1
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Dagenais P, Desjardins G, Legault P. An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme. Nucleic Acids Res 2021; 49:11959-11973. [PMID: 34718697 PMCID: PMC8599749 DOI: 10.1093/nar/gkab963] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
The divide-and-conquer strategy is commonly used for protein structure determination, but its applications to high-resolution structure determination of RNAs have been limited. Here, we introduce an integrative approach based on the divide-and-conquer strategy that was undertaken to determine the solution structure of an RNA model system, the Neurospora VS ribozyme. NMR and SAXS studies were conducted on a minimal trans VS ribozyme as well as several isolated subdomains. A multi-step procedure was used for structure determination that first involved pairing refined NMR structures with SAXS data to obtain structural subensembles of the various subdomains. These subdomain structures were then assembled to build a large set of structural models of the ribozyme, which was subsequently filtered using SAXS data. The resulting NMR-SAXS structural ensemble shares several similarities with the reported crystal structures of the VS ribozyme. However, a local structural difference is observed that affects the global fold by shifting the relative orientation of the two three-way junctions. Thus, this finding highlights a global conformational change associated with substrate binding in the VS ribozyme that is likely critical for its enzymatic activity. Structural studies of other large RNAs should benefit from similar integrative approaches that allow conformational sampling of assembled fragments.
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Affiliation(s)
- Pierre Dagenais
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| | - Geneviève Desjardins
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| | - Pascale Legault
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
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2
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Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme. Nat Chem 2020; 12:193-201. [PMID: 31959957 PMCID: PMC7389185 DOI: 10.1038/s41557-019-0391-x] [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: 03/12/2019] [Accepted: 11/13/2019] [Indexed: 11/09/2022]
Abstract
The Varkud satellite ribozyme catalyses site-specific RNA cleavage and ligation, and serves as an important model system to understand RNA catalysis. Here, we combine stereospecific phosphorothioate substitution, precision nucleobase mutation and linear free-energy relationship measurements with molecular dynamics, molecular solvation theory and ab initio quantum mechanical/molecular mechanical free-energy simulations to gain insight into the catalysis. Through this confluence of theory and experiment, we unify the existing body of structural and functional data to unveil the catalytic mechanism in unprecedented detail, including the degree of proton transfer in the transition state. Further, we provide evidence for a critical Mg2+ in the active site that interacts with the scissile phosphate and anchors the general base guanine in position for nucleophile activation. This novel role for Mg2+ adds to the diversity of known catalytic RNA strategies and unifies functional features observed in the Varkud satellite, hairpin and hammerhead ribozyme classes.
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3
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Lemkul JA, MacKerell AD. Polarizable force field for RNA based on the classical drude oscillator. J Comput Chem 2018; 39:2624-2646. [PMID: 30515902 PMCID: PMC6284239 DOI: 10.1002/jcc.25709] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 08/01/2018] [Accepted: 09/23/2018] [Indexed: 12/15/2022]
Abstract
RNA molecules are highly dynamic and capable of adopting a wide range of complex, folded structures. The factors driving the folding and dynamics of these structures are dependent on a balance of base pairing, hydration, base stacking, ion interactions, and the conformational sampling of the 2'-hydroxyl group in the ribose sugar. The representation of these features is a challenge for empirical force fields used in molecular dynamics simulations. Toward meeting this challenge, the inclusion of explicit electronic polarization is important in accurately modeling RNA structure. In this work, we present a polarizable force field for RNA based on the classical Drude oscillator model, which represents electronic degrees of freedom via negatively charged particles attached to their parent atoms by harmonic springs. Beginning with parametrization against quantum mechanical base stacking interaction energy and conformational energy data, we have extended the Drude-2017 nucleic acid force field to include RNA. The conformational sampling of a range of RNA sequences were used to validate the force field, including canonical A-form RNA duplexes, stem-loops, and complex tertiary folds that bind multiple Mg2+ ions. Overall, the Drude-2017 RNA force field reproduces important properties of these structures, including the conformational sampling of the 2'-hydroxyl and key interactions with Mg2+ ions. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
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4
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Krepl M, Vögele J, Kruse H, Duchardt-Ferner E, Wöhnert J, Sponer J. An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch. Nucleic Acids Res 2018; 46:6528-6543. [PMID: 29893898 PMCID: PMC6061696 DOI: 10.1093/nar/gky490] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/23/2018] [Indexed: 01/04/2023] Open
Abstract
The neomycin sensing riboswitch is the smallest biologically functional RNA riboswitch, forming a hairpin capped with a U-turn loop-a well-known RNA motif containing a conserved uracil. It was shown previously that a U→C substitution of the eponymous conserved uracil does not alter the riboswitch structure due to C protonation at N3. Furthermore, cytosine is evolutionary permitted to replace uracil in other U-turns. Here, we use molecular dynamics simulations to study the molecular basis of this substitution in the neomycin sensing riboswitch and show that a structure-stabilizing monovalent cation-binding site in the wild-type RNA is the main reason for its negligible structural effect. We then use NMR spectroscopy to confirm the existence of this cation-binding site and to demonstrate its effects on RNA stability. Lastly, using quantum chemical calculations, we show that the cation-binding site is altering the electronic environment of the wild-type U-turn so that it is more similar to the cytosine mutant. The study reveals an amazingly complex and delicate interplay between various energy contributions shaping up the 3D structure and evolution of nucleic acids.
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Affiliation(s)
- Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jennifer Vögele
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
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5
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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6
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Bergonzo C, Cheatham TE. Mg 2+ Binding Promotes SLV as a Scaffold in Varkud Satellite Ribozyme SLI-SLV Kissing Loop Junction. Biophys J 2017; 113:313-320. [PMID: 28669407 PMCID: PMC5529310 DOI: 10.1016/j.bpj.2017.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 11/07/2022] Open
Abstract
Though the structure of the substrate stem loop I (SLI)-stem loop V (SLV) kissing loop junction of the Varkud Satellite ribozyme has been experimentally characterized, the dynamics of this Mg2+-dependent loop-loop interaction have been elusive. Specifically, each hairpin loop contains a U-turn motif, but only SLV shows a conformational shift triggered by Mg2+ ion association. Here, we use molecular dynamics simulations to analyze the binding and dynamics of this kissing loop junction. We show that SLV acts as a scaffold, providing stability to the junction. Mg2+ ions associate with SLV when it is part of the junction in a manner similar to when it is unbound, but there is no specificity in Mg2+ binding for the SLI loop. This suggests that the entropic penalty of ordering the larger SLI is too high, allowing SLV to act as a scaffold for multiple substrate loop sequences.
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7
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Cunha RA, Bussi G. Unraveling Mg 2+-RNA binding with atomistic molecular dynamics. RNA (NEW YORK, N.Y.) 2017; 23:628-638. [PMID: 28148825 PMCID: PMC5393174 DOI: 10.1261/rna.060079.116] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/26/2016] [Indexed: 05/09/2023]
Abstract
Interaction with divalent cations is of paramount importance for RNA structural stability and function. We report here a detailed molecular dynamics study of all the possible binding sites for Mg2+ on an RNA duplex, including both direct (inner sphere) and indirect (outer sphere) binding. In order to tackle sampling issues, we develop a modified version of bias-exchange metadynamics, which allows us to simultaneously compute affinities with previously unreported statistical accuracy. Results correctly reproduce trends observed in crystallographic databases. Based on this, we simulate a carefully chosen set of models that allows us to quantify the effects of competition with monovalent cations, RNA flexibility, and RNA hybridization. Our simulations reproduce the decrease and increase of Mg2+ affinity due to ion competition and hybridization, respectively, and predict that RNA flexibility has a site-dependent effect. This suggests a nontrivial interplay between RNA conformational entropy and divalent cation binding.
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Affiliation(s)
- Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati-SISSA, 34136, Trieste, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati-SISSA, 34136, Trieste, Italy
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8
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Dagenais P, Girard N, Bonneau E, Legault P. Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28382748 PMCID: PMC5573960 DOI: 10.1002/wrna.1421] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/21/2017] [Accepted: 03/08/2017] [Indexed: 12/31/2022]
Abstract
Despite the large number of noncoding RNAs and their importance in several biological processes, our understanding of RNA structure and dynamics at atomic resolution is still very limited. Like many other RNAs, the Neurospora Varkud satellite (VS) ribozyme performs its functions through dynamic exchange of multiple conformational states. More specifically, the VS ribozyme recognizes and cleaves its stem-loop substrate via a mechanism that involves several structural transitions within its stem-loop substrate. The recent publications of high-resolution structures of the VS ribozyme, obtained by NMR spectroscopy and X-ray crystallography, offer an opportunity to integrate the data and closely examine the structural and dynamic properties of this model RNA system. Notably, these investigations provide a valuable example of the divide-and-conquer strategy for structural and dynamic characterization of a large RNA, based on NMR structures of several individual subdomains. The success of this divide-and-conquer approach reflects the modularity of RNA architecture and the great care taken in identifying the independently-folding modules. Together with previous biochemical and biophysical characterizations, the recent NMR and X-ray studies provide a coherent picture into how the VS ribozyme recognizes its stem-loop substrate. Such in-depth characterization of this RNA enzyme will serve as a model for future structural and engineering studies of dynamic RNAs and may be particularly useful in planning divide-and-conquer investigations. WIREs RNA 2017, 8:e1421. doi: 10.1002/wrna.1421 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Pierre Dagenais
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
| | - Nicolas Girard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
| | - Eric Bonneau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
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9
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Bergonzo C, Hall KB, Cheatham TE. Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics. J Chem Theory Comput 2016; 12:3382-9. [PMID: 27294370 PMCID: PMC4944181 DOI: 10.1021/acs.jctc.6b00173] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
We compare the performance of five
magnesium (Mg2+)
ion models in simulations of an RNA stem loop which has an experimentally
determined divalent ion dependent conformational shift. We show that
despite their differences in parametrization and resulting van der
Waals terms, including differences in the functional form of the nonbonded
potential, when the RNA adopts its folded conformation, all models
behave similarly across ten independent microsecond length simulations
with each ion model. However, when the entire structure ensemble is
accounted for, chelation of Mg2+ to RNA is seen in three
of the five models, most egregiously and likely artifactual in simulations
using a 12-6-4 model for the Lennard-Jones potential. Despite the
simple nature of the fixed point-charge and van der Waals sphere models
employed, and with the exception of the likely oversampled directed
chelation of the 12-6-4 potential models, RNA–Mg2+ interactions via first shell water molecules are surprisingly well
described by modern parameters, allowing us to observe the spontaneous
conformational shift from Mg2+ free RNA to Mg2+ associated RNA structure in unrestrained molecular dynamics simulations.
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Affiliation(s)
- Christina Bergonzo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States
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10
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Lacroix-Labonté J, Girard N, Dagenais P, Legault P. Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions. Nucleic Acids Res 2016; 44:6924-34. [PMID: 27166370 PMCID: PMC5001590 DOI: 10.1093/nar/gkw401] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/30/2016] [Indexed: 12/24/2022] Open
Abstract
The Neurospora VS ribozyme is a catalytic RNA that has the unique ability to specifically recognize and cleave a stem-loop substrate through formation of a highly stable kissing-loop interaction (KLI). In order to explore the engineering potential of the VS ribozyme to cleave alternate substrates, we substituted the wild-type KLI by other known KLIs using an innovative engineering method that combines rational and combinatorial approaches. A bioinformatic search of the protein data bank was initially performed to identify KLIs that are structurally similar to the one found in the VS ribozyme. Next, substrate/ribozyme (S/R) pairs that incorporate these alternative KLIs were kinetically and structurally characterized. Interestingly, several of the resulting S/R pairs allowed substrate cleavage with substantial catalytic efficiency, although with reduced activity compared to the reference S/R pair. Overall, this study describes an innovative approach for RNA engineering and establishes that the KLI of the trans VS ribozyme can be adapted to cleave other folded RNA substrates.
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Affiliation(s)
- Julie Lacroix-Labonté
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Nicolas Girard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Pierre Dagenais
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
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11
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Bergonzo C, Hall KB, Cheatham TE. Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions. J Phys Chem B 2015; 119:12355-64. [PMID: 26328924 PMCID: PMC4634716 DOI: 10.1021/acs.jpcb.5b05190] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Varkud Satellite RNA contains a self-cleaving ribozyme that has been shown to function independently of its surroundings. This 160 nucleotide ribozyme adopts a catalytically active tertiary structure that includes a kissing hairpin complex formed by stem-loop I and stem-loop V (SLV). The five-nucleotide 5'-rUGACU loop of the isolated SLV has been shown to adopt a Mg(2+)-dependent U-turn structure by solution NMR. This U-turn hairpin is examined here by molecular dynamics simulations in the presence of monovalent and divalent ions. Simulations confirm on an all-atom level the hypotheses for the role of the Mg(2+) ions in stabilizing the loop, as well as the role of the solvent exposed U700 base. Additionally, these simulations suggest the Mg(2+)-free stem-loop adopts a wide range of structures, including energetically favorable structures similar to the Mg(2+)-bound loop structure. We propose this structure is a "gatekeeper" or precursor to Mg(2+) binding when those ions are present.
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Affiliation(s)
- Christina Bergonzo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah , Salt Lake City, Utah 84112, United States
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12
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Bonneau E, Girard N, Lemieux S, Legault P. The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure. RNA (NEW YORK, N.Y.) 2015; 21:1621-32. [PMID: 26124200 PMCID: PMC4536322 DOI: 10.1261/rna.052076.115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/08/2015] [Indexed: 05/04/2023]
Abstract
As part of an effort to structurally characterize the complete Neurospora VS ribozyme, NMR solution structures of several subdomains have been previously determined, including the internal loops of domains I and VI, the I/V kissing-loop interaction and the III-IV-V junction. Here, we expand this work by determining the NMR structure of a 62-nucleotide RNA (J236) that encompasses the VS ribozyme II-III-VI three-way junction and its adjoining stems. In addition, we localize Mg(2+)-binding sites within this structure using Mn(2+)-induced paramagnetic relaxation enhancement. The NMR structure of the J236 RNA displays a family C topology with a compact core stabilized by continuous stacking of stems II and III, a cis WC/WC G•A base pair, two base triples and two Mg(2+) ions. Moreover, it reveals a remote tertiary interaction between the adenine bulges of stems II and VI. Additional NMR studies demonstrate that both this bulge-bulge interaction and Mg(2+) ions are critical for the stable folding of the II-III-VI junction. The NMR structure of the J236 RNA is consistent with biochemical studies on the complete VS ribozyme, but not with biophysical studies performed with a minimal II-III-VI junction that does not contain the II-VI bulge-bulge interaction. Together with previous NMR studies, our findings provide important new insights into the three-dimensional architecture of this unique ribozyme.
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Affiliation(s)
- Eric Bonneau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Nicolas Girard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Sébastien Lemieux
- Département d'Informatique et de Recherche Opérationnelle et Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
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13
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Kun Á, Szathmáry E. Fitness Landscapes of Functional RNAs. Life (Basel) 2015; 5:1497-517. [PMID: 26308059 PMCID: PMC4598650 DOI: 10.3390/life5031497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/26/2015] [Accepted: 08/03/2015] [Indexed: 11/16/2022] Open
Abstract
The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.
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Affiliation(s)
- Ádám Kun
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- MTA-ELTE-MTMT Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, Kirchplatz 1, 82049 Munich/Pullach, Germany.
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary.
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14
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Wunderlich CH, Juen MA, LeBlanc RM, Longhini AP, Dayie TK, Kreutz C. Stable isotope-labeled RNA phosphoramidites to facilitate dynamics by NMR. Methods Enzymol 2015; 565:461-94. [PMID: 26577742 DOI: 10.1016/bs.mie.2015.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Given that Ribonucleic acids (RNAs) are a central hub of various cellular processes, methods to synthesize these RNAs for biophysical studies are much needed. Here, we showcase the applicability of 6-(13)C-pyrimidine phosphoramidites to introduce isolated (13)C-(1)H spin pairs into RNAs up to 40 nucleotides long. The method allows the incorporation of 6-(13)C-uridine and -cytidine residues at any desired position within a target RNA. By site-specific positioning of the (13)C-label using RNA solid phase synthesis, these stable isotope-labeling patterns are especially well suited to resolve resonance assignment ambiguities. Of even greater importance, the labeling pattern affords accurate quantification of important functional transitions of biologically relevant RNAs (e.g., riboswitch aptamer domains, viral RNAs, or ribozymes) in the μs- to ms time regime and beyond without complications of one bond carbon scalar couplings. We outline the chemical synthesis of the 6-(13)C-pyrimidine building blocks and their use in RNA solid phase synthesis and demonstrate their utility in Carr Purcell Meiboom Gill relaxation dispersion, ZZ exchange, and chemical exchange saturation transfer NMR experiments.
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Affiliation(s)
- Christoph H Wunderlich
- Institute of Organic Chemistry and Center for Biomolecular Sciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Michael A Juen
- Institute of Organic Chemistry and Center for Biomolecular Sciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Regan M LeBlanc
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA
| | - Andrew P Longhini
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA
| | - T Kwaku Dayie
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA.
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Biomolecular Sciences Innsbruck, University of Innsbruck, Innsbruck, Austria.
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15
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Bonneau E, Legault P. Nuclear magnetic resonance structure of the III-IV-V three-way junction from the Varkud satellite ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement. Biochemistry 2014; 53:6264-75. [PMID: 25238589 DOI: 10.1021/bi500826n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The VS ribozyme is a catalytic RNA found within some natural isolates of Neurospora that is being used as a model system to improve our understanding of RNA structure, catalysis, and engineering. The catalytic domain contains five helical domains (SLII-SLVI) that are organized by two three-way junctions. The III-IV-V junction is required for high-affinity binding of the substrate domain (SLI) through formation of a kissing loop interaction with SLV. Here, we determine the high-resolution nuclear magnetic resonance (NMR) structure of a 47-nucleotide RNA containing the III-IV-V junction (J345). The J345 RNA adopts a Y-shaped fold typical of the family C three-way junctions, with coaxial stacking between stems III and IV and an acute angle between stems III and V. The NMR structure reveals that the core of the III-IV-V junction contains four stacked base triples, a U-turn motif, a cross-strand stacking interaction, an A-minor interaction, and a ribose zipper. In addition, the NMR structure shows that the cCUUGg tetraloop used to stabilize stem IV adopts a novel RNA tetraloop fold, different from the known gCUUGc tetraloop structure. Using Mn(2+)-induced paramagnetic relaxation enhancement, we identify six Mg(2+)-binding sites within J345, including one associated with the cCUUGg tetraloop and two with the junction core. The NMR structure of J345 likely represents the conformation of the III-IV-V junction in the context of the active VS ribozyme and suggests that this junction functions as a dynamic hinge that contributes to substrate recognition and catalysis. Moreover, this study highlights a new role for family C three-way junctions in long-range tertiary interactions.
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Affiliation(s)
- Eric Bonneau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal , C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
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16
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Bouchard P, Legault P. A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme. RNA (NEW YORK, N.Y.) 2014; 20:1451-64. [PMID: 25051972 PMCID: PMC4138328 DOI: 10.1261/rna.046144.114] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/03/2014] [Indexed: 05/20/2023]
Abstract
Kissing loops are tertiary structure elements that often play key roles in functional RNAs. In the Neurospora VS ribozyme, a kissing-loop interaction between the stem-loop I (SLI) substrate and stem-loop V (SLV) of the catalytic domain is known to play an important role in substrate recognition. In addition, this I/V kissing-loop interaction is associated with a helix shift in SLI that activates the substrate for catalysis. To better understand the role of this kissing-loop interaction in substrate recognition and activation by the VS ribozyme, we performed a thermodynamic characterization by isothermal titration calorimetry using isolated SLI and SLV stem-loops. We demonstrate that preshifted SLI variants have higher affinity for SLV than shiftable SLI variants, with an energetic cost of 1.8-3 kcal/mol for the helix shift in SLI. The affinity of the preshifted SLI for SLV is remarkably high, the interaction being more stable by 7-8 kcal/mol than predicted for a comparable duplex containing three Watson-Crick base pairs. The structural basis of this remarkable stability is discussed in light of previous NMR studies. Comparative thermodynamic studies reveal that kissing-loop complexes containing 6-7 Watson-Crick base pairs are as stable as predicted from comparable RNA duplexes; however, those with 2-3 Watson-Crick base pairs are more stable than predicted. Interestingly, the stability of SLI/ribozyme complexes is similar to that of SLI/SLV complexes. Thus, the I/V kissing loop interaction represents the predominant energetic contribution to substrate recognition by the trans-cleaving VS ribozyme.
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Affiliation(s)
- Patricia Bouchard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
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17
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Gottstein-Schmidtke SR, Duchardt-Ferner E, Groher F, Weigand JE, Gottstein D, Suess B, Wöhnert J. Building a stable RNA U-turn with a protonated cytidine. RNA (NEW YORK, N.Y.) 2014; 20:1163-72. [PMID: 24951555 PMCID: PMC4105743 DOI: 10.1261/rna.043083.113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 05/16/2014] [Indexed: 05/28/2023]
Abstract
The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5'-UNR-3' (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3' phosphate group of the R residue as well as a hydrogen bond between the 2'-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3' from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone.
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Affiliation(s)
- Sina R Gottstein-Schmidtke
- Institute of Molecular Biosciences, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
| | - Florian Groher
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Daniel Gottstein
- Institute for Biophysical Chemistry, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
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18
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Bonneau E, Legault P. NMR localization of divalent cations at the active site of the Neurospora VS ribozyme provides insights into RNA-metal-ion interactions. Biochemistry 2014; 53:579-90. [PMID: 24364590 PMCID: PMC3906864 DOI: 10.1021/bi401484a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metal cations represent key elements of RNA structure and function. In the Neurospora VS ribozyme, metal cations play diverse roles; they are important for substrate recognition, formation of the active site, and shifting the pKa's of two key nucleobases that contribute to the general acid-base mechanism. Recently, we determined the NMR structure of the A730 loop of the VS ribozyme active site (SLVI) that contributes the general acid (A756) in the enzymatic mechanism of the cleavage reaction. Our studies showed that magnesium (Mg(2+)) ions are essential to stabilize the formation of the S-turn motif within the A730 loop that exposes the A756 nucleobase for catalysis. In this article, we extend these NMR investigations by precisely mapping the Mg(2+)-ion binding sites using manganese-induced paramagnetic relaxation enhancement and cadmium-induced chemical-shift perturbation of phosphorothioate RNAs. These experiments identify five Mg(2+)-ion binding sites within SLVI. Four Mg(2+) ions in SLVI are associated with known RNA structural motifs, including the G-U wobble pair and the GNRA tetraloop, and our studies reveal novel insights about Mg(2+) ion binding to these RNA motifs. Interestingly, one Mg(2+) ion is specifically associated with the S-turn motif, confirming its structural role in the folding of the A730 loop. This Mg(2+) ion is likely important for formation of the active site and may play an indirect role in catalysis.
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Affiliation(s)
- Eric Bonneau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal , C.P. 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada
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19
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Bouchard P, Legault P. Structural insights into substrate recognition by the Neurospora Varkud satellite ribozyme: importance of U-turns at the kissing-loop junction. Biochemistry 2013; 53:258-69. [PMID: 24325625 PMCID: PMC3893828 DOI: 10.1021/bi401491g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Substrate
recognition by the Neurospora Varkud
satellite ribozyme depends on the formation of a magnesium-dependent
kissing-loop interaction between the stem-loop I (SLI) substrate and
stem-loop V (SLV) of the catalytic domain. From mutagenesis studies,
it has been established that this I/V kissing-loop interaction involves
three Watson–Crick base pairs and is associated with a structural
rearrangement of the SLI substrate that facilitates catalysis. Here,
we report the NMR structural characterization of this I/V kissing-loop
using isolated stem-loops. NMR studies were performed on different
SLI/SLV complexes containing a common SLV and shiftable, preshifted,
or double-stranded SLI variants. These studies confirm the presence
of three Watson–Crick base pairs at the kissing-loop junction
and provide evidence for the structural rearrangement of shiftable
SLI variants upon SLV binding. NMR structure determination of an SLI/SLV
complex demonstrates that both the SLI and SLV loops adopt U-turn
structures, which facilitates intermolecular Watson–Crick base
pairing. Several other interactions at the I/V interface, including
base triples and base stacking, help create a continuously stacked
structure. These NMR studies provide a structural basis to understand
the stability of the I/V kissing-loop interaction and lead us to propose
a kinetic model for substrate activation in the VS ribozyme.
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Affiliation(s)
- Patricia Bouchard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal , C.P. 6128, Succursale Centre-Ville, Montréal, Quebec H3C 3J7, Canada
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20
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Abstract
A single technique is insufficient to characterize the properties of an RNA molecule so this Guide provides advice and suggestions for use of several spectroscopic methods applied to RNA. It begins with a discussion of design features to synthesize a suitable molecule for study, assuming that the reader is familiar with in vitro enzymatic and chemical synthesis of RNA. With the RNA in hand, the application of UV melting studies to characterize its folding/unfolding transitions is presented, followed by instructions for fluorescence experiments to augment the UV data. Since RNAs are flexible molecules, it is important to characterize their mobility, and so time-resolved fluorescence data are analyzed. A brief exposition of the power of NMR spectroscopy to identify ion-binding sites is provided. RNA examples are described for each method to give a perspective on what can and cannot be learned.
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Affiliation(s)
- Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
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21
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Wunderlich CH, Spitzer R, Santner T, Fauster K, Tollinger M, Kreutz C. Synthesis of (6-(13)C)pyrimidine nucleotides as spin-labels for RNA dynamics. J Am Chem Soc 2012; 134:7558-69. [PMID: 22489874 DOI: 10.1021/ja302148g] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We present a (13)C-based isotope labeling protocol for RNA. Using (6-(13)C)pyrimidine phosphoramidite building blocks, site-specific labels can be incorporated into a target RNA via chemical oligonucleotide solid-phase synthesis. This labeling scheme is particularly useful for studying milli- to microsecond dynamics via NMR spectroscopy, as an isolated spin system is a crucial prerequisite to apply Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion type experiments. We demonstrate the applicability for the characterization and detection of functional dynamics on various time scales by incorporating the (6-(13)C)uridine and -cytidine labels into biologically relevant RNAs. The refolding kinetics of a bistable terminator antiterminator segment involved in the gene regulation process controlled by the preQ(1) riboswitch class I was investigated. Using (13)C CPMG relaxation dispersion NMR spectroscopy, the milli- to microsecond dynamics of the HIV-1 transactivation response element RNA and the Varkud satellite stem loop V motif was addressed.
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Affiliation(s)
- Christoph H Wunderlich
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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22
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Abstract
Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.
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Affiliation(s)
- Maria Pechlaner
- Institute of Inorganic Chemistry, University of Zürich, Zürich, Switzerland
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23
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Lacroix-Labonté J, Girard N, Lemieux S, Legault P. Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture. Nucleic Acids Res 2011; 40:2284-93. [PMID: 22086962 PMCID: PMC3299992 DOI: 10.1093/nar/gkr1018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure–function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS ribozyme, which form a kissing–loop interaction important for substrate recognition. To rapidly characterize the substrate specificity (kcat/KM) of several substrate/ribozyme pairs, a procedure was established for simultaneous kinetic characterization of multiple substrates. Several active substrate/ribozyme pairs were identified, indicating the presence of limited substrate promiscuity for stem Ib variants and helix-length compensation between stems Ib and V. 3D models of the I/V interaction were generated that are compatible with the kinetic data. These models further illustrate the adaptability of the VS ribozyme architecture for substrate cleavage and provide global structural information on the I/V kissing–loop interaction. By exploring higher-order compensatory mutations in RNA our approach brings a deeper understanding of the adaptability of RNA structure, while opening new avenues for RNA research.
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Affiliation(s)
- Julie Lacroix-Labonté
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada
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24
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Desjardins G, Bonneau E, Girard N, Boisbouvier J, Legault P. NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site. Nucleic Acids Res 2011; 39:4427-37. [PMID: 21266483 PMCID: PMC3105416 DOI: 10.1093/nar/gkq1244] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme. Here, we determined the high-resolution NMR structure of a stem–loop VI fragment containing the A730 internal loop, which forms part of the active site. In the presence of magnesium ions, the A730 loop adopts a structure that is consistent with existing biochemical data and most likely reflects its conformation in the VS ribozyme prior to docking with the cleavage site internal loop. Interestingly, the A730 loop adopts an S-turn motif that is also present in loop B within the hairpin ribozyme active site. The S-turn appears necessary to expose the Watson–Crick edge of a catalytically important residue (A756) so that it can fulfill its role in catalysis. The A730 loop and the cleavage site loop of the VS ribozyme display structural similarities to internal loops found in the active site of the hairpin ribozyme. These similarities provided a rationale to build a model of the VS ribozyme active site based on the crystal structure of the hairpin ribozyme.
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Affiliation(s)
- Geneviève Desjardins
- Département de Biochimie, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada
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25
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Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from? Molecules 2010; 15:5389-407. [PMID: 20714304 PMCID: PMC6257768 DOI: 10.3390/molecules15085389] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 07/29/2010] [Accepted: 08/04/2010] [Indexed: 11/17/2022] Open
Abstract
The hammerhead ribozyme was first considered as a metalloenzyme despite persistent inconsistencies between structural and functional data. In the last decade, metal ions were confirmed as catalysts in self-splicing ribozymes but displaced by nucleobases in self-cleaving ribozymes. However, a model of catalysis just relying on nucleobases as catalysts does not fully fit some recent data. Gathering and comparing data on metal ions in self-cleaving and self-splicing ribozymes, the roles of divalent metal ions and nucleobases are revisited. Hypothetical models based on cooperation between metal ions and nucleobases are proposed for the catalysis and evolution of this prototype in RNA catalysis.
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26
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Lamm G, Pack GR. Counterion condensation and shape within Poisson-Boltzmann theory. Biopolymers 2010; 93:619-39. [PMID: 20213767 DOI: 10.1002/bip.21421] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
An analytical approximation to the nonlinear Poisson-Boltzmann (PB) equation is applied to charged macromolecules that possess one-dimensional symmetry and can be modeled by a plane, infinite cylinder, or sphere. A functional substitution allows the nonlinear PB equation subject to linear boundary conditions to be transformed into an approximate linear (Debye-Hückel-type) equation subject to nonlinear boundary conditions. A simple analytical result for the surface potential of such polyelectrolytes follows, leading to expressions for the amount of condensed (or renormalized) charge and the electrostatic Helmholtz energy for polyelectrolytes. Analytical high-charge/low-salt and low-charge/high-salt limits are shown to be similar to results obtained by others based on PB or counterion condensation theory. Several important general observations concerning polyelectrolytes treated within the context of PB theory can be made including: (1) all charged surfaces display some counterion condensation for finite electrolyte concentration, (2) the effect of surface geometry is described primarily by the sum of the Debye constant and the mean curvature of the surface, (3) two surfaces with the same surface charge density and mean curvature condense approximately identical fractions of counterions, (4) the amount of condensation is not determined by a predefined "condensation distance" although such a distance can be determined uniquely from it, and (5) substantial condensation occurs if the Debye constant of the electrolyte is much less than the mean curvature of a highly charged polyelectrolyte.
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Affiliation(s)
- Gene Lamm
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
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27
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Mouse hepatitis virus stem-loop 2 adopts a uYNMG(U)a-like tetraloop structure that is highly functionally tolerant of base substitutions. J Virol 2009; 83:12084-93. [PMID: 19759148 DOI: 10.1128/jvi.00915-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Stem-loop 2 (SL2) of the 5'-untranslated region of the mouse hepatitis virus (MHV) contains a highly conserved pentaloop (C47-U48-U49-G50-U51) stacked on a 5-bp stem. Solution nuclear magnetic resonance experiments are consistent with a 5'-uYNMG(U)a or uCUYG(U)a tetraloop conformation characterized by an anti-C47-syn-G50 base-pairing interaction, with U51 flipped out into solution and G50 stacked on A52. Previous studies showed that U48C and U48A substitutions in MHV SL2 were lethal, while a U48G substitution was viable. Here, we characterize viruses harboring all remaining single-nucleotide substitutions in the pentaloop of MHV SL2 and also investigate the degree to which the sequence context of key pentaloop point mutations influences the MHV replication phenotype. U49 or U51 substitution mutants all are viable; C47 substitution mutants also are viable but produce slightly smaller plaques than wild-type virus. In contrast, G50A and G50C viruses are severely crippled and form much smaller plaques. Virus could not be recovered from G50U-containing mutants; rather, only true wild-type revertants or a virus, G50U/C47A, containing a second site mutation were recovered. These functional data suggest that the Watson-Crick edges of C47 and G50 (or A47 and U50 in the G50U/C47A mutant) are in close enough proximity to a hydrogen bond with U51 flipped out of the hairpin. Remarkably, increasing the helical stem stability rescues the previously lethal mutants U48C and G50U. These studies suggest that SL2 functions as an important, but rather plastic, structural element in stimulating subgenomic RNA synthesis in coronaviruses.
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28
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Suydam IT, Strobel SA. Fluorine substituted adenosines as probes of nucleobase protonation in functional RNAs. J Am Chem Soc 2008; 130:13639-48. [PMID: 18803382 DOI: 10.1021/ja803336y] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Ionized nucleobases are required for folding, conformational switching, or catalysis in a number of functional RNAs. A common strategy to study these sites employs nucleoside analogues with perturbed pKa, but the interpretation of these studies is often complicated by the chemical modification introduced, in particular modifications that add, remove, or translocate hydrogen bonding groups in addition to perturbing pKa values. In the present study we present a series of fluorine substituted adenosine analogues that produce large changes in N1 pKa values with minimal structural perturbation. These analogues include fluorine for hydrogen substitutions in the adenine ring of adenosine and 7-deaza-adenosine with resulting N1 pKa values spanning more than 4 pKa units. To demonstrate the utility of these analogues we have conducted a nucleotide analogue interference mapping (NAIM) study on a self-ligating construct of the Varkud Satellite (VS) ribozyme. We find that each of the analogues is readily incorporated by T7 RNA polymerase and produces fully active transcripts when substituted at the majority of sites. Strong interferences are observed for three sites known to be critical for VS ribozyme function, most notably A756. Substitutions at A756 lead to slight enhancements in activity for elevated pKa analogues and dramatic interferences in activity for reduced pKa analogues, supporting the proposed catalytic role for this base. The structural similarity of these analogues, combined with their even incorporation and selective interference, provides an improved method for identifying sites of adenosine protonation in a variety of systems.
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Affiliation(s)
- Ian T Suydam
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
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29
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Pereira MJB, Nikolova EN, Hiley SL, Jaikaran D, Collins RA, Walter NG. Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis. J Mol Biol 2008; 382:496-509. [PMID: 18656481 DOI: 10.1016/j.jmb.2008.07.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 07/01/2008] [Accepted: 07/08/2008] [Indexed: 01/18/2023]
Abstract
Non-coding RNAs of complex tertiary structure are involved in numerous aspects of the replication and processing of genetic information in many organisms; however, an understanding of the complex relationship between their structural dynamics and function is only slowly emerging. The Neurospora Varkud Satellite (VS) ribozyme provides a model system to address this relationship. First, it adopts a tertiary structure assembled from common elements, a kissing loop and two three-way junctions. Second, catalytic activity of the ribozyme is essential for replication of VS RNA in vivo and can be readily assayed in vitro. Here we exploit single molecule FRET to show that the VS ribozyme exhibits previously unobserved dynamic and heterogeneous hierarchical folding into an active structure. Readily reversible kissing loop formation combined with slow cleavage of the upstream substrate helix suggests a model whereby the structural dynamics of the VS ribozyme favor cleavage of the substrate downstream of the ribozyme core instead. This preference is expected to facilitate processing of the multimeric RNA replication intermediate into circular VS RNA, which is the predominant form observed in vivo.
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Affiliation(s)
- Miguel J B Pereira
- Department of Chemistry, Single Molecule Analysis Group, 930 N. University Ave., University of Michigan, Ann Arbor, MI 48109-1055, USA
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Bouchard P, Lacroix-Labonté J, Desjardins G, Lampron P, Lisi V, Lemieux S, Major F, Legault P. Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme. RNA (NEW YORK, N.Y.) 2008; 14:736-48. [PMID: 18314503 PMCID: PMC2271362 DOI: 10.1261/rna.824308] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Substrate recognition by the VS ribozyme involves a magnesium-dependent loop/loop interaction between the SLI substrate and the SLV hairpin from the catalytic domain. Recent NMR studies of SLV demonstrated that magnesium ions stabilize a U-turn loop structure and trigger a conformational change for the extruded loop residue U700, suggesting a role for U700 in SLI recognition. Here, we kinetically characterized VS ribozyme mutants to evaluate the contribution of U700 and other SLV loop residues to SLI recognition. To help interpret the kinetic data, we structurally characterized the SLV mutants by NMR spectroscopy and generated a three-dimensional model of the SLI/SLV complex by homology modeling with MC-Sym. We demonstrated that the mutation of U700 by A, C, or G does not significantly affect ribozyme activity, whereas deletion of U700 dramatically impairs this activity. The U700 backbone is likely important for SLI recognition, but does not appear to be required for either the structural integrity of the SLV loop or for direct interactions with SLI. Thus, deletion of U700 may affect other aspects of SLI recognition, such as magnesium ion binding and SLV loop dynamics. As part of our NMR studies, we developed a convenient assay based on detection of unusual (31)P and (15)N N7 chemical shifts to probe the formation of U-turn structures in RNAs. Our model of the SLI/SLV complex, which is compatible with biochemical data, leads us to propose novel interactions at the loop I/loop V interface.
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Affiliation(s)
- Patricia Bouchard
- Département de Biochimie, Université de Montréal, Montréal, H3C 3J7 Canada
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