1
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Mondal S, Sarvari G, Boehr DD. Picornavirus 3C Proteins Intervene in Host Cell Processes through Proteolysis and Interactions with RNA. Viruses 2023; 15:2413. [PMID: 38140654 PMCID: PMC10747604 DOI: 10.3390/v15122413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
The Picornaviridae family comprises a large group of non-enveloped viruses with enormous impact on human and animal health. The picornaviral genome contains one open reading frame encoding a single polyprotein that can be processed by viral proteases. The picornaviral 3C proteases share similar three-dimensional structures and play a significant role in the viral life cycle and virus-host interactions. Picornaviral 3C proteins also have conserved RNA-binding activities that contribute to the assembly of the viral RNA replication complex. The 3C protease is important for regulating the host cell response through the cleavage of critical host cell proteins, acting to selectively 'hijack' host factors involved in gene expression, promoting picornavirus replication, and inactivating key factors in innate immunity signaling pathways. The protease and RNA-binding activities of 3C are involved in viral polyprotein processing and the initiation of viral RNA synthesis. Most importantly, 3C modifies critical molecules in host organelles and maintains virus infection by subtly subverting host cell death through the blocking of transcription, translation, and nucleocytoplasmic trafficking to modulate cell physiology for viral replication. Here, we discuss the molecular mechanisms through which 3C mediates physiological processes involved in promoting virus infection, replication, and release.
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Affiliation(s)
| | | | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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2
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Pareek A, Kumar R, Mudgal R, Neetu N, Sharma M, Kumar P, Tomar S. Alphavirus antivirals targeting RNA‐dependent RNA polymerase domain of nsP4 divulged using surface plasmon resonance. FEBS J 2022; 289:4901-4924. [DOI: 10.1111/febs.16397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/13/2022] [Accepted: 02/11/2022] [Indexed: 01/01/2023]
Affiliation(s)
- Akshay Pareek
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Ravi Kumar
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Rajat Mudgal
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Neetu Neetu
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Monica Sharma
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
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3
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Lu H, Li J, Yang P, Jiang F, Liu H, Cui F. Mutation in the RNA-Dependent RNA Polymerase of a Symbiotic Virus Is Associated With the Adaptability of the Viral Host. Front Microbiol 2022; 13:883436. [PMID: 35432275 PMCID: PMC9005967 DOI: 10.3389/fmicb.2022.883436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Host adaptation has the potential to cause rapid genetic variation in symbiotic microorganisms in insects. How mutations in symbiotic viruses favor viral fitness in hosts and even influence host adaptability to new environments remains elusive. Here, we explored the role of genetic divergence at one site of a symbiotic virus, Acyrthosiphon pisum virus (APV), in the host aphid's adaptation to unfavorable plants. Based on the transcriptomes of the pea aphid Vicia faba colony and Vicia villosa colony, 46 single nucleotide polymorphism (SNP) sites were found in the APV genomes from the two aphid colonies. One SNP at site 5,990, G5990A, located at the RNA-dependent RNA polymerase (RdRp) domain, demonstrated a predominance from G to A when the host aphids were shifted from V. faba to the low-fitness plants V. villosa or Medicago sativa. This SNP resulted in a substitution from serine (S) to asparagine (N) at site 196 in RdRp. Although S196N was predicted to be located at a random coil far away from conserved functional motifs, the polymerase activity of the N196 type of RdRp was increased by 44.5% compared to that of the S196 type. The promoted enzymatic activity of RdRp was associated with a higher replication level of APV, which was beneficial for aphids as APV suppressed plant's resistance reactions toward aphids. The findings showed a novel case in which mutations selected in a symbiotic virus may confer a favor on the host as the host adapts to new environmental conditions.
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Affiliation(s)
- Hong Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Pengcheng Yang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fei Jiang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongran Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
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4
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Lethal Mutagenesis of RNA Viruses and Approved Drugs with Antiviral Mutagenic Activity. Viruses 2022; 14:v14040841. [PMID: 35458571 PMCID: PMC9024455 DOI: 10.3390/v14040841] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 12/11/2022] Open
Abstract
In RNA viruses, a small increase in their mutation rates can be sufficient to exceed their threshold of viability. Lethal mutagenesis is a therapeutic strategy based on the use of mutagens, driving viral populations to extinction. Extinction catastrophe can be experimentally induced by promutagenic nucleosides in cell culture models. The loss of HIV infectivity has been observed after passage in 5-hydroxydeoxycytidine or 5,6-dihydro-5-aza-2′-deoxycytidine while producing a two-fold increase in the viral mutation frequency. Among approved nucleoside analogs, experiments with polioviruses and other RNA viruses suggested that ribavirin can be mutagenic, although its mechanism of action is not clear. Favipiravir and molnupiravir exert an antiviral effect through lethal mutagenesis. Both drugs are broad-spectrum antiviral agents active against RNA viruses. Favipiravir incorporates into viral RNA, affecting the G→A and C→U transition rates. Molnupiravir (a prodrug of β-d-N4-hydroxycytidine) has been recently approved for the treatment of SARS-CoV-2 infection. Its triphosphate derivative can be incorporated into viral RNA and extended by the coronavirus RNA polymerase. Incorrect base pairing and inefficient extension by the polymerase promote mutagenesis by increasing the G→A and C→U transition frequencies. Despite having remarkable antiviral action and resilience to drug resistance, carcinogenic risks and genotoxicity are important concerns limiting their extended use in antiviral therapy.
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5
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Winston DS, Boehr DD. Allosteric and dynamic control of RNA-dependent RNA polymerase function and fidelity. Enzymes 2021; 49:149-193. [PMID: 34696831 DOI: 10.1016/bs.enz.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
All RNA viruses encode an RNA-dependent RNA polymerase (RdRp) responsible for genome replication. It is now recognized that enzymes in general, and RdRps specifically, are dynamic macromolecular machines such that their moving parts, including active site loops, play direct functional roles. While X-ray crystallography has provided deep insight into structural elements important for RdRp function, this methodology generally provides only static snapshots, and so is limited in its ability to report on dynamic fluctuations away from the lowest energy conformation. Nuclear magnetic resonance (NMR), molecular dynamics (MD) simulations and other biophysical techniques have brought new insight into RdRp function by their ability to characterize the trajectories, kinetics and thermodynamics of conformational motions. In particular, these methodologies have identified coordinated motions among conserved structural motifs necessary for nucleotide selection and incorporation. Disruption of these motions through amino acid substitutions or inhibitor binding impairs RdRp function. Understanding and re-engineering these motions thus provides exciting new avenues for anti-viral strategies. This chapter outlines the basics of these methodologies, summarizes the dynamic motions observed in different RdRps important for nucleotide selection and incorporation, and illustrates how this information can be leveraged towards rational vaccine strain development and anti-viral drug design.
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Affiliation(s)
- Dennis S Winston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States.
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6
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Maheden K, Todd B, Gordon CJ, Tchesnokov EP, Götte M. Inhibition of viral RNA-dependent RNA polymerases with clinically relevant nucleotide analogs. Enzymes 2021; 49:315-354. [PMID: 34696837 PMCID: PMC8517576 DOI: 10.1016/bs.enz.2021.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The treatment of viral infections remains challenging, in particular in the face of emerging pathogens. Broad-spectrum antiviral drugs could potentially be used as a first line of defense. The RNA-dependent RNA polymerase (RdRp) of RNA viruses serves as a logical target for drug discovery and development efforts. Herein we discuss compounds that target RdRp of poliovirus, hepatitis C virus, influenza viruses, respiratory syncytial virus, and the growing data on coronaviruses. We focus on nucleotide analogs and mechanisms of action and resistance.
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Affiliation(s)
- Kieran Maheden
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Brendan Todd
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Calvin J Gordon
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada; Li Ka Shing Institute of Virology at University of Alberta, Edmonton, AB, Canada.
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7
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Two RNA Tunnel Inhibitors Bind in Highly Conserved Sites in Dengue Virus NS5 Polymerase: Structural and Functional Studies. J Virol 2020; 94:JVI.01130-20. [PMID: 32907977 DOI: 10.1128/jvi.01130-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/29/2020] [Indexed: 11/20/2022] Open
Abstract
Dengue virus (DENV) NS5 RNA-dependent RNA polymerase (RdRp), an important drug target, synthesizes viral RNA and is essential for viral replication. While a number of allosteric inhibitors have been reported for hepatitis C virus RdRp, few have been described for DENV RdRp. Following a diverse compound screening campaign and a rigorous hit-to-lead flowchart combining biochemical and biophysical approaches, two DENV RdRp nonnucleoside inhibitors were identified and characterized. These inhibitors show low- to high-micromolar inhibition in DENV RNA polymerization and cell-based assays. X-ray crystallography reveals that they bind in the enzyme RNA template tunnel. One compound (NITD-434) induced an allosteric pocket at the junction of the fingers and palm subdomains by displacing residue V603 in motif B. Binding of another compound (NITD-640) ordered the fingers loop preceding the F motif, close to the RNA template entrance. Most of the amino acid residues that interacted with these compounds are highly conserved in flaviviruses. Both sites are important for polymerase de novo initiation and elongation activities and essential for viral replication. This work provides evidence that the RNA tunnel in DENV RdRp offers interesting target sites for inhibition.IMPORTANCE Dengue virus (DENV), an important arthropod-transmitted human pathogen that causes a spectrum of diseases, has spread dramatically worldwide in recent years. Despite extensive efforts, the only commercial vaccine does not provide adequate protection to naive individuals. DENV NS5 polymerase is a promising drug target, as exemplified by the development of successful commercial drugs against hepatitis C virus (HCV) polymerase and HIV-1 reverse transcriptase. High-throughput screening of compound libraries against this enzyme enabled the discovery of inhibitors that induced binding sites in the RNA template channel. Characterizations by biochemical, biophysical, and reverse genetics approaches provide a better understanding of the biological relevance of these allosteric sites and the way forward to design more-potent inhibitors.
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8
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Torres-Trenas A, Cañizares MC, García-Pedrajas MD, Pérez-Artés E. Molecular and Biological Characterization of the First Hypovirus Identified in Fusarium oxysporum. Front Microbiol 2020; 10:3131. [PMID: 32038565 PMCID: PMC6992542 DOI: 10.3389/fmicb.2019.03131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022] Open
Abstract
A novel mycovirus named Fusarium oxysporum f. sp. dianthi hypovirus 2 (FodHV2) has been identified infecting isolates Fod 408 and Fod 409 of Fusarium oxysporum f. sp. dianthi from Morocco. The genome of FodHV2 is 9,444 nucleotides long excluding the poly(A) tail, and has a single open reading frame encoding a polyprotein. The polyprotein contains three highly conserved domains of UDP glucose/sterol glucosyltransferase, RNA-dependent RNA polymerase, and viral RNA helicase. In addition, particular residues of Cys, Hys, and Gly detected in the N-terminal region suggest the presence of the catalytic site of a highly diverged papain-like protease. Genomic organization, presence of particular conserved motifs, and phylogenetic analyses based on multiple alignments clearly grouped FodHV2 with the members of the family Hypoviridae. FodHV2 was transferred by hyphal anastomosis to a recipient HygR-tagged virus-free strain. The comparison of the infected and non-infected isogenic strains showed that FodHV2 did not alter the vegetative growth, neither the conidiation nor the virulence of its fungal host. Efficiency of FodHV2 transmission through the conidia was 100% in both the original and the recipient infected-isolates. To the best of our knowledge, this is the first report of a hypovirus infecting the plant pathogen F. oxysporum, and also the first one of a hypovirus detected in a fungal strain from the African continent.
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Affiliation(s)
- Almudena Torres-Trenas
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - M. Carmen Cañizares
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - M. Dolores García-Pedrajas
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - Encarnación Pérez-Artés
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
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9
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RNA-Dependent RNA Polymerase Speed and Fidelity are not the Only Determinants of the Mechanism or Efficiency of Recombination. Genes (Basel) 2019; 10:genes10120968. [PMID: 31775299 PMCID: PMC6947342 DOI: 10.3390/genes10120968] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/14/2019] [Accepted: 11/21/2019] [Indexed: 01/05/2023] Open
Abstract
Using the RNA-dependent RNA polymerase (RdRp) from poliovirus (PV) as our model system, we have shown that Lys-359 in motif-D functions as a general acid in the mechanism of nucleotidyl transfer. A K359H (KH) RdRp derivative is slow and faithful relative to wild-type enzyme. In the context of the KH virus, RdRp-coding sequence evolves, selecting for the following substitutions: I331F (IF, motif-C) and P356S (PS, motif-D). We have evaluated IF-KH, PS-KH, and IF-PS-KH viruses and enzymes. The speed and fidelity of each double mutant are equivalent. Each exhibits a unique recombination phenotype, with IF-KH being competent for copy-choice recombination and PS-KH being competent for forced-copy-choice recombination. Although the IF-PS-KH RdRp exhibits biochemical properties within twofold of wild type, the virus is impaired substantially for recombination in cells. We conclude that there are biochemical properties of the RdRp in addition to speed and fidelity that determine the mechanism and efficiency of recombination. The interwoven nature of speed, fidelity, the undefined property suggested here, and recombination makes it impossible to attribute a single property of the RdRp to fitness. However, the derivatives described here may permit elucidation of the importance of recombination on the fitness of the viral population in a background of constant polymerase speed and fidelity.
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10
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Boehr AK, Arnold JJ, Oh HS, Cameron CE, Boehr DD. 2'-C-methylated nucleotides terminate virus RNA synthesis by preventing active site closure of the viral RNA-dependent RNA polymerase. J Biol Chem 2019; 294:16897-16907. [PMID: 31575662 PMCID: PMC6851289 DOI: 10.1074/jbc.ra119.010214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/28/2019] [Indexed: 01/25/2023] Open
Abstract
The 2'-C-methyl ribonucleosides are nucleoside analogs representing an important class of antiviral agents, especially against positive-strand RNA viruses. Their value is highlighted by the highly successful anti-hepatitis C drug sofosbuvir. When appropriately phosphorylated, these nucleotides are successfully incorporated into RNA by the virally encoded RNA-dependent RNA polymerase (RdRp). This activity prevents further RNA extension, but the mechanism is poorly characterized. Previously, we had identified NMR signatures characteristic of formation of RdRp-RNA binary and RdRp-RNA-NTP ternary complexes for the poliovirus RdRp, including an open-to-closed conformational change necessary to prepare the active site for catalysis of phosphoryl transfer. Here we used these observations as a framework for interpreting the effects of 2'-C-methyl adenosine analogs on RNA chain extension in solution-state NMR spectroscopy experiments, enabling us to gain additional mechanistic insights into 2'-C-methyl ribonucleoside-mediated RNA chain termination. Contrary to what has been proposed previously, poliovirus RdRp that was bound to RNA with an incorporated 2'-C-methyl nucleotide could still bind to the next incoming NTP. Our results also indicated that incorporation of the 2'-C-methyl nucleotide does not disrupt RdRp-RNA interactions and does not prevent translocation. Instead, incorporation of the 2'-C-methyl nucleotide blocked closure of the RdRp active site upon binding of the next correct incoming NTP, which prevented further nucleotide addition. We propose that other nucleotide analogs that act as nonobligate chain terminators may operate through a similar mechanism.
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Affiliation(s)
- Alyson K Boehr
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Hyung S Oh
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - David D Boehr
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
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11
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Shi J, Perryman JM, Yang X, Liu X, Musser DM, Boehr AK, Moustafa IM, Arnold JJ, Cameron CE, Boehr DD. Rational Control of Poliovirus RNA-Dependent RNA Polymerase Fidelity by Modulating Motif-D Loop Conformational Dynamics. Biochemistry 2019; 58:3735-3743. [PMID: 31424194 DOI: 10.1021/acs.biochem.9b00497] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The conserved structural motif D is an important determinant of the speed and fidelity of viral RNA-dependent RNA polymerases (RdRps). Structural and computational studies have suggested that conformational changes in the motif-D loop that help to reposition the catalytic lysine represent critical steps in nucleotide selection and incorporation. Conformations of the motif-D loop in the poliovirus RdRp are likely controlled in part by noncovalent interactions involving the motif-D residue Glu364. This residue swivels between making interactions with Lys228 and Asn370 to stabilize the open and closed loop conformations, respectively. We show here that we can rationally control the motif-D loop conformation by breaking these interactions. The K228A variant favors a more active closed conformation, leading to increased nucleotide incorporation rates and decreased nucleotide selectivity, and the N370A variant favors a less active open conformation, leading to decreased nucleotide incorporation rates and increased nucleotide selectivity. Similar competing interactions likely control nucleotide incorporation rates and fidelity in other viral RdRps. Rational engineering of these interactions may be important in the generation of live, attenuated vaccine strains, considering the established relationships between RdRp function and viral pathogenesis.
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Affiliation(s)
- Jingjing Shi
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Jacob M Perryman
- Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Xiaorong Yang
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Xinran Liu
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Derek M Musser
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Alyson K Boehr
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - David D Boehr
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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12
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Ogino T, Green TJ. RNA Synthesis and Capping by Non-segmented Negative Strand RNA Viral Polymerases: Lessons From a Prototypic Virus. Front Microbiol 2019; 10:1490. [PMID: 31354644 PMCID: PMC6636387 DOI: 10.3389/fmicb.2019.01490] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/14/2019] [Indexed: 12/26/2022] Open
Abstract
Non-segmented negative strand (NNS) RNA viruses belonging to the order Mononegavirales are highly diversified eukaryotic viruses including significant human pathogens, such as rabies, measles, Nipah, and Ebola. Elucidation of their unique strategies to replicate in eukaryotic cells is crucial to aid in developing anti-NNS RNA viral agents. Over the past 40 years, vesicular stomatitis virus (VSV), closely related to rabies virus, has served as a paradigm to study the fundamental molecular mechanisms of transcription and replication of NNS RNA viruses. These studies provided insights into how NNS RNA viruses synthesize 5′-capped mRNAs using their RNA-dependent RNA polymerase L proteins equipped with an unconventional mRNA capping enzyme, namely GDP polyribonucleotidyltransferase (PRNTase), domain. PRNTase or PRNTase-like domains are evolutionally conserved among L proteins of all known NNS RNA viruses and their related viruses belonging to Jingchuvirales, a newly established order, in the class Monjiviricetes, suggesting that they may have evolved from a common ancestor that acquired the unique capping system to replicate in a primitive eukaryotic host. This article reviews what has been learned from biochemical and structural studies on the VSV RNA biosynthesis machinery, and then focuses on recent advances in our understanding of regulatory and catalytic roles of the PRNTase domain in RNA synthesis and capping.
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Affiliation(s)
- Tomoaki Ogino
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, United States.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Todd J Green
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
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13
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Smertina E, Urakova N, Strive T, Frese M. Calicivirus RNA-Dependent RNA Polymerases: Evolution, Structure, Protein Dynamics, and Function. Front Microbiol 2019; 10:1280. [PMID: 31244803 PMCID: PMC6563846 DOI: 10.3389/fmicb.2019.01280] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/22/2019] [Indexed: 12/11/2022] Open
Abstract
The Caliciviridae are viruses with a positive-sense, single-stranded RNA genome that is packaged into an icosahedral, environmentally stable protein capsid. The family contains five genera (Norovirus, Nebovirus, Sapovirus, Lagovirus, and Vesivirus) that infect vertebrates including amphibians, reptiles, birds, and mammals. The RNA-dependent RNA polymerase (RdRp) replicates the genome of RNA viruses and can speed up evolution due to its error-prone nature. Studying calicivirus RdRps in the context of genuine virus replication is often hampered by a lack of suitable model systems. Enteric caliciviruses and RHDV in particular are notoriously difficult to propagate in cell culture; therefore, molecular studies of replication mechanisms are challenging. Nevertheless, research on recombinant proteins has revealed several unexpected characteristics of calicivirus RdRps. For example, the RdRps of RHDV and related lagoviruses possess the ability to expose a hydrophobic motif, to rearrange Golgi membranes, and to copy RNA at unusually high temperatures. This review is focused on the structural dynamics, biochemical properties, kinetics, and putative interaction partners of these RdRps. In addition, we discuss the possible existence of a conserved but as yet undescribed structural element that is shared amongst the RdRps of all caliciviruses.
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Affiliation(s)
- Elena Smertina
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Canberra, ACT, Australia
- Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Nadya Urakova
- Department of Entomology, Pennsylvania State University, University Park, PA, United States
| | - Tanja Strive
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Canberra, ACT, Australia
- Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, Australia
| | - Michael Frese
- Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
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14
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Beyond Members of the Flaviviridae Family, Sofosbuvir Also Inhibits Chikungunya Virus Replication. Antimicrob Agents Chemother 2019; 63:AAC.01389-18. [PMID: 30455237 DOI: 10.1128/aac.01389-18] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/31/2018] [Indexed: 12/30/2022] Open
Abstract
Chikungunya virus (CHIKV) causes a febrile disease associated with chronic arthralgia, which may progress to neurological impairment. Chikungunya fever (CF) is an ongoing public health problem in tropical and subtropical regions of the world, where control of the CHIKV vector, Aedes mosquitos, has failed. As there is no vaccine or specific treatment for CHIKV, patients receive only palliative care to alleviate pain and arthralgia. Thus, drug repurposing is necessary to identify antivirals against CHIKV. CHIKV RNA polymerase is similar to the orthologue enzyme of other positive-sense RNA viruses, such as members of the Flaviviridae family. Among the Flaviviridae, not only is hepatitis C virus RNA polymerase susceptible to sofosbuvir, a clinically approved nucleotide analogue, but so is dengue, Zika, and yellow fever virus replication. Here, we found that sofosbuvir was three times more selective in inhibiting CHIKV production in human hepatoma cells than ribavirin, a pan-antiviral drug. Although CHIKV replication in human induced pluripotent stem cell-derived astrocytes was less susceptible to sofosbuvir than were hepatoma cells, sofosbuvir nevertheless impaired virus production and cell death in a multiplicity of infection-dependent manner. Sofosbuvir also exhibited antiviral activity in vivo by preventing CHIKV-induced paw edema in adult mice at a dose of 20 mg/kg of body weight/day and prevented mortality in a neonate mouse model at 40- and 80-mg/kg/day doses. Our data demonstrate that a prototypic alphavirus, CHIKV, is also susceptible to sofosbuvir. As sofosbuvir is a clinically approved drug, our findings could pave the way to it becoming a therapeutic option against CF.
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Neupane A, Feng C, Feng J, Kafle A, Bücking H, Lee Marzano SY. Metatranscriptomic Analysis and In Silico Approach Identified Mycoviruses in the Arbuscular Mycorrhizal Fungus Rhizophagus spp. Viruses 2018; 10:E707. [PMID: 30545059 PMCID: PMC6316171 DOI: 10.3390/v10120707] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 12/27/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF), including Rhizophagus spp., can play important roles in nutrient cycling of the rhizosphere. However, the effect of virus infection on AMF's role in nutrient cycling cannot be determined without first knowing the diversity of the mycoviruses in AMF. Therefore, in this study, we sequenced the R. irregularis isolate-09 due to its previously demonstrated high efficiency in increasing the N/P uptake of the plant. We identified one novel mitovirus contig of 3685 bp, further confirmed by reverse transcription-PCR. Also, publicly available Rhizophagus spp. RNA-Seq data were analyzed to recover five partial virus sequences from family Narnaviridae, among which four were from R. diaphanum MUCL-43196 and one was from R. irregularis strain-C2 that was similar to members of the Mitovirus genus. These contigs coded genomes larger than the regular mitoviruses infecting pathogenic fungi and can be translated by either a mitochondrial translation code or a cytoplasmic translation code, which was also reported in previously found mitoviruses infecting mycorrhizae. The five newly identified virus sequences are comprised of functionally conserved RdRp motifs and formed two separate subclades with mitoviruses infecting Gigasporamargarita and Rhizophagusclarus, further supporting virus-host co-evolution theory. This study expands our understanding of virus diversity. Even though AMF is notably hard to investigate due to its biotrophic nature, this study demonstrates the utility of whole root metatranscriptome.
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Affiliation(s)
- Achal Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Chenchen Feng
- Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, Brookings, SD 57007, USA.
| | - Jiuhuan Feng
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
- Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, Brookings, SD 57007, USA.
| | - Arjun Kafle
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Heike Bücking
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Shin-Yi Lee Marzano
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
- Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, Brookings, SD 57007, USA.
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16
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Jordan PC, Stevens SK, Deval J. Nucleosides for the treatment of respiratory RNA virus infections. Antivir Chem Chemother 2018; 26:2040206618764483. [PMID: 29562753 PMCID: PMC5890544 DOI: 10.1177/2040206618764483] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/07/2018] [Indexed: 12/20/2022] Open
Abstract
Influenza virus, respiratory syncytial virus, human metapneumovirus, parainfluenza virus, coronaviruses, and rhinoviruses are among the most common viruses causing mild seasonal colds. These RNA viruses can also cause lower respiratory tract infections leading to bronchiolitis and pneumonia. Young children, the elderly, and patients with compromised cardiac, pulmonary, or immune systems are at greatest risk for serious disease associated with these RNA virus respiratory infections. In addition, swine and avian influenza viruses, together with severe acute respiratory syndrome-associated and Middle Eastern respiratory syndrome coronaviruses, represent significant pandemic threats to the general population. In this review, we describe the current medical need resulting from respiratory infections caused by RNA viruses, which justifies drug discovery efforts to identify new therapeutic agents. The RNA polymerase of respiratory viruses represents an attractive target for nucleoside and nucleotide analogs acting as inhibitors of RNA chain synthesis. Here, we present the molecular, biochemical, and structural fundamentals of the polymerase of the four major families of RNA respiratory viruses: Orthomyxoviridae, Pneumoviridae/Paramyxoviridae, Coronaviridae, and Picornaviridae. We summarize past and current efforts to develop nucleoside and nucleotide analogs as antiviral agents against respiratory virus infections. This includes molecules with very broad antiviral spectrum such as ribavirin and T-705 (favipiravir), and others targeting more specifically one or a few virus families. Recent advances in our understanding of the structure(s) and function(s) of respiratory virus polymerases will likely support the discovery and development of novel nucleoside analogs.
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Affiliation(s)
- Paul C Jordan
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, USA
| | - Sarah K Stevens
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, USA
| | - Jerome Deval
- Alios BioPharma, Inc., a Janssen Pharmaceutical Company of Johnson & Johnson, South San Francisco, USA
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17
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de la Higuera I, Ferrer-Orta C, de Ávila AI, Perales C, Sierra M, Singh K, Sarafianos SG, Dehouck Y, Bastolla U, Verdaguer N, Domingo E. Molecular and Functional Bases of Selection against a Mutation Bias in an RNA Virus. Genome Biol Evol 2017; 9:1212-1228. [PMID: 28460010 PMCID: PMC5433387 DOI: 10.1093/gbe/evx075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 12/12/2022] Open
Abstract
The selective pressures acting on viruses that replicate under enhanced mutation rates are largely unknown. Here, we describe resistance of foot-and-mouth disease virus to the mutagen 5-fluorouracil (FU) through a single polymerase substitution that prevents an excess of A to G and U to C transitions evoked by FU on the wild-type foot-and-mouth disease virus, while maintaining the same level of mutant spectrum complexity. The polymerase substitution inflicts upon the virus a fitness loss during replication in absence of FU but confers a fitness gain in presence of FU. The compensation of mutational bias was documented by in vitro nucleotide incorporation assays, and it was associated with structural modifications at the N-terminal region and motif B of the viral polymerase. Predictions of the effect of mutations that increase the frequency of G and C in the viral genome and encoded polymerase suggest multiple points in the virus life cycle where the mutational bias in favor of G and C may be detrimental. Application of predictive algorithms suggests adverse effects of the FU-directed mutational bias on protein stability. The results reinforce modulation of nucleotide incorporation as a lethal mutagenesis-escape mechanism (that permits eluding virus extinction despite replication in the presence of a mutagenic agent) and suggest that mutational bias can be a target of selection during virus replication.
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Affiliation(s)
- Ignacio de la Higuera
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain.,Christopher S. Bond Life Sciences Center and Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, Missouri
| | - Cristina Ferrer-Orta
- Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Ana I de Ávila
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Celia Perales
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain.,Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Macarena Sierra
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Kamalendra Singh
- Christopher S. Bond Life Sciences Center and Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, Missouri
| | - Stefan G Sarafianos
- Christopher S. Bond Life Sciences Center and Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, Missouri
| | - Yves Dehouck
- Machine Learning Group, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ugo Bastolla
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Nuria Verdaguer
- Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Barcelona, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
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18
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Kumar S, Subbarao BL, Kumari R, Hallan V. Molecular characterization of a novel cryptic virus infecting pigeonpea plants. PLoS One 2017; 12:e0181829. [PMID: 28771507 PMCID: PMC5542627 DOI: 10.1371/journal.pone.0181829] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/08/2017] [Indexed: 12/24/2022] Open
Abstract
A new member of the genus Deltapartitivirus was identified containing three dsRNAs with an estimated size of 1.71, 1.49 and 1.43 kb. The dsRNAs were extracted from symptomless pigeonpea [Cajanus cajan (L.) Millspaugh] plants cv. Erra Kandulu. This new virus with 4.64 kb genome was tentatively named Arhar cryptic virus-1 (ArCV-1). The genomic RNAs were amplified and characterized by sequence independent single primer amplification. The dsRNAs shared a highly conserved 16 nt 5' non-coding region (5'-GATAATGATCCAAGGA-3'). The largest dsRNA (dsRNA-1) was identified as the viral RNA dependent RNA polymerase (replicase), predicted to encode a putative 55.34 kDa protein (P1). The two other smaller dsRNAs (dsRNA-2 and dsRNA-3) predicted to encode for putative capsid proteins of 38.50kDa (P2) and 38.51kDa (P3), respectively. Phylogenetic analysis indicated that ArCV-1 formed a clade together with Fragaria chiloensis cryptic virus, Rosa multiflora cryptic virus and Rose cryptic virus-1, indicating that ArCV-1 could be a new member of the genus Deltapartitivirus. ArCV-1 3Dpol structure revealed several interesting features. The 3Dpol in its full-length shares structural similarities with members of the family Caliciviridaeand family Picornaviridae. In addition, fourth dsRNA molecule (dsRNA-2A), not related to ArCV-1 genome, was found in the same plant tissue. The dsRNA-2A (1.6 kb) encodes a protein (P4), with a predicted size of 44.5 kDa. P4 shares similarity with coat protein genes of several cryptic viruses, in particular the bipartite cryptic viruses including Raphanus sativus cryptic virus-3. This is the first report of occurrence of a cryptic virus in pigeonpea plants.
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Affiliation(s)
- Surender Kumar
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT) Campus, Palampur, India
- Department of Biotechnology, Plant Virus Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | | | - Reenu Kumari
- Department of Biotechnology, Plant Virus Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Vipin Hallan
- Department of Biotechnology, Plant Virus Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
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19
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Wada Y, Orba Y, Sasaki M, Kobayashi S, Carr MJ, Nobori H, Sato A, Hall WW, Sawa H. Discovery of a novel antiviral agent targeting the nonstructural protein 4 (nsP4) of chikungunya virus. Virology 2017; 505:102-112. [DOI: 10.1016/j.virol.2017.02.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/09/2017] [Accepted: 02/15/2017] [Indexed: 01/31/2023]
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20
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Amroun A, Priet S, de Lamballerie X, Quérat G. Bunyaviridae RdRps: structure, motifs, and RNA synthesis machinery. Crit Rev Microbiol 2017; 43:753-778. [PMID: 28418734 DOI: 10.1080/1040841x.2017.1307805] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Bunyaviridae family is the largest and most diverse family of RNA viruses. It has more than 350 members divided into five genera: Orthobunyavirus, Phlebovirus, Nairovirus, Hantavirus, and Tospovirus. They are present in the five continents, causing recurrent epidemics, epizootics, and considerable agricultural loss. The genome of bunyaviruses is divided into three segments of negative single-stranded RNA according to their relative size: L (Large), M (Medium) and S (Small) segment. Bunyaviridae RNA-dependent RNA polymerase (RdRp) is encoded by the L segment, and is in charge of the replication and transcription of the viral RNA in the cytoplasm of the infected cell. Viral RdRps share a characteristic right hand-like structure with three subdomains: finger, palm, and thumb subdomains that define the formation of the catalytic cavity. In addition to the N-terminal endonuclease domain, eight conserved motifs (A-H) have been identified in the RdRp of Bunyaviridae. In this review, we have summarized the recent insights from the structural and functional studies of RdRp to understand the roles of different motifs shared by RdRps, the mechanism of viral RNA replication, genome segment packaging by the nucleoprotein, cap-snatching, mRNA transcription, and other RNA mechanisms of bunyaviruses.
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Affiliation(s)
- Abdennour Amroun
- a Faculté de Médecine , UMR "Emergence des Pathologies Virales" (Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP), Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille , Marseille , France
| | - Stéphane Priet
- a Faculté de Médecine , UMR "Emergence des Pathologies Virales" (Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP), Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille , Marseille , France
| | - Xavier de Lamballerie
- a Faculté de Médecine , UMR "Emergence des Pathologies Virales" (Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP), Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille , Marseille , France
| | - Gilles Quérat
- a Faculté de Médecine , UMR "Emergence des Pathologies Virales" (Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP), Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille , Marseille , France
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21
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Peersen OB. Picornaviral polymerase structure, function, and fidelity modulation. Virus Res 2017; 234:4-20. [PMID: 28163093 PMCID: PMC5476519 DOI: 10.1016/j.virusres.2017.01.026] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/27/2017] [Indexed: 12/17/2022]
Abstract
Like all positive strand RNA viruses, the picornaviruses replicate their genomes using a virally encoded RNA-dependent RNA polymerase enzyme known as 3Dpol. Over the past decade we have made tremendous advances in our understanding of 3Dpol structure and function, including the discovery of a novel mechanism for closing the active site that allows these viruses to easily fine tune replication fidelity and quasispecies distributions. This review summarizes current knowledge of picornaviral polymerase structure and how the enzyme interacts with RNA and other viral proteins to form stable and processive elongation complexes. The picornaviral RdRPs are among the smallest viral polymerases, but their fundamental molecular mechanism for catalysis appears to be generally applicable as a common feature of all positive strand RNA virus polymerases.
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Affiliation(s)
- Olve B Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, United States.
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22
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Yang X, Liu X, Musser DM, Moustafa IM, Arnold JJ, Cameron CE, Boehr DD. Triphosphate Reorientation of the Incoming Nucleotide as a Fidelity Checkpoint in Viral RNA-dependent RNA Polymerases. J Biol Chem 2017; 292:3810-3826. [PMID: 28100782 DOI: 10.1074/jbc.m116.750638] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 01/16/2017] [Indexed: 11/06/2022] Open
Abstract
The nucleotide incorporation fidelity of the viral RNA-dependent RNA polymerase (RdRp) is important for maintaining functional genetic information but, at the same time, is also important for generating sufficient genetic diversity to escape the bottlenecks of the host's antiviral response. We have previously shown that the structural dynamics of the motif D loop are closely related to nucleotide discrimination. Previous studies have also suggested that there is a reorientation of the triphosphate of the incoming nucleotide, which is essential before nucleophilic attack from the primer RNA 3'-hydroxyl. Here, we have used 31P NMR with poliovirus RdRp to show that the binding environment of the triphosphate is different when correct versus incorrect nucleotide binds. We also show that amino acid substitutions at residues known to interact with the triphosphate can alter the binding orientation/environment of the nucleotide, sometimes lead to protein conformational changes, and lead to substantial changes in RdRp fidelity. The analyses of other fidelity variants also show that changes in the triphosphate binding environment are not always accompanied by changes in the structural dynamics of the motif D loop or other regions known to be important for RdRp fidelity, including motif B. Altogether, our studies suggest that the conformational changes in motifs B and D, and the nucleoside triphosphate reorientation represent separable, "tunable" fidelity checkpoints.
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Affiliation(s)
| | | | | | - Ibrahim M Moustafa
- Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jamie J Arnold
- Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Craig E Cameron
- Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
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23
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Wang J, Dong H, Chionh YH, McBee ME, Sirirungruang S, Cunningham RP, Shi PY, Dedon PC. The role of sequence context, nucleotide pool balance and stress in 2'-deoxynucleotide misincorporation in viral, bacterial and mammalian RNA. Nucleic Acids Res 2016; 44:8962-8975. [PMID: 27365049 PMCID: PMC5062971 DOI: 10.1093/nar/gkw572] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/06/2016] [Indexed: 11/16/2022] Open
Abstract
The misincorporation of 2′-deoxyribonucleotides (dNs) into RNA has important implications for the function of non-coding RNAs, the translational fidelity of coding RNAs and the mutagenic evolution of viral RNA genomes. However, quantitative appreciation for the degree to which dN misincorporation occurs is limited by the lack of analytical tools. Here, we report a method to hydrolyze RNA to release 2′-deoxyribonucleotide-ribonucleotide pairs (dNrN) that are then quantified by chromatography-coupled mass spectrometry (LC-MS). Using this platform, we found misincorporated dNs occurring at 1 per 103 to 105 ribonucleotide (nt) in mRNA, rRNAs and tRNA in human cells, Escherichia coli, Saccharomyces cerevisiae and, most abundantly, in the RNA genome of dengue virus. The frequency of dNs varied widely among organisms and sequence contexts, and partly reflected the in vitro discrimination efficiencies of different RNA polymerases against 2′-deoxyribonucleoside 5′-triphosphates (dNTPs). Further, we demonstrate a strong link between dN frequencies in RNA and the balance of dNTPs and ribonucleoside 5′-triphosphates (rNTPs) in the cellular pool, with significant stress-induced variation of dN incorporation. Potential implications of dNs in RNA are discussed, including the possibilities of dN incorporation in RNA as a contributing factor in viral evolution and human disease, and as a host immune defense mechanism against viral infections.
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Affiliation(s)
- Jin Wang
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Hongping Dong
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Yok Hian Chionh
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602 Department of Microbiology & Immunology Programme, Center for Life Sciences, National University of Singapore, Singapore 117545
| | - Megan E McBee
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Sasilada Sirirungruang
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Richard P Cunningham
- Department of Biological Sciences, The University at Albany, Albany, NY 12222, USA
| | - Pei-Yong Shi
- Departments of Biochemistry & Molecular Biology and Phamarcology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Peter C Dedon
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602 Department of Biological Engineering & Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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24
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Abstract
By now, it is well established that the error rate of the RNA-dependent RNA polymerase (RdRp) that replicates RNA virus genomes is a primary driver of the mutation frequencies observed in RNA virus populations-the basis for the RNA quasispecies. Over the last 10 years, a considerable amount of work has uncovered the molecular determinants of replication fidelity in this enzyme. The isolation of high- and low-fidelity variants for several RNA viruses, in an expanding number of viral families, provides evidence that nature has optimized the fidelity to facilitate genetic diversity and adaptation, while maintaining genetic integrity and infectivity. This chapter will provide an overview of what fidelity variants tell us about RNA virus biology and how they may be used in antiviral approaches.
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Affiliation(s)
- Esteban Domingo
- Campus de Cantoblanco, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Peter Schuster
- The Santa Fe Institute, Santa Fe, NM, USA and Institut f. Theoretische Chemie, Universität Wien, Vienna, Austria
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25
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Abstract
Hantaviruses are emerging zoonotic pathogens that belong to the Bunyaviridae family. They have been classified as category A pathogens by CDC (centers for disease control and prevention). Hantaviruses pose a serious threat to human health because their infection causes two highly fatal diseases, hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). These pathogens are transmitted to humans through aerosolized excreta of their infected rodent hosts. Hantaviruses have a tripartite-segmented negative-sense RNA genome. The three genomic RNA segments, S, M, and L, encode a nucleocapsid protein (N), a precursor glycoprotein that is processed into two envelope glycoproteins (Gn and Gc) and the viral RNA-dependent RNA polymerase (RdRp), respectively. N protein is the major structural component of the virus, its main function is to protect and encapsidate the three genomic RNAs forming three viral ribonucleocapsids. Recent studies have proposed that N in conjunction with RdRp plays important roles in the transcription and replication of viral genome. In addition, N preferentially facilitates the translation of viral mRNA in cells. Glycoproteins, Gn and Gc, play major roles in viral attachment and entry to the host cells, virulence, and assembly and packaging of new virions in infected cells. RdRp functions as RNA replicase and transcriptase to replicate and transcribe the viral RNA and is also thought to have endonuclease activity. Currently, no antiviral therapy or vaccine is available for the treatment of hantavirus-associated diseases. Understanding the molecular details of hantavirus life cycle will help in the identification of targets for antiviral therapeutics and in the design of potential antiviral drug for the treatment of HFRS and HCPS. Due to the alarming fatality of hantavirus diseases, development of an effective vaccine against hantaviruses is a necessity.
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Arterivirus RNA-dependent RNA polymerase: Vital enzymatic activity remains elusive. Virology 2015; 487:68-74. [PMID: 26499043 PMCID: PMC7111705 DOI: 10.1016/j.virol.2015.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/25/2015] [Accepted: 10/01/2015] [Indexed: 12/19/2022]
Abstract
All RNA viruses encode an RNA-dependent RNA polymerase (RdRp), which in arteriviruses is expressed as the C-terminal domain of nonstructural protein 9 (nsp9). Previously, potent primer-dependent RdRp activity has been demonstrated for the homologous polymerase subunit (nsp12) of the distantly related coronaviruses. The only previous study focusing on the in vitro activity of nsp9 of an arterivirus (equine arteritis virus; EAV) reported weak de novo polymerase activity on homopolymeric RNA templates. However, this activity was not retained when Mn2+ ions were omitted from the assay or when biologically relevant templates were supplied, which prompted us to revisit the biochemical properties of this polymerase. Based on the properties of active-site mutants, we conclude that the RNA-synthesizing activities observed in de novo and primer-dependent polymerase and terminal transferase assays cannot be attributed to recombinant EAV nsp9-RdRp. Our results illustrate the potential pitfalls of characterizing polymerases using highly sensitive biochemical assays. Several recombinant RdRp preparations of Equine arteritis virus (EAV) were purified. No primer-dependent or de novo RdRp or terminal transferase activity was shown. One RdRp preparation showed products resembling those of phage T7 RNA polymerase. Mutation of the RdRp active site aspartates to alanine crippled the EAV viability. Characterizing low activity RdRp in sensitive enzymatic assays requires extra care.
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27
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Functional insights from molecular modeling, docking, and dynamics study of a cypoviral RNA dependent RNA polymerase. J Mol Graph Model 2015; 61:160-74. [PMID: 26264734 DOI: 10.1016/j.jmgm.2015.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/27/2015] [Accepted: 07/18/2015] [Indexed: 11/20/2022]
Abstract
Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV) contains 11 double stranded RNA genome segments and infects tasar silkworm A. mylitta. RNA-dependent RNA polymerase (RdRp) is reported as a key enzyme responsible for propagation of the virus in the host cell but its structure function relationship still remains elusive. Here a computational approach has been taken to compare sequence and secondary structure of AmCPV RdRp with other viral RdRps to identify consensus motifs. Then a reliable pairwise sequence alignment of AmCPV RdRp with its closest sequence structure homologue λ3 RdRp is done to predict three dimensional structure of AmCPV RdRp. After comparing with other structurally known viral RdRps, important sequence and/or structural features involved in substrate entry or binding, polymerase reaction and the product release events have been identified. A conserved RNA pentanucleotide (5'-AGAGC-3') at the 3'-end of virus genome is predicted as cis-acting signal for RNA synthesis and its docking and simulation study along with the model of AmCPV RdRp has allowed to predict mode of template binding by the viral polymerase. It is found that template RNA enters into the catalytic center through nine sequence-independent and two sequence-dependent interactions with the specific amino acid residues. However, number of sequence dependent interactions remains almost same during 10 nano-second simulation time while total number of interactions decreases. Further, docking of N(7)-methyl-GpppG (mRNA cap) on the model as well as prediction of RNA secondary structure has shown the template entry process in the active site. These findings have led to postulate the mechanism of RNA-dependent RNA polymerization process by AmCPV RdRp. To our knowledge, this is the first report to evaluate structure function relationship of a cypoviral RdRp.
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Deval J, Hong J, Wang G, Taylor J, Smith LK, Fung A, Stevens SK, Liu H, Jin Z, Dyatkina N, Prhavc M, Stoycheva AD, Serebryany V, Liu J, Smith DB, Tam Y, Zhang Q, Moore ML, Fearns R, Chanda SM, Blatt LM, Symons JA, Beigelman L. Molecular Basis for the Selective Inhibition of Respiratory Syncytial Virus RNA Polymerase by 2'-Fluoro-4'-Chloromethyl-Cytidine Triphosphate. PLoS Pathog 2015; 11:e1004995. [PMID: 26098424 PMCID: PMC4476725 DOI: 10.1371/journal.ppat.1004995] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/02/2015] [Indexed: 01/23/2023] Open
Abstract
Respiratory syncytial virus (RSV) causes severe lower respiratory tract infections, yet no vaccines or effective therapeutics are available. ALS-8176 is a first-in-class nucleoside analog prodrug effective in RSV-infected adult volunteers, and currently under evaluation in hospitalized infants. Here, we report the mechanism of inhibition and selectivity of ALS-8176 and its parent ALS-8112. ALS-8176 inhibited RSV replication in non-human primates, while ALS-8112 inhibited all strains of RSV in vitro and was specific for paramyxoviruses and rhabdoviruses. The antiviral effect of ALS-8112 was mediated by the intracellular formation of its 5'-triphosphate metabolite (ALS-8112-TP) inhibiting the viral RNA polymerase. ALS-8112 selected for resistance-associated mutations within the region of the L gene of RSV encoding the RNA polymerase. In biochemical assays, ALS-8112-TP was efficiently recognized by the recombinant RSV polymerase complex, causing chain termination of RNA synthesis. ALS-8112-TP did not inhibit polymerases from host or viruses unrelated to RSV such as hepatitis C virus (HCV), whereas structurally related molecules displayed dual RSV/HCV inhibition. The combination of molecular modeling and enzymatic analysis showed that both the 2'F and the 4'ClCH2 groups contributed to the selectivity of ALS-8112-TP. The lack of antiviral effect of ALS-8112-TP against HCV polymerase was caused by Asn291 that is well-conserved within positive-strand RNA viruses. This represents the first comparative study employing recombinant RSV and HCV polymerases to define the selectivity of clinically relevant nucleotide analogs. Understanding nucleotide selectivity towards distant viral RNA polymerases could not only be used to repurpose existing drugs against new viral infections, but also to design novel molecules.
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Affiliation(s)
- Jerome Deval
- Alios BioPharma, Inc., South San Francisco, California, United States of America
- * E-mail: (JD); (LB)
| | - Jin Hong
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Guangyi Wang
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Josh Taylor
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Lucas K. Smith
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Amy Fung
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Sarah K. Stevens
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Hong Liu
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Zhinan Jin
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Natalia Dyatkina
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Marija Prhavc
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Antitsa D. Stoycheva
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Vladimir Serebryany
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Jyanwei Liu
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - David B. Smith
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Yuen Tam
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Qingling Zhang
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Martin L. Moore
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Children's Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Sushmita M. Chanda
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Lawrence M. Blatt
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Julian A. Symons
- Alios BioPharma, Inc., South San Francisco, California, United States of America
| | - Leo Beigelman
- Alios BioPharma, Inc., South San Francisco, California, United States of America
- * E-mail: (JD); (LB)
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Korboukh VK, Lee CA, Acevedo A, Vignuzzi M, Xiao Y, Arnold JJ, Hemperly S, Graci JD, August A, Andino R, Cameron CE. RNA virus population diversity, an optimum for maximal fitness and virulence. J Biol Chem 2014; 289:29531-44. [PMID: 25213864 DOI: 10.1074/jbc.m114.592303] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The ability of an RNA virus to exist as a population of genetically distinct variants permits the virus to overcome events during infections that would otherwise limit virus multiplication or drive the population to extinction. Viral genetic diversity is created by the ribonucleotide misincorporation frequency of the viral RNA-dependent RNA polymerase (RdRp). We have identified a poliovirus (PV) RdRp derivative (H273R) possessing a mutator phenotype. GMP misincorporation efficiency for H273R RdRp in vitro was increased by 2-3-fold that manifested in a 2-3-fold increase in the diversity of the H273R PV population in cells. Circular sequencing analysis indicated that some mutations were RdRp-independent. Consistent with the population genetics theory, H273R PV was driven to extinction more easily than WT in cell culture. Furthermore, we observed a substantial reduction in H273R PV virulence, measured as the ability to cause paralysis in the cPVR mouse model. Reduced virulence correlated with the inability of H273R PV to sustain replication in tissues/organs in which WT persists. Despite the attenuated phenotype, H273R PV was capable of replicating in mice to levels sufficient to induce a protective immune response, even when the infecting dose used was insufficient to elicit any visual signs of infection. We conclude that optimal RdRp fidelity is a virulence determinant that can be targeted for viral attenuation or antiviral therapies, and we suggest that the RdRp may not be the only source of mutations in a RNA virus genome.
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Affiliation(s)
| | - Cheri A Lee
- From the Departments of Biochemistry and Molecular Biology and
| | - Ashley Acevedo
- the Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94158
| | - Marco Vignuzzi
- the Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94158
| | - Yinghong Xiao
- the Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94158
| | - Jamie J Arnold
- From the Departments of Biochemistry and Molecular Biology and
| | | | - Jason D Graci
- From the Departments of Biochemistry and Molecular Biology and
| | - Avery August
- Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 and
| | - Raul Andino
- the Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94158
| | - Craig E Cameron
- From the Departments of Biochemistry and Molecular Biology and
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Subissi L, Decroly E, Selisko B, Canard B, Imbert I. A closed-handed affair: positive-strand RNA virus polymerases. Future Virol 2014. [DOI: 10.2217/fvl.14.53] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT RNA viruses are important emerging pathogens that cause human and animal infectious diseases. Antiviral therapies have to deal with the high mutational capacity of RNA viruses, which quickly adapt to new environments. A primary target for antiviral drug development is the viral RNA-dependent RNA polymerase (RdRp), which is the central enzyme of the viral RNA replication/transcription machinery. Here, we review the current mechanistic and structural knowledge on RdRps of positive-strand RNA viruses gained through crystallography and biochemistry. In addition, we review the growing body of information on RdRp-mediated strategies, such as proofreading and genome end repair, used by positive-strand RNA viruses to maintain their genome integrity.
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Affiliation(s)
- Lorenzo Subissi
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Etienne Decroly
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Barbara Selisko
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Bruno Canard
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
| | - Isabelle Imbert
- Centre National de la Recherche Scientifique, Aix-Marseille Université, CNRS UMR 7257, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
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31
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te Velthuis AJW. Common and unique features of viral RNA-dependent polymerases. Cell Mol Life Sci 2014; 71:4403-20. [PMID: 25080879 PMCID: PMC4207942 DOI: 10.1007/s00018-014-1695-z] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/29/2014] [Accepted: 07/28/2014] [Indexed: 12/12/2022]
Abstract
Eukaryotes and bacteria can be infected with a wide variety of RNA viruses. On average, these pathogens share little sequence similarity and use different replication and transcription strategies. Nevertheless, the members of nearly all RNA virus families depend on the activity of a virally encoded RNA-dependent polymerase for the condensation of nucleotide triphosphates. This review provides an overview of our current understanding of the viral RNA-dependent polymerase structure and the biochemistry and biophysics that is involved in replicating and transcribing the genetic material of RNA viruses.
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Affiliation(s)
- Aartjan J W te Velthuis
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands,
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32
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Černý J, Černá Bolfíková B, Valdés JJ, Grubhoffer L, Růžek D. Evolution of tertiary structure of viral RNA dependent polymerases. PLoS One 2014; 9:e96070. [PMID: 24816789 PMCID: PMC4015915 DOI: 10.1371/journal.pone.0096070] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 04/02/2014] [Indexed: 11/18/2022] Open
Abstract
Viral RNA dependent polymerases (vRdPs) are present in all RNA viruses; unfortunately, their sequence similarity is too low for phylogenetic studies. Nevertheless, vRdP protein structures are remarkably conserved. In this study, we used the structural similarity of vRdPs to reconstruct their evolutionary history. The major strength of this work is in unifying sequence and structural data into a single quantitative phylogenetic analysis, using powerful a Bayesian approach. The resulting phylogram of vRdPs demonstrates that RNA-dependent DNA polymerases (RdDPs) of viruses within Retroviridae family cluster in a clearly separated group of vRdPs, while RNA-dependent RNA polymerases (RdRPs) of dsRNA and +ssRNA viruses are mixed together. This evidence supports the hypothesis that RdRPs replicating +ssRNA viruses evolved multiple times from RdRPs replicating +dsRNA viruses, and vice versa. Moreover, our phylogram may be presented as a scheme for RNA virus evolution. The results are in concordance with the actual concept of RNA virus evolution. Finally, the methods used in our work provide a new direction for studying ancient virus evolution.
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Affiliation(s)
- Jiří Černý
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
- * E-mail:
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - James J. Valdés
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Libor Grubhoffer
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Daniel Růžek
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
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33
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The crystal structure of a cardiovirus RNA-dependent RNA polymerase reveals an unusual conformation of the polymerase active site. J Virol 2014; 88:5595-607. [PMID: 24600002 DOI: 10.1128/jvi.03502-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
UNLABELLED Encephalomyocarditis virus (EMCV) is a member of the Cardiovirus genus within the large Picornaviridae family, which includes a number of important human and animal pathogens. The RNA-dependent RNA polymerase (RdRp) 3Dpol is a key enzyme for viral genome replication. In this study, we report the X-ray structures of two different crystal forms of the EMCV RdRp determined at 2.8- and 2.15-Å resolution. The in vitro elongation and VPg uridylylation activities of the purified enzyme have also been demonstrated. Although the overall structure of EMCV 3Dpol is shown to be similar to that of the known RdRps of other members of the Picornaviridae family, structural comparisons show a large reorganization of the active-site cavity in one of the crystal forms. The rearrangement affects mainly motif A, where the conserved residue Asp240, involved in ribonucleoside triphosphate (rNTP) selection, and its neighbor residue, Phe239, move about 10 Å from their expected positions within the ribose binding pocket toward the entrance of the rNTP tunnel. This altered conformation of motif A is stabilized by a cation-π interaction established between the aromatic ring of Phe239 and the side chain of Lys56 within the finger domain. Other contacts, involving Phe239 and different residues of motif F, are also observed. The movement of motif A is connected with important conformational changes in the finger region flanked by residues 54 to 63, harboring Lys56, and in the polymerase N terminus. The structures determined in this work provide essential information for studies on the cardiovirus RNA replication process and may have important implications for the development of new antivirals targeting the altered conformation of motif A. IMPORTANCE The Picornaviridae family is one of the largest virus families known, including many important human and animal pathogens. The RNA-dependent RNA polymerase (RdRp) 3Dpol is a key enzyme for picornavirus genome replication and a validated target for the development of antiviral therapies. Solving the X-ray structure of the first cardiovirus RdRp, EMCV 3Dpol, we captured an altered conformation of a conserved motif in the polymerase active site (motif A) containing the aspartic acid residue involved in rNTP selection and binding. This altered conformation of motif A, which interferes with the correct positioning of the rNTP substrate in the active site, is stabilized by a number of residues strictly conserved among picornaviruses. The rearrangements observed suggest that this motif A segment is a dynamic element that can be modulated by external effectors, either activating or inhibiting enzyme activity, and this type of modulation appears to be general to all picornaviruses.
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34
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Morin B, Whelan SPJ. Sensitivity of the polymerase of vesicular stomatitis virus to 2' substitutions in the template and nucleotide triphosphate during initiation and elongation. J Biol Chem 2014; 289:9961-9. [PMID: 24526687 DOI: 10.1074/jbc.m113.542761] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The RNA synthesis machinery of non-segmented negative-sense RNA viruses comprises a ribonucleoprotein complex of the genomic RNA coated by a nucleocapsid protein (N) and associated with polymerase. Work with vesicular stomatitis virus (VSV), a prototype, supports a model of RNA synthesis whereby N is displaced from the template to allow the catalytic subunit of the polymerase, the large protein (L) to gain access to the RNA. Consistent with that model, purified L can copy synthetic RNA that contains requisite promoter sequences. Full processivity of L requires its phosphoprotein cofactor and the template-associated N. Here we demonstrate the importance of the 2' position of the RNA template and the substrate nucleotide triphosphates during initiation and elongation by L. The VSV polymerase can initiate on both DNA and RNA and can incorporate dNTPs. During elongation, the polymerase is sensitive to 2' modifications, although dNTPs can be incorporated, and mixed DNA-RNA templates can function. Modifications to the 2' position of the NTP, including 2',3'-ddCTP, arabinose-CTP, and 2'-O-methyl-CTP, inhibit polymerase, whereas 2'-amino-CTP is incorporated. The inhibitory effects of the NTPs were more pronounced on authentic N-RNA with the exception of dGTP, which is incorporated. This work underscores the sensitivity of the VSV polymerase to nucleotide modifications during initiation and elongation and highlights the importance of the 2'-hydroxyl of both template and substrate NTP. Moreover, this study demonstrates a critical role of the template-associated N protein in the architecture of the RNA-dependent RNA polymerase domain of L.
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Affiliation(s)
- Benjamin Morin
- From the Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
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35
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Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature 2013; 505:686-90. [PMID: 24284629 DOI: 10.1038/nature12861] [Citation(s) in RCA: 268] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 11/11/2013] [Indexed: 01/15/2023]
Abstract
RNA viruses exist as genetically diverse populations. It is thought that diversity and genetic structure of viral populations determine the rapid adaptation observed in RNA viruses and hence their pathogenesis. However, our understanding of the mechanisms underlying virus evolution has been limited by the inability to accurately describe the genetic structure of virus populations. Next-generation sequencing technologies generate data of sufficient depth to characterize virus populations, but are limited in their utility because most variants are present at very low frequencies and are thus indistinguishable from next-generation sequencing errors. Here we present an approach that reduces next-generation sequencing errors and allows the description of virus populations with unprecedented accuracy. Using this approach, we define the mutation rates of poliovirus and uncover the mutation landscape of the population. Furthermore, by monitoring changes in variant frequencies on serially passaged populations, we determined fitness values for thousands of mutations across the viral genome. Mapping of these fitness values onto three-dimensional structures of viral proteins offers a powerful approach for exploring structure-function relationships and potentially uncovering new functions. To our knowledge, our study provides the first single-nucleotide fitness landscape of an evolving RNA virus and establishes a general experimental platform for studying the genetic changes underlying the evolution of virus populations.
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36
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Shatskaya GS, Dmitrieva TM. Structural organization of viral RNA-dependent RNA polymerases. BIOCHEMISTRY (MOSCOW) 2013; 78:231-5. [PMID: 23586715 DOI: 10.1134/s0006297913030036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review describes available data on the structure of viral RNA-dependent RNA polymerases (RdRP) obtained from X-ray analysis and discusses the functional significance of the structural elements of these enzymes. Because most of the studies done to date relate to RdRP structures of picorna-, flavi-, and caliciviruses, here we consider mostly the structures of RdRP of these groups of viruses, and also include information about polymerases of other virus families.
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Affiliation(s)
- G S Shatskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
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37
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Liu X, Yang X, Lee CA, Moustafa IM, Smidansky ED, Lum D, Arnold JJ, Cameron CE, Boehr DD. Vaccine-derived mutation in motif D of poliovirus RNA-dependent RNA polymerase lowers nucleotide incorporation fidelity. J Biol Chem 2013; 288:32753-32765. [PMID: 24085299 DOI: 10.1074/jbc.m113.484428] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
All viral RNA-dependent RNA polymerases (RdRps) have a conserved structural element termed motif D. Studies of the RdRp from poliovirus (PV) have shown that a conformational change of motif D leads to efficient and faithful nucleotide addition by bringing Lys-359 into the active site where it serves as a general acid. The RdRp of the Sabin I vaccine strain has Thr-362 changed to Ile. Such a drastic change so close to Lys-359 might alter RdRp function and contribute in some way to the attenuated phenotype of Sabin type I. Here we present our characterization of the T362I RdRp. We find that the T362I RdRp exhibits a mutator phenotype in biochemical experiments in vitro. Using NMR, we show that this change in nucleotide incorporation fidelity correlates with a change in the structural dynamics of motif D. A recombinant PV expressing the T362I RdRp exhibits normal growth properties in cell culture but expresses a mutator phenotype in cells. For example, the T362I-containing PV is more sensitive to the mutagenic activity of ribavirin than wild-type PV. Interestingly, the T362I change was sufficient to cause a statistically significant reduction in viral virulence. Collectively, these studies suggest that residues of motif D can be targeted when changes in nucleotide incorporation fidelity are desired. Given the observation that fidelity mutants can serve as vaccine candidates, it may be possible to use engineering of motif D for this purpose.
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Affiliation(s)
| | | | - Cheri A Lee
- the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Ibrahim M Moustafa
- the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Eric D Smidansky
- the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | | | - Jamie J Arnold
- the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Craig E Cameron
- the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
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38
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Maláč K, Barvík I. Substrate recognition by norovirus polymerase: microsecond molecular dynamics study. J Comput Aided Mol Des 2013; 27:373-88. [PMID: 23619980 DOI: 10.1007/s10822-013-9652-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 04/18/2013] [Indexed: 01/02/2023]
Abstract
Molecular dynamics simulations of complexes between Norwalk virus RNA dependent RNA polymerase and its natural CTP and 2dCTP (both containing the O5'-C5'-C4'-O4' sequence of atoms bridging the triphosphate and sugar moiety) or modified coCTP (C5'-O5'-C4'-O4'), cocCTP (C5'-O5'-C4'-C4'') substrates were produced by means of CUDA programmable graphical processing units and the ACEMD software package. It enabled us to gain microsecond MD trajectories clearly showing that similar nucleoside triphosphates can bind surprisingly differently into the active site of the Norwalk virus RNA dependent RNA polymerase. It corresponds to their different modes of action (CTP-substrate, 2dCTP-poor substrate, coCTP-chain terminator, cocCTP-inhibitor). Moreover, extremely rare events-as repetitive pervasion of Arg182 into a potentially reaction promoting arrangement-were captured.
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Affiliation(s)
- Kamil Maláč
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, Prague 2, 121 16, Czech Republic
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39
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Garriga D, Ferrer-Orta C, Querol-Audí J, Oliva B, Verdaguer N. Role of motif B loop in allosteric regulation of RNA-dependent RNA polymerization activity. J Mol Biol 2013; 425:2279-87. [PMID: 23542342 DOI: 10.1016/j.jmb.2013.03.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 03/15/2013] [Accepted: 03/21/2013] [Indexed: 01/22/2023]
Abstract
Increasing amounts of data show that conformational dynamics are essential for protein function. Unveiling the mechanisms by which this flexibility affects the activity of a given enzyme and how it is controlled by other effectors opens the door to the design of a new generation of highly specific drugs. Viral RNA-dependent RNA polymerases (RdRPs) are not an exception. These enzymes, essential for the multiplication of all RNA viruses, catalyze the formation of phosphodiester bonds between ribonucleotides in an RNA-template-dependent fashion. Inhibition of RdRP activity will prevent genome replication and virus multiplication. Thus, RdRPs, like the reverse transcriptase of retroviruses, are validated targets for the development of antiviral therapeutics. X-ray crystallography of RdRPs trapped in multiple steps throughout the catalytic process, together with NMR data and molecular dynamics simulations, have shown that all polymerase regions contributing to conserved motifs required for substrate binding, catalysis and product release are highly flexible and some of them are predicted to display correlated motions. All these dynamic elements can be modulated by external effectors, which appear as useful tools for the development of effective allosteric inhibitors that block or disturb the flexibility of these enzymes, ultimately impeding their function. Among all movements observed, motif B, and the B-loop at its N-terminus in particular, appears as a new potential druggable site.
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Affiliation(s)
- Damià Garriga
- Institut de Biología Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Baldiri i Reixac 10-12, 08028 Barcelona, Spain
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40
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Ribavirin-resistant mutants of human enterovirus 71 express a high replication fidelity phenotype during growth in cell culture. J Virol 2012; 87:1759-69. [PMID: 23175376 DOI: 10.1128/jvi.02139-12] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
It has been shown in animal models that ribavirin-resistant poliovirus with a G64S mutation in its 3D polymerase has high replication fidelity coupled with attenuated virulence. Here, we describe the effects of mutagenesis in the human enterovirus 71 (HEV71) 3D polymerase on ribavirin resistance and replication fidelity. Seven substitutions were introduced at amino acid position 3D-G64 of a HEV71 full-length infectious cDNA clone (26M). Viable clone-derived virus populations were rescued from the G64N, G64R, and G64T mutant cDNA clones. The clone-derived G64R and G64T mutant virus populations were resistant to growth inhibition in the presence of 1,600 μM ribavirin, whereas the growth of parental 26M and the G64N mutant viruses were inhibited in the presence of 800 μM ribavirin. Nucleotide sequencing of the 2C and 3D coding regions revealed that the rate of random mutagenesis after 13 passages in the presence of 400 μM ribavirin was nearly 10 times higher in the 26M genome than in the mutant G64R virus genome. Furthermore, random mutations acquired in the 2C coding regions of 26M and G64N conferred resistance to growth inhibition in the presence of 0.5 mM guanidine, whereas the G64R and G64T mutant virus populations remained susceptible to growth inhibition by 0.5 mM guanidine. Interestingly, a S264L mutation identified in the 3D coding region of 26M after ribavirin selection was also associated with both ribavirin-resistant and high replication fidelity phenotypes. These findings are consistent with the hypothesis that the 3D-G64R, 3D-G64T, and 3D-S264L mutations confer resistance upon HEV71 to the antiviral mutagen ribavirin, coupled with a high replication fidelity phenotype during growth in cell culture.
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Weeks SA, Lee CA, Zhao Y, Smidansky ED, August A, Arnold JJ, Cameron CE. A Polymerase mechanism-based strategy for viral attenuation and vaccine development. J Biol Chem 2012; 287:31618-22. [PMID: 22854962 DOI: 10.1074/jbc.c112.401471] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Live, attenuated vaccines have prevented morbidity and mortality associated with myriad viral pathogens. Development of live, attenuated vaccines has traditionally relied on empirical methods, such as growth in nonhuman cells. These approaches require substantial time and expense to identify vaccine candidates and to determine their mechanisms of attenuation. With these constraints, at least a decade is required for approval of a live, attenuated vaccine for use in humans. We recently reported the discovery of an active site lysine residue that contributes to the catalytic efficiency of all nucleic acid polymerases (Castro, C., Smidansky, E. D., Arnold, J. J., Maksimchuk, K. R., Moustafa, I., Uchida, A., Götte, M., Konigsberg, W., and Cameron, C. E. (2009) Nat. Struct. Mol. Biol. 16, 212-218). Here we use a model RNA virus and its polymerase to show that mutation of this residue from lysine to arginine produces an attenuated virus that is genetically stable and elicits a protective immune response. Given the conservation of this residue in all viral polymerases, this study suggests that a universal, mechanism-based strategy may exist for viral attenuation and vaccine development.
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Affiliation(s)
- Spencer A Weeks
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University,University Park, Pennsylvania 16802, USA
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42
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Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. J Virol 2012; 86:5562-73. [PMID: 22379100 DOI: 10.1128/jvi.07196-11] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
There are no known RNA viruses that infect Archaea. Filling this gap in our knowledge of viruses will enhance our understanding of the relationships between RNA viruses from the three domains of cellular life and, in particular, could shed light on the origin of the enormous diversity of RNA viruses infecting eukaryotes. We describe here the identification of novel RNA viral genome segments from high-temperature acidic hot springs in Yellowstone National Park in the United States. These hot springs harbor low-complexity cellular communities dominated by several species of hyperthermophilic Archaea. A viral metagenomics approach was taken to assemble segments of these RNA virus genomes from viral populations isolated directly from hot spring samples. Analysis of these RNA metagenomes demonstrated unique gene content that is not generally related to known RNA viruses of Bacteria and Eukarya. However, genes for RNA-dependent RNA polymerase (RdRp), a hallmark of positive-strand RNA viruses, were identified in two contigs. One of these contigs is approximately 5,600 nucleotides in length and encodes a polyprotein that also contains a region homologous to the capsid protein of nodaviruses, tetraviruses, and birnaviruses. Phylogenetic analyses of the RdRps encoded in these contigs indicate that the putative archaeal viruses form a unique group that is distinct from the RdRps of RNA viruses of Eukarya and Bacteria. Collectively, our findings suggest the existence of novel positive-strand RNA viruses that probably replicate in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses that infect eukaryotes and even more distant from known bacterial RNA viruses. These positive-strand RNA viruses might be direct ancestors of RNA viruses of eukaryotes.
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Le Nouën C, Toquin D, Müller H, Raue R, Kean KM, Langlois P, Cherbonnel M, Eterradossi N. Different domains of the RNA polymerase of infectious bursal disease virus contribute to virulence. PLoS One 2012; 7:e28064. [PMID: 22253687 PMCID: PMC3258228 DOI: 10.1371/journal.pone.0028064] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 10/31/2011] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Infectious bursal disease virus (IBDV) is a pathogen of worldwide significance to the poultry industry. IBDV has a bi-segmented double-stranded RNA genome. Segments A and B encode the capsid, ribonucleoprotein and non-structural proteins, or the virus polymerase (RdRp), respectively. Since the late eighties, very virulent (vv) IBDV strains have emerged in Europe inducing up to 60% mortality. Although some progress has been made in understanding the molecular biology of IBDV, the molecular basis for the pathogenicity of vvIBDV is still not fully understood. METHODOLOGY, PRINCIPAL FINDINGS Strain 88180 belongs to a lineage of pathogenic IBDV phylogenetically related to vvIBDV. By reverse genetics, we rescued a molecular clone (mc88180), as pathogenic as its parent strain. To study the molecular basis for 88180 pathogenicity, we constructed and characterized in vivo reassortant or mosaic recombinant viruses derived from the 88180 and the attenuated Cu-1 IBDV strains. The reassortant virus rescued from segments A of 88180 (A88) and B of Cu-1 (BCU1) was milder than mc88180 showing that segment B is involved in 88180 pathogenicity. Next, the exchange of different regions of BCU1 with their counterparts in B88 in association with A88 did not fully restore a virulence equivalent to mc88180. This demonstrated that several regions if not the whole B88 are essential for the in vivo pathogenicity of 88180. CONCLUSION, SIGNIFICANCE The present results show that different domains of the RdRp, are essential for the in vivo pathogenicity of IBDV, independently of the replication efficiency of the mosaic viruses.
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Affiliation(s)
- Cyril Le Nouën
- Avian and Rabbit Virology, Immunology and Parasitology Unit, OIE Reference Laboratory for Infectious Bursal Disease, French Agency for Food, Environmental and Occupational Health Safety (Anses), Ploufragan, France
| | - Didier Toquin
- Avian and Rabbit Virology, Immunology and Parasitology Unit, OIE Reference Laboratory for Infectious Bursal Disease, French Agency for Food, Environmental and Occupational Health Safety (Anses), Ploufragan, France
| | - Hermann Müller
- Institute for Virology, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | - Rüdiger Raue
- Institute for Virology, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, Germany
| | | | - Patrick Langlois
- Virus Genetics and Biosecurity Unit, French Agency for Food, Environmental and Occupational Health Safety (ANSES), Ploufragan, France
| | - Martine Cherbonnel
- Avian and Rabbit Virology, Immunology and Parasitology Unit, OIE Reference Laboratory for Infectious Bursal Disease, French Agency for Food, Environmental and Occupational Health Safety (Anses), Ploufragan, France
| | - Nicolas Eterradossi
- Avian and Rabbit Virology, Immunology and Parasitology Unit, OIE Reference Laboratory for Infectious Bursal Disease, French Agency for Food, Environmental and Occupational Health Safety (Anses), Ploufragan, France
- * E-mail:
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Formation of higher-order foot-and-mouth disease virus 3D(pol) complexes is dependent on elongation activity. J Virol 2011; 86:2371-4. [PMID: 22156531 DOI: 10.1128/jvi.05696-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The replication of many viruses involves the formation of higher-order structures or replication "factories." We show that the key replication enzyme of foot-and-mouth disease virus (FMDV), the RNA-dependent RNA polymerase, forms fibrils in vitro. Although there are similarities with previously characterized poliovirus polymerase fibrils, FMDV fibrils are narrower, are composed of both protein and RNA, and, importantly, are seen only when all components of an elongation assay are present. Furthermore, an inhibitory RNA aptamer prevents fibril formation.
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45
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Amineva SP, Aminev AG, Gern JE, Palmenberg AC. Comparison of rhinovirus A infection in human primary epithelial and HeLa cells. J Gen Virol 2011; 92:2549-2557. [PMID: 21752966 DOI: 10.1099/vir.0.031302-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
HeLa cells are used to study the life cycles of many different viruses, including the human rhinoviruses (HRV) in the family Picornaviridae. Although the natural targets of HRV are human bronchial epithelial cells (hBE), it is generally more difficult to obtain and maintain the relevant primary cell cultures, relative to HeLa cells. Given that the HRV are now identified as a major cause of human asthma exacerbations, it becomes important to document how much of the virus biology learned from HeLa cells is common also to natural primary cells. When compared directly in matched infections using A01a virus, the kinetics of RNA replication, the synthesis and processing of viral proteins and the general subcellular localization of key non-structural proteins were resembled in hBE and HeLa cells. Viral-induced shutoff of host cell processes (e.g. nucleo-cytoplasmic trafficking) was also comparable.
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Affiliation(s)
- S P Amineva
- School of Medicine and Public Health, 600 Highland Avenue, University of Wisconsin, Madison, WI 53792, USA.,Institute for Molecular Virology, University of Wisconsin, 1525 Linden Drive, Madison, WI 53706, USA
| | - A G Aminev
- Institute for Molecular Virology, University of Wisconsin, 1525 Linden Drive, Madison, WI 53706, USA
| | - J E Gern
- School of Medicine and Public Health, 600 Highland Avenue, University of Wisconsin, Madison, WI 53792, USA
| | - A C Palmenberg
- Institute for Molecular Virology, University of Wisconsin, 1525 Linden Drive, Madison, WI 53706, USA
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Graham SC, Sarin LP, Bahar MW, Myers RA, Stuart DI, Bamford DH, Grimes JM. The N-terminus of the RNA polymerase from infectious pancreatic necrosis virus is the determinant of genome attachment. PLoS Pathog 2011; 7:e1002085. [PMID: 21731487 PMCID: PMC3121795 DOI: 10.1371/journal.ppat.1002085] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 04/11/2011] [Indexed: 12/30/2022] Open
Abstract
The RNA-dependent RNA polymerase VP1 of infectious pancreatic necrosis virus (IPNV) is a single polypeptide responsible for both viral RNA transcription and genome replication. Sequence analysis identifies IPNV VP1 as having an unusual active site topology. We have purified, crystallized and solved the structure of IPNV VP1 to 2.3 Å resolution in its apo form and at 2.2 Å resolution bound to the catalytically-activating metal magnesium. We find that recombinantly-expressed VP1 is highly active for RNA transcription and replication, yielding both free and polymerase-attached RNA products. IPNV VP1 also possesses terminal (deoxy)nucleotide transferase, RNA-dependent DNA polymerase (reverse transcriptase) and template-independent self-guanylylation activity. The N-terminus of VP1 interacts with the active-site cleft and we show that the N-terminal serine residue is required for formation of covalent RNA∶polymerase complexes, providing a mechanism for the genesis of viral genome∶polymerase complexes observed in vivo. Infectious pancreatic necrosis virus (IPNV) is highly contagious and causes severe disease in fish. As a result of intensive rearing conditions it has become a serious problem for the salmon and trout farming industries. IPNV, like many other viruses, replicates its genome using a protein (a ‘polymerase’) that is itself encoded by the viral genome. Unusually, in infectious IPNV particles the polymerase is found chemically linked to the viral genome. We have determined the atomic structure of IPNV polymerase using X-ray crystallography, revealing some significant differences in the fold of the protein chain compared to other well-characterized viral polymerases. By mutating an amino acid residue at the beginning of the protein we show how the chemical linkage to the viral genome can be disrupted. This provides an elegant mechanism for the attachment of the viral genome to the polymerase observed in vivo.
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Affiliation(s)
- Stephen C. Graham
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - L. Peter Sarin
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Biocenter 2, Helsinki, Finland
| | - Mohammad W. Bahar
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Reg A. Myers
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - David I. Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Dennis H. Bamford
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Biocenter 2, Helsinki, Finland
- * E-mail: (DHB); (JMG)
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (DHB); (JMG)
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Zemla AT, Lang DM, Kostova T, Andino R, Ecale Zhou CL. StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase. BMC Bioinformatics 2011; 12:226. [PMID: 21635786 PMCID: PMC3121648 DOI: 10.1186/1471-2105-12-226] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 06/02/2011] [Indexed: 12/15/2022] Open
Abstract
Background Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory--still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could help overcome these difficulties by facilitating the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Results Here we present StralSV (structure-alignment sequence variability), a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus, and we demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique, or that share structural similarity with proteins that would be considered distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local structural alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. Conclusions StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. StralSV is provided as a web service at http://proteinmodel.org/AS2TS/STRALSV/.
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Affiliation(s)
- Adam T Zemla
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
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Jiang H, Weng L, Zhang N, Arita M, Li R, Chen L, Toyoda T. Biochemical characterization of enterovirus 71 3D RNA polymerase. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:211-9. [PMID: 21220056 DOI: 10.1016/j.bbagrm.2011.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 12/27/2010] [Accepted: 01/03/2011] [Indexed: 11/24/2022]
Abstract
An unusual enterovirus 71 (EV71) epidemic has begun in China since 2008. EV71 RNA polymerases (3D(pol)) showed polymerase activity with an Mn(2+). Little activity was detected with Co(2+), and no activity was detected with Mg(2+), Ca(2+), Cu(2+), Ni(2+), Cd(2+), or Zn(2+). It is a primer-dependent polymerase, and the enzyme functioned with both di- and 10-nucleotide RNA primers. DNA primer, dT15, increased primer activity, similar to other enterovirus 3D(pol). However, EV71 3D(pol) initiated de novo transcription with a poly(C) template and genome RNA. Its RNA binding activity was weak. Terminal nucleotidyl transferase and reverse transcriptase activity were not detected. The Km and Vmax for EV71 3D(pol) were calculated from classic Lineweaver-Burk plots. The Km values were 2.35±0.05 (ATP), 5.40±0.93 (CTP), 1.12±0.10 (GTP) and 2.81±0.31 (UTP), and the Vmax values were 0.00078±0.00005/min (ATP), 0.011±0.0017/min (CTP), 0.050±0.0043/min (GTP) and 0.0027±0.0005/min (UTP). The Km of EV71 3D(pol) was similar to that of foot and mouth disease virus and rhinovirus. Polymerase activity of BrCr-TR strain and a strain from a clinical isolate in Beijing, 2008 were similar, indicating the potential for 3D(pol) as an antiviral drug target.
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Affiliation(s)
- Hongbing Jiang
- Unit of Viral Genome Regulation, Institut Pasteur of Shanghai, Key Laboratory of Molecular Virology & Immunology, Chinese Academy of Sciences, Shanghai, PR China
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Residues of the rotavirus RNA-dependent RNA polymerase template entry tunnel that mediate RNA recognition and genome replication. J Virol 2010; 85:1958-69. [PMID: 21147920 DOI: 10.1128/jvi.01689-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To replicate its segmented, double-stranded RNA (dsRNA) genome, the rotavirus RNA-dependent RNA polymerase, VP1, must recognize viral plus-strand RNAs (+RNAs) and guide them into the catalytic center. VP1 binds to the conserved 3' end of rotavirus +RNAs via both sequence-dependent and sequence-independent contacts. Sequence-dependent contacts permit recognition of viral +RNAs and specify an autoinhibited positioning of the template within the catalytic site. However, the contributions to dsRNA synthesis of sequence-dependent and sequence-independent VP1-RNA interactions remain unclear. To analyze the importance of VP1 residues that interact with +RNA on genome replication, we engineered mutant VP1 proteins and assayed their capacity to synthesize dsRNA in vitro. Our results showed that, individually, mutation of residues that interact specifically with RNA bases did not diminish replication levels. However, simultaneous mutations led to significantly lower levels of dsRNA product, presumably due to impaired recruitment of +RNA templates. In contrast, point mutations of sequence-independent RNA contact residues led to severely diminished replication, likely as a result of improper positioning of templates at the catalytic site. A noteworthy exception was a K419A mutation that enhanced the initiation capacity and product elongation rate of VP1. The specific chemistry of Lys419 and its position at a narrow region of the template entry tunnel appear to contribute to its capacity to moderate replication. Together, our findings suggest that distinct classes of VP1 residues interact with +RNA to mediate template recognition and dsRNA synthesis yet function in concert to promote viral RNA replication at appropriate times and rates.
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50
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Yang X, Welch JL, Arnold JJ, Boehr DD. Long-range interaction networks in the function and fidelity of poliovirus RNA-dependent RNA polymerase studied by nuclear magnetic resonance. Biochemistry 2010; 49:9361-71. [PMID: 20860410 DOI: 10.1021/bi100833r] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The fidelity of the poliovirus RNA-dependent RNA polymerase (3D(pol)) plays a direct role in the genomic evolution and pathogenesis of the virus. A single site mutation (Gly64Ser) that is remote from the catalytic center results in a higher fidelity polymerase. NMR studies with [methyl-(13)C]methionine-labeled protein were used to compare the solution structure and dynamics of wild-type and Gly64Ser 3D(pol). The chemical shifts for the Met6 resonance were significantly different between wild-type and Gly64Ser 3D(pol) when bound in ternary complexes with RNA and incorrect, but not with correct, nucleotide, suggesting that the Gly64Ser mutation induces structural changes in the N-terminal β-strand when the enzyme is bound to incorrect but not correct nucleotide. We also observe changes in the transverse relaxation times for methionines near regions important for nucleotide and RNA binding and catalysis. Our strategy to assign the [methyl-(13)C]methionine resonances involved separately mutating each of the 17 methionines. Several substitutions produced additional resonances for both Met6 and Met187, a reporter for RNA binding, and conformational changes in the highly conserved motif B loop, even though these methionines are greater than 20 Å apart. The results for Gly64Ser and the other mutants are intriguing considering that they can result in structural and/or dynamic changes to methionines distant from the site of mutation. We propose that there is a long-distance network operating throughout 3D(pol) that coordinates ligand binding, conformational changes, and catalysis. Mutation of Gly64 results in structural and/or dynamic changes to the network that may affect polymerase fidelity.
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Affiliation(s)
- Xiaorong Yang
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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