3′-overhang product ends. Ongoing studies are uncovering the functions of additional domains, including, inter alia, the dsRNA-binding and PAZ domains that cooperate with the RNase III domain to select target sites, regulate activity, confer processivity, and support the recognition of structurally diverse substrates. RNase III enzymes function in multicomponent assemblies that are regulated by diverse inputs, and at least one RNase III-related polypeptide can function as a noncatalytic, dsRNA-binding protein. This review summarizes the current knowledge of the mechanisms of catalysis and target site selection of RNase III family members, and also addresses less well understood aspects of these enzymes and their interactions with dsRNA. WIREs RNA 2014, 5:31–48. doi: 10.1002/wrna.1195
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Affiliation(s)
- Allen W Nicholson
- Department of Biology and Chemistry, College of Science & Technology, Temple University, Philadelphia, PA, USA
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19
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Ogawa A. Ligand-Dependent Upregulation of Ribosomal Shunting. Chembiochem 2013; 14:1539-43, 1509. [DOI: 10.1002/cbic.201300362] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Indexed: 12/25/2022]
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20
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Wang YH, Wei KY, Smolke CD. Synthetic biology: advancing the design of diverse genetic systems. Annu Rev Chem Biomol Eng 2013; 4:69-102. [PMID: 23413816 DOI: 10.1146/annurev-chembioeng-061312-103351] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A major objective of synthetic biology is to make the process of designing genetically encoded biological systems more systematic, predictable, robust, scalable, and efficient. Examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from simple genetic switches to search-and-destroy systems. While significant advances in DNA synthesis capabilities support the construction of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Thus, while synthetic biology offers much promise in developing systems to address challenges faced in the fields of manufacturing, environment and sustainability, and health and medicine, the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems.
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Affiliation(s)
- Yen-Hsiang Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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21
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Wachsmuth M, Findeiß S, Weissheimer N, Stadler PF, Mörl M. De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res 2012; 41:2541-51. [PMID: 23275562 PMCID: PMC3575828 DOI: 10.1093/nar/gks1330] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Riboswitches are regulatory RNA elements typically located in the 5′-untranslated region of certain mRNAs and control gene expression at the level of transcription or translation. These elements consist of a sensor and an adjacent actuator domain. The sensor usually is an aptamer that specifically interacts with a ligand. The actuator contains an intrinsic terminator or a ribosomal binding site for transcriptional or translational regulation, respectively. Ligand binding leads to structural rearrangements of the riboswitch and to presentation or masking of these regulatory elements. Based on this modular organization, riboswitches are an ideal target for constructing synthetic regulatory systems for gene expression. Although riboswitches for translational control have been designed successfully, attempts to construct synthetic elements regulating transcription have failed so far. Here, we present an in silico pipeline for the rational design of synthetic riboswitches that regulate gene expression at the transcriptional level. Using the well-characterized theophylline aptamer as sensor, we designed the actuator part as RNA sequences that can fold into functional intrinsic terminator structures. In the biochemical characterization, several of the designed constructs show ligand-dependent control of gene expression in Escherichia coli, demonstrating that it is possible to engineer riboswitches not only for translational but also for transcriptional regulation.
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Affiliation(s)
- Manja Wachsmuth
- Institute for Biochemistry, University of Leipzig, Brüderstr. 34, 04103 Leipzig, Germany
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22
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Abstract
Enzymes from the ribonuclease III family bind and cleave double-stranded RNA to initiate RNA processing and degradation of a large number of transcripts in bacteria and eukaryotes. This chapter focuses on the description of the diverse functions of fungal RNase III members in the processing and degradation of cellular RNAs, with a particular emphasis on the well-characterized representative in Saccharomyces cerevisiae, Rnt1p. RNase III enzymes fulfill important functions in the processing of the precursors of various stable noncoding RNAs such as ribosomal RNAs and small nuclear and nucleolar RNAs. In addition, they cleave and promote the degradation of specific mRNAs or improperly processed forms of certain mRNAs. The cleavage of these mRNAs serves both surveillance and regulatory functions. Finally, recent advances have shown that RNase III enzymes are involved in mediating fail-safe transcription termination by RNA polymerase II (Pol II), by cleaving intergenic stem-loop structures present downstream from Pol II transcription units. Many of these processing functions appear to be conserved in fungal species close to the Saccharomyces genus, and even in more distant eukaryotic species.
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Affiliation(s)
- Kevin Roy
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California, USA.
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23
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Ricci F, Vallée-Bélisle A, Porchetta A, Plaxco KW. Rational design of allosteric inhibitors and activators using the population-shift model: in vitro validation and application to an artificial biosensor. J Am Chem Soc 2012; 134:15177-80. [PMID: 22924432 PMCID: PMC3523727 DOI: 10.1021/ja304672h] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The population-shift mechanism can be used for rational re-engineering of structure-switching biosensors to enable their allosteric inhibition and activation. As a proof-of-principle example of this, we have introduced distal allosteric sites into molecular beacons, which are optical sensors for the detection of specific nucleic acid sequences. The binding of inhibitors and activators to these sites enabled the rational modulation of the sensor's target affinity-and thus its useful dynamic range-over 3 orders of magnitude. The convenience with which this was done suggests that the population-shift mechanism may prove to be a useful method by which allosteric regulation can be introduced into biosensors, "smart" biomaterials, and other artificial biotechnologies.
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Affiliation(s)
- Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Rome, Italy
| | - Alexis Vallée-Bélisle
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Center for Bioengineering, University of California, Santa Barbara, CA 93106 USA
| | - Alessandro Porchetta
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Consorzio Interuniversitario Biostrutture e Biosistemi “INBB”, Rome, Italy
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
- Center for Bioengineering, University of California, Santa Barbara, CA 93106 USA
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106 USA
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Abstract
Over the past decade, synthetic biology has emerged as an engineering discipline for biological systems. Compared with other substrates, biology poses a unique set of engineering challenges resulting from an incomplete understanding of natural biological systems and tools for manipulating them. To address these challenges, synthetic biology is advancing from developing proof-of-concept designs to focusing on core platforms for rational and high-throughput biological engineering. These platforms span the entire biological design cycle, including DNA construction, parts libraries, computational design tools, and interfaces for manipulating and probing synthetic circuits. The development of these enabling technologies requires an engineering mindset to be applied to biology, with an emphasis on generalizable techniques in addition to application-specific designs. This review aims to discuss the progress and challenges in synthetic biology and to illustrate areas where synthetic biology may impact biomedical engineering and human health.
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Affiliation(s)
- Allen A Cheng
- Synthetic Biology Group, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Chang AL, Wolf JJ, Smolke CD. Synthetic RNA switches as a tool for temporal and spatial control over gene expression. Curr Opin Biotechnol 2012; 23:679-88. [PMID: 22305712 DOI: 10.1016/j.copbio.2012.01.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 11/17/2022]
Abstract
The engineering of biological systems offers significant promise for advances in areas including health and medicine, chemical synthesis, energy production, and environmental sustainability. Realizing this potential requires tools that enable design of sophisticated genetic systems. The functional diversity of RNA makes it an attractive and versatile substrate for programming sensing, information processing, computation, and control functions. Recent advances in the design of synthetic RNA switches capable of detecting and responding to molecular and environmental signals enable dynamic modulation of gene expression through diverse mechanisms, including transcription, splicing, stability, RNA interference, and translation. Furthermore, implementation of these switches in genetic circuits highlights the potential for building synthetic cell systems targeted to applications in environmental remediation and next-generation therapeutics and diagnostics.
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Affiliation(s)
- Andrew L Chang
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
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26
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Blount BA, Weenink T, Ellis T. Construction of synthetic regulatory networks in yeast. FEBS Lett 2012; 586:2112-21. [DOI: 10.1016/j.febslet.2012.01.053] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 11/30/2022]
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27
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Kim IK, Roldão A, Siewers V, Nielsen J. A systems-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res 2012; 12:228-48. [DOI: 10.1111/j.1567-1364.2011.00779.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/05/2011] [Accepted: 12/09/2011] [Indexed: 12/01/2022] Open
Affiliation(s)
- Il-Kwon Kim
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - António Roldão
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - Verena Siewers
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
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28
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Engineering biological systems with synthetic RNA molecules. Mol Cell 2011; 43:915-26. [PMID: 21925380 DOI: 10.1016/j.molcel.2011.08.023] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 08/16/2011] [Accepted: 08/21/2011] [Indexed: 01/08/2023]
Abstract
RNA molecules play diverse functional roles in natural biological systems. There has been growing interest in designing synthetic RNA counterparts for programming biological function. The design of synthetic RNA molecules that exhibit diverse activities, including sensing, regulatory, information processing, and scaffolding activities, has highlighted the advantages of RNA as a programmable design substrate. Recent advances in implementing these engineered RNA molecules as key control elements in synthetic genetic networks are highlighting the functional relevance of this class of synthetic elements in programming cellular behaviors.
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Babiskin AH, Smolke CD. Synthetic RNA modules for fine-tuning gene expression levels in yeast by modulating RNase III activity. Nucleic Acids Res 2011; 39:8651-64. [PMID: 21737428 PMCID: PMC3201855 DOI: 10.1093/nar/gkr445] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The design of synthetic gene networks requires an extensive genetic toolbox to control the activities and levels of protein components to achieve desired cellular functions. Recently, a novel class of RNA-based control modules, which act through post-transcriptional processing of transcripts by directed RNase III (Rnt1p) cleavage, were shown to provide predictable control over gene expression and unique properties for manipulating biological networks. Here, we increase the regulatory range of the Rnt1p control elements, by modifying a critical region for enzyme binding to its hairpin substrates, the binding stability box (BSB). We used a high throughput, cell-based selection strategy to screen a BSB library for sequences that exhibit low fluorescence and thus high Rnt1p processing efficiencies. Sixteen unique BSBs were identified that cover a range of protein expression levels, due to the ability of the sequences to affect the hairpin cleavage rate and to form active cleavable complexes with Rnt1p. We further demonstrated that the activity of synthetic Rnt1p hairpins can be rationally programmed by combining the synthetic BSBs with a set of sequences located within a different region of the hairpin that directly modulate cleavage rates, providing a modular assembly strategy for this class of RNA-based control elements.
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Affiliation(s)
- Andrew H Babiskin
- Division of Chemistry and Chemical Engineering, 1200 E. California Blvd., MC 210-41, California Institute of Technology, Pasadena, CA 91125, USA
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