1
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Ogawa A, Fujikawa M, Onishi K, Takahashi H. Cell-Free Biosensors Based on Modular Eukaryotic Riboswitches That Function in One Pot at Ambient Temperature. ACS Synth Biol 2024; 13:2238-2245. [PMID: 38913391 DOI: 10.1021/acssynbio.4c00341] [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: 06/25/2024]
Abstract
Artificial riboswitches responsive to user-defined analytes can be constructed by successfully inserting in vitro selected aptamers, which bind to the analytes, into untranslated regions of mRNA. Among them, eukaryotic riboswitches are more promising as biosensors than bacterial ones because they function well at ambient temperature. In addition, cell-free expression systems allow the broader use of these riboswitches as cell-free biosensors in an environmentally friendly manner without cellular limitations. The current best cell-free eukaryotic riboswitch regulates eukaryotic canonical translation initiation through self-cleavage mediated by an implanted analyte-responsive ribozyme (i.e., an aptazyme, an aptamer-ribozyme fusion). However, it has critical flaws as a sensor: due to the less-active ribozyme used, self-cleavage and translation reactions must be conducted separately and sequentially, and a different aptazyme has to be selected to change the analyte specificity, even if an aptamer for the next analyte is available. We here stepwise engineered novel types of cell-free eukaryotic riboswitches that harness highly active self-cleavage and thus require no reaction partitioning. Despite the single-step and one-pot reaction, these riboswitches showed higher analyte dose dependency and sensitivities than the current best cell-free eukaryotic riboswitch requiring multistep reactions. In addition, the analyte specificity can be changed in an extremely facile way, simply by aptamer substitution (and the subsequent simple fine-tuning for giant aptamers). Given that cell-free systems can be lyophilized for storage and transport, the present one-pot and thus easy-to-handle cell-free biosensors utilizing eukaryotic riboswitches are expected to be widely used for on-the-spot sensing of analytes at ambient temperature.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 2-5 Bunkyo, Matsuyama ,Ehime 790-8577, Japan
| | - Masahiro Fujikawa
- Proteo-Science Center, Ehime University, 2-5 Bunkyo, Matsuyama ,Ehime 790-8577, Japan
| | - Kazuki Onishi
- Proteo-Science Center, Ehime University, 2-5 Bunkyo, Matsuyama ,Ehime 790-8577, Japan
| | - Hajime Takahashi
- Proteo-Science Center, Ehime University, 2-5 Bunkyo, Matsuyama ,Ehime 790-8577, Japan
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2
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Pietruschka G, Ranzani AT, Weber A, Patwari T, Pilsl S, Renzl C, Otte DM, Pyka D, Möglich A, Mayer G. An RNA Motif That Enables Optozyme Control and Light-Dependent Gene Expression in Bacteria and Mammalian Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304519. [PMID: 38227373 DOI: 10.1002/advs.202304519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/19/2023] [Indexed: 01/17/2024]
Abstract
The regulation of gene expression by light enables the versatile, spatiotemporal manipulation of biological function in bacterial and mammalian cells. Optoribogenetics extends this principle by molecular RNA devices acting on the RNA level whose functions are controlled by the photoinduced interaction of a light-oxygen-voltage photoreceptor with cognate RNA aptamers. Here light-responsive ribozymes, denoted optozymes, which undergo light-dependent self-cleavage and thereby control gene expression are described. This approach transcends existing aptamer-ribozyme chimera strategies that predominantly rely on aptamers binding to small molecules. The optozyme method thus stands to enable the graded, non-invasive, and spatiotemporally resolved control of gene expression. Optozymes are found efficient in bacteria and mammalian cells and usher in hitherto inaccessible optoribogenetic modalities with broad applicability in synthetic and systems biology.
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Affiliation(s)
- Georg Pietruschka
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
| | - Américo T Ranzani
- Lehrstuhl für Biochemie, Photobiochemie, University of Bayreuth, Universitätsstraße 30, 95440, Bayreuth, Germany
| | - Anna Weber
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Tejal Patwari
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
| | - Sebastian Pilsl
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
| | - Christian Renzl
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - David M Otte
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
| | - Daniel Pyka
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
| | - Andreas Möglich
- Lehrstuhl für Biochemie, Photobiochemie, University of Bayreuth, Universitätsstraße 30, 95440, Bayreuth, Germany
| | - Günter Mayer
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
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3
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Kläge D, Müller E, Hartig JS. A comparative survey of the influence of small self-cleaving ribozymes on gene expression in human cell culture. RNA Biol 2024; 21:1-11. [PMID: 38146121 PMCID: PMC10761166 DOI: 10.1080/15476286.2023.2296203] [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] [Accepted: 12/13/2023] [Indexed: 12/27/2023] Open
Abstract
Self-cleaving ribozymes are versatile tools for synthetic biologists when it comes to controlling gene expression. Up to date, 12 different classes are known, and over the past decades more and more details about their structure, cleavage mechanisms and natural environments have been uncovered. However, when these motifs are applied to mammalian gene expression constructs, the outcome can often be unexpected. A variety of factors, such as surrounding sequences and positioning of the ribozyme influences the activity and hence performance of catalytic RNAs. While some information about the efficiency of individual ribozymes (each tested in specific contexts) is known, general trends obtained from standardized, comparable experiments are lacking, complicating decisions such as which ribozyme to choose and where to insert it into the target mRNA. In many cases, application-specific optimization is required, which can be very laborious. Here, we systematically compared different classes of ribozymes within the 3'-UTR of a given reporter gene. We then examined position-dependent effects of the best-performing ribozymes. Moreover, we tested additional variants of already widely used hammerhead ribozymes originating from various organisms. We were able to identify functional structures suited for aptazyme design and generated highly efficient hammerhead ribozyme variants originating from the human genome. The present dataset will aide decisions about how to apply ribozymes for affecting gene expression as well as for developing ribozyme-based switches for controlling gene expression in human cells.
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Affiliation(s)
- Dennis Kläge
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Elisabeth Müller
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
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4
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Zhou S, Chen M, Yuan Y, Xu Y, Pu Q, Ai X, Liu S, Du F, Huang X, Dong J, Cui X, Tang Z. Trans-acting aptazyme for conditional gene knockdown in eukaryotic cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:367-375. [PMID: 37547296 PMCID: PMC10400872 DOI: 10.1016/j.omtn.2023.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Trans-acting hammerhead ribozyme inherits the advantages of being the smallest and best-characterized RNA-cleaving ribozyme, offering high modularity and the ability to cleave any desired sequence without the aid of any protein, as long as the target sequence contains a cleavage site. However, achieving precise control over the trans-acting hammerhead ribozyme would enable safer and more accurate regulation of gene expression. Herein, we described an intracellular selection of hammerhead aptazyme that contains a theophylline aptamer on stem II based on toxin protein IbsC. Based on the intracellular selection, we obtained three new cis-acting hammerhead aptazymes. Moreover, the corresponding trans-acting aptazymes could be efficiently induced by theophylline to knock down different targeted genes in eukaryotic cells. Notably, the best one, T195, exhibited a ligand-dependent and dose-dependent response to theophylline, and the cleavage efficiency could be enhanced by incorporating multiplex aptazymes.
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Affiliation(s)
- Shan Zhou
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Meiyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Yan Xu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Qinlin Pu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Xilei Ai
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Shuai Liu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
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5
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Vandierendonck J, Girardin Y, De Bruyn P, De Greve H, Loris R. A Multi-Layer-Controlled Strategy for Cloning and Expression of Toxin Genes in Escherichia coli. Toxins (Basel) 2023; 15:508. [PMID: 37624265 PMCID: PMC10467106 DOI: 10.3390/toxins15080508] [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] [Received: 04/05/2023] [Revised: 07/17/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Molecular cloning and controlled expression remain challenging when the target gene encodes a protein that is toxic to the host. We developed a set of multi-layer control systems to enable cloning of genes encoding proteins known to be highly toxic in Escherichia coli and other bacteria. The different multi-layer control systems combine a promoter-operator system on a transcriptional level with a riboswitch for translational control. Additionally, replicational control is ensured by using a strain that reduces the plasmid copy number. The use of weaker promoters (such as PBAD or PfdeA) in combination with the effective theophylline riboswitch is essential for cloning genes that encode notoriously toxic proteins that directly target translation and transcription. Controlled overexpression is possible, allowing the system to be used for evaluating in vivo effects of the toxin. Systems with a stronger promoter can be used for successful overexpression and purification of the desired protein but are limited to toxins that are more moderate and do not interfere with their own production.
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Affiliation(s)
| | | | | | - Henri De Greve
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie and Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium; (J.V.); (Y.G.)
| | - Remy Loris
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie and Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium; (J.V.); (Y.G.)
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6
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Wang Z, Cheng J, Dai G, Sun X, Yin X, Zhang Y. The Establishment of a Tobramycin-Responsive Whole-Cell Micro-Biosensor Based on an Artificial Ribozyme Switch. Life (Basel) 2023; 13:1553. [PMID: 37511928 PMCID: PMC10381313 DOI: 10.3390/life13071553] [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: 05/11/2023] [Revised: 06/25/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
In this study, a tobramycin concentration-dependent whole-cell micro-biosensor (tob-HHAz) was constructed by fusing a tobramycin aptamer with a hammerhead ribozyme (HHR) from Schistosoma mansoni. The biosensor was obtained by integrating all the modules into one complete RNA sequence, which was easily introduced into E. coli without suffering from harsh external environments. Three independent tobramycin-sensitive RNA structures were identified via high-throughput screening in vivo and were further verified in vitro to undergo the desired self-cleavage reaction. The computation prediction of the RNA structure was performed to help analyze the mechanisms of various conformations by performing a qualitative and rapid detection of tobramycin in practical samples; two sensors exhibited high responsiveness to spiked milk, with a detection limit of around 40 nM, which is below the EU's antibiotic maximum residual level. One of the structures provides a linear range from 30 to 650 nM with a minimum detection limit of 30 nM and showed relatively good selectivity in spiked urine. This study is the first in which in vivo screening was combined with computation analysis to optimize the pivotal structure of sensors. This strategy enables researchers to use artificial ribozyme-based biosensors not only for antibiotic detection but also as a generally applicable method for the further detection of substances in living cells.
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Affiliation(s)
- Zhenzhen Wang
- School of Life Science, Anhui Medical University, Hefei 230032, China
| | - Jiawen Cheng
- School of Life Science, Anhui Medical University, Hefei 230032, China
| | - Guimin Dai
- School of Life Science, Anhui Medical University, Hefei 230032, China
| | - Xiaoqi Sun
- School of Life Science, Anhui Medical University, Hefei 230032, China
| | - Xueli Yin
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Yuanyuan Zhang
- School of Life Science, Anhui Medical University, Hefei 230032, China
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7
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Kim M, Jo H, Jung GY, Oh SS. Molecular Complementarity of Proteomimetic Materials for Target-Specific Recognition and Recognition-Mediated Complex Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208309. [PMID: 36525617 DOI: 10.1002/adma.202208309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Indexed: 06/02/2023]
Abstract
As biomolecules essential for sustaining life, proteins are generated from long chains of 20 different α-amino acids that are folded into unique 3D structures. In particular, many proteins have molecular recognition functions owing to their binding pockets, which have complementary shapes, charges, and polarities for specific targets, making these biopolymers unique and highly valuable for biomedical and biocatalytic applications. Based on the understanding of protein structures and microenvironments, molecular complementarity can be exhibited by synthesizable and modifiable materials. This has prompted researchers to explore the proteomimetic potentials of a diverse range of materials, including biologically available peptides and oligonucleotides, synthetic supramolecules, inorganic molecules, and related coordination networks. To fully resemble a protein, proteomimetic materials perform the molecular recognition to mediate complex molecular functions, such as allosteric regulation, signal transduction, enzymatic reactions, and stimuli-responsive motions; this can also expand the landscape of their potential bio-applications. This review focuses on the recognitive aspects of proteomimetic designs derived for individual materials and their conformations. Recent progress provides insights to help guide the development of advanced protein mimicry with material heterogeneity, design modularity, and tailored functionality. The perspectives and challenges of current proteomimetic designs and tools are also discussed in relation to future applications.
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Affiliation(s)
- Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Seung Soo Oh
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
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8
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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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9
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Mao C, Mao Y, Zhu X, Chen G, Feng C. Synthetic biology-based bioreactor and its application in biochemical analysis. Crit Rev Anal Chem 2023:1-18. [PMID: 36803337 DOI: 10.1080/10408347.2023.2180319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
In the past few years, synthetic biologists have established some biological elements and bioreactors composed of nucleotides under the guidance of engineering methods. Following the concept of engineering, the common bioreactor components in recent years are introduced and compared. At present, biosensors based on synthetic biology have been applied to water pollution monitoring, disease diagnosis, epidemiological monitoring, biochemical analysis and other detection fields. In this paper, the biosensor components based on synthetic bioreactors and reporters are reviewed. In addition, the applications of biosensors based on cell system and cell-free system in the detection of heavy metal ions, nucleic acid, antibiotics and other substances are presented. Finally, the bottlenecks faced by biosensors and the direction of optimization are also discussed.
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Affiliation(s)
- Changqing Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Yichun Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, P. R. China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
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10
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Hoetzel J, Suess B. Structural changes in aptamers are essential for synthetic riboswitch engineering. J Mol Biol 2022; 434:167631. [PMID: 35595164 DOI: 10.1016/j.jmb.2022.167631] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/19/2022]
Abstract
Synthetic riboswitches are powerful tools in synthetic biology in which sensing and execution are consolidated in a single RNA molecule. By using SELEX to select aptamers in vitro, synthetic riboswitches can in theory be engineered against any ligand of choice. Surprisingly, very few in vitro selected aptamers have been used for the engineering of synthetic riboswitches. In-depth studies of these aptamers suggest that the key characteristics of such regulatory active RNAs are their structural switching abilities and their binding dynamics. Conventional SELEX approaches seem to be inadequate to select for these characteristics, which may explain the lack of in vitro selected aptamers suited for engineering of synthetic riboswitches. In this review, we explore the functional principles of synthetic riboswitches, identify key characteristics of regulatory active in vitro selected aptamers and integrate these findings in context with available in vitro selection methods. Based on these insights, we propose to use a combination of capture-SELEX and subsequent functional screening for a more successful in vitro selection of aptamers that can be applied for the engineering of synthetic riboswitches.
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Affiliation(s)
- Janis Hoetzel
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany. https://www.twitter.com/J_Hoetzel
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany; Center for Synthetic Biology, Technical University of Darmstadt, Germany.
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11
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Tabuchi T, Yokobayashi Y. High-throughput screening of cell-free riboswitches by fluorescence-activated droplet sorting. Nucleic Acids Res 2022; 50:3535-3550. [PMID: 35253887 PMCID: PMC8989549 DOI: 10.1093/nar/gkac152] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 11/14/2022] Open
Abstract
Cell-free systems that display complex functions without using living cells are emerging as new platforms to test our understanding of biological systems as well as for practical applications such as biosensors and biomanufacturing. Those that use cell-free protein synthesis (CFPS) systems to enable genetically programmed protein synthesis have relied on genetic regulatory components found or engineered in living cells. However, biological constraints such as cell permeability, metabolic stability, and toxicity of signaling molecules prevent development of cell-free devices using living cells even if cell-free systems are not subject to such constraints. Efforts to engineer regulatory components directly in CFPS systems thus far have been based on low-throughput experimental approaches, limiting the availability of basic components to build cell-free systems with diverse functions. Here, we report a high-throughput screening method to engineer cell-free riboswitches that respond to small molecules. Droplet-sorting of riboswitch variants in a CFPS system rapidly identified cell-free riboswitches that respond to compounds that are not amenable to bacterial screening methods. Finally, we used a histamine riboswitch to demonstrate chemical communication between cell-sized droplets.
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Affiliation(s)
- Takeshi Tabuchi
- 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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12
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Miller CA, Ho JML, Bennett MR. Strategies for Improving Small-Molecule Biosensors in Bacteria. BIOSENSORS 2022; 12:bios12020064. [PMID: 35200325 PMCID: PMC8869690 DOI: 10.3390/bios12020064] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 05/03/2023]
Abstract
In recent years, small-molecule biosensors have become increasingly important in synthetic biology and biochemistry, with numerous new applications continuing to be developed throughout the field. For many biosensors, however, their utility is hindered by poor functionality. Here, we review the known types of mechanisms of biosensors within bacterial cells, and the types of approaches for optimizing different biosensor functional parameters. Discussed approaches for improving biosensor functionality include methods of directly engineering biosensor genes, considerations for choosing genetic reporters, approaches for tuning gene expression, and strategies for incorporating additional genetic modules.
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Affiliation(s)
- Corwin A. Miller
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
| | - Joanne M. L. Ho
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
| | - Matthew R. Bennett
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
- Department of Bioengineering, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA
- Correspondence:
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13
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Peng H, Latifi B, Müller S, Lupták A, Chen IA. Self-cleaving ribozymes: substrate specificity and synthetic biology applications. RSC Chem Biol 2021; 2:1370-1383. [PMID: 34704043 PMCID: PMC8495972 DOI: 10.1039/d0cb00207k] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Various self-cleaving ribozymes appearing in nature catalyze the sequence-specific intramolecular cleavage of RNA and can be engineered to catalyze cleavage of appropriate substrates in an intermolecular fashion, thus acting as true catalysts. The mechanisms of the small, self-cleaving ribozymes have been extensively studied and reviewed previously. Self-cleaving ribozymes can possess high catalytic activity and high substrate specificity; however, substrate specificity is also engineerable within the constraints of the ribozyme structure. While these ribozymes share a common fundamental catalytic mechanism, each ribozyme family has a unique overall architecture and active site organization, indicating that several distinct structures yield this chemical activity. The multitude of catalytic structures, combined with some flexibility in substrate specificity within each family, suggests that such catalytic RNAs, taken together, could access a wide variety of substrates. Here, we give an overview of 10 classes of self-cleaving ribozymes and capture what is understood about their substrate specificity and synthetic applications. Evolution of these ribozymes in an RNA world might be characterized by the emergence of a new ribozyme family followed by rapid adaptation or diversification for specific substrates. Self-cleaving ribozymes have become important tools of synthetic biology. Here we summarize the substrate specificity and applications of the main classes of these ribozymes.![]()
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Affiliation(s)
- Huan Peng
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
| | - Brandon Latifi
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697 USA
| | - Sabine Müller
- Institute for Biochemistry, University Greifswald 17487 Greifswald Germany
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697 USA
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
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14
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Tabuchi T, Yokobayashi Y. Cell-free riboswitches. RSC Chem Biol 2021; 2:1430-1440. [PMID: 34704047 PMCID: PMC8496063 DOI: 10.1039/d1cb00138h] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/26/2021] [Indexed: 12/16/2022] Open
Abstract
The emerging community of cell-free synthetic biology aspires to build complex biochemical and genetic systems with functions that mimic or even exceed those in living cells. To achieve such functions, cell-free systems must be able to sense and respond to the complex chemical signals within and outside the system. Cell-free riboswitches can detect chemical signals via RNA-ligand interaction and respond by regulating protein synthesis in cell-free protein synthesis systems. In this article, we review synthetic cell-free riboswitches that function in both prokaryotic and eukaryotic cell-free systems reported to date to provide a current perspective on the state of cell-free riboswitch technologies and their limitations.
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Affiliation(s)
- Takeshi Tabuchi
- 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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15
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Engineering Aptazyme Switches for Conditional Gene Expression in Mammalian Cells Utilizing an In Vivo Screening Approach. Methods Mol Biol 2021. [PMID: 34086282 DOI: 10.1007/978-1-0716-1499-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Artificial RNA switches are an emerging class of genetic controllers suitable for synthetic biology applications. Aptazymes are fusions composed of an aptamer domain and a self-cleaving ribozyme. The utilization of aptazymes for conditional gene expression displays several advantages over employing conventional transcription factor-based techniques as aptazymes require minimal genomic space, fulfill their function without the need of protein cofactors and most importantly are reprogrammable with respect to ligand selectivity and the RNA function to be regulated. Technologies that enable the generation of aptazymes to defined input ligands are of interest for the construction of biocomputing devices and biosensing applications. In this chapter we present a method that facilitates the in vivo screening of randomized pools of aptazymes in mammalian cells.
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16
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Tickner ZJ, Farzan M. Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors. Pharmaceuticals (Basel) 2021; 14:ph14060554. [PMID: 34200913 PMCID: PMC8230432 DOI: 10.3390/ph14060554] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
Vectors developed from adeno-associated virus (AAV) are powerful tools for in vivo transgene delivery in both humans and animal models, and several AAV-delivered gene therapies are currently approved for clinical use. However, AAV-mediated gene therapy still faces several challenges, including limited vector packaging capacity and the need for a safe, effective method for controlling transgene expression during and after delivery. Riboswitches, RNA elements which control gene expression in response to ligand binding, are attractive candidates for regulating expression of AAV-delivered transgene therapeutics because of their small genomic footprints and non-immunogenicity compared to protein-based expression control systems. In addition, the ligand-sensing aptamer domains of many riboswitches can be exchanged in a modular fashion to allow regulation by a variety of small molecules, proteins, and oligonucleotides. Riboswitches have been used to regulate AAV-delivered transgene therapeutics in animal models, and recently developed screening and selection methods allow rapid isolation of riboswitches with novel ligands and improved performance in mammalian cells. This review discusses the advantages of riboswitches in the context of AAV-delivered gene therapy, the subsets of riboswitch mechanisms which have been shown to function in human cells and animal models, recent progress in riboswitch isolation and optimization, and several examples of AAV-delivered therapeutic systems which might be improved by riboswitch regulation.
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Affiliation(s)
- Zachary J. Tickner
- Department of Immunology and Microbiology, the Scripps Research Institute, Jupiter, FL 33458, USA;
- Correspondence:
| | - Michael Farzan
- Department of Immunology and Microbiology, the Scripps Research Institute, Jupiter, FL 33458, USA;
- Emmune, Inc., Jupiter, FL 33458, USA
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17
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Yu Q, Ren K, You M. Genetically encoded RNA nanodevices for cellular imaging and regulation. NANOSCALE 2021; 13:7988-8003. [PMID: 33885099 PMCID: PMC8122502 DOI: 10.1039/d0nr08301a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nucleic acid-based nanodevices have been widely used in the fields of biosensing and nanomedicine. Traditionally, the majority of these nanodevices were first constructed in vitro using synthetic DNA or RNA oligonucleotides and then delivered into cells. Nowadays, the emergence of genetically encoded RNA nanodevices has provided a promising alternative approach for intracellular analysis and regulation. These genetically encoded RNA-based nanodevices can be directly transcribed and continuously produced inside living cells. A variety of highly precise and programmable nanodevices have been constructed in this way during the last decade. In this review, we will summarize the recent advances in the design and function of these artificial genetically encoded RNA nanodevices. In particular, we will focus on their applications in regulating cellular gene expression, imaging, logic operation, structural biology, and optogenetics. We believe these versatile RNA-based nanodevices will be broadly used in the near future to probe and program cells and other biological systems.
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Affiliation(s)
- Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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18
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Schmidt CM, Smolke CD. A convolutional neural network for the prediction and forward design of ribozyme-based gene-control elements. eLife 2021; 10:59697. [PMID: 33860764 PMCID: PMC8128436 DOI: 10.7554/elife.59697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
Ribozyme switches are a class of RNA-encoded genetic switch that support conditional regulation of gene expression across diverse organisms. An improved elucidation of the relationships between sequence, structure, and activity can improve our capacity for de novo rational design of ribozyme switches. Here, we generated data on the activity of hundreds of thousands of ribozyme sequences. Using automated structural analysis and machine learning, we leveraged these large data sets to develop predictive models that estimate the in vivo gene-regulatory activity of a ribozyme sequence. These models supported the de novo design of ribozyme libraries with low mean basal gene-regulatory activities and new ribozyme switches that exhibit changes in gene-regulatory activity in the presence of a target ligand, producing functional switches for four out of five aptamers. Our work examines how biases in the model and the data set that affect prediction accuracy can arise and demonstrates that machine learning can be applied to RNA sequences to predict gene-regulatory activity, providing the basis for design tools for functional RNAs.
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Affiliation(s)
- Calvin M Schmidt
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, United States.,Chan Zuckerberg Biohub, San Francisco, United States
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19
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Aroonsri A, Kongsee J, Gunawan JD, Aubry DA, Shaw PJ. A cell-based ribozyme reporter system employing a chromosomally-integrated 5' exonuclease gene. BMC Mol Cell Biol 2021; 22:20. [PMID: 33726662 PMCID: PMC7967978 DOI: 10.1186/s12860-021-00357-7] [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: 06/26/2020] [Accepted: 02/28/2021] [Indexed: 11/10/2022] Open
Abstract
Background Bioinformatic genome surveys indicate that self-cleaving ribonucleic acids (ribozymes) appear to be widespread among all domains of life, although the functions of only a small number have been validated by biochemical methods. Alternatively, cell-based reporter gene assays can be used to validate ribozyme function. However, reporter activity can be confounded by phenomena unrelated to ribozyme-mediated cleavage of RNA. Results We established a ribozyme reporter system in Escherichia coli in which a significant reduction of reporter activity is manifest when an active ribozyme sequence is fused to the reporter gene and the expression of a foreign Bacillus subtilis RNaseJ1 5′ exonuclease is induced from a chromosomally-integrated gene in the same cell. Conclusions The reporter system could be useful for validating ribozyme function in candidate sequences identified from bioinformatics. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00357-7.
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Affiliation(s)
- Aiyada Aroonsri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Jindaporn Kongsee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Jeremy David Gunawan
- School of Life Science, Indonesia International Institute for Life Sciences (i3L), Jakarta, 13210, Indonesia
| | - Daniel Abidin Aubry
- School of Life Science, Indonesia International Institute for Life Sciences (i3L), Jakarta, 13210, Indonesia
| | - Philip James Shaw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
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20
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Brayshaw LL, Martinez-Fleites C, Athanasopoulos T, Southgate T, Jespers L, Herring C. The role of small molecules in cell and gene therapy. RSC Med Chem 2021; 12:330-352. [PMID: 34046619 PMCID: PMC8130622 DOI: 10.1039/d0md00221f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/25/2020] [Indexed: 01/22/2023] Open
Abstract
Cell and gene therapies have achieved impressive results in the treatment of rare genetic diseases using gene corrected stem cells and haematological cancers using chimeric antigen receptor T cells. However, these two fields face significant challenges such as demonstrating long-term efficacy and safety, and achieving cost-effective, scalable manufacturing processes. The use of small molecules is a key approach to overcome these barriers and can benefit cell and gene therapies at multiple stages of their lifecycle. For example, small molecules can be used to optimise viral vector production during manufacturing or used in the clinic to enhance the resistance of T cell therapies to the immunosuppressive tumour microenvironment. Here, we review current uses of small molecules in cell and gene therapy and highlight opportunities for medicinal chemists to further consolidate the success of cell and gene therapies.
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Affiliation(s)
- Lewis L Brayshaw
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Carlos Martinez-Fleites
- Protein Degradation Group, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Takis Athanasopoulos
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Thomas Southgate
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Laurent Jespers
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Christopher Herring
- Cell & Gene Therapy Discovery Research, Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
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21
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Brown W, Zhou W, Deiters A. Regulating CRISPR/Cas9 Function through Conditional Guide RNA Control. Chembiochem 2021; 22:63-72. [PMID: 32833316 PMCID: PMC7928076 DOI: 10.1002/cbic.202000423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/21/2020] [Indexed: 12/26/2022]
Abstract
Conditional control of CRISPR/Cas9 has been developed by using a variety of different approaches, many focusing on manipulation of the Cas9 protein itself. However, more recent strategies for governing CRISPR/Cas9 function are based on guide RNA (gRNA) modifications. They include control of gRNAs by light, small molecules, proteins, and oligonucleotides. These designs have unique advantages compared to other approaches and have allowed precise regulation of gene editing and transcription. Here, we discuss strategies for conditional control of gRNA function and compare effectiveness of these methods.
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Affiliation(s)
| | | | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 (USA)
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22
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Horne J, Beddingfield E, Knapp M, Mitchell S, Crawford L, Mills SB, Wrist A, Zhang S, Summers RM. Caffeine and Theophylline Inhibit β-Galactosidase Activity and Reduce Expression in Escherichia coli. ACS OMEGA 2020; 5:32250-32255. [PMID: 33376862 PMCID: PMC7758883 DOI: 10.1021/acsomega.0c03909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/03/2020] [Indexed: 05/04/2023]
Abstract
The β-galactosidase enzyme is a common reporter enzyme that has been used extensively in microbiological and synthetic biology research. Here, we demonstrate that caffeine and theophylline, common natural methylxanthine products found in many foods and pharmaceuticals, negatively impact both the expression and activity of β-galactosidase in Escherichia coli. The β-galactosidase activity in E. coli grown with increasing concentrations of caffeine and theophylline was reduced over sixfold in a dose-dependent manner. We also observed decreasing lacZ mRNA transcript levels with increasing methylxanthine concentrations in the growth media. Similarly, caffeine and theophylline inhibit the activity of the purified β-galactosidase enzyme, with an approximately 1.7-fold increase in K M toward o-nitrophenyl-β-galactoside and a concomitant decrease in v max. The authors recommend the use of alternative reporter systems when such methylxanthines are expected to be present.
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Affiliation(s)
| | - Elizabeth Beddingfield
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Madison Knapp
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Stephanie Mitchell
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Logan Crawford
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Shelby Brooks Mills
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Alexandra Wrist
- Department of Chemical and Biological
Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Shuyuan Zhang
- 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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23
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Verbič A, Praznik A, Jerala R. A guide to the design of synthetic gene networks in mammalian cells. FEBS J 2020; 288:5265-5288. [PMID: 33289352 DOI: 10.1111/febs.15652] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/06/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
Synthetic biology aims to harness natural and synthetic biological parts and engineering them in new combinations and systems, producing novel therapies, diagnostics, bioproduction systems, and providing information on the mechanism of function of biological systems. Engineering cell function requires the rewiring or de novo construction of cell information processing networks. Using natural and synthetic signal processing elements, researchers have demonstrated a wide array of signal sensing, processing and propagation modules, using transcription, translation, or post-translational modification to program new function. The toolbox for synthetic network design is ever-advancing and has still ample room to grow. Here, we review the diversity of synthetic gene networks, types of building modules, techniques of regulation, and their applications.
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Affiliation(s)
- Anže Verbič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
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24
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Abstract
Short regulatory RNA molecules underpin gene expression and govern cellular state and physiology. To establish an alternative layer of control over these processes, we generated chimeric regulatory RNAs that interact reversibly and light-dependently with the light-oxygen-voltage photoreceptor PAL. By harnessing this interaction, the function of micro RNAs (miRs) and short hairpin (sh) RNAs in mammalian cells can be regulated in a spatiotemporally precise manner. The underlying strategy is generic and can be adapted to near-arbitrary target sequences. Owing to full genetic encodability, it establishes optoribogenetic control of cell state and physiology. The method stands to facilitate the non-invasive, reversible and spatiotemporally resolved study of regulatory RNAs and protein function in cellular and organismal environments. Short hairpin RNAs can be used to modulate and regulate gene expression. Here the authors generate chimeric RNAs that interact with the photoreceptor PAL, allowing for optoribogenetic control of cell physiology.
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25
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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26
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Pu Q, Zhou S, Huang X, Yuan Y, Du F, Dong J, Chen G, Cui X, Tang Z. Intracellular Selection of Theophylline-Sensitive Hammerhead Aptazyme. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:400-408. [PMID: 32244167 PMCID: PMC7118274 DOI: 10.1016/j.omtn.2020.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/14/2020] [Accepted: 03/10/2020] [Indexed: 12/14/2022]
Abstract
Hammerhead ribozyme-based aptazyme (HHAz), inheriting the advantages of small size and high efficiency from the RNA-cleaving ribozyme and the specific recognition ability of aptamers to specific targets, exhibits the huge potential to be a transgene expression regulator. Herein, we report a selection strategy for HHAz by using a toxin protein IbsC as the reporter to offer a positive phenotype, thus realizing an easy-operating, time- and labor-saving selection of HHAz variants with desired properties. Based on this strategy, we obtained a new HHAz (TAP-1), which could react sensitively toward the extracellular regulatory molecule, theophylline, both in prokaryotic and eukaryotic systems. With fluorescent protein reporter, the intracellular switching efficiencies of TAP-1 and other reported theophylline-dependent HHAzs has been quantitatively evaluated, showing that TAP-1 not only exhibits the best downregulating ability at high concentration of theophylline but also maintains high activity with 0.1 mM theophylline, which is a safe concentration in the human body.
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Affiliation(s)
- Qinlin Pu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China; University of Chinese Academy of Sciences, Beijing 10049, P.R. China
| | - Shan Zhou
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China; University of Chinese Academy of Sciences, Beijing 10049, P.R. China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China.
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27
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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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28
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Ma L, Liu J. Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology. iScience 2020; 23:100815. [PMID: 31954323 PMCID: PMC6962706 DOI: 10.1016/j.isci.2019.100815] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/11/2019] [Accepted: 12/26/2019] [Indexed: 01/06/2023] Open
Abstract
Since the initial discovery of ribozymes in the early 1980s, catalytic nucleic acids have been used in different areas. Compared with protein enzymes, catalytic nucleic acids are programmable in structure, easy to modify, and more stable especially for DNA. We take a historic view to summarize a few main interdisciplinary areas of research on nucleic acid enzymes that may have broader impacts. Early efforts on ribozymes in the 1980s have broken the notion that all enzymes are proteins, supplying new evidence for the RNA world hypothesis. In 1994, the first catalytic DNA (DNAzyme) was reported. Since 2000, the biosensor applications of DNAzymes have emerged and DNAzymes are particularly useful for detecting metal ions, a challenging task for enzymes and antibodies. Combined with nanotechnology, DNAzymes are key building elements for switches allowing dynamic control of materials assembly. The search for new DNAzymes and ribozymes is facilitated by developments in DNA sequencing and computational algorithms, further broadening our fundamental understanding of their biochemistry.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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29
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Kato Y. Extremely Low Leakage Expression Systems Using Dual Transcriptional-Translational Control for Toxic Protein Production. Int J Mol Sci 2020; 21:ijms21030705. [PMID: 31973139 PMCID: PMC7037476 DOI: 10.3390/ijms21030705] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/25/2019] [Accepted: 01/19/2020] [Indexed: 02/01/2023] Open
Abstract
Expression systems for highly toxic protein genes must be conditional and suppress leakage expression to almost zero because even faint leakage expression may kill host cells, inhibit host growth, and cause loss of plasmids containing the toxic protein genes. The most widely used conditional expression systems are controlled only at the transcriptional level, and complete suppression of leakage expression is challenging. Recent progress on translational control has enabled construction of dual transcriptional-translational control systems in which leakage expression is strongly suppressed. This review summarizes the principles, features, and practical examples of dual transcriptional-translational control systems in bacteria, and provides future perspectives on these systems.
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Affiliation(s)
- Yusuke Kato
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan
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30
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Aptazymes: Expanding the Specificity of Natural Catalytic Nucleic Acids by Application of In Vitro Selected Oligonucleotides. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 170:107-119. [PMID: 30847536 DOI: 10.1007/10_2019_92] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Aptazymes are synthetic molecules composed of an aptamer domain and a catalytic active nucleic acid unit, which may be a ribozyme or a DNAzyme. In these constructs the aptamer domain serves as a molecular switch that can regulate the catalytic activity of the ribozyme or DNAzyme subunit. This regulation is triggered by binding of the aptamers target molecule, which causes significant structural changes in the aptamer and thus in the entire aptazyme. Therefore, aptazymes function similar to allosteric enzymes, whose catalytic activity is regulated by binding of ligands (effectors) to allosteric sites due to alteration of the three-dimensional structure of the active site of the enzyme. In case of aptazymes, the allosteric site is composed of an aptamer. Aptazymes can be designed for different applications and have already been used in analytical assays as well as for the regulation of gene expression.
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31
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Dohno C, Nakatani K. Molecular Glue for RNA: Regulating RNA Structure and Function through Synthetic RNA Binding Molecules. Chembiochem 2019; 20:2903-2910. [DOI: 10.1002/cbic.201900223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Chikara Dohno
- Department of Regulatory Bioorganic ChemistryThe Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki, Osaka 567-0047 Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic ChemistryThe Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki, Osaka 567-0047 Japan
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32
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Haines MC, Storch M, Oyarzún DA, Stan GB, Baldwin GS. Riboswitch identification using Ligase-Assisted Selection for the Enrichment of Responsive Ribozymes (LigASERR). Synth Biol (Oxf) 2019; 4:ysz019. [PMID: 32995542 PMCID: PMC7445825 DOI: 10.1093/synbio/ysz019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/22/2022] Open
Abstract
In vitro selection of ligand-responsive ribozymes can identify rare, functional sequences from large libraries. While powerful, key caveats of this approach include lengthy and demanding experimental workflows; unpredictable experimental outcomes and unknown functionality of enriched sequences in vivo. To address the first of these limitations, we developed Ligase-Assisted Selection for the Enrichment of Responsive Ribozymes (LigASERR). LigASERR is scalable, amenable to automation and requires less time to implement compared to alternative methods. To improve the predictability of experiments, we modeled the underlying selection process, predicting experimental outcomes based on sequence and population parameters. We applied this new methodology and model to the enrichment of a known, in vitro-selected sequence from a bespoke library. Prior to implementing selection, conditions were optimized and target sequence dynamics accurately predicted for the majority of the experiment. In addition to enriching the target sequence, we identified two new, theophylline-activated ribozymes. Notably, all three sequences yielded riboswitches functional in Escherichia coli, suggesting LigASERR and similar in vitro selection methods can be utilized for generating functional riboswitches in this organism.
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Affiliation(s)
- Matthew C Haines
- Department of Life Sciences, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Marko Storch
- Department of Life Sciences, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,London BioFoundry, Imperial College Translation & Innovation Hub, London, UK
| | - Diego A Oyarzún
- School of Informatics, University of Edinburgh, Edinburgh, UK.,School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Guy-Bart Stan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.,Department of Bioengineering, Imperial College London, London, UK
| | - Geoff S Baldwin
- Department of Life Sciences, Imperial College London, London, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
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33
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Matsumoto S, Caliskan N, Rodnina MV, Murata A, Nakatani K. Small synthetic molecule-stabilized RNA pseudoknot as an activator for -1 ribosomal frameshifting. Nucleic Acids Res 2019; 46:8079-8089. [PMID: 30085309 PMCID: PMC6144811 DOI: 10.1093/nar/gky689] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/31/2018] [Indexed: 12/02/2022] Open
Abstract
Programmed –1 ribosomal frameshifting (−1PRF) is a recoding mechanism to make alternative proteins from a single mRNA transcript. −1PRF is stimulated by cis-acting signals in mRNA, a seven-nucleotide slippery sequence and a downstream secondary structure element, which is often a pseudoknot. In this study we engineered the frameshifting pseudoknot from the mouse mammary tumor virus to respond to a rationally designed small molecule naphthyridine carbamate tetramer (NCTn). We demonstrate that NCTn can stabilize the pseudoknot structure in mRNA and activate –1PRF both in vitro and in human cells. The results illustrate how NCTn-inducible –1PRF may serve as an important component of the synthetic biology toolbox for the precise control of gene expression using small synthetic molecules.
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Affiliation(s)
- Saki Matsumoto
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research, Josef-Schneider-Str.2/D15, 97080, Würzburg, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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34
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Zhang J, Lan T, Lu Y. Molecular Engineering of Functional Nucleic Acid Nanomaterials toward In Vivo Applications. Adv Healthc Mater 2019; 8:e1801158. [PMID: 30725526 PMCID: PMC6426685 DOI: 10.1002/adhm.201801158] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/14/2019] [Indexed: 12/25/2022]
Abstract
Recent advances in nanotechnology and engineering have generated many nanomaterials with unique physical and chemical properties. Over the past decade, numerous nanomaterials are introduced into many research areas, such as sensors for environmental monitoring, food safety, point-of-care diagnostics, and as transducers for solar energy transfer. Meanwhile, functional nucleic acids (FNAs), including nucleic acid enzymes, aptamers, and aptazymes, have attracted major attention from the biomedical community due to their unique target recognition and catalytic properties. Benefiting from the recent progress of molecular engineering strategies, the physicochemical properties of nanomaterials are endowed by the target recognition and catalytic activity of FNAs in the presence of a target analyte, resulting in numerous smart nanoprobes for diverse applications including intracellular imaging, drug delivery, in vivo imaging, and tumor therapy. This progress report focuses on the recent advances in designing and engineering FNA-based nanomaterials, highlighting the functional outcomes toward in vivo applications. The challenges and opportunities for the future translation of FNA-based nanomaterials into clinical applications are also discussed.
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Affiliation(s)
- JingJing Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 601 S. Mathews Ave., Urbana, IL, 61801, USA
| | - Tian Lan
- GlucoSentient, Inc., 2100 S. Oak Street Suite 101, Champaign, IL, 61820, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 601 S. Mathews Ave., Urbana, IL, 61801, USA
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35
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Dwidar M, Yokobayashi Y. Riboswitch Signal Amplification by Controlling Plasmid Copy Number. ACS Synth Biol 2019; 8:245-250. [PMID: 30682247 DOI: 10.1021/acssynbio.8b00454] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Riboswitches are cis-acting RNA devices in mRNAs that control gene expression in response to chemical inputs. As RNA aptamers that recognize diverse classes of molecules can be isolated by in vitro selection, synthetic riboswitches hold promise for various applications in synthetic biology. One of the major drawbacks of riboswitches, however, is their limited dynamic range. A high level of gene expression in the OFF state (leakage) is also a common problem. To address these challenges, we designed and constructed a dual-riboswitch plasmid in which two genes are controlled by theophylline-activated riboswitches. One riboswitch controls the gene of interest, and another riboswitch controls RepL, a phage-derived replication protein that regulates the plasmid copy number. This single-plasmid system afforded an ON/OFF ratio as high as 3900. Furthermore, we used the system to control CRISPR interference (CRISPRi) targeting endogenous genes, and successfully observed expected phenotypic changes in Escherichia coli.
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Affiliation(s)
- Mohammed Dwidar
- 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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36
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Intracellular Imaging with Genetically Encoded RNA-based Molecular Sensors. NANOMATERIALS 2019; 9:nano9020233. [PMID: 30744040 PMCID: PMC6410142 DOI: 10.3390/nano9020233] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 01/10/2023]
Abstract
Genetically encodable sensors have been widely used in the detection of intracellular molecules ranging from metal ions and metabolites to nucleic acids and proteins. These biosensors are capable of monitoring in real-time the cellular levels, locations, and cell-to-cell variations of the target compounds in living systems. Traditionally, the majority of these sensors have been developed based on fluorescent proteins. As an exciting alternative, genetically encoded RNA-based molecular sensors (GERMS) have emerged over the past few years for the intracellular imaging and detection of various biological targets. In view of their ability for the general detection of a wide range of target analytes, and the modular and simple design principle, GERMS are becoming a popular choice for intracellular analysis. In this review, we summarize different design principles of GERMS based on various RNA recognition modules, transducer modules, and reporting systems. Some recent advances in the application of GERMS for intracellular imaging are also discussed. With further improvement in biostability, sensitivity, and robustness, GERMS can potentially be widely used in cell biology and biotechnology.
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37
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Stifel J, Spöring M, Hartig JS. Expanding the toolbox of synthetic riboswitches with guanine-dependent aptazymes. Synth Biol (Oxf) 2019; 4:ysy022. [PMID: 32995528 PMCID: PMC7445771 DOI: 10.1093/synbio/ysy022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/04/2018] [Accepted: 12/06/2018] [Indexed: 12/18/2022] Open
Abstract
Artificial riboswitches based on ribozymes serve as versatile tools for ligand-dependent gene expression regulation. Advantages of these so-called aptazymes are their modular architecture and the comparably little coding space they require. A variety of aptamer-ribozyme combinations were constructed in the past 20 years and the resulting aptazymes were applied in diverse contexts in prokaryotic and eukaryotic systems. Most in vivo functional aptazymes are OFF-switches, while ON-switches are more advantageous regarding potential applications in e.g. gene therapy vectors. We developed new ON-switching aptazymes in the model organism Escherichia coli and in mammalian cell culture using the intensely studied guanine-sensing xpt aptamer. Utilizing a high-throughput screening based on fluorescence-activated cell sorting in bacteria we identified up to 9.2-fold ON-switches and OFF-switches with a dynamic range up to 32.7-fold. For constructing ON-switches in HeLa cells, we used a rational design approach based on existing tetracycline-sensitive ON-switches. We discovered that communication modules responding to tetracycline are also functional in the context of guanine aptazymes, demonstrating a high degree of modularity. Here, guanine-responsive ON-switches with a four-fold dynamic range were designed. Summarizing, we introduce a series of novel guanine-dependent ribozyme switches operative in bacteria and human cell culture that significantly broaden the existing toolbox.
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Affiliation(s)
- Julia Stifel
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Maike Spöring
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Jörg Steffen Hartig
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
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38
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Neomycin-dependent hammerhead ribozymes for the direct control of gene expression in Saccharomyces cerevisiae. Methods 2019; 161:35-40. [PMID: 30639182 DOI: 10.1016/j.ymeth.2019.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/03/2019] [Accepted: 01/05/2019] [Indexed: 01/29/2023] Open
Abstract
Hammerhead ribozyme-based RNA switches have been proven to be powerful tools for conditional gene regulation in various organisms. We present neomycin-dependent hammerhead ribozymes (HHR) that influence gene expression in a ligand- and dose-dependent manner in S. cerevisiae. We utilized a novel design of fusing the aptamer domain to the HHR enabling for the first time the identification of genetic ON- and OFF-switches within the same library. For this purpose a neomycin aptamer was fused to stem 1 of a type 3 hammerhead ribozyme via an addressable three-way junction that shows high flexibility at the connection site. An in vivo screening approach identified sequences that allow to induce or repress gene expression 2- to 3-fold in response to neomycin addition. The ribozyme switches operate at neomycin concentrations that show no toxic effect on cell growth and pose powerful genetic tools to study and modulate cellular function in yeast.
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39
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Karunanayake Mudiyanselage APKK, Yu Q, Leon-Duque MA, Zhao B, Wu R, You M. Genetically Encoded Catalytic Hairpin Assembly for Sensitive RNA Imaging in Live Cells. J Am Chem Soc 2018; 140:8739-8745. [PMID: 29944357 PMCID: PMC6201751 DOI: 10.1021/jacs.8b03956] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA and RNA nanotechnology has been used for the development of dynamic molecular devices. In particular, programmable enzyme-free nucleic acid circuits, such as catalytic hairpin assembly, have been demonstrated as useful tools for bioanalysis and to scale up system complexity to an extent beyond current cellular genetic circuits. However, the intracellular functions of most synthetic nucleic acid circuits have been hindered by challenges in the biological delivery and degradation. On the other hand, genetically encoded and transcribed RNA circuits emerge as alternative powerful tools for long-term embedded cellular analysis and regulation. Herein, we reported a genetically encoded RNA-based catalytic hairpin assembly circuit for sensitive RNA imaging inside living cells. The split version of Broccoli, a fluorogenic RNA aptamer, was used as the reporter. One target RNA can catalytically trigger the fluorescence from tens-to-hundreds of Broccoli. As a result, target RNAs can be sensitively detected. We have further engineered our circuit to allow easy programming to image various target RNA sequences. This design principle opens the arena for developing a large variety of genetically encoded RNA circuits for cellular applications.
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Affiliation(s)
| | - Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Mark A. Leon-Duque
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Bin Zhao
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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40
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Ogawa A, Murashige Y, Takahashi H. Canonical translation-modulating OFF-riboswitches with a single aptamer binding to a small molecule that function in a higher eukaryotic cell-free expression system. Bioorg Med Chem Lett 2018; 28:2353-2357. [PMID: 29941191 DOI: 10.1016/j.bmcl.2018.06.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/16/2018] [Accepted: 06/18/2018] [Indexed: 12/30/2022]
Abstract
We have found that OFF-riboswitches that ligand-dependently downregulate the canonical translation in a higher eukaryotic expression system (wheat germ extract) can be easily created by inserting a single aptamer into the 5' untranslated region (UTR) of mRNA, even if its ligand is as small as theophylline. The key is the position of the inserted aptamer: the 5' end (+0 position) is much better than other positions for inhibiting canonical translation with the aptamer-ligand complex. The data showed that ribosome loading is suppressed by a rigid structure in the 5' end, and this suppression is dependent on the structure's stability but not on its size. Although this preference of aptamer insertion point contradicts the results in a lower eukaryote, it accords with the fact that the 5'-end structural hindrance is more effective for blocking the ribosome in higher eukaryotes. Therefore, the present type of OFF-riboswitch would function in various higher eukaryotic expression systems.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
| | - Yuta Murashige
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hajime Takahashi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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41
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Yokobayashi Y. Small Molecule-Responsive RNA Switches (Bacteria): Important Element of Programming Gene Expression in Response to Environmental Signals in Bacteria. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Yohei Yokobayashi
- Okinawa Institute of Science and Technology Graduate University; Nucleic Acid Chemistry and Engineering Unit Onna-son; Okinawa 9040415 Japan
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42
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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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43
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Wurmthaler LA, Klauser B, Hartig JS. Highly motif- and organism-dependent effects of naturally occurring hammerhead ribozyme sequences on gene expression. RNA Biol 2017; 15:231-241. [PMID: 29106331 DOI: 10.1080/15476286.2017.1397870] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recent bioinformatics studies have demonstrated a wide-spread occurrence of the hammerhead ribozyme (HHR) and similar small endonucleolytic RNA motifs in all domains of life. It is becoming increasingly evident that such ribozyme motifs participate in important genetic processes in diverse organisms. Although the HHR motif has been studied for more than three decades, only little is known about the consequences of ribozyme activity on gene expression. In the present study we analysed eight different naturally occurring HHR sequences in diverse genetic and organismal contexts. We investigated the influence of active ribozymes incorporated into mRNAs in mammalian, yeast and bacterial expression systems. The experiments show an unexpectedly high degree of organism-specific variability of ribozyme-mediated effects on gene expression. The presented findings demonstrate that ribozyme cleavage profoundly affect gene expression. However, the extent of this effect varies and depends strongly on the respective genetic context. The fast-cleaving type 3 HHRs [CChMVd(-) and sLTSV(-)] generally tended to cause the strongest effects on intracellular gene expression. The presented results are important in order to address potential functions of naturally occurring ribozymes in RNA processing and post-transcriptional regulation of gene expression. Additionally, our results are of interest for biotechnology and synthetic biology approaches that aim at the utilisation of self-cleaving ribozymes as widely applicable tools for controlling genetic processes.
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Affiliation(s)
- Lena A Wurmthaler
- a Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB) , University of Konstanz , Konstanz , Germany
| | - Benedikt Klauser
- a Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB) , University of Konstanz , Konstanz , Germany
| | - Jörg S Hartig
- a Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB) , University of Konstanz , Konstanz , Germany
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44
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Dohno C, Kimura M, Nakatani K. Restoration of Ribozyme Tertiary Contact and Function by Using a Molecular Glue for RNA. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Chikara Dohno
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki, Osaka 567-0047 Japan
| | - Maki Kimura
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki, Osaka 567-0047 Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki, Osaka 567-0047 Japan
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45
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Restoration of Ribozyme Tertiary Contact and Function by Using a Molecular Glue for RNA. Angew Chem Int Ed Engl 2017; 57:506-510. [DOI: 10.1002/anie.201709041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/14/2017] [Indexed: 11/07/2022]
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46
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Rodrigo G, Prakash S, Shen S, Majer E, Daròs JA, Jaramillo A. Model-based design of RNA hybridization networks implemented in living cells. Nucleic Acids Res 2017; 45:9797-9808. [PMID: 28934501 PMCID: PMC5766206 DOI: 10.1093/nar/gkx698] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/27/2017] [Indexed: 12/27/2022] Open
Abstract
Synthetic gene circuits allow the behavior of living cells to be reprogrammed, and non-coding small RNAs (sRNAs) are increasingly being used as programmable regulators of gene expression. However, sRNAs (natural or synthetic) are generally used to regulate single target genes, while complex dynamic behaviors would require networks of sRNAs regulating each other. Here, we report a strategy for implementing such networks that exploits hybridization reactions carried out exclusively by multifaceted sRNAs that are both targets of and triggers for other sRNAs. These networks are ultimately coupled to the control of gene expression. We relied on a thermodynamic model of the different stable conformational states underlying this system at the nucleotide level. To test our model, we designed five different RNA hybridization networks with a linear architecture, and we implemented them in Escherichia coli. We validated the network architecture at the molecular level by native polyacrylamide gel electrophoresis, as well as the network function at the bacterial population and single-cell levels with a fluorescent reporter. Our results suggest that it is possible to engineer complex cellular programs based on RNA from first principles. Because these networks are mainly based on physical interactions, our designs could be expanded to other organisms as portable regulatory resources or to implement biological computations.
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Affiliation(s)
- Guillermo Rodrigo
- Institute of Systems and Synthetic Biology, Université d'Évry Val d'Essonne-CNRS, F-91000 Évry, France.,Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Satya Prakash
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Shensi Shen
- Institute of Systems and Synthetic Biology, Université d'Évry Val d'Essonne-CNRS, F-91000 Évry, France
| | - Eszter Majer
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Alfonso Jaramillo
- Institute of Systems and Synthetic Biology, Université d'Évry Val d'Essonne-CNRS, F-91000 Évry, France.,Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.,Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, 46980 Paterna, Spain
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47
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Schneider C, Bronstein L, Diemer J, Koeppl H, Suess B. ROC'n'Ribo: Characterizing a Riboswitching Expression System by Modeling Single-Cell Data. ACS Synth Biol 2017; 6:1211-1224. [PMID: 28591515 DOI: 10.1021/acssynbio.6b00322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNA-engineered systems offer simple and versatile control over gene expression in many organisms. In particular, the design and implementation of riboswitches presents a unique opportunity to manipulate any reporter device in cis, executing tight temporal and spatial control at low metabolic costs. Assembled to higher order genetic circuits, such riboswitch-regulated devices may efficiently process logical operations. Here, we propose a hierarchical stochastic modeling approach to characterize an in silico repressor gate based on neomycin- and tetracycline-sensitive riboswitches. The model was calibrated on rich, transient in vivo single-cell data to account for cell-to-cell variability. To capture the effect of this variability on gate performance we employed the well-known ROC-analysis and derived a novel performance indicator for logic gates. Introduction of such a performance measure is necessary, since we aimed to assess the correct functionality of the gate at the single-cell level-a prerequisite for its further adaption to a genetic circuitry. Our results may be applied to other genetic devices to analyze their efficiency and ensure their correct performance in the light of cell-to-cell variability.
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Affiliation(s)
- Christopher Schneider
- Department
of Biology, Synthetic Genetic Circuits, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Leo Bronstein
- Department
of Electrical Engineering and Information Technology, Bioinspired
Communications, TU Darmstadt, Rundeturmstrasse 12, 64283 Darmstadt, Germany
| | - Jascha Diemer
- Department
of Electrical Engineering and Information Technology, Bioinspired
Communications, TU Darmstadt, Rundeturmstrasse 12, 64283 Darmstadt, Germany
| | - Heinz Koeppl
- Department
of Electrical Engineering and Information Technology, Bioinspired
Communications, TU Darmstadt, Rundeturmstrasse 12, 64283 Darmstadt, Germany
| | - Beatrix Suess
- Department
of Biology, Synthetic Genetic Circuits, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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48
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Kobori S, Takahashi K, Yokobayashi Y. Deep Sequencing Analysis of Aptazyme Variants Based on a Pistol Ribozyme. ACS Synth Biol 2017; 6:1283-1288. [PMID: 28398719 DOI: 10.1021/acssynbio.7b00057] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chemically regulated self-cleaving ribozymes, or aptazymes, are emerging as a promising class of genetic devices that allow dynamic control of gene expression in synthetic biology. However, further expansion of the limited repertoire of ribozymes and aptamers, and development of new strategies to couple the RNA elements to engineer functional aptazymes are highly desirable for synthetic biology applications. Here, we report aptazymes based on the recently identified self-cleaving pistol ribozyme class using a guanine aptamer as the molecular sensing element. Two aptazyme architectures were studied by constructing and assaying 17 728 mutants by deep sequencing. Although one of the architectures did not yield functional aptazymes, a novel aptazyme design in which the aptamer and the ribozyme were placed in tandem yielded a number of guanine-inhibited ribozymes. Detailed analysis of the extensive sequence-function data suggests a mechanism that involves a competition between two mutually exclusive RNA structures reminiscent of natural bacterial riboswitches.
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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
| | - Kei Takahashi
- 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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49
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Tang W, Hu JH, Liu DR. Aptazyme-embedded guide RNAs enable ligand-responsive genome editing and transcriptional activation. Nat Commun 2017; 8:15939. [PMID: 28656978 PMCID: PMC5493748 DOI: 10.1038/ncomms15939] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 05/12/2017] [Indexed: 01/01/2023] Open
Abstract
Programmable sequence-specific genome editing agents such as CRISPR-Cas9 have greatly advanced our ability to manipulate the human genome. Although canonical forms of genome-editing agents and programmable transcriptional regulators are constitutively active, precise temporal and spatial control over genome editing and transcriptional regulation activities would enable the more selective and potentially safer use of these powerful technologies. Here, by incorporating ligand-responsive self-cleaving catalytic RNAs (aptazymes) into guide RNAs, we developed a set of aptazyme-embedded guide RNAs that enable small molecule-controlled nuclease-mediated genome editing and small molecule-controlled base editing, as well as small molecule-dependent transcriptional activation in mammalian cells.
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Affiliation(s)
- Weixin Tang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Johnny H. Hu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - David R. Liu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
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50
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Müller A, Schneider JF, Degrossoli A, Lupilova N, Dick TP, Leichert LI. Fluorescence spectroscopy of roGFP2-based redox probes responding to various physiologically relevant oxidant species in vitro. Data Brief 2017; 11:617-627. [PMID: 28361106 PMCID: PMC5360222 DOI: 10.1016/j.dib.2017.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/07/2017] [Indexed: 12/04/2022] Open
Abstract
This article contains representative fluorescence excitation spectra of roGFP2-based probes used for ratiometric analysis of redox changes as presented in the article "Systematic in vitro assessment of responses of roGFP2-based probes to physiologically relevant oxidant species" [1]. The recombinant probes roGFP2, roGFP2-Orp1, and Grx1-roGFP2 were exposed to various oxidative and nitrosative species, including hydrogen peroxide (H2O2), aldrithiol-2 (AT-2), glutathione disulfide (GSSG), hypochlorous acid (HOCl), S-nitrosoglutathione (GSNO), peroxynitrite (ONOO−), potassium polysulfide (K2Sx), spermine NONOate (SperNO), and diethyl amino NONOate (DeaNO) at different molar ratios. Fluorescence excitation spectra of the probes were recorded in the excitation wavelength range between 350 and 500 nm and for a total of 60 min. Analysis and interpretation of the data is presented in an associated article [1].
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Affiliation(s)
- Alexandra Müller
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Jannis F Schneider
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Adriana Degrossoli
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Nataliya Lupilova
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Tobias P Dick
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Lars I Leichert
- Institute of Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
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