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Flemmich L, Bereiter R, Micura R. Chemical Synthesis of Modified RNA. Angew Chem Int Ed Engl 2024; 63:e202403063. [PMID: 38529723 DOI: 10.1002/anie.202403063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.
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Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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2
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Parmar S, Bume DD, Conelly C, Boer R, Prestwood PR, Wang Z, Labuhn H, Sinnadurai K, Feri A, Ouellet J, Homan P, Numata T, Schneekloth JS. Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.23.581746. [PMID: 38903087 PMCID: PMC11188086 DOI: 10.1101/2024.02.23.581746] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ1 riboswitches. Multiple X-ray co-crystal structures of synthetic ligands with the Thermoanaerobacter tengcongensis (Tte)-PreQ1 riboswitch confirm a common binding site with the cognate ligand, despite considerable chemical differences among the ligands. Structure probing assays demonstrate that one ligand causes conformational changes similar to PreQ1 in six structurally and mechanistically diverse PreQ1 riboswitch aptamers. Single-molecule force spectroscopy is used to demonstrate differential modes of riboswitch stabilization by the ligands. Binding of the natural ligand brings about the formation of a persistent, folded pseudoknot structure, whereas a synthetic ligand decreases the rate of unfolding through a kinetic mechanism. Single round transcription termination assays show the biochemical activity of the ligands, while a GFP reporter system reveals compound activity in regulating gene expression in live cells without toxicity. Taken together, this study reveals that diverse small molecules can impact gene expression in live cells by altering conformational changes in RNA structures through distinct mechanisms.
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Affiliation(s)
- Shaifaly Parmar
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Desta Doro Bume
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Colleen Conelly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Robert Boer
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Peri R. Prestwood
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Zhen Wang
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | | | | | - Adeline Feri
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | - Jimmy Ouellet
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | - Philip Homan
- Center for Cancer Research Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Tomoyuki Numata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - John S. Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
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Kumar S, Reddy G. Mechanism of Fluoride Ion Encapsulation by Magnesium Ions in a Bacterial Riboswitch. J Phys Chem B 2023; 127:9267-9281. [PMID: 37851949 DOI: 10.1021/acs.jpcb.3c03941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Riboswitches sense various ions in bacteria and activate gene expression to synthesize proteins that help maintain ion homeostasis. The crystal structure of the aptamer domain (AD) of the fluoride riboswitch shows that the F- ion is encapsulated by three Mg2+ ions bound to the ligand-binding domain (LBD) located at the core of the AD. The assembly mechanism of this intricate structure is unknown. To this end, we performed computer simulations using coarse-grained and all-atom RNA models to bridge multiple time scales involved in riboswitch folding and ion binding. We show that F- encapsulation by the Mg2+ ions bound to the riboswitch involves multiple sequential steps. Broadly, two Mg2+ ions initially interact with the phosphate groups of the LBD using water-mediated outer-shell coordination and transition to a direct inner-shell interaction through dehydration to strengthen their interaction with the LBD. We propose that the efficient binding mode of the third Mg2+ and F- is that they form a water-mediated ion pair and bind to the LBD simultaneously to minimize the electrostatic repulsion between three Mg2+ bound to the LBD. The tertiary stacking interactions among the LBD nucleobases alone are insufficient to stabilize the alignment of the phosphate groups to facilitate Mg2+ binding. We show that the stability of the whole assembly is an intricate balance of the interactions among the five phosphate groups, three Mg2+, and the encapsulated F- ion aided by the Mg2+ solvated water. These insights are helpful in the rational design of RNA-based ion sensors and fast-switching logic gates.
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Affiliation(s)
- Sunil Kumar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
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4
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Xu X, Egger M, Li C, Chen H, Micura R, Ren A. Structure-based investigations of the NAD+-II riboswitch. Nucleic Acids Res 2023; 51:54-67. [PMID: 36610789 PMCID: PMC9841397 DOI: 10.1093/nar/gkac1227] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 01/09/2023] Open
Abstract
Riboswitches are conserved non-coding domains in bacterial mRNA with gene regulation function that are essential for maintaining enzyme co-factor metabolism. Recently, the pnuC RNA motif was reported to selectively bind nicotinamide adenine dinucleotide (NAD+), defining a novel class of NAD+ riboswitches (NAD+-II) according to phylogenetic analysis. To reveal the three-dimensional architecture and the ligand-binding mode of this riboswitch, we solved the crystal structure of NAD+-II riboswitch in complex with NAD+. Strikingly and in contrast to class-I riboswitches that form a tight recognition pocket for the adenosine diphosphate (ADP) moiety of NAD+, the class-II riboswitches form a binding pocket for the nicotinamide mononucleotide (NMN) portion of NAD+ and display only unspecific interactions with the adenosine. We support this finding by an additional structure of the class-II RNA in complex with NMN alone. The structures define a novel RNA tertiary fold that was further confirmed by mutational analysis in combination with isothermal titration calorimetry (ITC), and 2-aminopurine-based fluorescence spectroscopic folding studies. Furthermore, we truncated the pnuC RNA motif to a short RNA helical scaffold with binding affinity comparable to the wild-type motif to allude to the potential of engineering the NAD+-II motif for biotechnological applications.
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Affiliation(s)
| | | | | | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ronald Micura
- Correspondence may also be addressed to Ronald Micura.
| | - Aiming Ren
- To whom correspondence should be addressed. Tel: +86 571 88981228; Fax: +86 571 88981227;
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5
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Kumar S, Reddy G. TPP Riboswitch Populates Holo-Form-like Structure Even in the Absence of Cognate Ligand at High Mg 2+ Concentration. J Phys Chem B 2022; 126:2369-2381. [PMID: 35298161 DOI: 10.1021/acs.jpcb.1c10794] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Riboswitches are noncoding RNA that regulate gene expression by folding into specific three-dimensional structures (holo-form) upon binding by their cognate ligand in the presence of Mg2+. Riboswitch functioning is also hypothesized to be under kinetic control requiring large cognate ligand concentrations. We ask the question under thermodynamic conditions, can the riboswitches populate structures similar to the holo-form only in the presence of Mg2+ and absence of cognate ligand binding. We addressed this question using thiamine pyrophosphate (TPP) riboswitch as a model system and computer simulations using a coarse-grained model for RNA. The folding free energy surface (FES) shows that with the initial increase in Mg2+ concentration ([Mg2+]), the aptamer domain (AD) of TPP riboswitch undergoes a barrierless collapse in its dimensions. On further increase in [Mg2+], intermediates separated by barriers appear on the FES, and one of the intermediates has a TPP ligand-binding competent structure. We show that site-specific binding of the Mg2+ aids in the formation of tertiary contacts. For [Mg2+] greater than physiological concentration, AD folds into a structure similar to the crystal structure of the TPP holo-form even in the absence of the TPP ligand. The folding kinetics shows that TPP AD populates an intermediate due to the misalignment of two arms present in the structure, which acts as a kinetic trap, leading to larger folding timescales. The predictions of the intermediate structures from the simulations are amenable for experimental verification.
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Affiliation(s)
- Sunil Kumar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
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Yang Z, Xu H, Wang J, Chen W, Zhao M. Single-Molecule Fluorescence Techniques for Membrane Protein Dynamics Analysis. APPLIED SPECTROSCOPY 2021; 75:491-505. [PMID: 33825543 DOI: 10.1177/00037028211009973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fluorescence-based single-molecule techniques, mainly including fluorescence correlation spectroscopy (FCS) and single-molecule fluorescence resonance energy transfer (smFRET), are able to analyze the conformational dynamics and diversity of biological macromolecules. They have been applied to analysis of the dynamics of membrane proteins, such as membrane receptors and membrane transport proteins, due to their superior ability in resolving spatio-temporal heterogeneity and the demand of trace amounts of analytes. In this review, we first introduced the basic principle involved in FCS and smFRET. Then we summarized the labeling and immobilization strategies of membrane protein molecules, the confocal-based and TIRF-based instrumental configuration, and the data processing methods. The applications to membrane protein dynamics analysis are described in detail with the focus on how to select suitable fluorophores, labeling sites, experimental setup, and analysis methods. In the last part, the remaining challenges to be addressed and further development in this field are also briefly discussed.
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Affiliation(s)
- Ziyu Yang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Haiqi Xu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Jiayu Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, 12465 Peking University, Beijing, China
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7
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Brown JA. Unraveling the structure and biological functions of RNA triple helices. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1598. [PMID: 32441456 PMCID: PMC7583470 DOI: 10.1002/wrna.1598] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
It has been nearly 63 years since the first characterization of an RNA triple helix in vitro by Gary Felsenfeld, David Davies, and Alexander Rich. An RNA triple helix consists of three strands: A Watson–Crick RNA double helix whose major‐groove establishes hydrogen bonds with the so‐called “third strand”. In the past 15 years, it has been recognized that these major‐groove RNA triple helices, like single‐stranded and double‐stranded RNA, also mediate prominent biological roles inside cells. Thus far, these triple helices are known to mediate catalysis during telomere synthesis and RNA splicing, bind to ligands and ions so that metabolite‐sensing riboswitches can regulate gene expression, and provide a clever strategy to protect the 3′ end of RNA from degradation. Because RNA triple helices play important roles in biology, there is a renewed interest in better understanding the fundamental properties of RNA triple helices and developing methods for their high‐throughput discovery. This review provides an overview of the fundamental biochemical and structural properties of major‐groove RNA triple helices, summarizes the structure and function of naturally occurring RNA triple helices, and describes prospective strategies to isolate RNA triple helices as a means to establish the “triplexome”. This article is categorized under:RNA Structure and Dynamics > RNA Structure and Dynamics RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems
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Affiliation(s)
- Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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8
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Dutta D, Wedekind JE. Nucleobase mutants of a bacterial preQ 1-II riboswitch that uncouple metabolite sensing from gene regulation. J Biol Chem 2020; 295:2555-2567. [PMID: 31659117 PMCID: PMC7049981 DOI: 10.1074/jbc.ra119.010755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/20/2019] [Indexed: 11/06/2022] Open
Abstract
Riboswitches are a class of nonprotein-coding RNAs that directly sense cellular metabolites to regulate gene expression. They are model systems for analyzing RNA-ligand interactions and are established targets for antibacterial agents. Many studies have analyzed the ligand-binding properties of riboswitches, but this work has outpaced our understanding of the underlying chemical pathways that govern riboswitch-controlled gene expression. To address this knowledge gap, we prepared 15 mutants of the preQ1-II riboswitch-a structurally and biochemically well-characterized HLout pseudoknot that recognizes the metabolite prequeuosine1 (preQ1). The mutants span the preQ1-binding pocket through the adjoining Shine-Dalgarno sequence (SDS) and include A-minor motifs, pseudoknot-insertion helix P4, U·A-U base triples, and canonical G-C pairs in the anti-SDS. As predicted-and confirmed by in vitro isothermal titration calorimetry measurements-specific mutations ablated preQ1 binding, but most aberrant binding effects were corrected by compensatory mutations. In contrast, functional analysis in live bacteria using a riboswitch-controlled GFPuv-reporter assay revealed that each mutant had a deleterious effect on gene regulation, even when compensatory changes were included. Our results indicate that effector binding can be uncoupled from gene regulation. We attribute loss of function to defects in a chemical interaction network that links effector binding to distal regions of the fold that support the gene-off RNA conformation. Our findings differentiate effector binding from biological function, which has ramifications for riboswitch characterization. Our results are considered in the context of synthetic ligands and drugs that bind tightly to riboswitches without eliciting a biological response.
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Affiliation(s)
- Debapratim Dutta
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Joseph E Wedekind
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642.
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9
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In vivo evolutionary engineering of riboswitch with high-threshold for N-acetylneuraminic acid production. Metab Eng 2020; 59:36-43. [PMID: 31954846 DOI: 10.1016/j.ymben.2020.01.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/26/2019] [Accepted: 01/04/2020] [Indexed: 11/22/2022]
Abstract
Riboswitches with desired properties, such as sensitivity, threshold, dynamic range, is important for its application. However, the property change of a natural riboswitch is difficult due to the lack of the understanding of aptamer ligand binding properties and a proper screening method for both rational and irrational design. In this study, an effective method to change the threshold of riboswitch was established in vivo based on growth coupled screening by combining both positive and negative selections. The feasibility of the method was verified by the model library. Using this method, an N-acetylneuraminic acid (NeuAc) riboswitch was evolved and modified riboswitches with high threshold and large dynamic range were obtained. Then, using a new NeuAc riboswitch, both ribosome binding sites and key gene in NeuAc biosynthesis pathway were optimized. The highest NeuAc production of 14.32 g/l that has been reported using glucose as sole carbon source was obtained.
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10
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Neuner E, Micura R. Practical synthesis of N-(di- n-butylamino)methylene-protected 2-aminopurine riboside phosphoramidite for RNA solid-phase synthesis. MONATSHEFTE FUR CHEMIE 2019; 150:1941-1946. [PMID: 31929656 PMCID: PMC6936340 DOI: 10.1007/s00706-019-02502-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/09/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Eva Neuner
- Institute of Organic Chemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck, Austria
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11
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Gasser C, Gebetsberger J, Gebetsberger M, Micura R. SHAPE probing pictures Mg2+-dependent folding of small self-cleaving ribozymes. Nucleic Acids Res 2019; 46:6983-6995. [PMID: 29924364 PMCID: PMC6101554 DOI: 10.1093/nar/gky555] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/07/2018] [Indexed: 12/28/2022] Open
Abstract
Self-cleaving ribozymes are biologically relevant RNA molecules which catalyze site-specific cleavage of the phosphodiester backbone. Gathering knowledge of their three-dimensional structures is critical toward an in-depth understanding of their function and chemical mechanism. Equally important is collecting information on the folding process and the inherent dynamics of a ribozyme fold. Over the past years, Selective-2′-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) turned out to be a significant tool to probe secondary and tertiary interactions of diverse RNA species at the single nucleotide level under varying environmental conditions. Small self-cleaving ribozymes, however, have not been investigated by this method so far. Here, we describe SHAPE probing of pre-catalytic folds of the recently discovered ribozyme classes twister, twister-sister (TS), pistol and hatchet. The study has implications on Mg2+-dependent folding and reveals potentially dynamic residues of these ribozymes that are otherwise difficult to identify. For twister, TS and pistol ribozymes the new findings are discussed in the light of their crystal structures, and in case of twister also with respect to a smFRET folding analysis. For the hatchet ribozyme where an atomic resolution structure is not yet available, the SHAPE data challenge the proposed secondary structure model and point at selected residues and putative long-distance interactions that appear crucial for structure formation and cleavage activity.
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Affiliation(s)
- Catherina Gasser
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
| | - Jennifer Gebetsberger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
| | - Manuel Gebetsberger
- Division for Biomedical Physics, Medical University of Innsbruck, Müllerstraße 44, Innsbruck 6020, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University, Innrain 80-82, Innsbruck 6020, Austria
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12
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Design and optimization of genetically encoded biosensors for high-throughput screening of chemicals. Curr Opin Biotechnol 2018; 54:18-25. [DOI: 10.1016/j.copbio.2018.01.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/08/2018] [Accepted: 01/11/2018] [Indexed: 02/07/2023]
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13
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Warnasooriya C, Ling C, Belashov IA, Salim M, Wedekind JE, Ermolenko DN. Observation of preQ 1-II riboswitch dynamics using single-molecule FRET. RNA Biol 2018; 16:1086-1092. [PMID: 30328747 DOI: 10.1080/15476286.2018.1536591] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PreQ1 riboswitches regulate the synthesis of the hypermodified tRNA base queuosine by sensing the pyrrolopyrimidine metabolite preQ1. Here, we use single-molecule FRET to interrogate the structural dynamics of apo and preQ1-bound states of the preQ1-II riboswitch from Lactobacillus rhamnosus. We find that the apo-form of the riboswitch spontaneously samples multiple conformations. Magnesium ions and preQ1 stabilize conformations that sequester the ribosome-binding site of the mRNA within the pseudoknotted structure, thus inhibiting translation initiation. Our results reveal that folding of the preQ1-II riboswitch is complex and provide evidence favoring a conformational selection model of effector binding by riboswitches of this class.
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Affiliation(s)
- Chandani Warnasooriya
- a Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
| | - Clarence Ling
- a Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
| | - Ivan A Belashov
- a Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
| | - Mohammad Salim
- a Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
| | - Joseph E Wedekind
- a Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
| | - Dmitri N Ermolenko
- a Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester , Rochester , NY , USA
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Ray S, Chauvier A, Walter NG. Kinetics coming into focus: single-molecule microscopy of riboswitch dynamics. RNA Biol 2018; 16:1077-1085. [PMID: 30328748 DOI: 10.1080/15476286.2018.1536594] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Riboswitches are dynamic RNA motifs that are mostly embedded in the 5'-untranslated regions of bacterial mRNAs, where they regulate gene expression transcriptionally or translationally by undergoing conformational changes upon binding of a small metabolite or ion. Due to the small size of typical ligands, relatively little free energy is available from ligand binding to overcome the often high energetic barrier of reshaping RNA structure. Instead, most riboswitches appear to take advantage of the directional and hierarchical folding of RNA by employing the ligand as a structural 'linchpin' to adjust the kinetic partitioning between alternate folds. In this model, even small, local structural and kinetic effects of ligand binding can cascade into global RNA conformational changes affecting gene expression. Single-molecule (SM) microscopy tools are uniquely suited to study such kinetically controlled RNA folding since they avoid the ensemble averaging of bulk techniques that loses sight of unsynchronized, transient, and/or multi-state kinetic behavior. This review summarizes how SM methods have begun to unravel riboswitch-mediated gene regulation.
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Affiliation(s)
- Sujay Ray
- a Single Molecule Analysis Group, Department of Chemistry, University of Michigan , Ann Arbor , MI , USA
| | - Adrien Chauvier
- a Single Molecule Analysis Group, Department of Chemistry, University of Michigan , Ann Arbor , MI , USA
| | - Nils G Walter
- a Single Molecule Analysis Group, Department of Chemistry, University of Michigan , Ann Arbor , MI , USA
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15
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Neuner E, Frener M, Lusser A, Micura R. Superior cellular activities of azido- over amino-functionalized ligands for engineered preQ 1 riboswitches in E.coli. RNA Biol 2018; 15:1376-1383. [PMID: 30332908 PMCID: PMC6284575 DOI: 10.1080/15476286.2018.1534526] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 10/05/2018] [Indexed: 01/29/2023] Open
Abstract
For this study, we utilized class-I and class-II preQ1-sensing riboswitches as model systems to decipher the structure-activity relationship of rationally designed ligand derivatives in vitro and in vivo. We found that synthetic preQ1 ligands with amino-modified side chains that protrude from the ligand-encapsulating binding pocket, and thereby potentially interact with the phosphate backbone in their protonated form, retain or even increase binding affinity for the riboswitches in vitro. They, however, led to significantly lower riboswitch activities in a reporter system in vivo in E. coli. Importantly, when we substituted the amino- by azido-modified side chains, the cellular activities of the ligands were restored for the class-I conditional gene expression system and even improved for the class-II counterpart. Kinetic analysis of ligand binding in vitro revealed enhanced on-rates for amino-modified derivatives while they were attenuated for azido-modified variants. This shows that neither high affinities nor fast on-rates are necessarily translated into efficient cellular activities. Taken together, our comprehensive study interconnects in vitro kinetics and in vitro thermodynamics of RNA-ligand binding with the ligands' in vivo performance and thereby encourages azido- rather than amino-functionalized design for enhanced cellular activity.
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Affiliation(s)
- Eva Neuner
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University, Innsbruck, Austria
| | - Marina Frener
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University, Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University, Innsbruck, Austria
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16
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Kesherwani M, N H V K, Velmurugan D. Conformational Dynamics of thiM Riboswitch To Understand the Gene Regulation Mechanism Using Markov State Modeling and the Residual Fluctuation Network Approach. J Chem Inf Model 2018; 58:1638-1651. [PMID: 29939019 DOI: 10.1021/acs.jcim.8b00155] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in the noncoding region of mRNA. The aptamer domain of TPP riboswitch detects the high abundance of coenzyme thiamine pyrophosphate (TPP) and modulates the gene expression for thiamine synthetic gene. The mechanistic understanding in recognition of TPP in aptamer domain and ligand-induced compactness for folding of expression platform are most important to designing novel modulators. To understand the dynamic behavior of TPP riboswitch upon TPP binding, molecular dynamics simulations were performed for 400 ns in both apo and TPP bound forms of thiM riboswitch from E. coli and analyzed in terms of eRMSD-based Markov state modeling and residual fluctuation network. Markov state models show good correlations in transition probability among metastable states from simulated trajectory and generated models. Structural compactness in TPP bound form is observed which is correlated with SAXS experiment. The importance of junction of P4 and P5 is evident during dynamics, which correlates with FRET analysis. The dynamic nature of two sensor forearms is due to the flexible P1 helix, which is its intrinsic property. The transient state in TPP-bound form was observed in the Markov state model, along with stable states. We believe that this transient state is responsible to assist the influx and outflux of ligand molecule by creating a solvent channel around the junction region of P4 and P5 and such a structure was anticipated in FRET analysis. The dynamic nature of riboswitch is dependent on the interaction between residues on distal loops L3 and L5/P3 and junction P4 and P5, J3/2 which stabilize the J2/4. It helps in the transfer of allosteric information between J2/4 and P3/L5 tertiary docking region through the active site residues. Understanding such information flow will benefit in highlighting crucial residues in highly dynamic and kinetic systems. Here, we report the residues and segments in riboswitch that play vital roles in providing stability and this can be exploited in designing inhibitors to regulate the functioning of riboswitches.
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Affiliation(s)
- Manish Kesherwani
- Centre for Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai - 600025 India
| | - Kutumbarao N H V
- Centre for Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai - 600025 India
| | - Devadasan Velmurugan
- Centre for Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai - 600025 India
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17
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Dutta D, Belashov IA, Wedekind JE. Coupling Green Fluorescent Protein Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria. Biochemistry 2018; 57:4620-4628. [PMID: 29897738 DOI: 10.1021/acs.biochem.8b00316] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncoding RNAs engage in numerous biological activities including gene regulation. To fully understand RNA function it is necessary to probe biologically relevant conformations in living cells. To address this challenge, we coupled RNA-mediated regulation of the green fluorescent protein (GFP)uv-reporter gene to icSHAPE (in cell Selective 2'-Hydroxyl Acylation analyzed by Primer Extension). Our transcript-specific approach provides sensitive, fluorescence-based readout of the regulatory-RNA status as a means to coordinate chemical modification experiments. We chose a plasmid-based reporter compatible with Escherichia coli to allow use of knockout strains that eliminate endogenous effector biosynthesis. The approach was piloted using the Lactobacillus rhamnosus ( Lrh) preQ1-II riboswitch, which senses the pyrrolopyrimidine metabolite preQ1. Using an E. coli Δ queF strain incapable of preQ1 anabolism, the Lrh riboswitch yielded nearly one log unit of GFPuv-gene repression resulting from exogenously added preQ1. We then subjected cells in gene "on" and "off" states to icSHAPE. The resulting differential analysis indicated reduction in Lrh riboswitch flexibility in the P3 helix of the pseudoknot, which comprises the ribosome-binding site (RBS) paired with the anti-RBS. Such expression platform modulation was not observed by in vitro chemical probing and demonstrates that the crowded cellular environment does not preclude detection of compact and loose RNA-regulatory conformations. Here we describe the design, methods, interpretation, and caveats of Reporter Coupled (ReCo) icSHAPE. We also describe mapping of the differential ReCo-icSHAPE results onto the Lrh riboswitch-preQ1 cocrystal structure. The approach should be readily applicable to functional RNAs triggered by effectors or environmental variations.
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Affiliation(s)
- Debapratim Dutta
- Department of Biochemistry & Biophysics and Center for RNA Biology , University of Rochester School of Medicine & Dentistry , Rochester , New York 14642 , United States
| | - Ivan A Belashov
- Department of Biochemistry & Biophysics and Center for RNA Biology , University of Rochester School of Medicine & Dentistry , Rochester , New York 14642 , United States
| | - Joseph E Wedekind
- Department of Biochemistry & Biophysics and Center for RNA Biology , University of Rochester School of Medicine & Dentistry , Rochester , New York 14642 , United States
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18
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Ray S, Widom JR, Walter NG. Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. Chem Rev 2018; 118:4120-4155. [PMID: 29363314 PMCID: PMC5918467 DOI: 10.1021/acs.chemrev.7b00519] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The emergence of single-molecule (SM) fluorescence techniques has opened up a vast new toolbox for exploring the molecular basis of life. The ability to monitor individual biomolecules in real time enables complex, dynamic folding pathways to be interrogated without the averaging effect of ensemble measurements. In parallel, modern biology has been revolutionized by our emerging understanding of the many functions of RNA. In this comprehensive review, we survey SM fluorescence approaches and discuss how the application of these tools to RNA and RNA-containing macromolecular complexes in vitro has yielded significant insights into the underlying biology. Topics covered include the three-dimensional folding landscapes of a plethora of isolated RNA molecules, their assembly and interactions in RNA-protein complexes, and the relation of these properties to their biological functions. In all of these examples, the use of SM fluorescence methods has revealed critical information beyond the reach of ensemble averages.
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Affiliation(s)
| | | | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA
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19
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Gleitsman KR, Sengupta RN, Herschlag D. Slow molecular recognition by RNA. RNA (NEW YORK, N.Y.) 2017; 23:1745-1753. [PMID: 28971853 PMCID: PMC5688996 DOI: 10.1261/rna.062026.117] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/26/2017] [Indexed: 05/28/2023]
Abstract
Molecular recognition is central to biological processes, function, and specificity. Proteins associate with ligands with a wide range of association rate constants, with maximal values matching the theoretical limit set by the rate of diffusional collision. As less is known about RNA association, we compiled association rate constants for all RNA/ligand complexes that we could find in the literature. Like proteins, RNAs exhibit a wide range of association rate constants. However, the fastest RNA association rates are considerably slower than those of the fastest protein associations and fall well below the diffusional limit. The apparently general observation of slow association with RNAs has implications for evolution and for modern-day biology. Our compilation highlights a quantitative molecular property that can contribute to biological understanding and underscores our need to develop a deeper physical understanding of molecular recognition events.
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Affiliation(s)
- Kristin R Gleitsman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Raghuvir N Sengupta
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
- Department of Chemical Engineering and Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, California 94305, USA
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20
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Jang S, Jang S, Xiu Y, Kang TJ, Lee SH, Koffas MAG, Jung GY. Development of Artificial Riboswitches for Monitoring of Naringenin In Vivo. ACS Synth Biol 2017; 6:2077-2085. [PMID: 28749656 DOI: 10.1021/acssynbio.7b00128] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Microbial strains are considered promising hosts for production of flavonoids because of their rapid growth rate and suitability for large-scale manufacturing. However, productivity and titer of current recombinant strains still do not meet the requirements of industrial processes. Genetically encoded biosensors have been applied for high-throughput screening or dynamic regulation of biosynthetic pathways for enhancing the performance of microbial strains that produce valuable chemicals. Currently, few protein sensor-regulators for flavonoids exist. Unlike the protein-based trans-regulating controllers, riboswitches can respond to their ligands faster and eliminate off-target effects. Here, we developed artificial riboswitches that activate gene expression in response to naringenin, an important flavonoid. RNA aptamers for naringenin were developed using SELEX and cloned upstream of a dual selectable marker gene to construct a riboswitch library. Two in vivo selection routes were applied separately to the library by supplementing naringenin at two different concentrations during enrichments to modulate the operational ranges of the riboswitches. The selected riboswitches were responsive to naringenin and activated gene expression up to 2.91-fold. Operational ranges of the riboswitches were distinguished on the basis of their selection route. Additionally, the specificity of the riboswitches was assessed, and their applicability as dynamic regulators was confirmed. Collectively, the naringenin riboswitches reported in this work will be valuable tools in metabolic engineering of microorganisms for the production of flavonoids.
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Affiliation(s)
- Sungho Jang
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Sungyeon Jang
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
| | - Yu Xiu
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Key Laboratory of Bioactive Substances and Functional Food, Beijing Union University, Beijing 100191, China
| | - Taek Jin Kang
- Department
of Chemical and Biochemical Engineering, Dongguk University, 30 Pildong-ro 1-gil, Jung-gu, Seoul, 04620, Korea
| | - Sang-Hyeup Lee
- Department
of Life Chemistry, Catholic University of Daegu, Hayang-ro 13-13,
Hayang-eup, Gyeongsan, Gyeongbuk 38430, Korea
| | - Mattheos A. G. Koffas
- Department
of Chemical and Biological Engineering, Center for Biotechnology and
Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Department
of Biological Sciences, Center for Biotechnology and Interdisciplinary
Studies, Rensselaer Polytechnic Institutee, Troy, New York 12180, United States
| | - Gyoo Yeol Jung
- Department
of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
- School
of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Korea
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21
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Vušurović N, Altman RB, Terry DS, Micura R, Blanchard SC. Pseudoknot Formation Seeds the Twister Ribozyme Cleavage Reaction Coordinate. J Am Chem Soc 2017; 139:8186-8193. [PMID: 28598157 PMCID: PMC5697751 DOI: 10.1021/jacs.7b01549] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The twister RNA is a recently discovered nucleolytic ribozyme that is present in both bacteria and eukarya. While its biological role remains unclear, crystal structure analyses and biochemical approaches have revealed critical features of its catalytic mechanism. Here, we set out to explore dynamic aspects of twister RNA folding along the cleavage reaction coordinate. To do so, we have employed both bulk and single-molecule fluorescence resonance energy transfer (FRET) methods to investigate a set of twister RNAs with labels strategically positioned at communicating segments. The data reveal that folding of the central pseudoknot (T1), the most crucial structural determinant to promote cleavage, exhibits reversible opening and closing dynamics at physiological Mg2+ concentration. Uncoupled folding, in which T1 formation precedes structuring for closing of stem P1, was confirmed using pre-steady-state three-color smFRET experiments initiated by Mg2+ injection. This finding suggests that the folding path of twister RNA requires proper orientation of the substrate prior to T1 closure such that the U5-A6 cleavage site becomes embraced to achieve its cleavage competent conformation. We also find that the cleaved 3'-fragment retains its compacted pseudoknot fold, despite the absence of the phylogenetically conserved stem P1, rationalizing the poor turnover efficiency of the twister ribozyme.
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Affiliation(s)
- Nikola Vušurović
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | - Roger B. Altman
- Weill Cornell Medicine, New York, New York 10065, United States
| | - Daniel S. Terry
- Weill Cornell Medicine, New York, New York 10065, United States
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
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22
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Jones CP, Ferré-D'Amaré AR. Long-Range Interactions in Riboswitch Control of Gene Expression. Annu Rev Biophys 2017; 46:455-481. [PMID: 28375729 DOI: 10.1146/annurev-biophys-070816-034042] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Riboswitches are widespread RNA motifs that regulate gene expression in response to fluctuating metabolite concentrations. Known primarily from bacteria, riboswitches couple specific ligand binding and changes in RNA structure to mRNA expression in cis. Crystal structures of the ligand binding domains of most of the phylogenetically widespread classes of riboswitches, each specific to a particular metabolite or ion, are now available. Thus, the bound states-one end point-have been thoroughly characterized, but the unbound states have been more elusive. Consequently, it is less clear how the unbound, sensing riboswitch refolds into the ligand binding-induced output state. The ligand recognition mechanisms of riboswitches are diverse, but we find that they share a common structural strategy in positioning their binding sites at the point of the RNA three-dimensional fold where the residues farthest from one another in sequence meet. We review how riboswitch folds adhere to this fundamental strategy and propose future research directions for understanding and harnessing their ability to specifically control gene expression.
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Affiliation(s)
- Christopher P Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824;
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824;
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23
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Jud L, Micura R. An Unconventional Acid-Labile Nucleobase Protection Concept for Guanosine Phosphoramidites in RNA Solid-Phase Synthesis. Chemistry 2017; 23:3406-3413. [PMID: 27943429 DOI: 10.1002/chem.201605056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Indexed: 12/14/2022]
Abstract
We present an innovative O6 -tert-butyl/N2 -tert-butyloxycarbonyl protection concept for guanosine (G) phosphoramidites. This concept is advantageous for 2'-modified G building blocks because of very efficient synthetic access when compared with existing routes that usually employ O6 -(4-nitrophenyl)ethyl/N2 -acyl protection or that start from 2-aminoadenosine involving enzymatic transformation into guanosine later on in the synthetic path. The new phosphoramidites are fully compatible with 2'-O-tBDMS or TOM phosphoramidites in standard RNA solid-phase synthesis and deprotection, and provide excellent quality of tailored RNAs for the growing range of applications in RNA biophysics, biochemistry, and biology.
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Affiliation(s)
- Lukas Jud
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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24
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Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation. Nat Commun 2017; 8:13892. [PMID: 28071751 PMCID: PMC5234074 DOI: 10.1038/ncomms13892] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/10/2016] [Indexed: 11/24/2022] Open
Abstract
On the basis of nascent transcript sequencing, it has been postulated but never demonstrated that transcriptional pausing at translation start sites is important for gene regulation. Here we show that the Escherichia coli thiamin pyrophosphate (TPP) thiC riboswitch contains a regulatory pause site in the translation initiation region that acts as a checkpoint for thiC expression. By biochemically probing nascent transcription complexes halted at defined positions, we find a narrow transcriptional window for metabolite binding, in which the downstream boundary is delimited by the checkpoint. We show that transcription complexes at the regulatory pause site favour the formation of a riboswitch intramolecular lock that strongly prevents TPP binding. In contrast, cotranscriptional metabolite binding increases RNA polymerase pausing and induces Rho-dependent transcription termination at the checkpoint. Early transcriptional pausing may provide a general mechanism, whereby transient transcriptional windows directly coordinate the sensing of environmental cues and bacterial mRNA regulation. Riboswitches are non-coding RNA elements that detect metabolites and control expression by regulating mRNA levels or translation. Here, the authors provide evidence that the E. coli thiC riboswitch has a pause site in the translation initiation region that acts as a checkpoint for thiC expression.
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25
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Börner R, Kowerko D, Miserachs HG, Schaffer MF, Sigel RK. Metal ion induced heterogeneity in RNA folding studied by smFRET. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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26
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Egloff D, Oleinich IA, Zhao M, König SLB, Sigel RKO, Freisinger E. Sequence-Specific Post-Synthetic Oligonucleotide Labeling for Single-Molecule Fluorescence Applications. ACS Chem Biol 2016; 11:2558-67. [PMID: 27409145 DOI: 10.1021/acschembio.6b00343] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The sequence-specific fluorescence labeling of nucleic acids is a prerequisite for various methods including single-molecule Förster resonance energy transfer (smFRET) for the detailed study of nucleic acid folding and function. Such nucleic acid derivatives are commonly obtained by solid-phase methods; however, yields decrease rapidly with increasing length and restrict the practicability of this approach for long strands. Here, we report a new labeling strategy for the postsynthetic incorporation of a bioorthogonal group into single stranded regions of both DNA and RNA of unrestricted length. A 12-alkyne-etheno-adenine modification is sequence-selectively formed using DNA-templated synthesis, followed by conjugation of the fluorophore Cy3 via a copper-catalyzed azide-alkyne cycloaddition (CuAAC). Evaluation of the labeled strands in smFRET measurements shows that the strategy developed here has the potential to be used for the study of long functional nucleic acids by (single-molecule) fluorescence or other methods. To prove the universal use of the method, its application was successfully extended to the labeling of a short RNA single strand. As a proof-of-concept, also the labeling of a large RNA molecule in form of a 633 nucleotide long construct derived from the Saccharomyces cerevisiae group II intron Sc.ai5γ was performed, and covalent attachment of the Cy3 fluorophore was shown with gel electrophoresis.
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Affiliation(s)
- David Egloff
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Igor A. Oleinich
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Meng Zhao
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Sebastian L. B. König
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Roland K. O. Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Eva Freisinger
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
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27
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Kushwaha M, Rostain W, Prakash S, Duncan JN, Jaramillo A. Using RNA as Molecular Code for Programming Cellular Function. ACS Synth Biol 2016; 5:795-809. [PMID: 26999422 DOI: 10.1021/acssynbio.5b00297] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA is involved in a wide-range of important molecular processes in the cell, serving diverse functions: regulatory, enzymatic, and structural. Together with its ease and predictability of design, these properties can lead RNA to become a useful handle for biological engineers with which to control the cellular machinery. By modifying the many RNA links in cellular processes, it is possible to reprogram cells toward specific design goals. We propose that RNA can be viewed as a molecular programming language that, together with protein-based execution platforms, can be used to rewrite wide ranging aspects of cellular function. In this review, we catalogue developments in the use of RNA parts, methods, and associated computational models that have contributed to the programmability of biology. We discuss how RNA part repertoires have been combined to build complex genetic circuits, and review recent applications of RNA-based parts and circuitry. We explore the future potential of RNA engineering and posit that RNA programmability is an important resource for firmly establishing an era of rationally designed synthetic biology.
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Affiliation(s)
- Manish Kushwaha
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - William Rostain
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
| | - Satya Prakash
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - John N. Duncan
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - Alfonso Jaramillo
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
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28
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Rugbjerg P, Genee HJ, Jensen K, Sarup-Lytzen K, Sommer MOA. Molecular Buffers Permit Sensitivity Tuning and Inversion of Riboswitch Signals. ACS Synth Biol 2016; 5:632-8. [PMID: 27138234 PMCID: PMC4949582 DOI: 10.1021/acssynbio.5b00213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Predictable integration
of foreign biological signals and parts
remains a key challenge in the systematic engineering of synthetic
cellular actuations, and general methods to improve signal transduction
and sensitivity are needed. To address this problem we modeled and
built a molecular signal buffer network in Saccharomyces cerevisiae inspired by chemical pH buffer systems. The molecular buffer system
context-insulates a riboswitch enabling synthetic control of colony
formation and modular signal manipulations. The riboswitch signal
is relayed to a transcriptional activation domain of a split transcription
factor, while interacting DNA-binding domains mediate the transduction
of signal and form an interacting molecular buffer. The molecular
buffer system enables modular signal inversion through integration
with repressor modules. Further, tuning of input sensitivity was achieved
through perturbation of the buffer pair ratio guided by a mathematical
model. Such buffered signal tuning networks will be useful for domestication
of RNA-based sensors enabling tunable outputs and library-wide selections
for drug discovery and metabolic engineering.
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Affiliation(s)
- Peter Rugbjerg
- Novo Nordisk Foundation Center
for Biosustainability, Technical University of Denmark, Kogle Allé
6, DK-2970 Hørsholm, Denmark
| | - Hans Jasper Genee
- Novo Nordisk Foundation Center
for Biosustainability, Technical University of Denmark, Kogle Allé
6, DK-2970 Hørsholm, Denmark
| | - Kristian Jensen
- Novo Nordisk Foundation Center
for Biosustainability, Technical University of Denmark, Kogle Allé
6, DK-2970 Hørsholm, Denmark
| | - Kira Sarup-Lytzen
- Novo Nordisk Foundation Center
for Biosustainability, Technical University of Denmark, Kogle Allé
6, DK-2970 Hørsholm, Denmark
| | - Morten Otto Alexander Sommer
- Novo Nordisk Foundation Center
for Biosustainability, Technical University of Denmark, Kogle Allé
6, DK-2970 Hørsholm, Denmark
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29
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McKeague M, Wong RS, Smolke CD. Opportunities in the design and application of RNA for gene expression control. Nucleic Acids Res 2016; 44:2987-99. [PMID: 26969733 PMCID: PMC4838379 DOI: 10.1093/nar/gkw151] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 02/29/2016] [Indexed: 12/15/2022] Open
Abstract
The past decade of synthetic biology research has witnessed numerous advances in the development of tools and frameworks for the design and characterization of biological systems. Researchers have focused on the use of RNA for gene expression control due to its versatility in sensing molecular ligands and the relative ease by which RNA can be modeled and designed compared to proteins. We review the recent progress in the field with respect to RNA-based genetic devices that are controlled through small molecule and protein interactions. We discuss new approaches for generating and characterizing these devices and their underlying components. We also highlight immediate challenges, future directions and recent applications of synthetic RNA devices in engineered biological systems.
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Affiliation(s)
- Maureen McKeague
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Remus S Wong
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Christina D Smolke
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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30
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The Complementarity of the Loop to the Stem in DNA Pseudoknots Gives Rise to Local TAT Base-Triplets. Methods Enzymol 2016. [PMID: 26794363 DOI: 10.1016/bs.mie.2015.07.029] [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: 10/15/2023]
Abstract
Pseudoknots belong to an RNA structural motif that has significant roles in the biological function of RNA. An example is ribosomal frameshifting; in this mechanism, the formation of a local triplex changes the reading frame that allows for differences in the translation of mRNAs. In this work, we have used a combination of temperature-dependent UV spectroscopy and differential scanning calorimetry (DSC) to determine the unfolding thermodynamics of a set of DNA pseudoknots with the following sequence: d(TCTCTTnAAAAAAAAGAGAT5TTTTTTT), where "Tn" is a thymine loop with n=5 (PsK-5), 7 (PsK-7), 9 (PsK-9), or 11 (PsK-11). All four oligonucleotides form intramolecular pseudoknots, and the increase in the length of this loop yielded more stable pseudoknots due to higher transition temperatures and higher unfolding enthalpies. This indicates formation of one and three TAT/TAT stacks in PsK-9 and PsK-11, respectively. We have flipped one AT for a TA base pair in the core stem of these pseudoknots, preventing in this way the formation of these base-triplet stacks. The DSC curves of these pseudoknots yielded lower unfolding enthalpies, confirming the formation of a local triplex in PsK-9 and PsK-11. Furthermore, we have investigated the reaction of PsK-5 and PsK-9 with their partially complementary strands: directly by isothermal titration calorimetry and indirectly by creating a Hess cycle with the DSC data. Relative to the PsK-5 reaction, PsK-9 reacts with its complementary strand with less favorable free energy and enthalpy contributions; this indicates PsK-9 is more stable and more compact due to the formation of a local triplex.
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31
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Espah Borujeni A, Mishler DM, Wang J, Huso W, Salis HM. Automated physics-based design of synthetic riboswitches from diverse RNA aptamers. Nucleic Acids Res 2016; 44:1-13. [PMID: 26621913 PMCID: PMC4705656 DOI: 10.1093/nar/gkv1289] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/30/2015] [Accepted: 11/05/2015] [Indexed: 01/31/2023] Open
Abstract
Riboswitches are shape-changing regulatory RNAs that bind chemicals and regulate gene expression, directly coupling sensing to cellular actuation. However, it remains unclear how their sequence controls the physics of riboswitch switching and activation, particularly when changing the ligand-binding aptamer domain. We report the development of a statistical thermodynamic model that predicts the sequence-structure-function relationship for translation-regulating riboswitches that activate gene expression, characterized inside cells and within cell-free transcription-translation assays. Using the model, we carried out automated computational design of 62 synthetic riboswitches that used six different RNA aptamers to sense diverse chemicals (theophylline, tetramethylrosamine, fluoride, dopamine, thyroxine, 2,4-dinitrotoluene) and activated gene expression by up to 383-fold. The model explains how aptamer structure, ligand affinity, switching free energy and macromolecular crowding collectively control riboswitch activation. Our model-based approach for engineering riboswitches quantitatively confirms several physical mechanisms governing ligand-induced RNA shape-change and enables the development of cell-free and bacterial sensors for diverse applications.
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Affiliation(s)
- Amin Espah Borujeni
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Dennis M Mishler
- Department of Biological Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jingzhi Wang
- Department of Biological Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Walker Huso
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Howard M Salis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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32
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Gupta A, Bansal M. The role of sequence in altering the unfolding pathway of an RNA pseudoknot: a steered molecular dynamics study. Phys Chem Chem Phys 2016; 18:28767-28780. [DOI: 10.1039/c6cp04617g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This work highlights a sequence dependent unfolding pathway of an RNA pseudoknot under force-induced pulling conditions.
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Affiliation(s)
- Asmita Gupta
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore-560012
- India
| | - Manju Bansal
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore-560012
- India
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33
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Aytenfisu AH, Liberman JA, Wedekind JE, Mathews DH. Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics. RNA (NEW YORK, N.Y.) 2015; 21:1898-907. [PMID: 26370581 PMCID: PMC4604430 DOI: 10.1261/rna.051367.115] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/02/2015] [Indexed: 05/06/2023]
Abstract
Riboswitches are RNA molecules that regulate gene expression using conformational change, affected by binding of small molecule ligands. A crystal structure of a ligand-bound class II preQ1 riboswitch has been determined in a previous structural study. To gain insight into the dynamics of this riboswitch in solution, eight total molecular dynamic simulations, four with and four without ligand, were performed using the Amber force field. In the presence of ligand, all four of the simulations demonstrated rearranged base pairs at the 3' end, consistent with expected base-pairing from comparative sequence analysis in a prior bioinformatic analysis; this suggests the pairing in this region was altered by crystallization. Additionally, in the absence of ligand, three of the simulations demonstrated similar changes in base-pairing at the ligand binding site. Significantly, although most of the riboswitch architecture remained intact in the respective trajectories, the P3 stem was destabilized in the ligand-free simulations in a way that exposed the Shine-Dalgarno sequence. This work illustrates how destabilization of two major groove base triples can influence a nearby H-type pseudoknot and provides a mechanism for control of gene expression by a fold that is frequently found in bacterial riboswitches.
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Affiliation(s)
- Asaminew H Aytenfisu
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Joseph A Liberman
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Joseph E Wedekind
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
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34
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McCown PJ, Liang JJ, Weinberg Z, Breaker RR. Structural, functional, and taxonomic diversity of three preQ1 riboswitch classes. ACTA ACUST UNITED AC 2015; 21:880-889. [PMID: 25036777 DOI: 10.1016/j.chembiol.2014.05.015] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 04/17/2014] [Accepted: 05/07/2014] [Indexed: 12/31/2022]
Abstract
Previously, two riboswitch classes have been identified that sense and respond to the hypermodified nucleobase called prequeuosine1 (preQ1). The enormous expansion of available genomic DNA sequence data creates new opportunities to identify additional representatives of the known riboswitch classes and to discover novel classes. We conducted bioinformatics searches on microbial genomic DNA data sets to discover numerous additional examples belonging to the two previously known riboswitch classes for preQ1 (classes preQ1-I and preQ1-II), including some structural variants that further restrict ligand specificity. Additionally, we discovered a third preQ1-binding riboswitch class (preQ1-III) that is structurally distinct from previously known classes. These findings demonstrate that numerous organisms monitor the concentrations of this modified nucleobase by exploiting one or more riboswitch classes for this widespread compound.
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Affiliation(s)
- Phillip J McCown
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Jonathan J Liang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Zasha Weinberg
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
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35
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Neuner S, Santner T, Kreutz C, Micura R. The "Speedy" Synthesis of Atom-Specific (15)N Imino/Amido-Labeled RNA. Chemistry 2015; 21:11634-11643. [PMID: 26237536 PMCID: PMC4946632 DOI: 10.1002/chem.201501275] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Although numerous reports on the synthesis of atom-specific (15)N-labeled nucleosides exist, fast and facile access to the corresponding phosphoramidites for RNA solid-phase synthesis is still lacking. This situation represents a severe bottleneck for NMR spectroscopic investigations on functional RNAs. Here, we present optimized procedures to speed up the synthesis of (15)N(1) adenosine and (15)N(1) guanosine amidites, which are the much needed counterparts of the more straightforward-to-achieve (15)N(3) uridine and (15)N(3) cytidine amidites in order to tap full potential of (1)H/(15)N/(15)N-COSY experiments for directly monitoring individual Watson-Crick base pairs in RNA. Demonstrated for two preQ1 riboswitch systems, we exemplify a versatile concept for individual base-pair labeling in the analysis of conformationally flexible RNAs when competing structures and conformational dynamics are encountered.
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Affiliation(s)
- Sandro Neuner
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Tobias Santner
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck (Austria)
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36
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Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics. Proc Natl Acad Sci U S A 2015; 112:E3485-94. [PMID: 26106162 DOI: 10.1073/pnas.1503955112] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PreQ1-III riboswitches are newly identified RNA elements that control bacterial genes in response to preQ1 (7-aminomethyl-7-deazaguanine), a precursor to the essential hypermodified tRNA base queuosine. Although numerous riboswitches fold as H-type or HLout-type pseudoknots that integrate ligand-binding and regulatory sequences within a single folded domain, the preQ1-III riboswitch aptamer forms a HLout-type pseudoknot that does not appear to incorporate its ribosome-binding site (RBS). To understand how this unusual organization confers function, we determined the crystal structure of the class III preQ1 riboswitch from Faecalibacterium prausnitzii at 2.75 Å resolution. PreQ1 binds tightly (KD,app 6.5 ± 0.5 nM) between helices P1 and P2 of a three-way helical junction wherein the third helix, P4, projects orthogonally from the ligand-binding pocket, exposing its stem-loop to base pair with the 3' RBS. Biochemical analysis, computational modeling, and single-molecule FRET imaging demonstrated that preQ1 enhances P4 reorientation toward P1-P2, promoting a partially nested, H-type pseudoknot in which the RBS undergoes rapid docking (kdock ∼ 0.6 s(-1)) and undocking (kundock ∼ 1.1 s(-1)). Discovery of such dynamic conformational switching provides insight into how a riboswitch with bipartite architecture uses dynamics to modulate expression platform accessibility, thus expanding the known repertoire of gene control strategies used by regulatory RNAs.
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37
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Reiling C, Khutsishvili I, Huang K, Marky LA. Loop Contributions to the Folding Thermodynamics of DNA Straight Hairpin Loops and Pseudoknots. J Phys Chem B 2015; 119:1939-46. [DOI: 10.1021/jp5116417] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Calliste Reiling
- Department of Pharmaceutical
Sciences, University of Nebraska Medical Center, 986025 Nebraska
Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Irine Khutsishvili
- Department of Pharmaceutical
Sciences, University of Nebraska Medical Center, 986025 Nebraska
Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Kai Huang
- Department of Pharmaceutical
Sciences, University of Nebraska Medical Center, 986025 Nebraska
Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Luis A. Marky
- Department of Pharmaceutical
Sciences, University of Nebraska Medical Center, 986025 Nebraska
Medical Center, Omaha, Nebraska 68198-6025, United States
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38
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Moschen T, Wunderlich CH, Spitzer R, Levic J, Micura R, Tollinger M, Kreutz C. Ligand-detected relaxation dispersion NMR spectroscopy: dynamics of preQ1-RNA binding. Angew Chem Int Ed Engl 2015; 54:560-3. [PMID: 25403518 PMCID: PMC4353840 DOI: 10.1002/anie.201409779] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 12/21/2022]
Abstract
An NMR-based approach to characterizing the binding kinetics of ligand molecules to biomolecules, like RNA or proteins, by ligand-detected Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments is described. A (15)N-modified preQ1 ligand is used to acquire relaxation dispersion experiments in the presence of low amounts of the Fsu class I preQ1 aptamer RNA, and increasing ligand concentrations to probe the RNA small molecule interaction. Our experimental data strongly support the conformational selection mechanism postulated. The approach gives direct access to two parameters of a ligand-receptor interaction: the off rate and the population of the small molecule-receptor complex. A detailed description of the kinetics underlying the ligand binding process is of crucial importance to fully understanding a riboswitch's function and to evaluate potential new antibiotics candidates targeting the noncoding RNA species. Ligand-detected NMR relaxation dispersion experiments represent a valuable diagnostic tool for the characterization of binding mechanisms.
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Affiliation(s)
- Thomas Moschen
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Christoph Hermann Wunderlich
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Romana Spitzer
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Jasmin Levic
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Ronald Micura
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Martin Tollinger
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
| | - Christoph Kreutz
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck (Austria)
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39
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Boudreault J, Perez-Gonzalez DC, Penedo JC, Lafontaine DA. Single-Molecule Approaches for the Characterization of Riboswitch Folding Mechanisms. Methods Mol Biol 2015; 1334:101-107. [PMID: 26404145 DOI: 10.1007/978-1-4939-2877-4_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Riboswitches are highly structured RNA molecules that control genetic expression by altering their structure as a function of metabolite binding. Accumulating evidence suggests that riboswitch structures are highly dynamic and perform conformational exchange between structural states that are important for the outcome of genetic regulation. To understand how ligand binding influences the folding of riboswitches, it is important to monitor in real time the riboswitch folding pathway as a function of experimental conditions. Single-molecule FRET (sm-FRET) is unique among biophysical techniques to study riboswitch conformational changes as it allows to both monitor steady-state populations of riboswitch conformers and associated interconversion dynamics. Since FRET fluorophores can be attached to virtually any nucleotide position, FRET assays can be adapted to monitor specific conformational changes, thus enabling to deduce complex riboswitch folding pathways. Herein, we show how to employ sm-FRET to study the folding pathway of the S-adenosylmethionine (SAM) and how this can be used to understand very specific conformational changes that are at the heart of riboswitch regulation mechanism.
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Affiliation(s)
- Julien Boudreault
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1
| | | | - J Carlos Penedo
- School of Physics and Astronomy, University of St. Andrews, St. Andrews, UK
| | - Daniel A Lafontaine
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada, J1K 2R1.
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40
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Narayan S, Kombrabail MH, Das S, Singh H, Chary KVR, Rao BJ, Krishnamoorthy G. Site-specific fluorescence dynamics in an RNA 'thermometer' reveals the role of ribosome binding in its temperature-sensitive switch function. Nucleic Acids Res 2014; 43:493-503. [PMID: 25477380 PMCID: PMC4288164 DOI: 10.1093/nar/gku1264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
RNA thermometers control the translation of several heat shock and virulence genes by their temperature-sensitive structural transitions. Changes in the structure and dynamics of MiniROSE RNA, which regulates translation in the temperature range of 20–45°C, were studied by site specifically replacing seven adenine residues with the fluorescent analog, 2-aminopurine (2-AP), one at a time. Dynamic fluorescence observables of 2-AP-labeled RNAs were compared in their free versus ribosome-bound states for the first time. Noticeably, position dependence of fluorescence observables, which was prominent at 20°C, was persistent even at 45ºC, suggesting the persistence of structural integrity up to 45ºC. Interestingly, position-dependent dispersion of fluorescence lifetime and quenching constant at 45°C was ablated in ribosome-bound state, when compared to those at 20°C, underscoring loss of structural integrity at 45°C, in ribosome-bound RNA. Significant increase in the value of mean lifetime for 2-AP corresponding to Shine–Dalgarno sequences, when the temperature was raised from 20 to 45°C, to values seen in the presence of urea at 45°C was a strong indicator of melting of the 3D structure of MiniROSE RNA at 45°C, only when it was ribosome bound. Taken all together, we propose a model where we invoke that ribosome binding of the RNA thermometer critically regulates temperature sensing functions in MiniROSE RNA.
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Affiliation(s)
- Satya Narayan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Mamta H Kombrabail
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Sudipta Das
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500075, India
| | - Himanshu Singh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Kandala V R Chary
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Basuthkar J Rao
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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41
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Holmstrom ED, Polaski JT, Batey RT, Nesbitt DJ. Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch. J Am Chem Soc 2014; 136:16832-43. [PMID: 25325398 PMCID: PMC4277777 DOI: 10.1021/ja5076184] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Riboswitches
represent a family of highly structured regulatory
elements found primarily in the leader sequences of bacterial mRNAs.
They function as molecular switches capable of altering gene expression;
commonly, this occurs via a conformational change in a regulatory
element of a riboswitch that results from ligand binding in the aptamer
domain. Numerous studies have investigated the ligand binding process,
but little is known about the structural changes in the regulatory
element. A mechanistic description of both processes is essential
for deeply understanding how riboswitches modulate gene expression.
This task is greatly facilitated by studying all aspects of riboswitch
structure/dynamics/function in the same model system. To this end,
single-molecule fluorescence resonance energy transfer (smFRET) techniques
have been used to directly observe the conformational dynamics of
a hydroxocobalamin (HyCbl) binding riboswitch (env8HyCbl) with a known crystallographic structure.1 The single-molecule RNA construct studied in this work
is unique in that it contains all of the structural elements both
necessary and sufficient for regulation of gene expression in a biological
context. The results of this investigation reveal that the undocking
rate constant associated with the disruption of a long-range kissing-loop
(KL) interaction is substantially decreased when the ligand is bound
to the RNA, resulting in a preferential stabilization of the docked
conformation. Notably, the formation of this tertiary KL interaction
directly sequesters the Shine-Dalgarno sequence (i.e., the ribosome
binding site) via base-pairing, thus preventing translation initiation.
These results reveal that the conformational dynamics of this regulatory
switch are quantitatively described by a four-state kinetic model,
whereby ligand binding promotes formation of the KL interaction. The
results of complementary cell-based gene expression experiments conducted
in Escherichia coli are highly correlated
with the smFRET results, suggesting that KL formation is directly
responsible for regulating gene expression.
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Affiliation(s)
- Erik D Holmstrom
- JILA, University of Colorado and National Institute of Standards and Technology, and ‡Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0440, United States
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Moschen T, Wunderlich CH, Spitzer R, Levic J, Micura R, Tollinger M, Kreutz C. Ligand-Detected Relaxation Dispersion NMR Spectroscopy: Dynamics of preQ1-RNA Binding. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409779] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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43
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Ruff KM, Strobel SA. Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy. RNA (NEW YORK, N.Y.) 2014; 20:1775-88. [PMID: 25246650 PMCID: PMC4201829 DOI: 10.1261/rna.047266.114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 08/22/2014] [Indexed: 05/21/2023]
Abstract
The glycine riboswitch predominantly exists as a tandem structure, with two adjacent, homologous ligand-binding domains (aptamers), followed by a single expression platform. The recent identification of a leader helix, the inclusion of which eliminates cooperativity between the aptamers, has reopened the debate over the purpose of the tandem structure of the glycine riboswitch. An equilibrium dialysis-based assay was combined with binding-site mutations to monitor glycine binding in each ligand-binding site independently to understand the role of each aptamer in glycine binding and riboswitch tertiary interactions. A series of mutations disrupting the dimer interface was used to probe how dimerization impacts ligand binding by the tandem glycine riboswitch. While the wild-type tandem riboswitch binds two glycine equivalents, one for each aptamer, both individual aptamers are capable of binding glycine when the other aptamer is unoccupied. Intriguingly, glycine binding by aptamer-1 is more sensitive to dimerization than glycine binding by aptamer-2 in the context of the tandem riboswitch. However, monomeric aptamer-2 shows dramatically weakened glycine-binding affinity. In addition, dimerization of the two aptamers in trans is dependent on glycine binding in at least one aptamer. We propose a revised model for tandem riboswitch function that is consistent with these results, wherein ligand binding in aptamer-1 is linked to aptamer dimerization and stabilizes the P1 stem of aptamer-2, which controls the expression platform.
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Affiliation(s)
- Karen M Ruff
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
| | - Scott A Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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44
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Levic J, Micura R. Syntheses of (15)N-labeled pre-queuosine nucleobase derivatives. Beilstein J Org Chem 2014; 10:1914-8. [PMID: 25246950 PMCID: PMC4168690 DOI: 10.3762/bjoc.10.199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 07/14/2014] [Indexed: 01/21/2023] Open
Abstract
Pre-queuosine or queuine (preQ1) is a guanine derivative that is involved in the biosynthetic pathway of the hypermodified tRNA nucleoside queuosine (Que). The core structure of preQ1 is represented by 7-(aminomethyl)-7-deazaguanine (preQ1 base). Here, we report the synthesis of three preQ1 base derivatives with complementary (15)N-labeling patterns, utilizing [(15)N]-KCN, [(15)N]-phthalimide, and [(15)N3]-guanidine as cost-affordable (15)N sources. Such derivatives are required to explore the binding process of the preQ1 base to RNA targets using advanced NMR spectroscopic methods. PreQ1 base specifically binds to bacterial mRNA domains and thereby regulates genes that are required for queuosine biosynthesis.
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Affiliation(s)
- Jasmin Levic
- Institute of Organic Chemistry, University of Innsbruck and Center for Molecular Biosciences Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, University of Innsbruck and Center for Molecular Biosciences Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
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45
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Peselis A, Serganov A. Structure and function of pseudoknots involved in gene expression control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:803-22. [PMID: 25044223 DOI: 10.1002/wrna.1247] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/09/2014] [Accepted: 05/21/2014] [Indexed: 11/08/2022]
Abstract
Natural RNA molecules can have a high degree of structural complexity but even the most complexly folded RNAs are assembled from simple structural building blocks. Among the simplest RNA elements are double-stranded helices that participate in the formation of different folding topologies and constitute the major fraction of RNA structures. One common folding motif of RNA is a pseudoknot, defined as a bipartite helical structure formed by base-pairing of the apical loop in the stem-loop structure with an outside sequence. Pseudoknots constitute integral parts of the RNA structures essential for various cellular activities. Among many functions of pseudoknotted RNAs is feedback regulation of gene expression, carried out through specific recognition of various molecules. Pseudoknotted RNAs autoregulate ribosomal and phage protein genes in response to downstream encoded proteins, while many metabolic and transport genes are controlled by cellular metabolites interacting with pseudoknotted RNA elements from the riboswitch family. Modulation of some genes also depends on metabolite-induced messenger RNA (mRNA) cleavage performed by pseudoknotted ribozymes. Several regulatory pseudoknots have been characterized biochemically and structurally in great detail. These studies have demonstrated a plethora of pseudoknot-based folds and have begun uncovering diverse molecular principles of the ligand-dependent gene expression control. The pseudoknot-mediated mechanisms of gene control and many unexpected and interesting features of the regulatory pseudoknots have significantly advanced our understanding of the genetic circuits and laid the foundation for modulation of their outcomes.
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Affiliation(s)
- Alla Peselis
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
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Büttner L, Javadi-Zarnaghi F, Höbartner C. Site-specific labeling of RNA at internal ribose hydroxyl groups: terbium-assisted deoxyribozymes at work. J Am Chem Soc 2014; 136:8131-7. [PMID: 24825547 DOI: 10.1021/ja503864v] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A general and efficient single-step method was established for site-specific post-transcriptional labeling of RNA. Using Tb(3+) as accelerating cofactor for deoxyribozymes, various labeled guanosines were site-specifically attached to 2'-OH groups of internal adenosines in in vitro transcribed RNA. The DNA-catalyzed 2',5'-phosphodiester bond formation proceeded efficiently with fluorescent, spin-labeled, biotinylated, or cross-linker-modified guanosine triphosphates. The sequence context of the labeling site was systematically analyzed by mutating the nucleotides flanking the targeted adenosine. Labeling of adenosines in a purine-rich environment showed the fastest reactions and highest yields. Overall, practically useful yields >70% were obtained for 13 out of 16 possible nucleotide (nt) combinations. Using this approach, we demonstrate preparative labeling under mild conditions for up to ~160-nt-long RNAs, including spliceosomal U6 small nuclear RNA and a cyclic-di-AMP binding riboswitch RNA.
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Affiliation(s)
- Lea Büttner
- Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
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Price IR, Grigg JC, Ke A. Common themes and differences in SAM recognition among SAM riboswitches. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:931-938. [PMID: 24863160 DOI: 10.1016/j.bbagrm.2014.05.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/13/2014] [Accepted: 05/15/2014] [Indexed: 12/19/2022]
Abstract
The recent discovery of short cis-acting RNA elements termed riboswitches has caused a paradigm shift in our understanding of genetic regulatory mechanisms. The three distinct superfamilies of S-adenosyl-l-methionine (SAM) riboswitches are the most commonly found riboswitch classes in nature. These RNAs represent three independent evolutionary solutions to achieve specific SAM recognition. This review summarizes research on 1) modes of gene regulatory mechanisms, 2) common themes and differences in ligand recognition, and 3) ligand-induced conformational dynamics among SAM riboswitch families. The body of work on the SAM riboswitch families constitutes a useful primer to the topic of gene regulatory RNAs as a whole. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Ian R Price
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jason C Grigg
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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48
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Eichhorn CD, Kang M, Feigon J. Structure and function of preQ 1 riboswitches. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:939-950. [PMID: 24798077 DOI: 10.1016/j.bbagrm.2014.04.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/22/2014] [Accepted: 04/25/2014] [Indexed: 12/17/2022]
Abstract
PreQ1 riboswitches help regulate the biosynthesis and transport of preQ1 (7-aminomethyl-7-deazaguanine), a precursor of the hypermodified guanine nucleotide queuosine (Q), in a number of Firmicutes, Proteobacteria, and Fusobacteria. Queuosine is almost universally found at the wobble position of the anticodon in asparaginyl, tyrosyl, histidyl and aspartyl tRNAs, where it contributes to translational fidelity. Two classes of preQ1 riboswitches have been identified (preQ1-I and preQ1-II), and structures of examples from both classes have been determined. Both classes form H-type pseudoknots upon preQ1 binding, each of which has distinct unusual features and modes of preQ1 recognition. These features include an unusually long loop 2 in preQ1-I pseudoknots and an embedded hairpin in loop 3 in preQ1-II pseudoknots. PreQ1-I riboswitches are also notable for their unusually small aptamer domain, which has been extensively investigated by NMR, X-ray crystallography, FRET, and other biophysical methods. Here we review the discovery, structural biology, ligand specificity, cation interactions, folding, dynamics, and applications to biotechnology of preQ1 riboswitches. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Mijeong Kang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
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49
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Wachter A. Gene regulation by structured mRNA elements. Trends Genet 2014; 30:172-81. [PMID: 24780087 DOI: 10.1016/j.tig.2014.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/20/2014] [Indexed: 01/19/2023]
Abstract
The precise temporal and spatial coordination of gene activity, based on the integration of internal and external signals, is crucial for the accurate functioning of all biological processes. Although the basic principles of gene expression were established some 60 years ago, recent research has revealed a surprising complexity in the control of gene activity. Many of these gene regulatory mechanisms occur at the level of the mRNA, including sophisticated gene control tasks mediated by structured mRNA elements. We now know that mRNA folds can serve as highly specific receptors for various types of molecules, as exemplified by metabolite-binding riboswitches, and interfere with pro- and eukaryotic gene expression at the level of transcription, translation, and RNA processing. Gene regulation by structured mRNA elements comprises versatile strategies including self-cleaving ribozymes, RNA-folding-mediated occlusion or presentation of cis-regulatory sequences, and sequestration of trans-acting factors including other RNAs and proteins.
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Affiliation(s)
- Andreas Wachter
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
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Savinov A, Perez CF, Block SM. Single-molecule studies of riboswitch folding. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1030-1045. [PMID: 24727093 DOI: 10.1016/j.bbagrm.2014.04.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/27/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
The folding dynamics of riboswitches are central to their ability to modulate gene expression in response to environmental cues. In most cases, a structural competition between the formation of a ligand-binding aptamer and an expression platform (or some other competing off-state) determines the regulatory outcome. Here, we review single-molecule studies of riboswitch folding and function, predominantly carried out using single-molecule FRET or optical trapping approaches. Recent results have supplied new insights into riboswitch folding energy landscapes, the mechanisms of ligand binding, the roles played by divalent ions, the applicability of hierarchical folding models, and kinetic vs. thermodynamic control schemes. We anticipate that future work, based on improved data sets and potentially combining multiple experimental techniques, will enable the development of more complete models for complex RNA folding processes. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Andrew Savinov
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | | | - Steven M Block
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.
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