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Bocobza SE, Aharoni A. Small molecules that interact with RNA: riboswitch-based gene control and its involvement in metabolic regulation in plants and algae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:693-703. [PMID: 24773387 DOI: 10.1111/tpj.12540] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 03/20/2014] [Accepted: 04/15/2014] [Indexed: 05/28/2023]
Abstract
Riboswitches are RNA elements that bind small molecules and in turn regulate gene expression. This mechanism allows the cell to sense the intracellular concentration of these small molecules. A particular riboswitch typically regulates its adjacent gene by altering the transcription, the translation or the splicing of this gene. Recently, a riboswitch that binds thiamin pyrophosphate (TPP) was characterized and found to regulate thiamin biosynthesis in plants and algae. Furthermore, it appears that this element is an essential regulator of primary metabolism in plants. Manipulation of endogenous riboswitch activity resulted in metabolic phenotypes that underlined the role of these elements and their ligands in preserving metabolic homeostasis. This situation supports the hypothesis that riboswitches could be remnants of the most ancient metabolic regulators. Here, we review the mode of action of the plant and algal TPP riboswitch and its relevance to the metabolic network. We also discuss the potential engineering of riboswitches as metabolite sensors in plants and platforms for gene control. Whether additional such RNA-based mechanisms exist in plants and in algae is still an open question, yet, the importance of these elements to metabolic regulation is beyond doubt.
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Affiliation(s)
- Samuel E Bocobza
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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52
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Groher F, Suess B. Synthetic riboswitches - A tool comes of age. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:964-973. [PMID: 24844178 DOI: 10.1016/j.bbagrm.2014.05.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/29/2014] [Accepted: 05/08/2014] [Indexed: 12/14/2022]
Abstract
Within the last decade, it has become obvious that RNA plays an important role in regulating gene expression. This has led to a plethora of approaches aiming at exploiting the outstanding chemical properties of RNA to develop synthetic RNA regulators for conditional gene expression systems. Consequently, many different regulators have been developed to act on various stages of gene expression. They can be engineered to respond to almost any ligand of choice and are, therefore, of great interest for applications in synthetic biology. This review presents an overview of such engineered riboswitches, discusses their applicability and points out recent trends in their development. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Florian Groher
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany.
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53
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Xia X, Piao X, Bong D. Bifacial peptide nucleic acid as an allosteric switch for aptamer and ribozyme function. J Am Chem Soc 2014; 136:7265-8. [PMID: 24796374 DOI: 10.1021/ja5032584] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We demonstrate herein that bifacial peptide nucleic acid (bPNA) hybrid triplexes functionally substitute for duplex DNA or RNA. Structure-function loss in three non-coding nucleic acids was inflicted by replacement of a duplex stem with unstructured oligo-T/U strands, which are bPNA binding sites. Functional rescue was observed on refolding of the oligo-T/U strands into bPNA triplex hybrid stems. Bifacial PNA binding was thus used to allosterically switch-on protein and small-molecule binding in DNA and RNA aptamers, as well as catalytic bond scission in a ribozyme. Duplex stems that support the catalytic site of a minimal type I hammerhead ribozyme were replaced with oligo-U loops, severely crippling or ablating the native RNA splicing function. Refolding of the U-loops into bPNA triplex stems completely restored splicing function in the hybrid system. These studies indicate that bPNA may have general utility as an allosteric trigger for a wide range of functions in non-coding nucleic acids.
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Affiliation(s)
- Xin Xia
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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54
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A versatile framework for microbial engineering using synthetic non-coding RNAs. Nat Rev Microbiol 2014; 12:341-54. [DOI: 10.1038/nrmicro3244] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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55
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Kang Z, Zhang C, Zhang J, Jin P, Zhang J, Du G, Chen J. Small RNA regulators in bacteria: powerful tools for metabolic engineering and synthetic biology. Appl Microbiol Biotechnol 2014; 98:3413-24. [DOI: 10.1007/s00253-014-5569-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 12/17/2022]
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56
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Ren R, Wang LL, Ding TR, Li XM. Enzyme-free amplified detection of nucleic acids based on self-sustained replication of RNAzyme and its application in tumor cell detection. Biosens Bioelectron 2013; 54:122-7. [PMID: 24262777 DOI: 10.1016/j.bios.2013.10.063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 10/22/2013] [Accepted: 10/29/2013] [Indexed: 11/17/2022]
Abstract
A system based on exponential amplification of self-sustained replication of RNAzyme was developed for quantitative detection of linker DNA that can be recognized by base complementarity. The hybridization of the linker DNA with two RNA ligase subunits formed an RNA enzyme that catalyzes the joining of two oligonucleotide substrates. The ligated product opens a hairpin molecular beacon, resulting in the generation of a higher fluorescence intensity. The product of this reaction depends on the concentration of the linker DNA, allowing one to determine the concentration of target DNA in a sample. Furthermore, based on the high specificity and affinity of cell aptamer with its target cells, this amplification strategy has been successfully applied in detection of cancer cells. The exceptional amplification power of the RNAzyme along with the simple assay protocol makes direct cell detection possible in real-world samples with minimal sample pretreatments. This process is analogous to quantitative PCR (qPCR) but can be applied to the detection of nucleic acid and cells, as well as proteins and small molecules that are relevant to medical diagnostics.
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Affiliation(s)
- Rui Ren
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, PR China
| | - Lin-Lin Wang
- State Key Laboratory Base of Eco-chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Tian-Rong Ding
- State Key Laboratory Base of Eco-chemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Xue-Mei Li
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, PR China.
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57
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Chappell J, Takahashi MK, Meyer S, Loughrey D, Watters KE, Lucks J. The centrality of RNA for engineering gene expression. Biotechnol J 2013; 8:1379-95. [PMID: 24124015 PMCID: PMC4033574 DOI: 10.1002/biot.201300018] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/19/2013] [Accepted: 08/15/2013] [Indexed: 12/25/2022]
Abstract
Synthetic biology holds promise as both a framework for rationally engineering biological systems and a way to revolutionize how we fundamentally understand them. Essential to realizing this promise is the development of strategies and tools to reliably and predictably control and characterize sophisticated patterns of gene expression. Here we review the role that RNA can play towards this goal and make a case for why this versatile, designable, and increasingly characterizable molecule is one of the most powerful substrates for engineering gene expression at our disposal. We discuss current natural and synthetic RNA regulators of gene expression acting at key points of control – transcription, mRNA degradation, and translation. We also consider RNA structural probing and computational RNA structure predication tools as a way to study RNA structure and ultimately function. Finally, we discuss how next-generation sequencing methods are being applied to the study of RNA and to the characterization of RNA's many properties throughout the cell.
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Affiliation(s)
- James Chappell
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
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58
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Li X, Song J, Wang Y, Cheng T. Cyclically amplified fluorescent detection of theophylline and thiamine pyrophosphate by coupling self-cleaving RNA ribozyme with endonuclease. Anal Chim Acta 2013; 797:95-101. [DOI: 10.1016/j.aca.2013.08.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/09/2013] [Accepted: 08/13/2013] [Indexed: 01/10/2023]
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59
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Nakahira Y, Ogawa A, Asano H, Oyama T, Tozawa Y. Theophylline-Dependent Riboswitch as a Novel Genetic Tool for Strict Regulation of Protein Expression in Cyanobacterium Synechococcus elongatus PCC 7942. ACTA ACUST UNITED AC 2013; 54:1724-35. [DOI: 10.1093/pcp/pct115] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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60
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Ogawa A. Ligand-Dependent Upregulation of Ribosomal Shunting. Chembiochem 2013; 14:1539-43, 1509. [DOI: 10.1002/cbic.201300362] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Indexed: 12/25/2022]
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61
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Wachsmuth M, Findeiß S, Weissheimer N, Stadler PF, Mörl M. De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res 2012; 41:2541-51. [PMID: 23275562 PMCID: PMC3575828 DOI: 10.1093/nar/gks1330] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Riboswitches are regulatory RNA elements typically located in the 5′-untranslated region of certain mRNAs and control gene expression at the level of transcription or translation. These elements consist of a sensor and an adjacent actuator domain. The sensor usually is an aptamer that specifically interacts with a ligand. The actuator contains an intrinsic terminator or a ribosomal binding site for transcriptional or translational regulation, respectively. Ligand binding leads to structural rearrangements of the riboswitch and to presentation or masking of these regulatory elements. Based on this modular organization, riboswitches are an ideal target for constructing synthetic regulatory systems for gene expression. Although riboswitches for translational control have been designed successfully, attempts to construct synthetic elements regulating transcription have failed so far. Here, we present an in silico pipeline for the rational design of synthetic riboswitches that regulate gene expression at the transcriptional level. Using the well-characterized theophylline aptamer as sensor, we designed the actuator part as RNA sequences that can fold into functional intrinsic terminator structures. In the biochemical characterization, several of the designed constructs show ligand-dependent control of gene expression in Escherichia coli, demonstrating that it is possible to engineer riboswitches not only for translational but also for transcriptional regulation.
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Affiliation(s)
- Manja Wachsmuth
- Institute for Biochemistry, University of Leipzig, Brüderstr. 34, 04103 Leipzig, Germany
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62
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Kobori S, Ichihashi N, Kazuta Y, Matsuura T, Yomo T. Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system: modeling of ligand-dependent and -independent expression. RNA (NEW YORK, N.Y.) 2012; 18:1458-1465. [PMID: 22733807 PMCID: PMC3404367 DOI: 10.1261/rna.032748.112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 05/26/2012] [Indexed: 06/01/2023]
Abstract
Aptazymes are useful as RNA-based switches of gene expression responsive to several types of compounds. One of the most important properties of the switching ability is the signal/noise (S/N) ratio, i.e., the ratio of gene expression in the presence of ligand to that in the absence of ligand. The present study was performed to gain a quantitative understanding of how the aptazyme S/N ratio is determined by factors involved in gene expression, such as transcription, RNA self-cleavage, RNA degradation, protein translation, and their ligand dependencies. We performed switching of gene expression using two on-switch aptazymes with different properties in a cell-free translation system, and constructed a kinetic model that quantitatively describes the dynamics of RNA and protein species involved in switching. Both theoretical and experimental analyses consistently demonstrated that factors determining both the absolute value and the dynamics of the S/N ratio are highly dependent on the routes of translation in the absence of ligand: translation from the ligand-independently cleaved RNA or leaky translation from the noncleaved RNA. The model obtained here is useful to assess the factors that restrict the S/N ratio and to improve aptazymes more efficiently.
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Affiliation(s)
- Shungo Kobori
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Norikazu Ichihashi
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka 565-0871, Japan
| | - Yasuaki Kazuta
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka 565-0871, Japan
| | - Tomoaki Matsuura
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka 565-0871, Japan
- Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
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63
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Kashida S, Inoue T, Saito H. Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation. Nucleic Acids Res 2012; 40:9369-78. [PMID: 22810207 PMCID: PMC3467064 DOI: 10.1093/nar/gks668] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The three-dimensional (3D) structures of many biomacromolecules have been solved to reveal the functions of these molecules. However, these 3D structures have rarely been applied to constructing efficient molecular devices that function in living cells. Here, we demonstrate a 3D structure-based molecular design principle for constructing short hairpin RNA (shRNA)-mediated genetic information converters; these converters respond to specific proteins and trigger the desired gene expression by modulating the function of the RNA-processing enzyme Dicer. The inhibitory effect on Dicer cleavage against the shRNA designed to specifically bind to U1A spliceosomal protein was correlated with the degree of steric hindrance between Dicer and the shRNA-protein complex in vitro: The level of the hindrance was predicted based on the models. Moreover, the regulation of gene expression was achieved by using the shRNA converters designed to bind to the target U1A or nuclear factor-κB (NF-κB) p50 proteins expressed in human cells. The 3D molecular design approach is widely applicable for developing new devices in synthetic biology.
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Affiliation(s)
- Shunnichi Kashida
- Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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64
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Eby DM, Harbaugh S, Tatum RN, Farrington KE, Kelley-Loughnane N, Johnson GR. Bacterial sunscreen: layer-by-layer deposition of UV-absorbing polymers on whole-cell biosensors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:10521-10527. [PMID: 22694254 DOI: 10.1021/la3014514] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
UV-protective coatings on live bacterial cells were created from the assembly of cationic and UV-absorbing anionic polyelectrolytes using layer-by-layer (LbL) methodology. A cationic polymer (polyallylamine) and three different anionic polymers with varying absorbance in the UV range (poly(vinyl sulfate), poly(4-styrenesulfonic acid), and humic acid) were used to encapsulate Escherichia coli cells with two different green fluorescent protein (GFP) expression systems: constitutive expression of a UV-excitable GFP (GFPuv) and regulated expression of the intensely fluorescent GFP from amphioxus (GFPa1) through a theophylline-inducible riboswitch. Riboswitches activate protein expression after specific ligand-RNA binding events. Hence, they operate as a cellular biosensor that will activate reporter protein synthesis after exposure to a ligand target. E. coli cells coated with UV-absorbing polymers demonstrated enhanced protection of GFP stability, metabolic activity, and viability after prolonged exposure to radiation from a germicidal lamp. The results show the effectiveness of LbL coatings to provide UV protection to living cells for biotechnological applications.
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Affiliation(s)
- D Matthew Eby
- Universal Technology Corporation and Air Force Research Laboratory, Materials and Manufacturing Directorate, Tyndall Air Force Base, 139 Barnes Drive, Building 1117, Tyndall AFB, Florida 32403, United States.
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65
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Quarta G, Sin K, Schlick T. Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function. PLoS Comput Biol 2012; 8:e1002368. [PMID: 22359488 PMCID: PMC3280964 DOI: 10.1371/journal.pcbi.1002368] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 12/19/2011] [Indexed: 11/23/2022] Open
Abstract
Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant “downhill” pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design. Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way that sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we mimic transcription by computing energy landscapes which describe accessible secondary structures for a range of sequence lengths. Consistent with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: Low-barrier landscape with an ensemble of conformations in equilibrium before encountering a substrate; barrier-free landscape with a dominant “downhill” pathway to the minimum free energy structure; and barrier-dominated landscape with two isolated conformational states with different functions. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved between riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design.
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Affiliation(s)
- Giulio Quarta
- Department of Chemistry, New York University, New York, New York, United States of America
- Howard Hughes Medical Institute - Medical Research Fellows Program, Chevy Chase, Maryland, United States of America
| | - Ken Sin
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, New York, United States of America
- Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
- * E-mail:
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66
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Chang AL, Wolf JJ, Smolke CD. Synthetic RNA switches as a tool for temporal and spatial control over gene expression. Curr Opin Biotechnol 2012; 23:679-88. [PMID: 22305712 DOI: 10.1016/j.copbio.2012.01.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 11/17/2022]
Abstract
The engineering of biological systems offers significant promise for advances in areas including health and medicine, chemical synthesis, energy production, and environmental sustainability. Realizing this potential requires tools that enable design of sophisticated genetic systems. The functional diversity of RNA makes it an attractive and versatile substrate for programming sensing, information processing, computation, and control functions. Recent advances in the design of synthetic RNA switches capable of detecting and responding to molecular and environmental signals enable dynamic modulation of gene expression through diverse mechanisms, including transcription, splicing, stability, RNA interference, and translation. Furthermore, implementation of these switches in genetic circuits highlights the potential for building synthetic cell systems targeted to applications in environmental remediation and next-generation therapeutics and diagnostics.
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Affiliation(s)
- Andrew L Chang
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
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67
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Ogawa A. Rational construction of eukaryotic OFF-riboswitches that downregulate internal ribosome entry site-mediated translation in response to their ligands. Bioorg Med Chem Lett 2012; 22:1639-42. [DOI: 10.1016/j.bmcl.2011.12.118] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 12/26/2011] [Accepted: 12/26/2011] [Indexed: 11/16/2022]
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68
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Zeng Y, Pratumyot Y, Piao X, Bong D. Discrete Assembly of Synthetic Peptide–DNA Triplex Structures from Polyvalent Melamine–Thymine Bifacial Recognition. J Am Chem Soc 2011; 134:832-5. [PMID: 22201288 DOI: 10.1021/ja2099326] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yingying Zeng
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
| | - Yaowalak Pratumyot
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
| | - Xijun Piao
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
| | - Dennis Bong
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210,
United States
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69
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Fujita Y, Tanaka T, Furuta H, Ikawa Y. Functional roles of a tetraloop/receptor interacting module in a cyclic di-GMP riboswitch. J Biosci Bioeng 2011; 113:141-5. [PMID: 22074990 DOI: 10.1016/j.jbiosc.2011.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 09/26/2011] [Accepted: 10/07/2011] [Indexed: 12/27/2022]
Abstract
Riboswitches are a class of structural RNAs that regulate transcription and translation through specific recognition of small molecules. Riboswitches are attractive not only as drug targets for novel antibiotics but also as modular tools for controlling gene expression. Sequence comparison of a class of riboswitches that sense cyclic di-GMP (type-I c-di-GMP riboswitches) revealed that this type of riboswitch frequently shows a GAAA loop/receptor interaction between P1 and P3 elements. In the crystal structures of a type-I c-di-GMP riboswitch from Vibrio cholerae (the Vc2 riboswitch), the GNRA loop/receptor interaction assembled P2 and P3 stems to organize a ligand-binding pocket. In this study, the functional importance of the GAAA loop-receptor interaction in the Vc2 riboswitch was examined. A series of variant Vc2 riboswitches with mutations in the GAAA loop/receptor interaction were assayed for their switching abilities. In mutants with mutations in the P2 GAAA loop, expression of the reporter gene was reduced to approximately 40% - 60% of that in the wild-type. However, mutants in which the P3 receptor motif was substituted with base pairs were as active as the wild-type. These results suggested that the GAAA loop/receptor interaction does not simply establish the RNA 3D structure but docking of P2 GAAA loop reduces the flexibility of the GAAA receptor motif in the P3 element. This mechanism was supported by a variant riboswitch bearing a theophylline aptamer module in P3 the structural rigidity of which could be modulated by the small molecule theophylline.
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Affiliation(s)
- Yuki Fujita
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan
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70
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Abstract
Aptamers are useful for allosteric regulation because they are nucleic acid-based structures in which ligand binding induces conformational changes that may alter the function of a connected oligonucleotide at a distant site. Through this approach, a specific input is efficiently converted into an altered output. This property makes these biomolecules ideally suited to function as sensors or switches in biochemical assays or inside living cells. The ability to select oligonucleotide-based recognition elements in vitro in combination with the availability of nucleic acids with enzymatic activity has led to the development of a wide range of engineered allosteric aptasensors and aptazymes. Here, we discuss recent progress in the screening, design and diversity of these conformational switching oligonucleotides. We cover their application in vitro and for regulating gene expression in both prokaryotes and eukaryotes.
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Affiliation(s)
- Jan L Vinkenborg
- Life & Medical Sciences Institute, Chemical Biology & Medicinal Chemistry Unit, Laboratory of Chemical Biology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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71
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Ogawa A. Multiple-Catalytic Sensing of Nucleic Acid Sequences by Utilising a DNA-RNA-DNA Chimeric Antisense Probe and RNase H with a Eukaryotic Cell-Free Translation System. Chembiochem 2011; 12:881-5. [DOI: 10.1002/cbic.201000744] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Indexed: 02/05/2023]
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72
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Ogawa A, Doi Y, Matsushita N. Improvement of in vitro-transcribed amber suppressor tRNAs toward higher suppression efficiency in wheat germ extract. Org Biomol Chem 2011; 9:8495-503. [DOI: 10.1039/c1ob06351k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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