1
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Lou Y, Woodson SA. Co-transcriptional folding of the glmS ribozyme enables a rapid response to metabolite. Nucleic Acids Res 2024; 52:872-884. [PMID: 38000388 PMCID: PMC10810187 DOI: 10.1093/nar/gkad1120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/24/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The glmS ribozyme riboswitch, located in the 5' untranslated region of the Bacillus subtilis glmS messenger RNA (mRNA), regulates cell wall biosynthesis through ligand-induced self-cleavage and decay of the glmS mRNA. Although self-cleavage of the refolded glmS ribozyme has been studied extensively, it is not known how early the ribozyme folds and self-cleaves during transcription. Here, we combine single-molecule fluorescence with kinetic modeling to show that self-cleavage can occur during transcription before the ribozyme is fully synthesized. Moreover, co-transcriptional folding of the RNA at a physiological elongation rate allows the ribozyme catalytic core to react without the downstream peripheral stability domain. Dimethyl sulfate footprinting further revealed how slow sequential folding favors formation of the native core structure through fraying of misfolded helices and nucleation of a native pseudoknot. Ribozyme self-cleavage at an early stage of transcription may benefit glmS regulation in B. subtilis, as it exposes the mRNA to exoribonuclease before translation of the open reading frame can begin. Our results emphasize the importance of co-transcriptional folding of RNA tertiary structure for cis-regulation of mRNA stability.
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Affiliation(s)
- Yuan Lou
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
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2
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Lee HK, Lee YT, Fan L, Wilt HM, Conrad CE, Yu P, Zhang J, Shi G, Ji X, Wang YX, Stagno JR. Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state. Structure 2023; 31:848-859.e3. [PMID: 37253356 PMCID: PMC10335363 DOI: 10.1016/j.str.2023.05.003] [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: 12/22/2022] [Revised: 03/16/2023] [Accepted: 05/03/2023] [Indexed: 06/01/2023]
Abstract
The thiamine pyrophosphate (TPP)-sensing riboswitch is one of the earliest discovered and most widespread riboswitches. Numerous structural studies have been reported for this riboswitch bound with various ligands. However, the ligand-free (apo) structure remains unknown. Here, we report a 3.1 Å resolution crystal structure of Escherichia coli TPP riboswitch in the apo state, which exhibits an extended, Y-shaped conformation further supported by small-angle X-ray scattering data and driven molecular dynamics simulations. The loss of ligand interactions results in helical uncoiling of P5 and disruption of the key tertiary interaction between the sensory domains. Opening of the aptamer propagates to the gene-regulatory P1 helix and generates the key conformational flexibility needed for the switching behavior. Much of the ligand-binding site at the three-way junction is unaltered, thereby maintaining a partially preformed pocket. Together, these results paint a dynamic picture of the ligand-induced conformational changes in TPP riboswitches that confer conditional gene regulation.
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Affiliation(s)
- Hyun Kyung Lee
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yun-Tzai Lee
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-Ray Scattering Core Facility of National Cancer Institute, Frederick, MD 21702, USA
| | - Haley M Wilt
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Chelsie E Conrad
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ping Yu
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Genbin Shi
- Biomolecular Structure Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Xinhua Ji
- Biomolecular Structure Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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3
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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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4
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Binding of 30S Ribosome Induces Single-stranded Conformation Within and Downstream of the Expression Platform in a Translational Riboswitch. J Mol Biol 2022; 434:167668. [PMID: 35667471 DOI: 10.1016/j.jmb.2022.167668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/29/2022] [Accepted: 05/31/2022] [Indexed: 11/23/2022]
Abstract
Translational riboswitches are bacterial gene regulatory elements found in the 5'-untranslated region of mRNAs. They operate through a conformational refolding reaction that is triggered by a concentration change of a modulating small molecular ligand. The translation initiation region (TIR) is either released from or incorporated into base pairing interactions through the conformational switch. Hence, initiation of translation is regulated by the accessibility of the Shine-Dalgarno sequence and start codon. Interaction with the 30S ribosome is indispensable for the structural switch between functional OFF and ON states. However, on a molecular level it is still not fully resolved how the ribosome is accommodated near or at the translation initiation region in the context of translational riboswitches. The standby model of translation initiation postulates a binding site where the mRNA enters the ribosome and where it resides until the initiation site becomes unstructured and accessible. We here investigated the adenine-sensing riboswitch from Vibrio vulnificus. By application of a 19F labelling strategy for NMR spectroscopy that utilizes ligation techniques to synthesize differentially 19F labelled riboswitch molecules we show that nucleotides directly downstream of the riboswitch domain are first involved in productive interaction with the 30S ribosomal subunit. Upon the concerted action of ligand and the ribosomal protein rS1 the TIR becomes available and subsequently the 30S ribosome can slide towards the TIR. It will be interesting to see whether this is a general feature in translational riboswitches or if riboswitches exist where this region is structured and represent yet another layer of regulation.
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5
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Riboswitch RS thiT as a molecular tool in Lactococcus lactis. Appl Environ Microbiol 2021; 88:e0176421. [PMID: 34936833 PMCID: PMC8862789 DOI: 10.1128/aem.01764-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Previous RNA sequencing has allowed the identification of 129 long 5′ untranslated regions (UTRs) in the Lactococcus lactis MG1363 transcriptome. These sequences potentially harbor cis-acting riboswitches. One of the identified extended 5′ UTRs is a putative thiamine pyrophosphate (TPP) riboswitch. It is located immediately upstream of the thiamine transporter gene thiT (llmg_0334). To confirm this assumption, the 5′-UTR sequence was placed upstream of the gene encoding the superfolder green fluorescent protein (sfGFP), sfgfp, allowing the examination of the expression of sfGFP in the presence or absence of thiamine in the medium. The results show that this sequence indeed represents a thiamine-responsive TPP riboswitch. This RNA-based genetic control device was used to successfully restore the mutant phenotype of an L. lactis strain lacking the major autolysin gene, acmA. The L. lactisthiT TPP riboswitch (RSthiT) is a useful molecular genetic tool enabling the gradual downregulation of the expression of genes under its control by adjusting the thiamine concentration. IMPORTANCE The capacity of microbes with biotechnological importance to adapt to and survive under quickly changing industrial conditions depends on their ability to adequately control gene expression. Riboswitches are important RNA-based elements involved in rapid and precise gene regulation. Here, we present the identification of a natural thiamine-responsive riboswitch of Lactococcus lactis, a bacterium used worldwide in the production of dairy products. We used it to restore a genetic defect in an L. lactis mutant and show that it is a valuable addition to the ever-expanding L. lactis genetic toolbox.
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6
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Xu X, Egger M, Chen H, Bartosik K, Micura R, Ren A. Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition. Nucleic Acids Res 2021; 49:7139-7153. [PMID: 34125892 PMCID: PMC8266621 DOI: 10.1093/nar/gkab486] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/29/2021] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson–Crick base pair to junction J2. Xanthine inserts between a G–U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.
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Affiliation(s)
- Xiaochen Xu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Michaela Egger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Karolina Bartosik
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck 6020, Austria
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
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7
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Ganser LR, Chu CC, Bogerd HP, Kelly ML, Cullen BR, Al-Hashimi HM. Probing RNA Conformational Equilibria within the Functional Cellular Context. Cell Rep 2021; 30:2472-2480.e4. [PMID: 32101729 DOI: 10.1016/j.celrep.2020.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/24/2019] [Accepted: 01/31/2020] [Indexed: 12/17/2022] Open
Abstract
Low-abundance short-lived non-native conformations referred to as excited states (ESs) are increasingly observed in vitro and implicated in the folding and biological activities of regulatory RNAs. We developed an approach for assessing the relative abundance of RNA ESs within the functional cellular context. Nuclear magnetic resonance (NMR) spectroscopy was used to estimate the degree to which substitution mutations bias conformational equilibria toward the inactive ES in vitro. The cellular activity of the ES-stabilizing mutants was used as an indirect measure of the conformational equilibria within the functional cellular context. Compensatory mutations that restore the ground-state conformation were used to control for changes in sequence. Using this approach, we show that the ESs of two regulatory RNAs from HIV-1, the transactivation response element (TAR) and the Rev response element (RRE), likely form in cells with abundances comparable to those measured in vitro, and their targeted stabilization may provide an avenue for developing anti-HIV therapeutics.
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Affiliation(s)
- Laura R Ganser
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Chia-Chieh Chu
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Hal P Bogerd
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, NC 27710, USA
| | - Megan L Kelly
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Bryan R Cullen
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
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8
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Abdelsattar AS, Mansour Y, Aboul-Ela F. The Perturbed Free-Energy Landscape: Linking Ligand Binding to Biomolecular Folding. Chembiochem 2021; 22:1499-1516. [PMID: 33351206 DOI: 10.1002/cbic.202000695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/19/2020] [Indexed: 12/24/2022]
Abstract
The effects of ligand binding on biomolecular conformation are crucial in drug design, enzyme mechanisms, the regulation of gene expression, and other biological processes. Descriptive models such as "lock and key", "induced fit", and "conformation selection" are common ways to interpret such interactions. Another historical model, linked equilibria, proposes that the free-energy landscape (FEL) is perturbed by the addition of ligand binding energy for the bound population of biomolecules. This principle leads to a unified, quantitative theory of ligand-induced conformation change, building upon the FEL concept. We call the map of binding free energy over biomolecular conformational space the "binding affinity landscape" (BAL). The perturbed FEL predicts/explains ligand-induced conformational changes conforming to all common descriptive models. We review recent experimental and computational studies that exemplify the perturbed FEL, with emphasis on RNA. This way of understanding ligand-induced conformation dynamics motivates new experimental and theoretical approaches to ligand design, structural biology and systems biology.
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Affiliation(s)
- Abdallah S Abdelsattar
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Youssef Mansour
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Fareed Aboul-Ela
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
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9
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Chen H, Egger M, Xu X, Flemmich L, Krasheninina O, Sun A, Micura R, Ren A. Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding. Nucleic Acids Res 2020; 48:12394-12406. [PMID: 33170270 PMCID: PMC7708056 DOI: 10.1093/nar/gkaa1029] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 11/13/2022] Open
Abstract
Riboswitches are important gene regulatory elements frequently encountered in bacterial mRNAs. The recently discovered nadA riboswitch contains two similar, tandemly arrayed aptamer domains, with the first domain possessing high affinity for nicotinamide adenine dinucleotide (NAD+). The second domain which comprises the ribosomal binding site in a putative regulatory helix, however, has withdrawn from detection of ligand-induced structural modulation thus far, and therefore, the identity of the cognate ligand and the regulation mechanism have remained unclear. Here, we report crystal structures of both riboswitch domains, each bound to NAD+. Furthermore, we demonstrate that ligand binding to domain 2 requires significantly higher concentrations of NAD+ (or ADP retaining analogs) compared to domain 1. Using a fluorescence spectroscopic approach, we further shed light on the structural features which are responsible for the different ligand affinities, and describe the Mg2+-dependent, distinct folding and pre-organization of their binding pockets. Finally, we speculate about possible scenarios for nadA RNA gene regulation as a putative two-concentration sensor module for a time-controlled signal that is primed and stalled by the gene regulation machinery at low ligand concentrations (domain 1), and finally triggers repression of translation as soon as high ligand concentrations are reached in the cell (domain 2).
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Affiliation(s)
- Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Michaela Egger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, 6020, Austria
| | - Xiaochen Xu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Laurin Flemmich
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, 6020, Austria
| | - Olga Krasheninina
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, 6020, Austria
| | - Aiai Sun
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, 6020, Austria
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
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10
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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11
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Nam H, Becette O, LeBlanc RM, Oh D, Case DA, Dayie TK. Deleterious effects of carbon-carbon dipolar coupling on RNA NMR dynamics. JOURNAL OF BIOMOLECULAR NMR 2020; 74:321-331. [PMID: 32363430 DOI: 10.1007/s10858-020-00315-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/18/2020] [Indexed: 06/11/2023]
Abstract
Many regulatory RNAs undergo dynamic exchanges that are crucial for their biological functions and NMR spectroscopy is a versatile tool for monitoring dynamic motions of biomolecules. Meaningful information on biomolecular dynamics requires an accurate measurement of relaxation parameters such as longitudinal (R1) rates, transverse (R2) rates and heteronuclear Overhauser effect (hNOE). However, earlier studies have shown that the large 13C-13C interactions complicate analysis of the carbon relaxation parameters. To investigate the effect of 13C-13C interactions on RNA dynamic studies, we performed relaxation measurements on various RNA samples with different labeling patterns and compared these measurements with the computational simulations. For uniformly labeled samples, contributions of the neighboring carbon to R1 measurements were observed. These contributions increased with increasing magnetic field and overall correlation time ([Formula: see text]) for R1 rates, necessitating more careful analysis for uniformly labeled large RNAs. In addition, the hNOE measurements were also affected by the adjacent carbon nuclei. Unlike R1 rates, R1ρ rates showed relatively good agreement between uniformly- and site-selectively labeled samples, suggesting no dramatic effect from their attached carbon, in agreement with previous observations. Overall, having more accurate rate measurements avoids complex analysis and will be a key for interpreting 13C relaxation rates for molecular motion that can provide valuable insights into cellular molecular recognition events.
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Affiliation(s)
- Hyeyeon Nam
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Owen Becette
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Regan M LeBlanc
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Daniel Oh
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Theodore K Dayie
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.
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12
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Fürtig B, Oberhauser EM, Zetzsche H, Klötzner DP, Heckel A, Schwalbe H. Refolding through a Linear Transition State Enables Fast Temperature Adaptation of a Translational Riboswitch. Biochemistry 2020; 59:1081-1086. [PMID: 32134253 DOI: 10.1021/acs.biochem.9b01044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The adenine-sensing riboswitch from the Gram-negative bacterium Vibrio vulnificus is an RNA-based gene regulatory element that acts in response to both its cognate low-molecular weight ligand and temperature. The combined sensitivity to environmental temperature and ligand concentration is maintained by an equilibrium of three distinct conformations involving two ligand-free states and one ligand-bound state. The key structural element that undergoes refolding in the ligand-free states comprises a 35-nucleotide temperature response module. Here, we present the structural characterization of this temperature response module. We employ high-resolution NMR spectroscopy and photocaged RNAs as molecular probes to decipher the kinetic and thermodynamic framework of the secondary structure transition in the apo state of the riboswitch. We propose a model for the transition state adopted during the thermal refolding of the temperature response module that connects two mutually exclusive long-lived and stable conformational states. This transition state is characterized by a comparatively low free activation enthalpy. A pseudoknot conformation in the transition state, as commonly seen in RNA refolding, is therefore unlikely. More likely, the transition state of the adenine-sensing riboswitch temperature response module features a linear conformation.
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Affiliation(s)
- Boris Fürtig
- Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max von Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Eva Marie Oberhauser
- Institute of Organic Chemistry and Chemical Biology, Max von Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Heidi Zetzsche
- Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max von Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Dean-Paulos Klötzner
- Institute of Organic Chemistry and Chemical Biology, Max von Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Max von Laue Strasse 7, 60438 Frankfurt/Main, Germany
| | - Harald Schwalbe
- Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Max von Laue Strasse 7, 60438 Frankfurt/Main, Germany
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13
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McCluskey K, Boudreault J, St-Pierre P, Perez-Gonzalez C, Chauvier A, Rizzi A, Beauregard PB, Lafontaine DA, Penedo JC. Unprecedented tunability of riboswitch structure and regulatory function by sub-millimolar variations in physiological Mg2. Nucleic Acids Res 2020; 47:6478-6487. [PMID: 31045204 PMCID: PMC6614840 DOI: 10.1093/nar/gkz316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
Riboswitches are cis-acting regulatory RNA biosensors that rival the efficiency of those found in proteins. At the heart of their regulatory function is the formation of a highly specific aptamer–ligand complex. Understanding how these RNAs recognize the ligand to regulate gene expression at physiological concentrations of Mg2+ ions and ligand is critical given their broad impact on bacterial gene expression and their potential as antibiotic targets. In this work, we used single-molecule FRET and biochemical techniques to demonstrate that Mg2+ ions act as fine-tuning elements of the amino acid-sensing lysC aptamer's ligand-free structure in the mesophile Bacillus subtilis. Mg2+ interactions with the aptamer produce encounter complexes with strikingly different sensitivities to the ligand in different, yet equally accessible, physiological ionic conditions. Our results demonstrate that the aptamer adapts its structure and folding landscape on a Mg2+-tunable scale to efficiently respond to changes in intracellular lysine of more than two orders of magnitude. The remarkable tunability of the lysC aptamer by sub-millimolar variations in the physiological concentration of Mg2+ ions suggests that some single-aptamer riboswitches have exploited the coupling of cellular levels of ligand and divalent metal ions to tightly control gene expression.
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Affiliation(s)
- Kaley McCluskey
- SUPA School of Physics and Astronomy, University of St. Andrews, Scotland KY16 9SS, UK
| | - Julien Boudreault
- Département de Biologie, Université de Sherbrooke, Québec, Canada J1K 2R1
| | - Patrick St-Pierre
- Département de Biologie, Université de Sherbrooke, Québec, Canada J1K 2R1
| | - Cibran Perez-Gonzalez
- SUPA School of Physics and Astronomy, University of St. Andrews, Scotland KY16 9SS, UK.,Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Adrien Chauvier
- Département de Biologie, Université de Sherbrooke, Québec, Canada J1K 2R1
| | - Adrien Rizzi
- Département de Chimie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Pascale B Beauregard
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | | | - J Carlos Penedo
- SUPA School of Physics and Astronomy, University of St. Andrews, Scotland KY16 9SS, UK.,Biomedical Sciences Research Complex, School of Biology, University of St. Andrews, Scotland KY16 9ST, UK
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14
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Chu CC, Plangger R, Kreutz C, Al-Hashimi HM. Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site. Nucleic Acids Res 2019; 47:7105-7117. [PMID: 31199872 PMCID: PMC6649712 DOI: 10.1093/nar/gkz498] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/21/2019] [Accepted: 06/07/2019] [Indexed: 01/01/2023] Open
Abstract
The HIV-1 Rev response element (RRE) RNA element mediates the nuclear export of intron containing viral RNAs by forming an oligomeric complex with the viral protein Rev. Stem IIB and nearby stem II three-way junction nucleate oligomerization through cooperative binding of two Rev molecules. Conformational flexibility at this RRE region has been shown to be important for Rev binding. However, the nature of the flexibility has remained elusive. Here, using NMR relaxation dispersion, including a new strategy for directly observing transient conformational states in large RNAs, we find that stem IIB alone or when part of the larger RREII three-way junction robustly exists in dynamic equilibrium with non-native excited state (ES) conformations that have a combined population of ∼20%. The ESs disrupt the Rev-binding site by changing local secondary structure, and their stabilization via point substitution mutations decreases the binding affinity to the Rev arginine-rich motif (ARM) by 15- to 80-fold. The ensemble clarifies the conformational flexibility observed in stem IIB, reveals long-range conformational coupling between stem IIB and the three-way junction that may play roles in cooperative Rev binding, and also identifies non-native RRE conformational states as new targets for the development of anti-HIV therapeutics.
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Affiliation(s)
- Chia-Chieh Chu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Universität Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Universität Innsbruck, 6020 Innsbruck, Austria
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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15
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Abstract
Riboswitches are RNA elements that recognize diverse chemical and biomolecular inputs, and transduce this recognition process to genetic, fluorescent, and other engineered outputs using RNA conformational changes. These systems are pervasive in cellular biology and are a promising biotechnology with applications in genetic regulation and biosensing. Here, we derive a simple expression bounding the activation ratio-the proportion of RNA in the active vs. inactive states-for both ON and OFF riboswitches that operate near thermodynamic equilibrium: 1+[I]/KdI, where [I] is the input ligand concentration and KdI is the intrinsic dissociation constant of the aptamer module toward the input ligand. A survey of published studies of natural and synthetic riboswitches confirms that the vast majority of empirically measured activation ratios have remained well below this thermodynamic limit. A few natural and synthetic riboswitches achieve activation ratios close to the limit, and these molecules highlight important principles for achieving high riboswitch performance. For several applications, including "light-up" fluorescent sensors and chemically-controlled CRISPR/Cas complexes, the thermodynamic limit has not yet been achieved, suggesting that current tools are operating at suboptimal efficiencies. Future riboswitch studies will benefit from comparing observed activation ratios to this simple expression for the optimal activation ratio. We present experimental and computational suggestions for how to make these quantitative comparisons and suggest new molecular mechanisms that may allow non-equilibrium riboswitches to surpass the derived limit.
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Affiliation(s)
| | - Michelle Wu
- Program in Biomedical Informatics, Stanford University, Stanford, CA, United States
| | - Michael Gotrik
- Department of Biochemistry, Stanford University, Stanford, CA, United States
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, CA, United States; Department of Physics, Stanford University, Stanford, CA, United States.
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16
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Sengupta RN, Herschlag D. Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor. Biochemistry 2019; 58:2760-2768. [PMID: 31117387 PMCID: PMC6586055 DOI: 10.1021/acs.biochem.9b00231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
The diverse biological
processes mediated by RNA rest upon its
recognition of various ligands, including small molecules and nucleic
acids. Nevertheless, a recent literature survey suggests that RNA
molecular recognition of these ligands is slow, with association rate
constants orders of magnitude below the diffusional limit. Thus, we
were prompted to consider strategies for increasing RNA association
kinetics. Proteins can accelerate ligand association via electrostatic
forces, and here, using the Tetrahymena group I ribozyme,
we provide evidence that electrostatic forces can accelerate RNA/ligand
association. This RNA enzyme (E) catalyzes cleavage of an oligonucleotide
substrate (S) by an exogenous guanosine (G) cofactor. The G 2′-
and 3′-OH groups interact with an active site metal ion, termed
MC, within E·S·G, and we perturbed each of these
contacts via −NH3+ substitution. New
and prior data indicate that G(2′NH3+) and G(3′NH3+) bind as strongly as
G, suggesting that the −NH3+ substituents
of these analogues avoid repulsive interactions with MC and make alternative interactions. Unexpectedly, removal of the
adjacent −OH via −H substitution to give G(2′H,3′NH3+) and G(2′NH3+,3′H) enhanced binding, in stark contrast to the deleterious
effect of these substitutions on G binding. Pulse–chase experiments
indicate that the −NH3+ moiety of G(2′H,3′NH3+) increases the rate of G association. These results
suggest that the positively charged −NH3+ group can act as a molecular “anchor” to increase
the residence time of the encounter complex and thereby enhance productive
binding. Electrostatic anchors may provide a broadly applicable strategy
for the development of fast binding RNA ligands and RNA-targeted therapeutics.
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Affiliation(s)
- Raghuvir N Sengupta
- Department of Biochemistry , Stanford University , Stanford , California 94305 , United States
| | - Daniel Herschlag
- Department of Biochemistry , Stanford University , Stanford , California 94305 , United States.,Departments of Chemical Engineering and Chemistry , Stanford University , Stanford , California 94305 , United States.,Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health) , Stanford University , Stanford , California 94305 , United States
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17
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Abstract
RNA-binding proteins chaperone the biological functions of noncoding RNA by reducing RNA misfolding, improving matchmaking between regulatory RNA and targets, and exerting quality control over RNP biogenesis. Recent studies of Escherichia coli CspA, HIV NCp, and E. coli Hfq are beginning to show how RNA-binding proteins remodel RNA structures. These different protein families use common strategies for disrupting or annealing RNA double helices, which can be used to understand the mechanisms by which proteins chaperone RNA-dependent regulation in bacteria.
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18
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Classification of riboswitch sequences using k-mer frequencies. Biosystems 2018; 174:63-76. [PMID: 30205141 DOI: 10.1016/j.biosystems.2018.09.001] [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] [Received: 05/31/2018] [Revised: 08/16/2018] [Accepted: 09/05/2018] [Indexed: 12/24/2022]
Abstract
Riboswitches are non-coding RNAs that regulate gene expression by altering the structural conformation of mRNA transcripts. Their regulation mechanism might be exploited for interesting biomedical applications such as drug targets and biosensors. A major challenge consists in accurately identifying metabolite-binding RNA switches which are structurally complex and diverse. In this regard, we investigated the classification of 16 riboswitch families using supervised learning algorithms trained solely with sequence-based features. We generated a reduced feature set and proposed a visual representation to explore its components. We induced Support Vector Machine, Random Forest, Naive Bayes, J48, and HyperPipes classifiers with our proposed feature set and tested their performance over independent data. Our best multi-class classifier achieved F-measure values of 0.996 and 0.966 in the training and test phases, respectively, outperforming those of a previous approach. When compared against BLAST, our best classifiers yielded competitive results. This work shows that the classifiers trained with our sequence-based feature set accurately discriminate riboswitches.
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19
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LeBlanc RM, Longhini AP, Tugarinov V, Dayie TK. NMR probing of invisible excited states using selectively labeled RNAs. JOURNAL OF BIOMOLECULAR NMR 2018; 71:165-172. [PMID: 29858959 DOI: 10.1007/s10858-018-0184-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments are invaluable for probing sparsely and transiently populated biomolecular states that cannot be directly detected by traditional NMR experiments and that are invisible by other biophysical approaches. A notable gap for RNA is the absence of CPMG experiments for measurement of methine base 1H and methylene C5' chemical shifts of ribose moieties in the excited state, partly because of complications from homonuclear 13C-13C scalar couplings. Here we present site-specific 13C labeling that makes possible the design of pulse sequences for recording accurate 1H-13C MQ and SQ CPMG experiments for ribose methine H1'-C1' and H2'-C2', base and ribose 1H CPMG, as well as a new 1H-13C TROSY-detected methylene (CH2) C5' CPMG relaxation pulse schemes. We demonstrate the utility of these experiments for two RNAs, the A-Site RNA known to undergo exchange and the IRE RNA suspected of undergoing exchange on microseconds to millisecond time-scale. We anticipate the new labeling approaches will facilitate obtaining structures of invisible states and provide insights into the relevance of such states for RNA-drug interactions.
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Affiliation(s)
- Regan M LeBlanc
- Department of Chemistry & Biochemistry, University of Maryland, College Park, 8314 Paint Branch Dr, College Park, MD, 20782, USA
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Andrew P Longhini
- Department of Chemistry & Biochemistry, University of Maryland, College Park, 8314 Paint Branch Dr, College Park, MD, 20782, USA
- University of California, Santa Barbara, CA, 93106, USA
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-052, USA
| | - T Kwaku Dayie
- Department of Chemistry & Biochemistry, University of Maryland, College Park, 8314 Paint Branch Dr, College Park, MD, 20782, USA.
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20
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Nichols PJ, Henen MA, Born A, Strotz D, Güntert P, Vögeli B. High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints. Commun Biol 2018; 1:61. [PMID: 30271943 PMCID: PMC6123705 DOI: 10.1038/s42003-018-0067-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/09/2018] [Indexed: 11/29/2022] Open
Abstract
RNA not only translates the genetic code into proteins, but also carries out important cellular functions. Understanding such functions requires knowledge of the structure and dynamics at atomic resolution. Almost half of the published RNA structures have been solved by nuclear magnetic resonance (NMR). However, as a result of severe resonance overlap and low proton density, high-resolution RNA structures are rarely obtained from nuclear Overhauser enhancement (NOE) data alone. Instead, additional semi-empirical restraints and labor-intensive techniques are required for structural averages, while there are only a few experimentally derived ensembles representing dynamics. Here we show that our exact NOE (eNOE) based structure determination protocol is able to define a 14-mer UUCG tetraloop structure at high resolution without other restraints. Additionally, we use eNOEs to calculate a two-state structure, which samples its conformational space. The protocol may open an avenue to obtain high-resolution structures of small RNA of unprecedented accuracy with moderate experimental efforts.
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Affiliation(s)
- Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora,, CO, 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora,, CO, 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora,, CO, 80045, USA
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zürich, ETH-Hönggerberg, Zürich, 8093, Switzerland
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, ETH-Hönggerberg, Zürich, 8093, Switzerland
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, 60438, Germany
- Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, 192-0397, Japan
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora,, CO, 80045, USA.
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21
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Manz C, Kobitski AY, Samanta A, Jäschke A, Nienhaus GU. The multi-state energy landscape of the SAM-I riboswitch: A single-molecule Förster resonance energy transfer spectroscopy study. J Chem Phys 2018; 148:123324. [DOI: 10.1063/1.5003783] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Christoph Manz
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Andrei Yu. Kobitski
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Ayan Samanta
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Andres Jäschke
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Nanotechnology and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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22
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Tian S, Kladwang W, Das R. Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping. eLife 2018; 7:29602. [PMID: 29446752 PMCID: PMC5847336 DOI: 10.7554/elife.29602] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 02/13/2018] [Indexed: 12/23/2022] Open
Abstract
The structural interconversions that mediate the gene regulatory functions of RNA molecules may be different from classic models of allostery, but the relevant structural correlations have remained elusive in even intensively studied systems. Here, we present a four-dimensional expansion of chemical mapping called lock-mutate-map-rescue (LM2R), which integrates multiple layers of mutation with nucleotide-resolution chemical mapping. This technique resolves the core mechanism of the adenine-responsive V. vulnificus add riboswitch, a paradigmatic system for which both Monod-Wyman-Changeux (MWC) conformational selection models and non-MWC alternatives have been proposed. To discriminate amongst these models, we locked each functionally important helix through designed mutations and assessed formation or depletion of other helices via compensatory rescue evaluated by chemical mapping. These LM2R measurements give strong support to the pre-existing correlations predicted by MWC models, disfavor alternative models, and suggest additional structural heterogeneities that may be general across ligand-free riboswitches.
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Affiliation(s)
- Siqi Tian
- Department of Biochemistry, Stanford University, Stanford, United States
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University, Stanford, United States
| | - Rhiju Das
- Department of Physics, Stanford University, Stanford, United States
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23
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Trigo-Mouriño P, Griesinger C, Lee D. Label-free NMR-based dissociation kinetics determination. JOURNAL OF BIOMOLECULAR NMR 2017; 69:229-235. [PMID: 29143948 DOI: 10.1007/s10858-017-0150-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/03/2017] [Indexed: 06/07/2023]
Abstract
Understanding the dissociation of molecules is the basis to modulate interactions of biomedical interest. Optimizing drugs for dissociation rates is found to be important for their efficacy, selectivity, and safety. Here, we show an application of the high-power relaxation dispersion (RD) method to the determination of the dissociation rates of weak binding ligands from receptors. The experiment probes proton RD on the ligand and, therefore, avoids the need for any isotopic labeling. The large ligand excess eases the detection significantly. Importantly, the use of large spin-lock fields allows the detection of faster dissociation rates than other relaxation approaches. Moreover, this experimental approach allows to access directly the off-rate of the binding process without the need for analyzing a series of samples with increasing ligand saturation. The validity of the method is shown with small molecule interactions using two macromolecules, bovine serum albumin and tubulin heterodimers.
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Affiliation(s)
- Pablo Trigo-Mouriño
- Department of NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Donghan Lee
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, 40202, USA.
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24
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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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25
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Hanke CA, Gohlke H. Tertiary Interactions in the Unbound Guanine-Sensing Riboswitch Focus Functional Conformational Variability on the Binding Site. J Chem Inf Model 2017; 57:2822-2832. [DOI: 10.1021/acs.jcim.7b00567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christian A. Hanke
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute for Complex Systems - Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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26
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Warhaut S, Mertinkus KR, Höllthaler P, Fürtig B, Heilemann M, Hengesbach M, Schwalbe H. Ligand-modulated folding of the full-length adenine riboswitch probed by NMR and single-molecule FRET spectroscopy. Nucleic Acids Res 2017; 45:5512-5522. [PMID: 28204648 PMCID: PMC5605240 DOI: 10.1093/nar/gkx110] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/06/2017] [Indexed: 01/20/2023] Open
Abstract
The full-length translation-regulating add adenine riboswitch (Asw) from Vibrio vulnificus has a more complex conformational space than its isolated aptamer domain. In addition to the predicted apo (apoA) and holo conformation that feature the conserved three-way junctional purine riboswitch aptamer, it adopts a second apo (apoB) conformation with a fundamentally different secondary structure. Here, we characterized the ligand-dependent conformational dynamics of the full-length add Asw by NMR and by single-molecule FRET (smFRET) spectroscopy. Both methods revealed an adenine-induced secondary structure switch from the apoB-form to the apoA-form that involves no tertiary structural interactions between aptamer and expression platform. This strongly suggests that the add Asw triggers translation by capturing the apoA-form secondary structure in the holo state. Intriguingly, NMR indicated a homogenous, docked aptamer kissing loop fold for apoA and holo, while smFRET showed persistent aptamer kissing loop docking dynamics between comparably stable, undocked and docked substates of the apoA and the holo conformation. Unraveling the folding of large junctional riboswitches thus requires the integration of complementary solution structural techniques such as NMR and smFRET.
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Affiliation(s)
- Sven Warhaut
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Klara Rebecca Mertinkus
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Philipp Höllthaler
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Boris Fürtig
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Martin Hengesbach
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main, Hessen 60438, Germany
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27
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Manz C, Kobitski AY, Samanta A, Keller BG, Jäschke A, Nienhaus GU. Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nat Chem Biol 2017; 13:1172-1178. [DOI: 10.1038/nchembio.2476] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 08/03/2017] [Indexed: 11/09/2022]
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28
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Clay MC, Ganser LR, Merriman DK, Al-Hashimi HM. Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics. Nucleic Acids Res 2017; 45:e134. [PMID: 28609788 PMCID: PMC5737546 DOI: 10.1093/nar/gkx525] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/01/2017] [Accepted: 06/05/2017] [Indexed: 11/15/2022] Open
Abstract
Recent studies have shown that RNAs exist in dynamic equilibrium with short-lived low-abundance 'excited states' that form by reshuffling base pairs in and around non-canonical motifs. These conformational states are proposed to be rich in non-canonical motifs and to play roles in the folding and regulatory functions of non-coding RNAs but their structure proves difficult to characterize given their transient nature. Here, we describe an approach for determining sugar pucker conformation in RNA excited states through nuclear magnetic resonance measurements of C1΄ and C4΄ rotating frame spin relaxation (R1ρ) in uniformly 13C/15N labeled RNA samples. Application to HIV-1 TAR exposed slow modes of sugar repuckering dynamics at the μs and ms timescale accompanying transitions between non-helical (C2΄-endo) to helical (C3΄-endo) conformations during formation of two distinct excited states. In contrast, we did not obtain any evidence for slow sugar repuckering dynamics for nucleotides in a variety of structural contexts that do not undergo non-helical to helical transitions. Our results outline a route for significantly improving the conformational characterization of RNA excited states and suggest that slow modes of repuckering dynamics gated by transient changes in secondary structure are quite common in RNA.
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Affiliation(s)
- Mary C. Clay
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Laura R. Ganser
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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29
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Hanke CA, Gohlke H. Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch. PLoS One 2017; 12:e0179271. [PMID: 28640851 PMCID: PMC5480868 DOI: 10.1371/journal.pone.0179271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 05/27/2017] [Indexed: 12/18/2022] Open
Abstract
Riboswitches are genetic regulatory elements that control gene expression depending on ligand binding. The guanine-sensing riboswitch (Gsw) binds ligands at a three-way junction formed by paired regions P1, P2, and P3. Loops L2 and L3 cap the P2 and P3 helices and form tertiary interactions. Part of P1 belongs to the switching sequence dictating the fate of the mRNA. Previous studies revealed an intricate relationship between ligand binding and presence of the tertiary interactions, and between ligand binding and influence on the P1 region. However, no information is available on the interplay among these three main regions in Gsw. Here we show that stabilization of the L2-L3 region by tertiary interactions, and the ligand binding site by ligand binding, cooperatively influences the structural stability of terminal base pairs in the P1 region in the presence of Mg2+ ions. The results are based on molecular dynamics simulations with an aggregate simulation time of ~10 μs across multiple systems of the unbound state of the Gsw aptamer and a G37A/C61U mutant, and rigidity analyses. The results could explain why the three-way junction is a central structural element also in other riboswitches and how the cooperative effect could become contextual with respect to intracellular Mg2+ concentration. The results suggest that the transmission of allosteric information to P1 can be entropy-dominated.
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Affiliation(s)
- Christian A. Hanke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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30
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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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31
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Etzel M, Mörl M. Synthetic Riboswitches: From Plug and Pray toward Plug and Play. Biochemistry 2017; 56:1181-1198. [PMID: 28206750 DOI: 10.1021/acs.biochem.6b01218] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In synthetic biology, metabolic engineering, and gene therapy, there is a strong demand for orthogonal or externally controlled regulation of gene expression. Here, RNA-based regulatory devices represent a promising emerging alternative to proteins, allowing a fast and direct control of gene expression, as no synthesis of regulatory proteins is required. Besides programmable ribozyme elements controlling mRNA stability, regulatory RNA structures in untranslated regions are highly interesting for engineering approaches. Riboswitches are especially well suited, as they show a modular composition of sensor and response elements, allowing a free combination of different modules in a plug-and-play-like mode. The sensor or aptamer domain specifically interacts with a trigger molecule as a ligand, modulating the activity of the adjacent response domain that controls the expression of the genes located downstream, in most cases at the level of transcription or translation. In this review, we discuss the recent advances and strategies for designing such synthetic riboswitches based on natural or artificial components and readout systems, from trial-and-error approaches to rational design strategies. As the past several years have shown dramatic development in this fascinating field of research, we can give only a limited overview of the basic riboswitch design principles that is far from complete, and we apologize for not being able to consider every successful and interesting approach described in the literature.
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Affiliation(s)
- Maja Etzel
- Institute for Biochemistry, Leipzig University , Brüderstrasse 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University , Brüderstrasse 34, 04103 Leipzig, Germany
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32
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Cantara WA, Hatterschide J, Wu W, Musier-Forsyth K. RiboCAT: a new capillary electrophoresis data analysis tool for nucleic acid probing. RNA (NEW YORK, N.Y.) 2017; 23:240-249. [PMID: 27821510 PMCID: PMC5238798 DOI: 10.1261/rna.058404.116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/02/2016] [Indexed: 06/06/2023]
Abstract
Chemical and enzymatic probing of RNA secondary structure and RNA/protein interactions provides the basis for understanding the functions of structured RNAs. However, the ability to rapidly perform such experiments using capillary electrophoresis has been hampered by relatively labor-intensive data analysis software. While these computationally robust programs have been shown to calculate residue-specific reactivities to a high degree of accuracy, they often require time-consuming manual intervention and lack the ability to be easily modified by users. To alleviate these issues, RiboCAT (Ribonucleic acid capillary-electrophoresis analysis tool) was developed as a user-friendly, Microsoft Excel-based tool that reduces the need for manual intervention, thereby significantly shortening the time required for data analysis. Features of this tool include (i) the use of an Excel platform, (ii) a method of intercapillary signal alignment using internal size standards, (iii) a peak-sharpening algorithm to more accurately identify peaks, and (iv) an open architecture allowing for simple user intervention. Furthermore, a complementary tool, RiboDOG (RiboCAT data output generator) was designed to facilitate the comparison of multiple data sets, highlighting potential inconsistencies and inaccuracies that may have occurred during analysis. Using these new tools, the secondary structure of the HIV-1 5' untranslated region (5'UTR) was determined using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), matching the results of previous work.
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Affiliation(s)
- William A Cantara
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Joshua Hatterschide
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Weixin Wu
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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33
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Borkar AN, Vallurupalli P, Camilloni C, Kay LE, Vendruscolo M. Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop. Phys Chem Chem Phys 2017; 19:2797-2804. [PMID: 28067358 PMCID: PMC6529357 DOI: 10.1039/c6cp08313g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA molecules in solution tend to undergo structural fluctuations of relatively large amplitude and to populate a range of different conformations some of which with low populations. It is still very challenging, however, to characterise the structures of these low populated states and to understand their functional roles. In the present study, we address this problem by using NMR residual dipolar couplings (RDCs) as structural restraints in replica-averaged metadynamics (RAM) simulations. By applying this approach to a 14-mer RNA hairpin containing the prototypical UUCG tetraloop motif, we show that it is possible to construct the free energy landscape of this RNA molecule. This free energy landscapes reveals the surprisingly rich dynamics of the UUCG tetraloop and identifies the multiple substates that exist in equilibrium owing to thermal fluctuations. The approach that we present is general and can be applied to the study of the free energy landscapes of other RNA or RNA-protein systems.
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Affiliation(s)
- Aditi N Borkar
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Pramodh Vallurupalli
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Canada M5S 1A8
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Canada M5S 1A8
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34
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Edelmann FT, Schlundt A, Heym RG, Jenner A, Niedner-Boblenz A, Syed MI, Paillart JC, Stehle R, Janowski R, Sattler M, Jansen RP, Niessing D. Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex. Nat Struct Mol Biol 2017; 24:152-161. [PMID: 28092367 DOI: 10.1038/nsmb.3351] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/07/2016] [Indexed: 12/20/2022]
Abstract
mRNA localization is an essential mechanism of gene regulation and is required for processes such as stem-cell division, embryogenesis and neuronal plasticity. It is not known which features in the cis-acting mRNA localization elements (LEs) are specifically recognized by motor-containing transport complexes. To the best of our knowledge, no high-resolution structure is available for any LE in complex with its cognate protein complex. Using X-ray crystallography and complementary techniques, we carried out a detailed assessment of an LE of the ASH1 mRNA from yeast, its complex with its shuttling RNA-binding protein She2p, and its highly specific, cytoplasmic complex with She3p. Although the RNA alone formed a flexible stem loop, She2p binding induced marked conformational changes. However, only joining by the unstructured She3p resulted in specific RNA recognition. The notable RNA rearrangements and joint action of a globular and an unfolded RNA-binding protein offer unprecedented insights into the step-wise maturation of an mRNA-transport complex.
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Affiliation(s)
- Franziska Theresia Edelmann
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Andreas Schlundt
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany
| | - Roland Gerhard Heym
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Andreas Jenner
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Annika Niedner-Boblenz
- Biomedical Center of the Ludwig-Maximilians-Universität München, Department of Cell Biology, Planegg-Martinsried, Germany
| | | | - Jean-Christophe Paillart
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Ralf Stehle
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany
| | - Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany
| | - Ralf-Peter Jansen
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Biomedical Center of the Ludwig-Maximilians-Universität München, Department of Cell Biology, Planegg-Martinsried, Germany
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35
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Colameco S, Elliot MA. Non-coding RNAs as antibiotic targets. Biochem Pharmacol 2016; 133:29-42. [PMID: 28012959 DOI: 10.1016/j.bcp.2016.12.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/12/2016] [Indexed: 02/07/2023]
Abstract
Antibiotics inhibit a wide range of essential processes in the bacterial cell, including replication, transcription, translation and cell wall synthesis. In many instances, these antibiotics exert their effects through association with non-coding RNAs. This review highlights many classical antibiotic targets (e.g. rRNAs and the ribosome), explores a number of emerging targets (e.g. tRNAs, RNase P, riboswitches and small RNAs), and discusses the future directions and challenges associated with non-coding RNAs as antibiotic targets.
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Affiliation(s)
- Savannah Colameco
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Marie A Elliot
- Department of Biology and Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
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36
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Neuner S, Kreutz C, Micura R. The synthesis of 15N(7)-Hoogsteen face-labeled adenosine phosphoramidite for solid-phase RNA synthesis. MONATSHEFTE FUR CHEMIE 2016; 148:149-155. [PMID: 28127100 PMCID: PMC5225212 DOI: 10.1007/s00706-016-1882-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 11/21/2016] [Indexed: 01/08/2023]
Abstract
ABSTRACT We have developed an efficient route for the synthesis of 15N(7)-labeled adenosine as phosphoramidite building block for site- and atom-specific incorporation into RNA by automated solid-phase synthesis. Such labeled RNA is required for the evaluation of selected non-canonical base pair interactions in folded RNA using NMR spectroscopic methods. GRAPHICAL ABSTRACT
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Affiliation(s)
- Sandro Neuner
- Institute of Organic Chemistry, Leopold-Franzens University, Innrain 80-82, Innsbruck, Austria
| | - Christoph Kreutz
- 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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37
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Merriman DK, Xue Y, Yang S, Kimsey IJ, Shakya A, Clay M, Al-Hashimi HM. Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales. Biochemistry 2016; 55:4445-56. [PMID: 27232530 DOI: 10.1021/acs.biochem.6b00285] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Helix-junction-helix (HJH) motifs are flexible building blocks of RNA architecture that help define the orientation and dynamics of helical domains. They are also frequently involved in adaptive recognition of proteins and small molecules and in the formation of tertiary contacts. Here, we use a battery of nuclear magnetic resonance techniques to examine how deleting a single bulge residue (C24) from the human immunodeficiency virus type 1 (HIV-1) transactivation response element (TAR) trinucleotide bulge (U23-C24-U25) affects dynamics over a broad range of time scales. Shortening the bulge has an effect on picosecond-to-nanosecond interhelical and local bulge dynamics similar to that casued by increasing the Mg(2+) and Na(+) concentration, whereby a preexisting two-state equilibrium in TAR is shifted away from a bent flexible conformation toward a coaxial conformation, in which all three bulge residues are flipped out and flexible. Surprisingly, the point deletion minimally affects microsecond-to-millisecond conformational exchange directed toward two low-populated and short-lived excited conformational states that form through reshuffling of bases pairs throughout TAR. The mutant does, however, adopt a slightly different excited conformational state on the millisecond time scale, in which U23 is intrahelical, mimicking the expected conformation of residue C24 in the excited conformational state of wild-type TAR. Thus, minor changes in HJH topology preserve motional modes in RNA occurring over the picosecond-to-millisecond time scales but alter the relative populations of the sampled states or cause subtle changes in their conformational features.
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Affiliation(s)
- Dawn K Merriman
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Yi Xue
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Shan Yang
- Baxter Health Care (Suzhou) Company, Ltd. , Suzhou, Jiang Su 215028, China
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Anisha Shakya
- Department of Chemistry and Biophysics, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Mary Clay
- Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
| | - Hashim M Al-Hashimi
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University Medical Center , Durham, North Carolina 27710, United States
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38
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Mehdizadeh Aghdam E, Hejazi MS, Barzegar A. Riboswitches: From living biosensors to novel targets of antibiotics. Gene 2016; 592:244-59. [PMID: 27432066 DOI: 10.1016/j.gene.2016.07.035] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 07/11/2016] [Accepted: 07/14/2016] [Indexed: 12/24/2022]
Abstract
Riboswitches are generally located in 5'-UTR region of mRNAs and specifically bind small ligands. Following ligand binding, gene expression is controlled mostly by transcription termination, translation inhibition or mRNA degradation processes. More than 30 classes of known riboswitches have been identified by now. Most riboswitches consist of an aptamer domain and an expression platform. The aptamer domain of each class of riboswitch is a conserved structure and stabilizes specific structures of the expression platforms through binding to specific compounds. In this review, we are highlighting most aspects of riboswitch research including the novel riboswitch discoveries, routine methods for discovering and investigating riboswitches along with newly discovered classes and mechanistic principles of riboswitch-mediated gene expression control. Moreover, we will give an overview about the potential of riboswitches as therapeutic targets for antibiotic design and also their utilization as biosensors for molecular detection.
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Affiliation(s)
- Elnaz Mehdizadeh Aghdam
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Saeid Hejazi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolfazl Barzegar
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran; The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran
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39
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Patel KA, Sethi R, Dhara AR, Roy I. Challenges with osmolytes as inhibitors of protein aggregation: Can nucleic acid aptamers provide an answer? Int J Biol Macromol 2016; 100:75-88. [PMID: 27156694 DOI: 10.1016/j.ijbiomac.2016.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 02/07/2023]
Abstract
Protein aggregation follows some common motifs. Whether in the formation of inclusion bodies in heterologous overexpression systems or inclusions in protein conformational diseases, or aggregation during storage or transport of protein formulations, aggregates form cross beta-sheet structures and stain with amyloidophilic dyes like Thioflavin T and Congo Red, irrespective of the concerned protein. Traditionally, osmolytes are used to stabilize proteins against stress conditions. They are employed right from protein expression, through production and purification, to formulation and administration. As osmolytes interact with the solvent, the differential effect of the stress condition on the solvent mostly determines the effect of the osmolyte on protein stability. Nucleic acid aptamers, on the other hand, are highly specific for their targets. When selected against monomeric, natively folded proteins, they bind to them with very high affinity. This binding inhibits the unfolding of the protein and/or monomer-monomer interaction which are the initial common steps of protein aggregation. Thus, by changing the approach to a protein-centric model, aptamers are able to function as universal stabilizers of proteins. The review discusses cases where osmolytes were unable to provide stabilization to proteins against different stress conditions, a gap which the aptamers seem to be able to fill.
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Affiliation(s)
- Kinjal A Patel
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ratnika Sethi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Anita R Dhara
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India.
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40
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Chemo-enzymatic labeling for rapid assignment of RNA molecules. Methods 2016; 103:11-7. [PMID: 27090003 DOI: 10.1016/j.ymeth.2016.03.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 03/17/2016] [Accepted: 03/22/2016] [Indexed: 11/22/2022] Open
Abstract
Even though Nuclear Magnetic Resonance (NMR) spectroscopy is one of the few techniques capable of determining atomic resolution structures of RNA, it is constrained by two major problems of chemical shift overlap of resonances and rapid signal loss due to line broadening. Emerging tools to tackle these problems include synthesis of atom specifically labeled or chemically modified nucleotides. Herein we review the synthesis of these nucleotides, the design and production of appropriate RNA samples, and the application and analysis of the NMR experiments that take advantage of these labels.
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41
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Chen B, LeBlanc R, Dayie TK. SAM-II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition. Angew Chem Int Ed Engl 2016; 55:2724-7. [PMID: 26800479 DOI: 10.1002/anie.201509997] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/18/2015] [Indexed: 11/10/2022]
Abstract
Conformational equilibria are increasingly recognized as pivotal for biological function. Traditional structural analyses provide a static image of conformers in solution that sometimes present conflicting views. From (13) C and (1) H chemical exchange saturation transfer experiments, in concert with ligation and selective labeling strategies, we show that in the absence of metabolite, a Mg(2+) (0-0.5 mm)-bound apo SAM-II riboswitch RNA exists in a minor (≈10 %) partially closed state that rapidly exchanges with a predominantly (≈90 %) open form with a lifetime of ≈32 ms. The base and sugar (H6,C6, H1',C1') chemical shifts of C43 for the dominant conformer are similar to those of a free CMP, but those of the minor apo species are comparable to shifts of CMPs in helical RNA regions. Our results suggest that these transient, low populated states stabilized by Mg(2+) will likely enhance rapid ligand recognition and, we anticipate, will play potentially ubiquitous roles in RNA signaling.
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Affiliation(s)
- Bin Chen
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA
| | - Regan LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA
| | - T Kwaku Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sciences Building (296), 8314 Paint Branch Dr., College Park, MD, 20782, USA.
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42
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Chen B, LeBlanc R, Dayie TK. SAM‐II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509997] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Bin Chen
- Center for Biomolecular Structure and Organization Department of Chemistry and Biochemistry University of Maryland Biomolecular Sciences Building (296), 8314 Paint Branch Dr. College Park MD 20782 USA
| | - Regan LeBlanc
- Center for Biomolecular Structure and Organization Department of Chemistry and Biochemistry University of Maryland Biomolecular Sciences Building (296), 8314 Paint Branch Dr. College Park MD 20782 USA
| | - T. Kwaku Dayie
- Center for Biomolecular Structure and Organization Department of Chemistry and Biochemistry University of Maryland Biomolecular Sciences Building (296), 8314 Paint Branch Dr. College Park MD 20782 USA
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Ma CW, Zhou LB, Zeng AP. Engineering Biomolecular Switches for Dynamic Metabolic Control. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:45-76. [DOI: 10.1007/10_2016_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Fadouloglou VE, Lin HTV, Tria G, Hernández H, Robinson CV, Svergun DI, Luisi BF. Maturation of 6S regulatory RNA to a highly elongated structure. FEBS J 2015; 282:4548-64. [PMID: 26367381 PMCID: PMC7610929 DOI: 10.1111/febs.13516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 09/04/2015] [Accepted: 09/10/2015] [Indexed: 12/11/2022]
Abstract
As bacterial populations leave the exponential growth phase and enter the stationary phase, their patterns of gene expression undergo marked changes. A key effector of this change is 6S RNA, which is a highly conserved regulatory RNA that impedes the transcription of genes associated with exponential growth by forming an inactivating ternary complex with RNA polymerase and sigma factor σ(70) (σ(70)-RNAP). In Escherichia coli, the endoribonuclease RNase E generates 6S RNA by specific cleavage of a precursor that is nearly twice the size of the 58 kDa mature form. We have explored recognition of the precursor by RNase E, and observed that processing is inhibited under conditions of excess substrate. This finding supports a largely distributive mechanism, meaning that each round of catalysis results in enzyme dissociation and re-binding to the substrate. We show that the precursor molecule and the mature 6S share a structural core dominated by an A-type helix, indicating that processing is not accompanied by extensive refolding. Both precursor and mature forms of 6S have a highly stable secondary structure, adopt an elongated shape, and show the potential to form dimers under specific conditions; nonetheless, 6S has a high structural plasticity that probably enables it to be structurally adapted upon binding to its cognate protein partners. Analysis of the 6S-σ(70)-RNAP complex by native mass spectrometry reveals a stable association with a stoichiometry of 1:1:1. A theoretical 3D model of mature 6S is presented, which is consistent with the experimental data and supports a previously proposed structure with a small stem-loop inside the central bubble.
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Affiliation(s)
- Vasiliki E Fadouloglou
- Department of Biochemistry, University of Cambridge, UK
- Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Giancarlo Tria
- European Molecular Biology Laboratory, Hamburg Outstation, European Molecular Biology Laboratory/Deutsches Elektronen Synchrotron, Hamburg, Germany
| | | | | | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, European Molecular Biology Laboratory/Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, UK
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Aboul-ela F, Huang W, Abd Elrahman M, Boyapati V, Li P. Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design. WILEY INTERDISCIPLINARY REVIEWS. RNA 2015; 6:631-50. [PMID: 26361734 PMCID: PMC5049679 DOI: 10.1002/wrna.1300] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 11/23/2022]
Abstract
The power of riboswitches in regulation of bacterial metabolism derives from coupling of two characteristics: recognition and folding. Riboswitches contain aptamers, which function as biosensors. Upon detection of the signaling molecule, the riboswitch transduces the signal into a genetic decision. The genetic decision is coupled to refolding of the expression platform, which is distinct from, although overlapping with, the aptamer. Early biophysical studies of riboswitches focused on recognition of the ligand by the aptamer-an important consideration for drug design. A mechanistic understanding of ligand-induced riboswitch RNA folding can further enhance riboswitch ligand design, and inform efforts to tune and engineer riboswitches with novel properties. X-ray structures of aptamer/ligand complexes point to mechanisms through which the ligand brings together distal strand segments to form a P1 helix. Transcriptional riboswitches must detect the ligand and form this P1 helix within the timescale of transcription. Depending on the cell's metabolic state and cellular environmental conditions, the folding and genetic outcome may therefore be affected by kinetics of ligand binding, RNA folding, and transcriptional pausing, among other factors. Although some studies of isolated riboswitch aptamers found homogeneous, prefolded conformations, experimental, and theoretical studies point to functional and structural heterogeneity for nascent transcripts. Recently it has been shown that some riboswitch segments, containing the aptamer and partial expression platforms, can form binding-competent conformers that incorporate an incomplete aptamer secondary structure. Consideration of the free energy landscape for riboswitch RNA folding suggests models for how these conformers may act as transition states-facilitating rapid, ligand-mediated aptamer folding.
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Affiliation(s)
- Fareed Aboul-ela
- Center for X-Ray Determination of the Structure of Matter, University of Science and Technology at Zewail City, Giza, Egypt
| | - Wei Huang
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA
| | - Maaly Abd Elrahman
- Center for X-Ray Determination of the Structure of Matter, University of Science and Technology at Zewail City, Giza, Egypt
- Therapeutical Chemistry Department, National Research Center, El Buhouth St., Dokki, Cairo, Egypt
| | - Vamsi Boyapati
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Pan Li
- Department of Biological Sciences, University at Albany-SUNY, Albany, NY, USA
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Salmon L, Giambaşu GM, Nikolova EN, Petzold K, Bhattacharya A, Case DA, Al-Hashimi HM. Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings. J Am Chem Soc 2015; 137:12954-65. [PMID: 26306428 PMCID: PMC4748170 DOI: 10.1021/jacs.5b07229] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the measurement of abundant experimental data. NMR residual dipolar couplings (RDCs) carry rich dynamics information, however, difficulties in modulating overall alignment of nucleic acids have limited the ability to fully extract this information. We present a strategy for modulating RNA alignment that is based on introducing variable dynamic kinks in terminal helices. With this strategy, we measured seven sets of RDCs in a cUUCGg apical loop and used this rich data set to test the accuracy of an 0.8 μs MD simulation computed using the Amber ff10 force field as well as to determine an atomic resolution ensemble. The MD-generated ensemble quantitatively reproduces the measured RDCs, but selection of a sub-ensemble was required to satisfy the RDCs within error. The largest discrepancies between the RDC-selected and MD-generated ensembles are observed for the most flexible loop residues and backbone angles connecting the loop to the helix, with the RDC-selected ensemble resulting in more uniform dynamics. Comparison of the RDC-selected ensemble with NMR spin relaxation data suggests that the dynamics occurs on the ps-ns time scales as verified by measurements of R(1ρ) relaxation-dispersion data. The RDC-satisfying ensemble samples many conformations adopted by the hairpin in crystal structures indicating that intrinsic plasticity may play important roles in conformational adaptation. The approach presented here can be applied to test nucleic acid force fields and to characterize dynamics in diverse RNA motifs at atomic resolution.
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Affiliation(s)
- Loïc Salmon
- Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - George M. Giambaşu
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Evgenia N. Nikolova
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | | | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, North Carolina, USA
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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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