1
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O'Loughlin S, Capece MC, Klimova M, Wills NM, Coakley A, Samatova E, O'Connor PBF, Loughran G, Weissman JS, Baranov PV, Rodnina MV, Puglisi JD, Atkins JF. Polysomes Bypass a 50-Nucleotide Coding Gap Less Efficiently Than Monosomes Due to Attenuation of a 5' mRNA Stem-Loop and Enhanced Drop-off. J Mol Biol 2020; 432:4369-4387. [PMID: 32454154 PMCID: PMC7245268 DOI: 10.1016/j.jmb.2020.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 01/03/2023]
Abstract
Efficient translational bypassing of a 50-nt non-coding gap in a phage T4 topoisomerase subunit gene (gp60) requires several recoding signals. Here we investigate the function of the mRNA stem–loop 5′ of the take-off codon, as well as the importance of ribosome loading density on the mRNA for efficient bypassing. We show that polysomes are less efficient at mediating bypassing than monosomes, both in vitro and in vivo, due to their preventing formation of a stem–loop 5′ of the take-off codon and allowing greater peptidyl-tRNA drop off. A ribosome profiling analysis of phage T4-infected Escherichia coli yielded protected mRNA fragments within the normal size range derived from ribosomes stalled at the take-off codon. However, ribosomes at this position also yielded some 53-nucleotide fragments, 16 longer. These were due to protection of the nucleotides that form the 5′ stem–loop. NMR shows that the 5′ stem–loop is highly dynamic. The importance of different nucleotides in the 5′ stem–loop is revealed by mutagenesis studies. These data highlight the significance of the 5′ stem–loop for the 50-nt bypassing and further enhance appreciation of relevance of the extent of ribosome loading for recoding. Monosomes are more efficient than polysome in mediating 50-nt translational bypassing. A 5′ mRNA stem–loop facilitates translational bypassing by monosomes. Ribosome profiling yields an extra-long, 53-nt, protected fragment of mRNA.
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Affiliation(s)
- Sinéad O'Loughlin
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland; School of Microbiology, University College Cork, Western Gateway Building, Western Road, Cork, T12 YT57, Ireland
| | - Mark C Capece
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-4090, USA
| | - Mariia Klimova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Norma M Wills
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Arthur Coakley
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland
| | - Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Patrick B F O'Connor
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland
| | - Gary Loughran
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Pavel V Baranov
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-4090, USA
| | - John F Atkins
- School of Biochemistry, University College Cork, Western Gateway Building, Western Road, Cork, T12 XF62, Ireland; School of Microbiology, University College Cork, Western Gateway Building, Western Road, Cork, T12 YT57, Ireland; Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA.
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2
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Weickhmann AK, Keller H, Wurm JP, Strebitzer E, Juen MA, Kremser J, Weinberg Z, Kreutz C, Duchardt-Ferner E, Wöhnert J. The structure of the SAM/SAH-binding riboswitch. Nucleic Acids Res 2019; 47:2654-2665. [PMID: 30590743 PMCID: PMC6411933 DOI: 10.1093/nar/gky1283] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/12/2018] [Accepted: 12/26/2018] [Indexed: 12/16/2022] Open
Abstract
S-adenosylmethionine (SAM) is a central metabolite since it is used as a methyl group donor in many different biochemical reactions. Many bacteria control intracellular SAM concentrations using riboswitch-based mechanisms. A number of structurally different riboswitch families specifically bind to SAM and mainly regulate the transcription or the translation of SAM-biosynthetic enzymes. In addition, a highly specific riboswitch class recognizes S-adenosylhomocysteine (SAH)—the product of SAM-dependent methyl group transfer reactions—and regulates enzymes responsible for SAH hydrolysis. High-resolution structures are available for many of these riboswitch classes and illustrate how they discriminate between the two structurally similar ligands SAM and SAH. The so-called SAM/SAH riboswitch class binds both ligands with similar affinities and is structurally not yet characterized. Here, we present a high-resolution nuclear magnetic resonance structure of a member of the SAM/SAH-riboswitch class in complex with SAH. Ligand binding induces pseudoknot formation and sequestration of the ribosome binding site. Thus, the SAM/SAH-riboswitches are translational ‘OFF’-switches. Our results establish a structural basis for the unusual bispecificity of this riboswitch class. In conjunction with genomic data our structure suggests that the SAM/SAH-riboswitches might be an evolutionary late invention and not a remnant of a primordial RNA-world as suggested for other riboswitches.
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Affiliation(s)
- A Katharina Weickhmann
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany
| | - Heiko Keller
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany
| | - Jan P Wurm
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Bavaria, Germany
| | - Elisabeth Strebitzer
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Michael A Juen
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Johannes Kremser
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Institute of Informatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Christoph Kreutz
- Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/M., Germany
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3
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Rennella E, Sára T, Juen M, Wunderlich C, Imbert L, Solyom Z, Favier A, Ayala I, Weinhäupl K, Schanda P, Konrat R, Kreutz C, Brutscher B. RNA binding and chaperone activity of the E. coli cold-shock protein CspA. Nucleic Acids Res 2017; 45:4255-4268. [PMID: 28126922 PMCID: PMC5397153 DOI: 10.1093/nar/gkx044] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/17/2017] [Indexed: 11/14/2022] Open
Abstract
Ensuring the correct folding of RNA molecules in the cell is of major importance for a large variety of biological functions. Therefore, chaperone proteins that assist RNA in adopting their functionally active states are abundant in all living organisms. An important feature of RNA chaperone proteins is that they do not require an external energy source to perform their activity, and that they interact transiently and non-specifically with their RNA targets. So far, little is known about the mechanistic details of the RNA chaperone activity of these proteins. Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that have been reported to bind single-stranded RNA and DNA. Here, we have used advanced NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting activity of CspA, the major cold shock protein of Escherichia coli, upon binding to different RNA hairpins. Real-time NMR provides detailed information on the folding kinetics and folding pathways. Finally, comparison of wild-type CspA with single-point mutants and small peptides yields insights into the complementary roles of aromatic and positively charged amino-acid side chains for the RNA chaperone activity of the protein.
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Affiliation(s)
- Enrico Rennella
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Tomáš Sára
- Department of Computational & Structural Biology, Max F. Perutz Laboratories, Campus, Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Michael Juen
- Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Wunderlich
- Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Lionel Imbert
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Zsofia Solyom
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Adrien Favier
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Isabel Ayala
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Katharina Weinhäupl
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Paul Schanda
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
| | - Robert Konrat
- Department of Computational & Structural Biology, Max F. Perutz Laboratories, Campus, Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble 1, 71 avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Grenoble, France.,Centre National de Recherche Scientifique (CNRS), Grenoble, France
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4
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Applications of NMR to structure determination of RNAs large and small. Arch Biochem Biophys 2017; 628:42-56. [PMID: 28600200 DOI: 10.1016/j.abb.2017.06.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 05/31/2017] [Accepted: 06/04/2017] [Indexed: 02/07/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to investigate the structure and dynamics of RNA, because many biologically important RNAs have conformationally flexible structures, which makes them difficult to crystallize. Functional, independently folded RNA domains, range in size between simple stem-loops of as few as 10-20 nucleotides, to 50-70 nucleotides, the size of tRNA and many small ribozymes, to a few hundred nucleotides, the size of more complex RNA enzymes and of the functional domains of non-coding transcripts. In this review, we discuss new methods for sample preparation, assignment strategies and structure determination for independently folded RNA domains of up to 100 kDa in molecular weight.
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5
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Marchanka A, Simon B, Carlomagno T. A Suite of Solid-State NMR Experiments for RNA Intranucleotide Resonance Assignment in a 21 kDa Protein-RNA Complex. Angew Chem Int Ed Engl 2013; 52:9996-10001. [DOI: 10.1002/anie.201304779] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Indexed: 02/06/2023]
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6
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Marchanka A, Simon B, Carlomagno T. A Suite of Solid-State NMR Experiments for RNA Intranucleotide Resonance Assignment in a 21 kDa Protein-RNA Complex. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304779] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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7
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Coggins BE, Venters RA, Zhou P. Radial sampling for fast NMR: Concepts and practices over three decades. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:381-419. [PMID: 20920757 PMCID: PMC2951763 DOI: 10.1016/j.pnmrs.2010.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 07/16/2010] [Indexed: 05/04/2023]
Affiliation(s)
- Brian E. Coggins
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
| | - Ronald A. Venters
- Duke University NMR Center, Duke University Medical Center, Durham, NC 27710
| | - Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
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8
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Abstract
The use of contemporary nuclear magnetic resonance (NMR) methods in the studies of model systems between microRNA (miRNA) and messenger RNA (mRNA) is reviewed. We describe our studies on structural features of 33-nt RNA model construct between let-7 miRNA and lin-41 mRNA at the second binding site. let-7 miRNA inhibits translation of lin-41 gene through formation of two complexes with the target sequence within 3' untranslated region of lin-41 mRNA in Caenorhabditis elegans. The base pairing, asymmetric internal loops, and adenine bulge in both the complementary sites are important for regulation of gene expression. NMR study on the uniformly (13)C- and (15)N-labeled RNA construct has shown that RNA molecule folds into a stable structure consisting of two stem regions separated by a well-defined asymmetric internal loop. Solution-state NMR can make important contribution toward deeper understanding of assembly, folding, and structural features of miRNA:mRNA complexes.
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Affiliation(s)
- Mirko Cevec
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
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9
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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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10
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Desaulniers JP, Chang YC, Aduri R, Abeysirigunawardena SC, SantaLucia J, Chow CS. Pseudouridines in rRNA helix 69 play a role in loop stacking interactions. Org Biomol Chem 2008; 6:3892-5. [PMID: 18931791 DOI: 10.1039/b812731j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The (1)H NMR spectra of RNAs representing E. coli 23S rRNA helix 69 with [1,3-(15)N]pseudouridine modification at specific sites reveal unique roles for pseudouridine in stabilizing base-stacking interactions in the hairpin loop region.
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11
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Hennig M, Williamson JR, Brodsky AS, Battiste JL. Recent advances in RNA structure determination by NMR. ACTA ACUST UNITED AC 2008; Chapter 7:Unit 7.7. [PMID: 18428875 DOI: 10.1002/0471142700.nc0707s02] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Despite recent advances in the solution of NMR structures of RNA and RNA-ligand complexes, the rate limiting step remains the gathering of a large number of NOE and torsion restraints. Additional sources of information for structure determination of larger RNA molecules have recently become available, and it is possible to supplement NOE and J-coupling data with the measurement of dipolar couplings and cross-correlated relaxation rates in high-resolution NMR spectroscopy.
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Affiliation(s)
- M Hennig
- The Scripps Research Institute, La Jolla, California, USA
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12
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Cevec M, Thibaudeau C, Plavec J. Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans. Nucleic Acids Res 2008; 36:2330-7. [PMID: 18296482 PMCID: PMC2367737 DOI: 10.1093/nar/gkn088] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Let-7 microRNA (miRNA) regulates heterochronic genes in developmental timing of the nematode Caenorhabditis elegans. Binding of miRNA to messenger RNA (mRNA) and structural features of the complex are crucial for gene silencing. We herein present the NMR solution structure of a model mimicking the interaction of let-7 miRNA with its complementary site (LCS 2) in the 3' untranslated region (3'-UTR) of the lin-41 mRNA. A structural study was performed by NMR spectroscopy using NOE restraints, torsion angle restraints and residual dipolar couplings. The 33-nt RNA construct folds into a stem-loop structure that features two stem regions which are separated by an asymmetric internal loop. One of the stems comprises a GU wobble base pair, which does not alter its overall A-form RNA conformation. The asymmetric internal loop adopts a single, well-defined structure in which three uracils form a base triple, while two adenines form a base pair. The 3D structure of the construct gives insight into the structural aspects of interactions between let-7 miRNA and lin-41 mRNA.
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Affiliation(s)
- Mirko Cevec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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13
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Webba da Silva M. NMR methods for studying quadruplex nucleic acids. Methods 2008; 43:264-77. [PMID: 17967697 DOI: 10.1016/j.ymeth.2007.05.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 05/16/2007] [Indexed: 12/22/2022] Open
Abstract
Solution NMR spectroscopy has traditionally played a central role in examining quadruplex structure, dynamics, and interactions. Here, an overview is given of the methods currently applied to structural, dynamics, thermodynamics, and kinetics studies of nucleic acid quadruplexes and associated cations.
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Affiliation(s)
- Mateus Webba da Silva
- School of Biomedical Sciences, University of Ulster, Cromore Road, Coleraine BT52 1SA, UK.
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14
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Abstract
This chapter reviews the methodologies for RNA structure determination by liquid-state nuclear magnetic resonance (NMR). The routine production of milligram quantities of isotopically labeled RNA remains critical to the success of NMR-based structure studies. The standard method for the preparation of isotopically labeled RNA for structural studies in solution is in vitro transcription from DNA oligonucleotide templates using T7 RNA polymerase and unlabeled or isotopically labeled nucleotide triphosphates (NTPs). The purification of the desired RNA can be performed by either denaturing polyacrylamide gel electrophoresis (PAGE) or anion-exchange chromatography. Our basic strategy for studying RNA in solution by NMR is outlined. The topics covered include RNA resonance assignment, restraint collection, and the structure calculation process. Selected examples of NMR spectra are given for a correctly folded 30 nucleotide-containing RNA.
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15
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Jin H, Loria JP, Moore PB. Solution structure of an rRNA substrate bound to the pseudouridylation pocket of a box H/ACA snoRNA. Mol Cell 2007; 26:205-15. [PMID: 17466623 DOI: 10.1016/j.molcel.2007.03.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Revised: 02/13/2007] [Accepted: 03/14/2007] [Indexed: 11/15/2022]
Abstract
Base pairing between the RNA components of box H/ACA small nucleolar ribonucleoproteins (snoRNPs) and sequences in other eukaryotic RNAs target specific uridines for pseudouridylation. An RNA called HJ1 has been developed that interacts with the rRNA sequence targeted by the 5' pseudouridylation pocket of human U65 snoRNA the same way as intact U65 snoRNA. Sequences on both strands of the analog of the U65 snoRNP pseudouridylation pocket in HJ1 pair with its substrate sequence, and the resulting complex, called HJ3, is strongly stabilized by Mg(2+). The solution structure of HJ3 reveals an Omega-shaped RNA interaction motif that has not previously been described, which is likely to be common to all box H/ACA snoRNP-substrate complexes. The topology of the complex explains why the access of substrate sequences to snoRNPs is facile and how uridine selection may occur when these complexes form.
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Affiliation(s)
- Hong Jin
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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16
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Joli F, Bouchemal N, Laigle A, Hartmann B, Hantz E. Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides. Nucleic Acids Res 2006; 34:5740-51. [PMID: 17041234 PMCID: PMC1694020 DOI: 10.1093/nar/gkl617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A preferential target of antisense oligonucleotides directed against human PGY/MDR1 mRNA is a hairpin containing a stem with a G*U wobble pair, capped by the purine-rich 5'r(GGGAUG)3' hexaloop. This hairpin is studied by multidimensional NMR and restrained molecular dynamics, with special emphasis on the conformation of south sugars and non-standard phosphate linkages evidenced in both the stem and the loop. The hairpin is found to be highly structured. The G*U wobble pair, a strong counterion binding site, displays structural particularities that are characteristic of this type of mismatch. The upper part of the stem undergoes distortions that optimize its interactions with the beginning of the loop. The loop adopts a new fold in which the single-stranded GGGA purine tract is structured in A-like conformation stacked in continuity of the stem and displays an extensive hydrogen bonding surface for recognition. The remarkable hairpin stability results from classical inter- and intra-strand interactions reinforced by numerous hydrogen bonds involving unusual backbone conformations and ribose 2'-hydroxyl groups. Overall, this work emphasizes numerous features that account for the well-ordered structure of the whole hairpin and highlights the loop properties that facilitate interaction with antisense oligonucleotides.
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Affiliation(s)
- Flore Joli
- Laboratoire BioMoCeTi, CNRS UMR 7033UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
- Laboratoire de Biochimie Théorique, CNRS UPR 9080Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- To whom correspondence should be addressed. Tel: +33 158415167; Fax: +33 158415026;
| | - Nadia Bouchemal
- Laboratoire BioMoCeTi, CNRS UMR 7033UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
| | - Alain Laigle
- Laboratoire BioMoCeTi, CNRS UMR 7033UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
| | - Brigitte Hartmann
- Laboratoire de Biochimie Théorique, CNRS UPR 9080Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- To whom correspondence should be addressed. Tel: +33 158415167; Fax: +33 158415026;
| | - Edith Hantz
- Laboratoire BioMoCeTi, CNRS UMR 7033UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France
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17
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Joli F, Bouchemal N, Hartmann B, Hantz E. NMR and molecular modelling studies of an RNA hairpin containing a G-rich hexaloop. CR CHIM 2006. [DOI: 10.1016/j.crci.2005.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Van Melckebeke H, Pardi A, Boisbouvier J, Simorre JP, Brutscher B. Resolution-enhanced base-type-edited HCN experiment for RNA. JOURNAL OF BIOMOLECULAR NMR 2005; 32:263-71. [PMID: 16211480 DOI: 10.1007/s10858-005-8872-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Accepted: 06/07/2005] [Indexed: 05/04/2023]
Abstract
New base-type-edited transverse-relaxation optimized CT-HCN(C) experiments are presented that yield intra-base and sugar-to-base correlations for 13C-15N labeled RNA. High spectral resolution in the 13C and 15N dimensions is achieved by constant time (CT) frequency editing. A spectral editing filter applied during the CT 15N labeling period separates the correlation peaks arising from G/U and A/C nucleotide bases. This provides the increased spectral resolution required to unambiguously connect the 1H and 13C resonances in sugar and base moieties of RNA nucleotides. In addition, the experiment allows base type identification for each residue, and therefore presents an attractive spectroscopic alternative to nucleotide-specific isotope labeling. Application to a 33-nucleotide RNA aptamer demonstrates the performance of the new pulse scheme.
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Affiliation(s)
- Hélène Van Melckebeke
- Laboratoire de RMN, Institut de Biologie Structurale--Jean-Pierre Ebel, UMR, 5075 CNRS-CEA-UJF, 41, rue Jules Horowitz, 38027, Cedex, Grenoble, France
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19
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Dayie KT. Resolution enhanced homonuclear carbon decoupled triple resonance experiments for unambiguous RNA structural characterization. JOURNAL OF BIOMOLECULAR NMR 2005; 32:129-39. [PMID: 16034664 DOI: 10.1007/s10858-005-5093-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Accepted: 03/21/2005] [Indexed: 05/03/2023]
Abstract
Large RNAs (>30 nucleotides) suffer from extensive resonance overlap that can seriously hamper unambiguous structural characterization. Here we present a set of 3D multinuclear NMR experiments with improved and optimized resolution and sensitivity for aiding with the assignment of RNA molecules. In all these experiments strong base and ribose carbon-carbon couplings are eliminated by homonuclear band-selective decoupling, leading to improved signal to noise and resolution of the C5, C6, and C1' carbon resonances. This decoupling scheme is applied to base-type selective 13C-edited NOESY, 13C-edited TOCSY (HCCH, CCH), HCCNH, and ribose H1C1C2 experiments. The 3D implementation of the HCCNH experiment with both carbon and nitrogen evolution enables direct correlation of 13C and 15N resonances at different proton resonant frequencies. The advantages of the new experiments are demonstrated on a 36 nucleotides hairpin RNA from domain 5 (D5) of the group II intron Pylaiella littoralis using an abbreviated assignment strategy. These four experiments provided additional separation for regions of the RNA that have overlapped chemical shift resonances, and enabled the assignment of critical D5 bulge nucleotides that could not be assigned using current experimental schemes.
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Affiliation(s)
- Kwaku T Dayie
- Department of Molecular Genetics and Program in Structural Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA.
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20
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Campbell DO, Legault P. Nuclear magnetic resonance structure of the Varkud satellite ribozyme stem-loop V RNA and magnesium-ion binding from chemical-shift mapping. Biochemistry 2005; 44:4157-70. [PMID: 15766243 DOI: 10.1021/bi047963l] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An important step in the substrate recognition of the Neurospora Varkud Satellite (VS) ribozyme is the formation of a magnesium-dependent loop/loop interaction between the terminal loops of stem-loops I and V. We have studied the structure of stem-loop V by nuclear magnetic resonance spectroscopy and shown that it adopts a U-turn conformation, a common motif found in RNA. Structural comparisons indicate that the U-turn of stem-loop V fulfills some but not all of the structural characteristics found in canonical U-turn structures. This U-turn conformation exposes the Watson-Crick faces of the bases within stem-loop V (G697, A698, and C699) and makes them accessible for interaction with stem-loop I. Using chemical-shift mapping, we show that magnesium ions interact with the loop of the isolated stem-loop V and induce a conformational change that may be important for interaction with stem-loop I. This study expands our understanding of the role of U-turn motifs in RNA structure and function and provides insights into the mechanism of substrate recognition in the VS ribozyme.
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Affiliation(s)
- Dean O Campbell
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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21
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Abstract
NMR spectroscopy is a powerful tool for studying proteins and nucleic acids in solution. This is illustrated by the fact that nearly half of all current RNA structures were determined by using NMR techniques. Information about the structure, dynamics, and interactions with other RNA molecules, proteins, ions, and small ligands can be obtained for RNA molecules up to 100 nucleotides. This review provides insight into the resonance assignment methods that are the first and crucial step of all NMR studies, into the determination of base-pair geometry, into the examination of local and global RNA conformation, and into the detection of interaction sites of RNA. Examples of NMR investigations of RNA are given by using several different RNA molecules to illustrate the information content obtainable by NMR spectroscopy and the applicability of NMR techniques to a wide range of biologically interesting RNA molecules.
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Affiliation(s)
- Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany
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22
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Bondensgaard K, Mollova ET, Pardi A. The global conformation of the hammerhead ribozyme determined using residual dipolar couplings. Biochemistry 2002; 41:11532-42. [PMID: 12269797 DOI: 10.1021/bi012167q] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The global structure of the hammerhead ribozyme was determined in the absence of Mg(2+) by solution NMR experiments. The hammerhead ribozyme motif forms a branched structure consisting of three helical stems connected to a catalytic core. The (1)H-(15)N and (1)H-(13)C residual dipolar couplings were measured in a set of differentially (15)N/(13)C-labeled ribozymes complexed with an unlabeled noncleavable substrate. The residual dipolar couplings provide orientation information on both the local and the global structure of the molecule. Analysis of the residual dipolar couplings demonstrated that the local structure of the three helical stems in solution is well modeled by an A-form conformation. However, the global structure of the hammerhead in solution in the absence of Mg(2+) is not consistent with the Y-shaped conformation observed in crystal structures of the hammerhead. The residual dipolar couplings for the helical stems were combined with standard NOE and J coupling constant NMR data from the catalytic core. The NOE data show formation of sheared G-A base pairs in domain 2. These NMR data were used to determine the global orientation of the three helical stems in the hammerhead. The hammerhead forms a rather extended structure under these conditions with a large angle between stems I and II ( approximately 153 degrees ), a smaller angle between stems II and III ( approximately 100 degrees ), and the smallest angle between stems I and III ( approximately 77 degrees ). The residual dipolar coupling data also contain information on the dynamics of the molecule and were used here to provide qualitative information on the flexibility of the helical domains in the hammerhead ribozyme-substrate complex.
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Affiliation(s)
- Kent Bondensgaard
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
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23
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Abstract
DNA oligonucleotides that have repetitive tracts of guanine bases can form G-quadruplex structures that display an amazing polymorphism. Structures of several new G-quadruplexes have been solved recently that greatly expand the known structural motifs observed in nucleic acid quadruplexes. Base triads, base hexads, and quartets that contain cytosine have recently been identified stacked over the familiar G-quartets. The current status of the diverse array of structural features in quadruplexes is described and used to provide insight into the polymorphism and folding pathways. This review also summarizes recent progress in the techniques used to probe the structures of G-quadruplexes and discusses the role of ion binding in quadruplex formation. Several of the quadruplex structures featured in this review can be accessed in the online version of this review as CHIME representations.
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Affiliation(s)
- M A Keniry
- Research School of Chemistry, The Australian National University, Canberra, ACT 0200, Australia.
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24
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Cromsigt J, van Buuren B, Schleucher J, Wijmenga S. Resonance assignment and structure determination for RNA. Methods Enzymol 2002; 338:371-99. [PMID: 11460559 DOI: 10.1016/s0076-6879(02)38229-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Affiliation(s)
- J Cromsigt
- Department of Medical Biosciences-Medical Biophysics, Umea University, S-901 87 Umea, Sweden
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25
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Abstract
Over the last decade, a vast number of useful nuclear magnetic resonance (NMR) experiments have been developed and successfully employed to determine the structure and dynamics of RNA oligonucleotides. Despite this progress, high-resolution RNA structure determination by NMR spectroscopy still remains a lengthy process and requires programming and extensive calibrations to perform NMR experiments successfully. To accelerate RNA structure determination by NMR spectroscopy, we have designed and programmed a package of RNA NMR experiments, called RNAPack. The user-friendly package contains a set of semiautomated single, double, and triple resonance NMR experiments, which are fully optimized for high-resolution RNA solution structure determination on Varian NMR spectrometers. RNAPack provides an autocalibration feature that allows rapid calibration of all NMR experiments in a single step and thereby speeds up the NMR data collection and eliminates user errors. In our laboratory, we have successfully employed this technology to solve RNA solution structures of domains of the internal ribosome entry site of the genomic hepatitis C viral RNA in less than 3 months. RNAPack therefore makes NMR spectroscopy an attractive and rapid structural tool and allows integration of atomic resolution structural information into biochemical studies of large RNA systems.
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Affiliation(s)
- P J Lukavsky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
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26
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Abstract
Aminoglycoside antibiotics, including paromomycin, neomycin and gentamicin, target a region of highly conserved nucleotides in the decoding region aminoacyl-tRNA site (A site) of 16 S rRNA on the 30 S subunit. Change of a single nucleotide, A1408 to G, reduces the affinity of many aminoglycosides for the ribosome; G1408 distinguishes between prokaryotic and eukaryotic ribosomes. The structures of a prokaryotic decoding region A-site oligonucleotide free in solution and bound to the aminoglycosides paromomycin and gentamicin C1a were determined previously. Here, the structure of a eukaryotic decoding region A-site oligonucleotide bound to paromomycin has been determined using NMR spectroscopy and compared to the prokaryotic A-site-paromomycin structure. A conformational change in three adenosine residues of an internal loop, critical for high-affinity antibiotic binding, was observed in the prokaryotic RNA-paromomycin complex in comparison to its free form. This conformational change is not observed in the eukaryotic RNA-paromomycin complex, disrupting the binding pocket for ring I of the antibiotic. The lack of the conformational change supports footprinting and titration calorimetry data that demonstrate approximately 25-50-fold weaker binding of paromomycin to the eukaryotic decoding-site oligonucleotide. Neomycin, which is much less active against Escherichia coli ribosomes with an A1408G mutation, binds non-specifically to the oligonucleotide. These results suggest that eukaryotic ribosomal RNA has a shallow binding pocket for aminoglycosides, which accommodates only certain antibiotics.
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MESH Headings
- Adenosine/chemistry
- Anti-Bacterial Agents/chemistry
- Anti-Bacterial Agents/metabolism
- Drug Resistance, Microbial/genetics
- Guanosine/chemistry
- Magnetic Resonance Spectroscopy/methods
- Molecular Structure
- Neomycin/metabolism
- Paromomycin/metabolism
- RNA, Bacterial/chemistry
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- Species Specificity
- Structure-Activity Relationship
- Substrate Specificity
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Affiliation(s)
- S R Lynch
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
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27
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Abstract
The aminoglycoside antibiotics target a region of highly conserved nucleotides in the aminoacyl-tRNA site (A site) of 16 S RNA on the 30 S subunit. The structures of a prokaryotic decoding region A-site oligonucleotide free in solution and bound to the aminoglycosides paromomycin and gentamicin C1A have been determined. Here, the structure of a eukaryotic decoding region A-site oligonucleotide has been determined using homonuclear and heteronuclear NMR spectroscopy, and compared to the unbound prokaryotic rRNA structure. The two structures are similar, with a U1406-U1495 base-pair, a C1407-G1494 Watson-Crick base-pair, and a G1408-A1493 base-pair instead of the A1408-A1493 base-pair of the prokaryotic structure. The two structures differ in the orientation of the 1408 position with respect to A1493; G1408 is rotated toward the major groove, which is the binding pocket for aminoglycosides. The structures also differ in the stacking geometry of G1494 on A1493, which could have slight long-range conformational effects.
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Affiliation(s)
- S R Lynch
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
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28
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Lynch SR, Recht MI, Puglisi JD. Biochemical and nuclear magnetic resonance studies of aminoglycoside-RNA complexes. Methods Enzymol 2000; 317:240-61. [PMID: 10829284 DOI: 10.1016/s0076-6879(00)17018-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- S R Lynch
- Department of Structural Biology, Stanford University School of Medicine, California 94305-5126, USA
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29
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Wöhnert J, Ramachandran R, Görlach M, Brown LR. Triple-resonance experiments for correlation of H5 and exchangeable pyrimidine base hydrogens in (13)C,(15)N-labeled RNA. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1999; 139:430-433. [PMID: 10423381 DOI: 10.1006/jmre.1999.1797] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Triple-resonance two-dimensional H5(C5C4N)H experiments are described that provide through-bond H5 to imino/amino connectivities in uridines and cytidines in (13)C, (15)N-labeled RNAs. The experiments employ selective INEPT steps for transferring magnetization from the H5 hydrogens through the intervening C5, C4, and N3/N4 nuclei to the imino/amino hydrogens. The improved sensitivity of these experiments for assignments in a large 43-nucleotide RNA is demonstrated.
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Affiliation(s)
- J Wöhnert
- Abteilung für Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V., Postfach 100813, Jena, D-07708, Germany
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30
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Legault P, Hoogstraten CG, Metlitzky E, Pardi A. Order, dynamics and metal-binding in the lead-dependent ribozyme. J Mol Biol 1998; 284:325-35. [PMID: 9813121 DOI: 10.1006/jmbi.1998.2181] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The in vitro selected lead-dependent ribozyme is among the smallest and simplest of the known catalytic RNA motifs and has a unique metal ion specificity for divalent lead. The conformation and dynamics of this ribozyme are analyzed here by NMR and chemical probing experiments. Complete assignments of the 1H, 13C, and 15N resonances have been made, and the NMR chemical shift changes in the presence of Pb2+, Mg2+ or high concentrations of Na+ show that there is no significant structural change upon addition of either activating (Pb2+) or inhibitory (Mg2+) divalent ions. The 13C NMR relaxation data indicate substantial dynamic fluctuations on various time-scales for active-site residues in this ribozyme. The combination of chemical probing and NMR experiments reveals a picture of the active site for the lead-dependent ribozyme that has both ordered and dynamic features.
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Affiliation(s)
- P Legault
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, CO, 80309-0215, USA
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31
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Abstract
Aminoglycoside antibiotics that bind to the ribosomal A site cause misreading of the genetic code and inhibit translocation. The clinically important aminoglycoside, gentamicin C, is a mixture of three components. Binding of each gentamicin component to the ribosome and to a model RNA oligonucleotide was studied biochemically and the structure of the RNA complexed to gentamicin C1a was solved using magnetic resonance nuclear spectroscopy. Gentamicin C1a binds in the major groove of the RNA. Rings I and II of gentamicin direct specific RNA-drug interactions. Ring III of gentamicin, which distinguishes this subclass of aminoglycosides, also directs specific RNA interactions with conserved base pairs. The structure leads to a general model for specific ribosome recognition by aminoglycoside antibiotics and a possible mechanism for translational inhibition and miscoding. This study provides a structural rationale for chemical synthesis of novel aminoglycosides.
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Affiliation(s)
- S Yoshizawa
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5400, USA
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32
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Fourmy D, Yoshizawa S, Puglisi JD. Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA. J Mol Biol 1998; 277:333-45. [PMID: 9514734 DOI: 10.1006/jmbi.1997.1551] [Citation(s) in RCA: 202] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aminoglycoside antibiotics that bind to ribosomal RNA in the aminoacyl-tRNA site (A-site) cause misreading of the genetic code and inhibit translocation. An A-site RNA oligonucleotide specifically binds to aminoglycoside antibiotics and the structure of the RNA-paromomycin complex was previously determined by nuclear magnetic resonance (NMR) spectroscopy. Here, the A-site RNA structure in its free form has been determined using heteronuclear NMR and compared to the structure of the paromomycin-RNA complex. As in the complex with paromomycin, the asymmetric internal loop is closed by a Watson-Crick base-pair (C1407.G1494) and by two non-canonical base-pairs (U1406.U1495, A1408.A1493). A1492 stacks below A1493 and is intercalated between the upper and lower stems. The comparison of the free and bound conformations of the RNA shows that two universally conserved residues of the A site of 16 S rRNA, A1492 and A1493, are displaced towards the minor groove of the RNA helix in presence of antibiotic. These changes in the RNA conformation place the N1 positions of A1492 and A1493 on the minor groove side of the A-site RNA and suggest a mechanism of action of aminoglycosides on translation.
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Affiliation(s)
- D Fourmy
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA
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33
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Simorre JP, Legault P, Baidya N, Uhlenbeck OC, Maloney L, Wincott F, Usman N, Beigelman L, Pardi A. Structural variation induced by different nucleotides at the cleavage site of the hammerhead ribozyme. Biochemistry 1998; 37:4034-44. [PMID: 9521724 DOI: 10.1021/bi972493z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The hammerhead ribozyme is capable of cleaving RNA substrates at 5' UX 3' sequences (where the cleavage site, X, can be A, C, or U). Hammerhead complexes containing dC, dA, dI, or rG nucleotides at the cleavage site have been studied by NMR. The rG at the cleavage site forms a Watson-Crick base pair with C3 in the conserved core of the hammerhead, indicating that rG substrates inhibit the cleavage reaction by stabilizing an inactive conformation of the molecule. Isotope-edited NMR experiments on the hammerhead complexes show that there are different short proton-proton distances between neighboring residues depending upon whether there is a dC or dA at the cleavage site. These NMR data demonstrate that there are significant differences in the structure and/or dynamics of the active-site residues in these hammerhead complexes. Molecular dynamics calculations were used to model the conformations of the cleavage-site variants consistent with the NMR data. The solution conformations of the hammerhead ribozyme-substrate complexes are compared with the X-ray structure of the hammerhead ribozyme and are used to help understand the thermodynamic and kinetic differences among the cleavage-site variants.
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Affiliation(s)
- J P Simorre
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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34
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Addess KJ, Basilion JP, Klausner RD, Rouault TA, Pardi A. Structure and dynamics of the iron responsive element RNA: implications for binding of the RNA by iron regulatory binding proteins. J Mol Biol 1997; 274:72-83. [PMID: 9398517 DOI: 10.1006/jmbi.1997.1377] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The iron responsive element (IRE) is a approximately 30 nucleotide RNA hairpin that is located in the 5' untranslated region of all ferritin mRNAs and in the 3' untranslated region of all transferrin receptor mRNAs. The IREs are bound by two related IRE-binding proteins (IRPs) which help control intracellular levels of iron by regulating the expression of both ferritin and transferrin receptor genes. Multi-dimensional NMR and computational approaches were used to study the structure and dynamics of the IRE RNA in solution. The NMR data are consistent with formation of A-form helical stem regions, a one-base internal bulge and a Watson-Crick C.G base-pair between the first and fifth nucleotides in the loop. A superposition of refined structures indicates that the conserved C in the internal bulge, and three residues in the six-nucleotide hairpin loop are quite dynamic in this RNA. The structural roles of the stems, the loop and the bulge in the function of the IRE RNA and in possible interactions with the iron regulatory protein are discussed.
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Affiliation(s)
- K J Addess
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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35
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Puglisi EV, Green R, Noller HF, Puglisi JD. Structure of a conserved RNA component of the peptidyl transferase centre. NATURE STRUCTURAL BIOLOGY 1997; 4:775-8. [PMID: 9334738 DOI: 10.1038/nsb1097-775] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The structure of a conserved hairpin loop involved in peptidyl-tRNA recognition by 50S ribosomal subunits has been solved by NMR. The loop is closed by a novel G-C base pair and presents guanine residues for RNA recognition.
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36
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Zimmermann GR, Jenison RD, Wick CL, Simorre JP, Pardi A. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. NATURE STRUCTURAL BIOLOGY 1997; 4:644-9. [PMID: 9253414 DOI: 10.1038/nsb0897-644] [Citation(s) in RCA: 213] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To visualize the interplay of RNA structural interactions in a ligand binding site, we have determined the solution structure of a high affinity RNA-theophylline complex using NMR spectroscopy. The structure provides insight into the ability of this in vitro selected RNA to discriminate theophylline from the structurally similar molecule caffeine. Numerous RNA structural motifs combine to form a well-ordered binding pocket where an intricate network of hydrogen bonds and stacking interactions lock the theophylline into the complex. Two internal loops interact to form the binding site which consists of a sandwich of three base triples. The complex also contains novel base-zipper and 1-3-2 stacking motifs, in addition to an adenosine platform and a reversed sugar. An important feature of the RNA is that many of the conserved core residues participate in multiple overlapping tertiary interactions. This complex illustrates how interlocking structural motifs can be assembled into a highly specific ligand-binding site that possesses high levels of affinity and molecular discrimination.
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Affiliation(s)
- G R Zimmermann
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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37
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Legault P, Pardi A. Unusual Dynamics and pKa Shift at the Active Site of a Lead-Dependent Ribozyme. J Am Chem Soc 1997. [DOI: 10.1021/ja9640051] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pascale Legault
- Contribution from the Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215
| | - Arthur Pardi
- Contribution from the Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215
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38
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Szyperski T, Braun D, Banecki B, Wüthrich K. Useful Information from Axial Peak Magnetization in Projected NMR Experiments. J Am Chem Soc 1996. [DOI: 10.1021/ja961015t] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- T. Szyperski
- Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule-Hönggerberg CH-8093 Zürich, Switzerland
| | - D. Braun
- Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule-Hönggerberg CH-8093 Zürich, Switzerland
| | - B. Banecki
- Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule-Hönggerberg CH-8093 Zürich, Switzerland
| | - K. Wüthrich
- Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule-Hönggerberg CH-8093 Zürich, Switzerland
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39
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Simorre JP, Zimmermann GR, Mueller L, Pardi A. Triple-Resonance Experiments for Assignment of Adenine Base Resonances in13C/15N-Labeled RNA. J Am Chem Soc 1996. [DOI: 10.1021/ja954208+] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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