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Abstract
The nonsegmented, negative-strand RNA viruses (nsNSVs), also known as the order Mononegavirales, have a genome consisting of a single strand of negative-sense RNA. Integral to the nsNSV replication cycle is the viral polymerase, which is responsible for transcribing the viral genome, to produce an array of capped and polyadenylated messenger RNAs, and replicating it to produce new genomes. To perform the different steps that are necessary for these processes, the nsNSV polymerases undergo a series of coordinated conformational transitions. While much is still to be learned regarding the intersection of nsNSV polymerase dynamics, structure, and function, recently published polymerase structures, combined with a history of biochemical and molecular biology studies, have provided new insights into how nsNSV polymerases function as dynamic machines. In this review, we consider each of the steps involved in nsNSV transcription and replication and suggest how these relate to solved polymerase structures.
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Affiliation(s)
- Mohamed Ouizougun-Oubari
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA;
| | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA;
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Cheng N, Jiang N, Fu Y, Xu Z, Peng X, Yu J, Cen S, Wang Y, Zhang G, Zheng Y, He J. The mechanism and pharmacodynamics of 2-((1H-indol-3-yl)thio/sulfinyl)-N-pheny acetamide derivative as a novel inhibitor against human respiratory syncytial virus. J Enzyme Inhib Med Chem 2022; 37:2598-2604. [PMID: 36131622 PMCID: PMC9518288 DOI: 10.1080/14756366.2022.2123804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Human respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infection worldwide. Until now, there are no licenced vaccines or effective antiviral drugs against RSV infections. In our previous work, we found 2-((1H-indol-3-yl)thio/sulfinyl)-N-pheny acetamide derivatives (4-49 C and 1-HB-63) being a novel inhibitor against RSV in vitro. Here, we explored the underlying mechanism of 2-((1H-indol-3-yl)thio/sulfinyl)-N-pheny acetamide derivatives to inhibit RSV replication in vitro and disclosed that 4–49 C worked as the inhibitor of membrane fusion and 1-HB-63 functioned at the stage of RSV genome replication/transcription. Yet, both of them could not inhibit RSV infection of BALB/c mice by using RSV-Luc, in vivo imaging and RT-qPCR analyses, for which it may be due to the fast metabolism in vivo. Our work suggests that further structural modification and optimisation of 2-((1H-indol-3-yl) thio/sulfinyl)-N-pheny acetamide derivative are needed to obtain drug candidates with effective anti-RSV activities in vivo.
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Affiliation(s)
- Ningning Cheng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Nan Jiang
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Yuanhui Fu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Zhuxin Xu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Xianglei Peng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Jiemei Yu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yanpeng Zheng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Jinsheng He
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
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Donovan-Banfield I, Milligan R, Hall S, Gao T, Murphy E, Li J, Shawli GT, Hiscox J, Zhuang X, McKeating JA, Fearns R, Matthews DA. Direct RNA sequencing of respiratory syncytial virus infected human cells generates a detailed overview of RSV polycistronic mRNA and transcript abundance. PLoS One 2022; 17:e0276697. [PMID: 36355791 PMCID: PMC9648745 DOI: 10.1371/journal.pone.0276697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 10/11/2022] [Indexed: 11/12/2022] Open
Abstract
To characterize species of viral mRNA transcripts generated during respiratory syncytial virus (RSV) infection, human fibroblast-like MRC-5 lung cells were infected with subgroup A RSV for 6, 16 and 24 hours. In addition, we characterised the viral transcriptome in infected Calu-3 lung epithelial cells at 48 hours post infection. Total RNA was harvested and polyadenylated mRNA was enriched and sequenced by direct RNA sequencing using an Oxford nanopore device. This platform yielded over 450,000 direct mRNA transcript reads which were mapped to the viral genome and analysed to determine the relative mRNA levels of viral genes using our in-house ORF-centric pipeline. We examined the frequency of polycistronic readthrough mRNAs were generated and assessed the length of the polyadenylated tails for each group of transcripts. We show a general but non-linear decline in gene transcript abundance across the viral genome, as predicted by the model of RSV gene transcription. However, the decline in transcript abundance is not uniform. The polyadenylate tails generated by the viral polymerase are similar in length to those generated by the host polyadenylation machinery and broadly declined in length for most transcripts as the infection progressed. Finally, we observed that the steady state abundance of transcripts with very short polyadenylate tails less than 20 nucleotides is less for N, SH and G transcripts in both cell lines compared to NS1, NS2, P, M, F and M2 which may reflect differences in mRNA stability and/or translation rates within and between the cell lines.
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Affiliation(s)
- I’ah Donovan-Banfield
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
- Department of Infection Biology and Microbiome, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Rachel Milligan
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Sophie Hall
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Tianyi Gao
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Eleanor Murphy
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Jack Li
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Ghada T. Shawli
- Department of Infection Biology and Microbiome, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Julian Hiscox
- Department of Infection Biology and Microbiome, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Xiaodong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jane A. McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Rachel Fearns
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail: (DAM); (RF)
| | - David A. Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
- * E-mail: (DAM); (RF)
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Ogino M, Green TJ, Ogino T. GDP polyribonucleotidyltransferase domain of vesicular stomatitis virus polymerase regulates leader-promoter escape and polyadenylation-coupled termination during stop-start transcription. PLoS Pathog 2022; 18:e1010287. [PMID: 35108335 PMCID: PMC8843114 DOI: 10.1371/journal.ppat.1010287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/14/2022] [Accepted: 01/19/2022] [Indexed: 11/23/2022] Open
Abstract
The unconventional mRNA capping enzyme (GDP polyribonucleotidyltransferase, PRNTase) domain of the vesicular stomatitis virus (VSV) L protein possesses a dual-functional "priming-capping loop" that governs terminal de novo initiation for leader RNA synthesis and capping of monocistronic mRNAs during the unique stop-start transcription cycle. Here, we investigated the roles of basic amino acid residues on a helix structure directly connected to the priming-capping loop in viral RNA synthesis and identified single point mutations that cause previously unreported defective phenotypes at different steps of stop-start transcription. Mutations of residue R1183 (R1183A and R1183K) dramatically reduced the leader RNA synthesis activity by hampering early elongation, but not terminal de novo initiation or productive elongation, suggesting that the mutations negatively affect escape from the leader promoter. On the other hand, mutations of residue R1178 (R1178A and R1178K) decreased the efficiency of polyadenylation-coupled termination of mRNA synthesis at the gene junctions, but not termination of leader RNA synthesis at the leader-to-N-gene junction, resulting in the generation of larger amounts of aberrant polycistronic mRNAs. In contrast, both the R1183 and R1178 residues are not essential for cap-forming activities. The R1183K mutation was lethal to VSV, whereas the R1178K mutation attenuated VSV and triggered the production of the polycistronic mRNAs in infected cells. These observations suggest that the PRNTase domain plays multiple roles in conducting accurate stop-start transcription beyond its known role in pre-mRNA capping. Vesicular stomatitis virus (VSV), an animal rhabdovirus closely related to rabies virus, has served as a paradigm for understanding the basic molecular mechanisms of transcription and replication by rhabdoviruses (e.g., rabies) and other non-segmented negative strand (NNS) RNA viruses, such as measles and Ebola. NNS RNA viral polymerases sequentially synthesize the non-coding leader RNA and monocistronic mRNAs from the 3′-terminal leader region and internal genes, respectively, on their genomes by the stop-start transcription mechanism. A hallmark of NNS RNA viral polymerases is the presence of a unique enzymatic domain, called GDP polyribonucleotidyltransferase (PRNTase), which catalyzes pre-mRNA 5′-capping, one of the essential mRNA modifications. Our recent study revealed that the VSV PRNTase domain directs transcription initiation at the 3′-end of the genome as well as pre-mRNA capping with the dual functional priming-capping loop during stop-start transcription. Here, we further show that a helix structure flanked by the priming-capping loop regulates not only transcription elongation at an early phase of leader RNA synthesis but also polyadenylation-coupled transcription termination at gene junctions. These findings indicate that the PRNTase domain acts as a key regulatory domain for stop-start transcription as well as a catalytic domain for pre-mRNA capping.
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Affiliation(s)
- Minako Ogino
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, United States of America
| | - Todd J. Green
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Tomoaki Ogino
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, United States of America
- * E-mail:
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Braun MR, Noton SL, Blanchard EL, Shareef A, Santangelo PJ, Johnson WE, Fearns R. Respiratory syncytial virus M2-1 protein associates non-specifically with viral messenger RNA and with specific cellular messenger RNA transcripts. PLoS Pathog 2021; 17:e1009589. [PMID: 34003848 PMCID: PMC8162694 DOI: 10.1371/journal.ppat.1009589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 05/28/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a major cause of respiratory disease in infants and the elderly. RSV is a non-segmented negative strand RNA virus. The viral M2-1 protein plays a key role in viral transcription, serving as an elongation factor to enable synthesis of full-length mRNAs. M2-1 contains an unusual CCCH zinc-finger motif that is conserved in the related human metapneumovirus M2-1 protein and filovirus VP30 proteins. Previous biochemical studies have suggested that RSV M2-1 might bind to specific virus RNA sequences, such as the transcription gene end signals or poly A tails, but there was no clear consensus on what RSV sequences it binds. To determine if M2-1 binds to specific RSV RNA sequences during infection, we mapped points of M2-1:RNA interactions in RSV-infected cells at 8 and 18 hours post infection using crosslinking immunoprecipitation with RNA sequencing (CLIP-Seq). This analysis revealed that M2-1 interacts specifically with positive sense RSV RNA, but not negative sense genome RNA. It also showed that M2-1 makes contacts along the length of each viral mRNA, indicating that M2-1 functions as a component of the transcriptase complex, transiently associating with nascent mRNA being extruded from the polymerase. In addition, we found that M2-1 binds specific cellular mRNAs. In contrast to the situation with RSV mRNA, M2-1 binds discrete sites within cellular mRNAs, with a preference for A/U rich sequences. These results suggest that in addition to its previously described role in transcription elongation, M2-1 might have an additional role involving cellular RNA interactions.
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Affiliation(s)
- Molly R. Braun
- Department of Microbiology, Boston University School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Emmeline L. Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - Afzaal Shareef
- Department of Microbiology, Boston University School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
| | - Philip J. Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - W. Evan Johnson
- Division of Computational Biomedicine and Bioinformatics Program and Department of Biostatistics, Boston University, Boston, Massachusetts, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, United States of America
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A Respiratory Syncytial Virus Attachment Gene Variant Associated with More Severe Disease in Infants Decreases Fusion Protein Expression, Which May Facilitate Immune Evasion. J Virol 2020; 95:JVI.01201-20. [PMID: 33115881 DOI: 10.1128/jvi.01201-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023] Open
Abstract
This study identified a genotype of respiratory syncytial virus (RSV) associated with increased acute respiratory disease severity in a cohort of previously healthy term infants. The genotype (2stop+A4G) consists of two components. The A4G component is a prevalent point mutation in the 4th position of the gene end transcription termination signal of the G gene of currently circulating RSV strains. The 2stop component is two tandem stop codons at the G gene terminus, preceding the gene end transcription termination signal. To investigate the biological role of these RSV G gene mutations, recombinant RSV strains harboring either a wild-type A2 strain G gene (one stop codon preceding a wild-type gene end signal), an A4G gene end signal preceded by one stop codon, or the 2stop+A4G virulence-associated combination were generated and characterized. Infection with the recombinant A4G (rA4G) RSV mutant resulted in transcriptional readthrough and lower G and fusion (F) protein levels than for the wild type. Addition of a second stop codon preceding the A4G point mutation (2stop+A4G) restored G protein expression but retained lower F protein levels. These data suggest that RSV G and F glycoprotein expression is regulated by transcriptional and translational readthrough. Notably, while rA4G and r2stop+A4G RSV were attenuated in cells and in naive BALB/c mice compared to that for wild-type RSV, the r2stop+A4G RSV was better able to infect BALB/c mice in the presence of preexisting immunity than rA4G RSV. Together, these factors may contribute to the maintenance and virulence of the 2stop+A4G genotype in currently circulating RSV-A strains.IMPORTANCE Strain-specific differences in respiratory syncytial virus (RSV) isolates are associated with differential pathogenesis in mice. However, the role of RSV genotypes in human infection is incompletely understood. This work demonstrates that one such genotype, 2stop+A4G, present in the RSV attachment (G) gene terminus is associated with greater infant disease severity. The genotype consists of two tandem stop codons preceding an A-to-G point mutation in the 4th position of the G gene end transcription termination signal. Virologically, the 2stop+A4G RSV genotype results in reduced levels of the RSV fusion (F) glycoprotein. A recombinant 2stop+A4G RSV was better able to establish infection in the presence of existing RSV immunity than a virus harboring the common A4G mutation. These data suggest that regulation of G and F expression has implications for virulence and, potentially, immune evasion.
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Slovic A, Kosutic-Gulija T, Santak M, Ivancic-Jelecki J, Jagusic M, Ljubin-Sternak S, Mlinarić-Galinović G, Vilibić-Čavlek T, Tabain I, Forcic D. Genetic Variability and Sequence Relatedness of Matrix Protein in Viruses of the Families Paramyxoviridae and Pneumoviridae. Intervirology 2018; 60:181-189. [PMID: 29510403 DOI: 10.1159/000487049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/22/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The families Paramyxoviridae and Pneumoviridae comprise a broad spectrum of viral pathogens that affect human health. The matrix (M) protein of these viruses has a central role in their life cycle. In line with this, molecular characteristics of the M proteins from variable viruses that circulated in Croatia were investigated. METHODS Sequences of the M proteins of human parainfluenza virus (HPIV) 1-3 within the family Paramyxoviridae, human metapneumovirus (HMPV), and human respiratory syncytial virus from the family Pneumoviridae were obtained and analyzed. RESULTS M proteins were very diverse among HPIVs, but highly conserved within each virus. More variability was seen in nucleotide sequences of M proteins from the Pneumoviridae family. An insertion of 8 nucleotides in the 3' untranslated region in 1 HMPV M gene sequence was discovered (HR347-12). As there are no samples with such an insertion in the database, this insertion is of interest and requires further research. CONCLUSION While we have confirmed that M proteins were conserved among individual viruses, any changes that are observed should be given attention and further researched. Of special interest is inclusion of HPIV2 M proteins in this analysis, as these proteins have not been studied to the same extent as other paramyxoviruses.
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Affiliation(s)
- Anamarija Slovic
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
| | - Tanja Kosutic-Gulija
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
| | - Maja Santak
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
| | - Jelena Ivancic-Jelecki
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
| | - Maja Jagusic
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
| | - Sunčanica Ljubin-Sternak
- Teaching Institute of Public Health "Dr. Andrija Štampar", Zagreb, Croatia.,School of Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Tatjana Vilibić-Čavlek
- School of Medicine, University of Zagreb, Zagreb, Croatia.,Croatian National Institute of Public Health, Zagreb, Croatia
| | - Irena Tabain
- Croatian National Institute of Public Health, Zagreb, Croatia
| | - Dubravko Forcic
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Zagreb, Croatia.,Center of Excellence for Viral Immunology and Vaccines, CERVirVac, Zagreb, Croatia
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Fearns R, Plemper RK. Polymerases of paramyxoviruses and pneumoviruses. Virus Res 2017; 234:87-102. [PMID: 28104450 DOI: 10.1016/j.virusres.2017.01.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 11/13/2022]
Abstract
The paramyxo- and pneumoviruses are members of the order Mononegavirales, a group of viruses with non-segmented, negative strand RNA genomes. The polymerases of these viruses are multi-functional complexes, capable of transcribing subgenomic capped and polyadenylated mRNAs and replicating the genome. Although there is no native structure available for any complete paramyxo- or pneumovirus polymerase, functional and structural studies of a fragment of a pneumovirus polymerase protein and mutation analyses and resistance profiling of small-molecule inhibitors have generated a wealth of mechanistic information. This review integrates these data with the structure of a related polymerase, identifying similarities, differences, gaps in knowledge, and avenues for antiviral drug development.
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Affiliation(s)
- Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, United States.
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, United States
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Barik S. What Really Rigs Up RIG-I? J Innate Immun 2016; 8:429-36. [PMID: 27438016 PMCID: PMC6738806 DOI: 10.1159/000447947] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/23/2016] [Accepted: 06/23/2016] [Indexed: 12/24/2022] Open
Abstract
RIG-I (retinoic acid-inducible gene 1) is an archetypal member of the cytoplasmic DEAD-box dsRNA helicase family (RIG-I-like receptors or RLRs), the members of which play essential roles in the innate immune response of the metazoan cell. RIG-I functions as a pattern recognition receptor that detects nonself RNA as a pathogen-associated molecular pattern (PAMP). However, the exact molecular nature of the viral RNAs that act as a RIG-I ligand has remained a mystery and a matter of debate. In this article, we offer a critical review of the actual viral RNAs that act as PAMPs to activate RIG-I, as seen from the perspective of a virologist, including a recent report that the viral Leader-read-through transcript is a novel and effective RIG-I ligand.
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Affiliation(s)
- Sailen Barik
- Department of Biological, Geological and Environmental Sciences, and Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio, USA
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Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach. J Virol 2016; 90:4876-4888. [PMID: 26656699 PMCID: PMC4859727 DOI: 10.1128/jvi.02349-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/18/2015] [Indexed: 11/20/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is a major cause of serious respiratory tract infection. Treatment options include administration of ribavirin, a purine analog, although the mechanism of its anti-HRSV activity is unknown. We used transcriptome sequencing (RNA-seq) to investigate the genome mutation frequency and viral mRNA accumulation in HRSV-infected cells that were left untreated or treated with ribavirin. In the absence of ribavirin, HRSV-specific transcripts accounted for up to one-third of total RNA reads from the infected-cell RNA population. Ribavirin treatment resulted in a >90% reduction in abundance of viral mRNA reads, while at the same time no such reduction was detected for the abundance of cellular transcripts. The presented data reveal that ribavirin significantly increases the frequency of HRSV-specific RNA mutations, suggesting a direct influence on the fidelity of the HRSV polymerase. The presented data show that transitions and transversions occur during HRSV replication and that these changes occur in hot spots along the HRSV genome. Examination of nucleotide substitution rates in the viral genome indicated an increase in the frequency of transition but not transversion mutations in the presence of ribavirin. In addition, our data indicate that in the continuous cell types used and at the time points analyzed, the abundances of some HRSV mRNAs do not reflect the order in which the mRNAs are transcribed. IMPORTANCE Human respiratory syncytial virus (HRSV) is a major pediatric pathogen. Ribavirin can be used in children who are extremely ill to reduce the amount of virus and to lower the burden of disease. Ribavirin is used as an experimental therapy with other viruses. The mechanism of action of ribavirin against HRSV is not well understood, although it is thought to increase the mutation rate of the viral polymerase during replication. To investigate this hypothesis, we used a high-resolution approach that allowed us to determine the genetic sequence of the virus to a great depth of coverage. We found that ribavirin did not cause a detectable change in the relative amounts of viral mRNA transcripts. However, we found that ribavirin treatment did indeed cause an increase in the number of mutations, which was associated with a decrease in virus production.
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Transcriptional Regulation in Ebola Virus: Effects of Gene Border Structure and Regulatory Elements on Gene Expression and Polymerase Scanning Behavior. J Virol 2015; 90:1898-909. [PMID: 26656691 DOI: 10.1128/jvi.02341-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/24/2015] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED The highly pathogenic Ebola virus (EBOV) has a nonsegmented negative-strand (NNS) RNA genome containing seven genes. The viral genes either are separated by intergenic regions (IRs) of variable length or overlap. The structure of the EBOV gene overlaps is conserved throughout all filovirus genomes and is distinct from that of the overlaps found in other NNS RNA viruses. Here, we analyzed how diverse gene borders and noncoding regions surrounding the gene borders influence transcript levels and govern polymerase behavior during viral transcription. Transcription of overlapping genes in EBOV bicistronic minigenomes followed the stop-start mechanism, similar to that followed by IR-containing gene borders. When the gene overlaps were extended, the EBOV polymerase was able to scan the template in an upstream direction. This polymerase feature seems to be generally conserved among NNS RNA virus polymerases. Analysis of IR-containing gene borders showed that the IR sequence plays only a minor role in transcription regulation. Changes in IR length were generally well tolerated, but specific IR lengths led to a strong decrease in downstream gene expression. Correlation analysis revealed that these effects were largely independent of the surrounding gene borders. Each EBOV gene contains exceptionally long untranslated regions (UTRs) flanking the open reading frame. Our data suggest that the UTRs adjacent to the gene borders are the main regulators of transcript levels. A highly complex interplay between the different cis-acting elements to modulate transcription was revealed for specific combinations of IRs and UTRs, emphasizing the importance of the noncoding regions in EBOV gene expression control. IMPORTANCE Our data extend those from previous analyses investigating the implication of noncoding regions at the EBOV gene borders for gene expression control. We show that EBOV transcription is regulated in a highly complex yet not easily predictable manner by a set of interacting cis-active elements. These findings are important not only for the design of recombinant filoviruses but also for the design of other replicon systems widely used as surrogate systems to study the filovirus replication cycle under low biosafety levels. Insights into the complex regulation of EBOV transcription conveyed by noncoding sequences will also help to interpret the importance of mutations that have been detected within these regions, including in isolates of the current outbreak.
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Noton SL, Aljabr W, Hiscox JA, Matthews DA, Fearns R. Factors affecting de novo RNA synthesis and back-priming by the respiratory syncytial virus polymerase. Virology 2014; 462-463:318-27. [PMID: 25010481 DOI: 10.1016/j.virol.2014.05.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 05/20/2014] [Accepted: 05/30/2014] [Indexed: 01/15/2023]
Abstract
Respiratory syncytial virus RNA dependent RNA polymerase (RdRp) initiates RNA synthesis from the leader (le) and trailer-complement (trc) promoters. The RdRp can also add nucleotides to the 3' end of the trc promoter by back-priming, but there is no evidence this occurs at the le promoter in infected cells. We examined how environmental factors and RNA sequence affect de novo RNA synthesis versus back-priming using an in vitro assay. We found that replacing Mg(2+) with Mn(2+) in the reaction buffer increased de novo initiation relative to back-priming, and different lengths of trc sequence were required for the two activities. Experiments with le RNA showed that back-priming occurred with this sequence in vitro, but less efficiently than with trc RNA. These findings indicate that during infection, the RdRp is governed between de novo RNA synthesis and back-priming by RNA sequence and environment, including a factor missing from the in vitro assay.
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Affiliation(s)
- Sarah L Noton
- Department of Microbiology, Boston University Medical Campus, 72 East Concord Street, Boston, MA 02118, USA.
| | - Waleed Aljabr
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool L3 5RF, UK.
| | - Julian A Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool L3 5RF, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, ic2 Building, Liverpool L3 5RF, UK.
| | - David A Matthews
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK.
| | - Rachel Fearns
- Department of Microbiology, Boston University Medical Campus, 72 East Concord Street, Boston, MA 02118, USA.
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13
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Kumar N, Maherchandani S, Kashyap SK, Singh SV, Sharma S, Chaubey KK, Ly H. Peste des petits ruminants virus infection of small ruminants: a comprehensive review. Viruses 2014; 6:2287-327. [PMID: 24915458 PMCID: PMC4074929 DOI: 10.3390/v6062287] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/26/2014] [Accepted: 05/28/2014] [Indexed: 12/14/2022] Open
Abstract
Peste des petits ruminants (PPR) is caused by a Morbillivirus that belongs to the family Paramyxoviridae. PPR is an acute, highly contagious and fatal disease primarily affecting goats and sheep, whereas cattle undergo sub-clinical infection. With morbidity and mortality rates that can be as high as 90%, PPR is classified as an OIE (Office International des Epizooties)-listed disease. Considering the importance of sheep and goats in the livelihood of the poor and marginal farmers in Africa and South Asia, PPR is an important concern for food security and poverty alleviation. PPR virus (PPRV) and rinderpest virus (RPV) are closely related Morbilliviruses. Rinderpest has been globally eradicated by mass vaccination. Though a live attenuated vaccine is available against PPR for immunoprophylaxis, due to its instability in subtropical climate (thermo-sensitivity), unavailability of required doses and insufficient coverage (herd immunity), the disease control program has not been a great success. Further, emerging evidence of poor cross neutralization between vaccine strain and PPRV strains currently circulating in the field has raised concerns about the protective efficacy of the existing PPR vaccines. This review summarizes the recent advancement in PPRV replication, its pathogenesis, immune response to vaccine and disease control. Attempts have also been made to highlight the current trends in understanding the host susceptibility and resistance to PPR.
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Affiliation(s)
- Naveen Kumar
- Virology Laboratory, Division of Animal Health, Central Institute for Research on Goats, Makhdoom, P.O. Farah, Mathura, UP 281122, India.
| | - Sunil Maherchandani
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, Rajasthan 334001, India.
| | - Sudhir Kumar Kashyap
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, Rajasthan 334001, India.
| | - Shoor Vir Singh
- Virology Laboratory, Division of Animal Health, Central Institute for Research on Goats, Makhdoom, P.O. Farah, Mathura, UP 281122, India.
| | - Shalini Sharma
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India.
| | - Kundan Kumar Chaubey
- Virology Laboratory, Division of Animal Health, Central Institute for Research on Goats, Makhdoom, P.O. Farah, Mathura, UP 281122, India.
| | - Hinh Ly
- Veterinary and Biomedical Sciences Department, University of Minnesota, 1988 Fitch Ave., Ste 295, Saint Paul, MN 55108, USA.
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14
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Kanduc D, Fasano C, Bavaro SL, Novello G, Lucchese G, Capone G. Peptide profiling of the route from Mahoney to Sabin, and return. J Basic Microbiol 2014; 54:369-77. [DOI: 10.1002/jobm.201200642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 02/07/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
| | - Candida Fasano
- Department of Biosciences, Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
| | - Simona Lucia Bavaro
- Department of Biosciences, Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
| | - Giuseppe Novello
- Department of Biosciences, Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
| | - Guglielmo Lucchese
- Department of Biosciences, Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
| | - Giovanni Capone
- Department of Biosciences, Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
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15
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Respiratory syncytial virus: virology, reverse genetics, and pathogenesis of disease. Curr Top Microbiol Immunol 2013; 372:3-38. [PMID: 24362682 DOI: 10.1007/978-3-642-38919-1_1] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human respiratory syncytial virus (RSV) is an enveloped, nonsegmented negative-strand RNA virus of family Paramyxoviridae. RSV is the most complex member of the family in terms of the number of genes and proteins. It is also relatively divergent and distinct from the prototype members of the family. In the past 30 years, we have seen a tremendous increase in our understanding of the molecular biology of RSV based on a succession of advances involving molecular cloning, reverse genetics, and detailed studies of protein function and structure. Much remains to be learned. RSV disease is complex and variable, and the host and viral factors that determine tropism and disease are poorly understood. RSV is notable for a historic vaccine failure in the 1960s involving a formalin-inactivated vaccine that primed for enhanced disease in RSV naïve recipients. Live vaccine candidates have been shown to be free of this complication. However, development of subunit or other protein-based vaccines for pediatric use is hampered by the possibility of enhanced disease and the difficulty of reliably demonstrating its absence in preclinical studies.
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16
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Brown PA, Lupini C, Catelli E, Clubbe J, Ricchizzi E, Naylor CJ. A single polymerase (L) mutation in avian metapneumovirus increased virulence and partially maintained virus viability at an elevated temperature. J Gen Virol 2010; 92:346-54. [DOI: 10.1099/vir.0.026740-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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17
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Murphy AM, Moerdyk-Schauwecker M, Mushegian A, Grdzelishvili VZ. Sequence-function analysis of the Sendai virus L protein domain VI. Virology 2010; 405:370-82. [PMID: 20609457 PMCID: PMC2923248 DOI: 10.1016/j.virol.2010.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 04/16/2010] [Accepted: 06/08/2010] [Indexed: 11/26/2022]
Abstract
The large (about 2200 amino acids) L polymerase protein of nonsegmented negative-strand RNA viruses (order Mononegavirales) has six conserved sequence regions (“domains”) postulated to constitute the specific enzymatic activities involved in viral mRNA synthesis, 5′-end capping, cap methylation, 3′ polyadenylation, and genomic RNA replication. Previous studies with vesicular stomatitis virus identified amino acid residues within the L protein domain VI required for mRNA cap methylation. In our recent study we analyzed four amino acid residues within domain VI of the Sendai virus L protein and our data indicated that there could be differences in L protein sequence requirements for cap methylation in two different families of Mononegavirales — rhabdoviruses and paramyxoviruses. In this study, we conducted a more comprehensive mutational analysis by targeting the entire SeV L protein domain VI, creating twenty-four L mutants, and testing these mutations for their effects on viral mRNA synthesis, cap methylation, viral genome replication and virus growth kinetics. Our analysis identified several residues required for successful cap methylation and virus replication and clearly showed the importance of the K-D-K-E tetrad and glycine-rich motif in the SeV cap methylation. This study is the first extensive sequence analysis of the L protein domain VI in the family Paramyxoviridae, and it confirms structural and functional similarity of this domain across different families of the order Mononegavirales.
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Affiliation(s)
- Andrea M Murphy
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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18
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Minet C, Yami M, Egzabhier B, Gil P, Tangy F, Brémont M, Libeau G, Diallo A, Albina E. Sequence analysis of the large (L) polymerase gene and trailer of the peste des petits ruminants virus vaccine strain Nigeria 75/1: Expression and use of the L protein in reverse genetics. Virus Res 2009; 145:9-17. [DOI: 10.1016/j.virusres.2009.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 06/04/2009] [Accepted: 06/05/2009] [Indexed: 10/20/2022]
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19
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Song W, Liu G, Bosworth CA, Walker JR, Megaw GA, Lazrak A, Abraham E, Sullender WM, Matalon S. Respiratory syncytial virus inhibits lung epithelial Na+ channels by up-regulating inducible nitric-oxide synthase. J Biol Chem 2009; 284:7294-306. [PMID: 19131335 PMCID: PMC2652346 DOI: 10.1074/jbc.m806816200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 01/06/2009] [Indexed: 12/13/2022] Open
Abstract
Respiratory syncytial virus (RSV) infection has been shown to reduce Na+-driven alveolar fluid clearance in BALB/c mice in vivo. To investigate the cellular mechanisms by which RSV inhibits amiloride-sensitive epithelial Na+ channels (ENaC), the main pathways through which Na+ ions enter lung epithelial cells, we infected human Clara-like lung (H441) cells with RSV that expresses green fluorescent protein (rRA2). 3-6 days later patch clamp recordings showed that infected cells (i.e. cells expressing green fluorescence; GFP+) had significantly lower whole-cell amiloride-sensitive currents and single channel activity (NPo) as compared with non-infected (GFP-), non-inoculated, or cells infected with UV-inactivated RSV. Both alpha and beta ENaC mRNA levels were significantly reduced in GFP+ cells as measured by real-time reverse transcription-PCR. Infection with RSV increased expression of the inducible nitric-oxide synthase (iNOS) and nitrite concentration in the culture medium; nuclear translocation of NF-kappaB p65 subunit and NF-kappaB activation were also up-regulated. iNOS up-regulation in GFP+ cells was prevented by knocking down IkappaB kinase gamma before infection. Furthermore, pretreatment of H441 cells with the specific iNOS inhibitor 1400W (1 microM) resulted in a doubling of the amiloride-sensitive Na+ current in GFP+ cells. Additionally, preincubation of H441 cells with A77-1726 (20 microM), a de novo UTP synthesis inhibitor, and 1400W completely reversed the RSV inhibition of amiloride-sensitive currents in GFP+ cells. Thus, both UTP- and iNOS-generated reactive species contribute to ENaC down-regulation in RSV-infected airway epithelial cells.
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Affiliation(s)
- Weifeng Song
- Department of Anesthesiology, Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama 35233, USA
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20
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Chen L, Song W, Davis IC, Shrestha K, Schwiebert E, Sullender WM, Matalon S. Inhibition of Na+ transport in lung epithelial cells by respiratory syncytial virus infection. Am J Respir Cell Mol Biol 2008; 40:588-600. [PMID: 18952569 DOI: 10.1165/rcmb.2008-0034oc] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We investigated the mechanisms by which respiratory syncytial virus (RSV) infection decreases vectorial Na+ transport across respiratory epithelial cells. Mouse tracheal epithelial (MTE) cells from either BALB/c or C57BL/6 mice and human airway H441 cells were grown on semipermeable supports under an air-liquid interface. Cells were infected with RSV-A2 and mounted in Ussing chambers for measurements of short-circuit currents (I(sc)). Infection with RSV for 24 hours (multiplicity of infection = 1) resulted in positive immunofluorescence for RSV antigen in less than 10% of MTE or H441 cells. In spite of the limited number of cells infected, RSV reduced both basal and amiloride-sensitive I(sc) in both MTE and H441 cells by approximately 50%, without causing a concomitant reduction in transepithelial resistance. Agents that increased intracellular cAMP (forskolin, cpt-CAMP, and IBMX) increased mainly Cl(-) secretion in MTE cells and Na+ absorption in H441 cells. RSV infection for 24 hours blunted both variables. In contrast, ouabain sensitive I(sc), measured across apically permeabilized H441 monolayers, remained unchanged. Western blot analysis of H441 cell lysates demonstrated reductions in alpha- but not gamma-ENaC subunit protein levels at 24 hours after RSV infection. The reduction in amiloride-sensitive I(sc) in H441 cells was prevented by pretreatment with inhibitors of de novo pyrimidine or purine synthesis (A77-1726 and 6-MP, respectively, 50 microM). Our results suggest that infection of both murine and human respiratory epithelial cells with RSV inhibits vectorial Na+ transport via nucleotide release. These findings are consistent with our previous studies showing reduced alveolar fluid clearance after RSV infection of BALB/c mice.
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Affiliation(s)
- Lan Chen
- Department of Anesthesiology, University of Alabama at Birmingham, Birmingham, AL 35205-3703, USA
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21
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Asenjo A, Calvo E, Villanueva N. Phosphorylation of human respiratory syncytial virus P protein at threonine 108 controls its interaction with the M2-1 protein in the viral RNA polymerase complex. J Gen Virol 2006; 87:3637-3642. [PMID: 17098979 DOI: 10.1099/vir.0.82165-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human respiratory syncytial virus (HRSV) P protein is phosphorylated, with different turnover rates, at several serine (S) and threonine (T) residues. The role of phosphothreonines in viral RNA synthesis was studied by using P protein substitution variants and the HRSV-based minigenome pM/SH. By using liquid chromatography coupled to ion-trap mass spectrometry, it was found that P protein T108 was phosphorylated by addition of a high-turnover phosphate group. This phosphorylation occurs in P protein expressed transiently and during HRSV infection. The results suggest that phosphorylation at P protein T108 affects M2-1 transcriptional activities, because this modification prevents interaction between the P and M2-1 proteins. Therefore, P protein phosphorylation-dephosphorylation at T108 could distinguish the role of the P protein in viral transcription and replication.
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Affiliation(s)
- Ana Asenjo
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Crta Majadahonda-Pozuelo km 2, Majadahonda, 28220 Madrid, Spain
| | - Enrique Calvo
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández de Almagro 3, 28029 Madrid, Spain
| | - Nieves Villanueva
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Crta Majadahonda-Pozuelo km 2, Majadahonda, 28220 Madrid, Spain
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22
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Cowton VM, McGivern DR, Fearns R. Unravelling the complexities of respiratory syncytial virus RNA synthesis. J Gen Virol 2006; 87:1805-1821. [PMID: 16760383 DOI: 10.1099/vir.0.81786-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Human respiratory syncytial virus (RSV) is the leading cause of paediatric respiratory disease and is the focus of antiviral- and vaccine-development programmes. These goals have been aided by an understanding of the virus genome architecture and the mechanisms by which it is expressed and replicated. RSV is a member of the order Mononegavirales and, as such, has a genome consisting of a single strand of negative-sense RNA. At first glance, transcription and genome replication appear straightforward, requiring self-contained promoter regions at the 3' ends of the genome and antigenome RNAs, short cis-acting elements flanking each of the genes and one polymerase. However, from these minimal elements, the virus is able to generate an array of capped, methylated and polyadenylated mRNAs and encapsidated antigenome and genome RNAs, all in the appropriate ratios to facilitate virus replication. The apparent simplicity of genome expression and replication is a consequence of considerable complexity in the polymerase structure and its cognate cis-acting sequences; here, our understanding of mechanisms by which the RSV polymerase proteins interact with signals in the RNA template to produce different RNA products is reviewed.
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MESH Headings
- Base Sequence
- DNA-Directed RNA Polymerases/metabolism
- Genome, Viral
- Humans
- Models, Biological
- Molecular Sequence Data
- Mononegavirales/genetics
- Mononegavirales/physiology
- Nucleocapsid/biosynthesis
- Nucleocapsid/genetics
- RNA, Antisense/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- Respiratory Syncytial Virus, Human/genetics
- Respiratory Syncytial Virus, Human/pathogenicity
- Respiratory Syncytial Virus, Human/physiology
- Transcription, Genetic
- Viral Proteins/metabolism
- Virus Replication
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Affiliation(s)
- Vanessa M Cowton
- Division of Pathology and Neuroscience, University of Dundee Medical School, Dundee DD1 9SY, UK
| | - David R McGivern
- Division of Pathology and Neuroscience, University of Dundee Medical School, Dundee DD1 9SY, UK
| | - Rachel Fearns
- Division of Pathology and Neuroscience, University of Dundee Medical School, Dundee DD1 9SY, UK
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23
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Melero JA. Molecular Biology of Human Respiratory Syncytial Virus. RESPIRATORY SYNCYTIAL VIRUS 2006. [DOI: 10.1016/s0168-7069(06)14001-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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24
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Grdzelishvili VZ, Smallwood S, Tower D, Hall RL, Hunt DM, Moyer SA. A single amino acid change in the L-polymerase protein of vesicular stomatitis virus completely abolishes viral mRNA cap methylation. J Virol 2005; 79:7327-37. [PMID: 15919887 PMCID: PMC1143665 DOI: 10.1128/jvi.79.12.7327-7337.2005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The vesicular stomatitis virus (VSV) RNA polymerase synthesizes viral mRNAs with 5'-cap structures methylated at the guanine-N7 and 2'-O-adenosine positions (7mGpppA(m)). Previously, our laboratory showed that a VSV host range (hr) and temperature-sensitive (ts) mutant, hr1, had a complete defect in mRNA cap methylation and that the wild-type L protein could complement the hr1 defect in vitro. Here, we sequenced the L, P, and N genes of mutant hr1 and found only two amino acid substitutions, both residing in the L-polymerase protein, which differentiate hr1 from its wild-type parent. These mutations (N505D and D1671V) were introduced separately and together into the L gene, and their effects on VSV in vitro transcription and in vivo chloramphenicol acetyltransferase minigenome replication were studied under conditions that are permissive and nonpermissive for hr1. Neither L mutation significantly affected viral RNA synthesis at 34 degrees C in permissive (BHK) and nonpermissive (HEp-2) cells, but D1671V reduced in vitro transcription and genome replication by about 50% at 40 degrees C in both cell lines. Recombinant VSV bearing each mutation were isolated, and the hr and ts phenotypes in infected cells were the result of a single D1671V substitution in the L protein. While the mutations did not significantly affect mRNA synthesis by purified viruses, 5'-cap analyses of product mRNAs clearly demonstrated that the D1671V mutation abrogated all methyltransferase activity. Sequence analysis suggests that an aspartic acid at amino acid 1671 is a critical residue within a putative conserved S-adenosyl-l-methionine-binding domain of the L protein.
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Affiliation(s)
- Valery Z Grdzelishvili
- University of Florida College of Medicine, Department of Molecular Genetics and Microbiology, 1600 S.W. Archer Road, P.O. Box 100266, Gainesville, FL 32610-0266, USA
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25
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Moudy RM, Sullender WM, Wertz GW. Variations in intergenic region sequences of Human respiratory syncytial virus clinical isolates: analysis of effects on transcriptional regulation. Virology 2004; 327:121-33. [PMID: 15327903 DOI: 10.1016/j.virol.2004.06.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Revised: 06/01/2004] [Accepted: 06/08/2004] [Indexed: 11/18/2022]
Abstract
Sequences at the beginnings and ends of Human respiratory syncytial virus (HRSV) genes are necessary for efficient initiation and termination of transcription. The gene start sequences are well conserved and contain signals required for initiation, while the semi-conserved sequences at the gene ends direct transcriptional termination with varying efficiencies. The intergenic regions, which lie between the gene ends and the downstream gene start sequences, are not conserved in length or sequence, and certain positions have been reported to play a role in transcriptional regulation. We have previously shown that the gene end sequences in HRSV subgroup A clinical isolates are variable and that variations found at certain gene ends decreased transcriptional termination and downstream mRNA expression. Here, we have extended this work to examine variation in the intergenic regions between the genes of clinical isolates. We determined the sequences of the eight intergenic regions and the M2/L overlap from clinical isolates from the US and UK and found that all of these regions contained variations from the prototype A2 strain. The amount of variation observed was disparate among the different intergenic regions and did not correlate with length. The effects of selected variant sequences on transcription were examined in the context of subgenomic replicons. While some changes in the intergenic regions had minor effects, certain sequence variations significantly altered transcription termination or initiation. A single nucleotide deletion in the M/SH intergenic region decreased initiation at the SH gene start seven-fold, while changes in the F/M2 intergenic region were found that in some cases increased and in others decreased termination at the F gene end. The P/M intergenic region was the most variable, but none of the changes examined affected either termination at the P gene end or initiation of the downstream M gene start. These results show that in HRSV clinical isolates the intergenic region sequences are variable and that changes in these regions have the potential to affect transcriptional control at the gene junctions.
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Affiliation(s)
- Robin M Moudy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294,USA
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26
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Rodríguez L, Cuesta I, Asenjo A, Villanueva N. Human respiratory syncytial virus matrix protein is an RNA-binding protein: binding properties, location and identity of the RNA contact residues. J Gen Virol 2004; 85:709-719. [PMID: 14993657 DOI: 10.1099/vir.0.19707-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human respiratory syncytial virus (HRSV) matrix (M) protein is a structural internal membrane protein. Here we have shown that, like its orthomyxovirus and rhabdovirus counterparts, it has RNA-binding capacity, as determined by retardation of (32)P-labelled riboprobes in gel electrophoresis, cross-linking with UV light and Northern-Western assays. Its binding to RNA was neither sequence-specific nor showed a length requirement, although it had cooperative kinetics with a K(d) of 25 nM and probably two different types of RNA-binding sites. After preparative cross-linking of (32)P-labelled riboprobes with purified, renatured HRSV Long strain M protein (256 residues), the residues in contact with RNA were located between amino acids 120 and 170, in the central part of the molecule. Lysine (positions 121, 130, 156 and 157) and arginine (position 170) residues located within this region and conserved among pneumovirus M proteins of different origins were found to be essential for RNA contact. M protein expression did not affect the replication and transcription of HRSV RNA analogues in vivo (except when expressed in large amounts), in contrast to the in vitro transcription inhibition described previously. In addition, M protein was found to aggregate into high-molecular-mass oligomers, both in the presence and absence of its RNA-binding activity. The formation of these structures has been related in other viruses to either viral or host-cell RNA metabolism.
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Affiliation(s)
- Lorena Rodríguez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo Km 2, Majadahonda, Madrid 28220, Spain
| | - Isabel Cuesta
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo Km 2, Majadahonda, Madrid 28220, Spain
| | - Ana Asenjo
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo Km 2, Majadahonda, Madrid 28220, Spain
| | - Nieves Villanueva
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra Majadahonda-Pozuelo Km 2, Majadahonda, Madrid 28220, Spain
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27
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Easton AJ, Domachowske JB, Rosenberg HF. Animal pneumoviruses: molecular genetics and pathogenesis. Clin Microbiol Rev 2004; 17:390-412. [PMID: 15084507 PMCID: PMC387412 DOI: 10.1128/cmr.17.2.390-412.2004] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pneumoviruses are single-stranded, negative-sense, nonsegmented RNA viruses of the family Paramyxoviridae, subfamily Pneumovirinae, and include pathogens that infect humans (respiratory syncytial virus and human metapneumovirus), domestic mammals (bovine, ovine, and caprine respiratory syncytial viruses), rodents (pneumonia virus of mice), and birds (avian metapneumovirus). Among the topics considered in this review are recent studies focused on the roles of the individual virus-encoded components in promoting virus replication as well as in altering and evading innate antiviral host defenses. Advances in the molecular technology of pneumoviruses and the emergence of recombinant pneumoviruses that are leading to improved virus-based vaccine formulations are also discussed. Since pneumovirus infection in natural hosts is associated with a profound inflammatory response that persists despite adequate antiviral therapy, we also review the recent experimental treatment strategies that have focused on combined antiviral, anti-inflammatory, and immunomodulatory approaches.
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28
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Abstract
BACKGROUND Human respiratory syncytial virus (HRSV) is a leading cause of serious pediatric respiratory disease worldwide. Natural infection provides only partial protection as repeat infections occur throughout life. A brief review of the extent of antigenic and genetic variation observed in HRSV clinical isolates is presented. METHODS AND RESULTS Recent experimental research is reviewed, describing key factors that may explain the ability of HRSV to cause multiple infections in the same individual even in the presence of an existing immune response. It is well-appreciated that variability of the G protein, both between and within antigenic subgroups A and B, is partially responsible for repeat HRSV infections. A high level of nucleotide change resulting in amino acid change provides strong evidence for selective pressure for change in G sequences, thus new HRSV variants. Although little variation in gene-coding sequences is observed in the F protein (the second major protective antigen), new evidence of genetic variation has identified alteration of gene expression levels by selection of changes in the gene end termination signal that precedes the gene encoding the F protein. Due to obligatory sequential transcription, these changes affect downstream gene expression levels. These data suggest that modulation of F protein levels may provide a selective advantage in the presence of a preexisting immune response. CONCLUSIONS Experimental data in HRSV demonstrate that variation exists not only in gene-coding sequences but also in the signals that control gene expression. Thus alteration in the expression of key proteins provides a second type of antigenic "variation." A better understanding of these differences is critical to the development of an effective vaccine.
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Affiliation(s)
- Gail W Wertz
- Department of Microbiology, University of Alabama at Birmingham, USA.
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Moudy RM, Harmon SB, Sullender WM, Wertz GW. Variations in transcription termination signals of human respiratory syncytial virus clinical isolates affect gene expression. Virology 2003; 313:250-60. [PMID: 12951037 DOI: 10.1016/s0042-6822(03)00299-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Human respiratory syncytial virus (HRSV) has a single-stranded, negative-sense RNA genome with 10 genes encoding 11 proteins. Sequences at the beginning of the HRSV genes are highly conserved; however, the gene end sequences vary around a semiconserved consensus sequence, and the nontranscribed intergenic regions vary in both length and sequence. The regions at the junctions between HRSV genes (the gene end sequence of an upstream gene, intergenic region, and the gene start sequence of a downstream gene) contain elements required for efficient termination of the upstream gene and transcription of the downstream gene. Previous studies have examined variation in the HRSV coding sequences, but none have systematically analyzed the noncoding transcriptional control regions for variability. We determined the gene start and gene end sequences of each of the 10 HRSV genes from 14 clinical isolates for variations from the sequence of the prototype A2 strain. No changes were found in any of the gene start sequences. Eight of the 10 gene end sequences, however, contained variations. Several of these, a U(4)-tract instead of a U(6)- or U(5)-tract at the M and SH gene ends, respectively, (U(4)A) and an A-to-G change at position four in the G gene end (A4G), were predicted to affect termination and were examined for their effects on transcription. The changes were found to inhibit transcriptional termination, resulting in increased polycistronic readthrough and correspondingly reduced initiation of the downstream monocistronic mRNA. Viruses with the A4G variant G gene end sequence produced less F protein than those with A2-like G gene end sequences. Examination of additional G gene end sequences available in GenBank revealed that the observed A4G variation was restricted to one phylogenetic lineage of HRSV. All viruses examined within this lineage possessed this variant G gene end sequence. The data presented show that the gene end sequences of naturally occurring HRSV clinical isolates vary from those of the prototypic A2 strain and that certain of these changes inhibit efficient transcriptional termination and downstream gene expression.
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Affiliation(s)
- Robin M Moudy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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