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Warden MS, Cai K, Cornilescu G, Burke JE, Ponniah K, Butcher SE, Pascal SM. Conformational flexibility in the enterovirus RNA replication platform. RNA (NEW YORK, N.Y.) 2019; 25:376-387. [PMID: 30578285 PMCID: PMC6380274 DOI: 10.1261/rna.069476.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/19/2018] [Indexed: 05/06/2023]
Abstract
A presumed RNA cloverleaf (5'CL), located at the 5'-most end of the noncoding region of the enterovirus genome, is the primary established site for initiation of genomic replication. Stem-loop B (SLB) and stem-loop D (SLD), the two largest stem-loops within the 5'CL, serve as recognition sites for protein interactions that are essential for replication. Here we present the solution structure of rhinovirus serotype 14 5'CL using a combination of nuclear magnetic resonance spectroscopy and small-angle X-ray scattering. In the absence of magnesium, the structure adopts an open, somewhat extended conformation. In the presence of magnesium, the structure compacts, bringing SLB and SLD into close contact, a geometry that creates an extensive accessible major groove surface, and permits interaction between the proteins that target each stem-loop.
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Affiliation(s)
- Meghan S Warden
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Kai Cai
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jordan E Burke
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, USA
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2
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Warden MS, Tonelli M, Cornilescu G, Liu D, Hopersberger LJ, Ponniah K, Pascal SM. Structure of RNA Stem Loop B from the Picornavirus Replication Platform. Biochemistry 2017; 56:2549-2557. [PMID: 28459542 DOI: 10.1021/acs.biochem.7b00141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The presumptive RNA cloverleaf at the start of the 5'-untranslated region of the picornavirus genome is an essential element in replication. Stem loop B (SLB) of the cloverleaf is a recognition site for the host polyC-binding protein, which initiates a switch from translation to replication. Here we present the solution structure of human rhinovirus isotype 14 SLB using nuclear magnetic resonance spectroscopy. SLB adopts a predominantly A-form helical structure. The stem contains five Watson-Crick base pairs and one wobble base pair and is capped by an eight-nucleotide loop. The wobble base pair introduces perturbations into the helical parameters but does not appear to introduce flexibility. However, the helix major groove appears to be accessible. Flexibility is seen throughout the loop and in the terminal nucleotides. The pyrimidine-rich region of the loop, the apparent recognition site for the polyC-binding protein, is the most disordered region of the structure.
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Affiliation(s)
- Meghan S Warden
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Dong Liu
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Lorelei J Hopersberger
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Komala Ponniah
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
| | - Steven M Pascal
- Department of Chemistry and Biochemistry, Old Dominion University , Norfolk, Virginia 23529, United States
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3
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Thulasi P, Pandya LK, Znosko BM. Thermodynamic characterization of RNA triloops. Biochemistry 2010; 49:9058-62. [PMID: 20843054 DOI: 10.1021/bi101164s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Relatively few thermodynamic parameters are available for RNA triloops. Therefore, 24 stem-loop sequences containing naturally occurring triloops were optically melted, and the thermodynamic parameters ΔH°, ΔS°, ΔG°(37), and T(M) for each stem-loop were determined. These new experimental values, on average, are 0.5 kcal/mol different from the values predicted for these triloops using the model proposed by Mathews et al. [Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M., and Turner, D. H. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 7287-7292]. The data for the 24 triloops reported here were then combined with the data for five triloops that were published previously. A new model was derived to predict the free energy contribution of previously unmeasured triloops. The average absolute difference between the measured values and the values predicted using this proposed model is 0.3 kcal/mol. These new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA stem-loops containing triloops and, furthermore, should allow for improved prediction of secondary structure from sequence.
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Affiliation(s)
- Praneetha Thulasi
- Department of Chemistry, Saint Louis University, Saint Louis, Missouri 63103, United States
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4
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Claridge JK, Headey SJ, Chow JYH, Schwalbe M, Edwards PJ, Jeffries CM, Venugopal H, Trewhella J, Pascal SM. A picornaviral loop-to-loop replication complex. J Struct Biol 2009; 166:251-62. [PMID: 19268541 PMCID: PMC7172786 DOI: 10.1016/j.jsb.2009.02.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 01/30/2009] [Accepted: 02/21/2009] [Indexed: 11/28/2022]
Abstract
Picornaviruses replicate their RNA genomes through a highly conserved mechanism that involves an interaction between the principal viral protease (3C(pro)) and the 5'-UTR region of the viral genome. The 3C(pro) catalytic site is the target of numerous replication inhibitors. This paper describes the first structural model of a complex between a picornaviral 3C(pro) and a region of the 5'-UTR, stem-loop D (SLD). Using human rhinovirus as a model system, we have combined NMR contact information, small-angle X-ray scattering (SAXS) data, and previous mutagenesis results to determine the shape, position and relative orientation of the 3C(pro) and SLD components. The results clearly identify a 1:1 binding stoichiometry, with pronounced loops from each molecule providing the key binding determinants for the interaction. Binding between SLD and 3C(pro) induces structural changes in the proteolytic active site that is positioned on the opposite side of the protease relative to the RNA/protein interface, suggesting that subtle conformational changes affecting catalytic activity are relayed through the protein.
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Affiliation(s)
- Jolyon K Claridge
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
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Cordey S, Gerlach D, Junier T, Zdobnov EM, Kaiser L, Tapparel C. The cis-acting replication elements define human enterovirus and rhinovirus species. RNA (NEW YORK, N.Y.) 2008; 14:1568-1578. [PMID: 18541697 PMCID: PMC2491478 DOI: 10.1261/rna.1031408] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Accepted: 04/24/2008] [Indexed: 05/26/2023]
Abstract
Replication of picornaviruses is dependent on VPg uridylylation, which is linked to the presence of the internal cis-acting replication element (cre). Cre are located within the sequence encoding polyprotein, yet at distinct positions as demonstrated for poliovirus and coxsackievirus-B3, cardiovirus, and human rhinovirus (HRV-A and HRV-B), overlapping proteins 2C, VP2, 2A, and VP1, respectively. Here we report a novel distinct cre element located in the VP2 region of the recently reported HRV-A2 species and provide evolutionary evidence of its functionality. We also experimentally interrogated functionality of recently identified HRV-B cre in the 2C region that is orthologous to the human enterovirus (HEV) cre and show that it is dispensable for replication and appears to be a nonfunctional evolutionary relic. In addition, our mutational analysis highlights two amino acids in the 2C protein that are crucial for replication. Remarkably, we conclude that each genetic clade of HRV and HEV is characterized by a unique functional cre element, where evolutionary success of a new genetic lineage seems to be associated with an invention of a novel cre motif and decay of the ancestral one. Therefore, we propose that cre element could be considered as an additional criterion for human rhinovirus and enterovirus classification.
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Affiliation(s)
- Samuel Cordey
- Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 1211 Geneva 14, Switzerland.
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Amborski AN, Johnson PE. Enhanced NMR signal detection of imino protons in RNA molecules containing 3' dangling nucleotides. JOURNAL OF BIOMOLECULAR NMR 2008; 40:183-188. [PMID: 18273681 DOI: 10.1007/s10858-008-9220-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Revised: 01/07/2008] [Accepted: 01/10/2008] [Indexed: 05/25/2023]
Abstract
We present a method for improving the quality of nuclear magnetic resonance (NMR) spectra involving exchangeable protons near the base of the stem of RNA hairpin molecules. NMR spectra of five different RNA hairpins were compared. These hairpins consisted of a native RNA structure and four molecules each having different unpaired, or dangling, nucleotides at the 3' end. NMR experiments were acquired in water for each construct and the quality of the imino proton spectral regions were examined. The imino resonances near the base of the stem of the wild type RNA structure were not observed due to breathing motions. However, a significant increase in spectral quality for molecules with dangling 3' adenosine or guanosine nucleotides was observed, with imino protons detected in these constructs that were not observed in the wild type construct. A modest improvement in spectral quality was seen for the construct with a 3' unpaired uridine, whereas no significant improvement was observed for a 3' unpaired cytidine. This improvement in NMR spectral quality mirrors the increased thermodynamic stability observed for 3' unpaired nucleotides which is dependant on the stacking interactions of these nucleotides against the base of the stem. The use of a dangling 3' adenosine nucleotide represents an easy method to significantly improve the quality of NMR spectra of RNA molecules.
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Affiliation(s)
- Andrew N Amborski
- Department of Chemistry, York University, M3J 1P3, Toronto, ON, Canada
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7
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Abstract
RNA interference (RNAi) is a conserved sequence-specific, gene-silencing mechanism that is induced by double-stranded RNA. RNAi holds great promise as a novel nucleic acid-based therapeutic against a wide variety of diseases, including cancer, infectious diseases and genetic disorders. Antiviral RNAi strategies have received much attention and several compounds are currently being tested in clinical trials. Although induced RNAi is able to trigger profound and specific inhibition of virus replication, it is becoming clear that RNAi therapeutics are not as straightforward as we had initially hoped. Difficulties concerning toxicity and delivery to the right cells that earlier hampered the development of antisense-based therapeutics may also apply to RNAi. In addition, there are indications that viruses have evolved ways to escape from RNAi. Proper consideration of all of these issues will be necessary in the design of RNAi-based therapeutics for successful clinical intervention of human pathogenic viruses.
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Affiliation(s)
- Joost Haasnoot
- Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Meibergdreef 15, Amsterdam, 1105 AZ The Netherlands
| | - Ellen M Westerhout
- Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Meibergdreef 15, Amsterdam, 1105 AZ The Netherlands
| | - Ben Berkhout
- Department of Medical Microbiology, Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Meibergdreef 15, Amsterdam, 1105 AZ The Netherlands
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Lisi V, Major F. A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships. RNA (NEW YORK, N.Y.) 2007; 13:1537-45. [PMID: 17652406 PMCID: PMC1950765 DOI: 10.1261/rna.597507] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Despite an increasing number of experimentally determined RNA structures, the gap between the number of structures and that of RNA families is still growing. To overcome this limitation, efficient and reliable RNA modeling methodologies must be developed. In order to reach this goal, here, we show how triloop sequence-structure relationships have been inferred through a systematic analysis of all triloops found in available high-resolution structures. The structural annotation of all triloops allowed us to define discrete states of the triloop's conformational space, and therefore an explicit sequence-to-structure relation. The sequence-structure relationships inferred from this explicit relation are presented in a convenient modeling table that provides a limited set of possible three-dimensional structures given any triloop sequence. The table is indexed by the two nucleotides that form the triloop's flanking base pair, since they are shown to provide the most information about the triloop three-dimensional structures. We also report the observations in the X-ray crystallographic structures of important conformational variations, which we believe might be the result of RNA dynamic.
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Affiliation(s)
- Véronique Lisi
- Institute for Research in Immunology and Cancer, Department of Computer Science and Operations Research, Université de Montréal, Québec, Canada
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Tapparel C, Junier T, Gerlach D, Cordey S, Van Belle S, Perrin L, Zdobnov EM, Kaiser L. New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features. BMC Genomics 2007; 8:224. [PMID: 17623054 PMCID: PMC1949831 DOI: 10.1186/1471-2164-8-224] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 07/10/2007] [Indexed: 12/15/2022] Open
Abstract
Background Human rhinoviruses (HRV), the most frequent cause of respiratory infections, include 99 different serotypes segregating into two species, A and B. Rhinoviruses share extensive genomic sequence similarity with enteroviruses and both are part of the picornavirus family. Nevertheless they differ significantly at the phenotypic level. The lack of HRV full-length genome sequences and the absence of analysis comparing picornaviruses at the whole genome level limit our knowledge of the genomic features supporting these differences. Results Here we report complete genome sequences of 12 HRV-A and HRV-B serotypes, more than doubling the current number of available HRV sequences. The whole-genome maximum-likelihood phylogenetic analysis suggests that HRV-B and human enteroviruses (HEV) diverged from the last common ancestor after their separation from HRV-A. On the other hand, compared to HEV, HRV-B are more related to HRV-A in the capsid and 3B-C regions. We also identified the presence of a 2C cis-acting replication element (cre) in HRV-B that is not present in HRV-A, and that had been previously characterized only in HEV. In contrast to HEV viruses, HRV-A and HRV-B share also markedly lower GC content along the whole genome length. Conclusion Our findings provide basis to speculate about both the biological similarities and the differences (e.g. tissue tropism, temperature adaptation or acid lability) of these three groups of viruses.
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Affiliation(s)
- Caroline Tapparel
- Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 24 Rue Micheli-du-Crest, 1211 Geneva 14, Switzerland
| | - Thomas Junier
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 14, Switzerland
| | - Daniel Gerlach
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 14, Switzerland
| | - Samuel Cordey
- Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 24 Rue Micheli-du-Crest, 1211 Geneva 14, Switzerland
| | - Sandra Van Belle
- Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 24 Rue Micheli-du-Crest, 1211 Geneva 14, Switzerland
| | - Luc Perrin
- Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 24 Rue Micheli-du-Crest, 1211 Geneva 14, Switzerland
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 14, Switzerland
- Swiss Institute of Bioinformatics, 1 Rue Michel-Servet, 1211 Geneva 14, Switzerland
- Imperial College London, South Kensington Campus, SW7 2AZ London, UK
| | - Laurent Kaiser
- Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 24 Rue Micheli-du-Crest, 1211 Geneva 14, Switzerland
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Headey SJ, Huang H, Claridge JK, Soares GA, Dutta K, Schwalbe M, Yang D, Pascal SM. NMR structure of stem-loop D from human rhinovirus-14. RNA (NEW YORK, N.Y.) 2007; 13:351-60. [PMID: 17194719 PMCID: PMC1800519 DOI: 10.1261/rna.313707] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Accepted: 10/31/2006] [Indexed: 05/13/2023]
Abstract
The 5'-cloverleaf of the picornavirus RNA genome is essential for the assembly of a ribonucleoprotein replication complex. Stem-loop D (SLD) of the cloverleaf is the recognition site for the multifunctional viral protein 3Cpro. This protein is the principal viral protease, and its interaction with SLD also helps to position the viral RNA-dependent RNA polymerase (3Dpol) for replication. Human rhinovirus-14 (HRV-14) is distinct from the majority of picornaviruses in that its SLD forms a cUAUg triloop instead of the more common uYACGg tetraloop. This difference appears to be functionally significant, as 3Cpro from tetraloop-containing viruses cannot bind the HRV-14 SLD. We have determined the solution structure of the HRV-14 SLD using NMR spectroscopy. The structure is predominantly an A-form helix, but with a central pyrimidine-pyrimidine base-paired region and a significantly widened major groove. The stabilizing hydrogen bonding present in the uYACGg tetraloop was not found in the cUAUg triloop. However, the triloop uses different structural elements to present a largely similar surface: sequence and underlying architecture are not conserved, but key aspects of the surface structure are. Important structural differences do exist, though, and may account for the observed cross-isotype binding specificities between 3Cpro and SLD.
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Affiliation(s)
- Stephen J Headey
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Kienberger F, Zhu R, Moser R, Blaas D, Hinterdorfer P. Monitoring RNA release from human rhinovirus by dynamic force microscopy. J Virol 2004; 78:3203-9. [PMID: 15016841 PMCID: PMC371065 DOI: 10.1128/jvi.78.7.3203-3209.2004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human rhinoviruses were imaged under physiological conditions by dynamic force microscopy. Topographical images revealed various polygonal areas on the surfaces of the 30-nm viral particles. RNA release was initiated by exposure to a low-pH buffer. The lengths of the RNAs that were released but still connected to the virus capsid varied between 40 and 330 nm, whereas RNA molecules that were completely released from the virus were observed with lengths up to 1 micro m. Fork-like structure elements with 30-nm extensions were sometimes resolved at one end of the RNA molecules. They possibly correspond to the characteristic multi-stem-loop conformation, the internal ribosomal entry site, located at the 5' region of the genome. This study demonstrates that dynamic force microscopy can be used to study viral RNA release in situ under physiological conditions.
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Affiliation(s)
- Ferry Kienberger
- Institute for Biophysics, J. Kepler University, A-4040 Linz, Austria
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Ohlenschläger O, Wöhnert J, Bucci E, Seitz S, Häfner S, Ramachandran R, Zell R, Görlach M. The structure of the stemloop D subdomain of coxsackievirus B3 cloverleaf RNA and its interaction with the proteinase 3C. Structure 2004; 12:237-48. [PMID: 14962384 DOI: 10.1016/j.str.2004.01.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2003] [Revised: 10/24/2003] [Accepted: 10/24/2003] [Indexed: 11/25/2022]
Abstract
Stemloop D (SLD) of the 5' cloverleaf RNA is the cognate ligand of the coxsackievirus B3 (CVB3) 3C proteinase (3Cpro). Both are indispensable components of the viral replication initiation complex. SLD is a structurally autonomous subunit of the 5' cloverleaf. The SLD structure was solved by NMR spectroscopy to an rms deviation of 0.66 A (all heavy atoms). SLD contains a novel triple pyrimidine mismatch motif with a central Watson-Crick type C:U pair. SLD is capped by an apical uCACGg tetraloop adopting a structure highly similar to stable cUNCGg tetraloops. Binding of CVB3 3Cpro induces changes in NMR spectra for nucleotides adjacent to the triple pyrimidine mismatch and of the tetraloop implying them as sites of specific SLD:3Cpro interaction. The binding of 3Cpro to SLD requires the integrity of those structural elements, strongly suggesting that 3Cpro recognizes a structural motif instead of a specific sequence.
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Affiliation(s)
- Oliver Ohlenschläger
- Institut für Molekulare Biotechnologie eV, Bentenbergstr 100813, D-07745 Jena, Germany
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