1
|
Kleiner VA, Fearns R. How does the polymerase of non-segmented negative strand RNA viruses commit to transcription or genome replication? J Virol 2024:e0033224. [PMID: 39078194 DOI: 10.1128/jvi.00332-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024] Open
Abstract
The Mononegavirales, or non-segmented negative-sense RNA viruses (nsNSVs), includes significant human pathogens, such as respiratory syncytial virus, parainfluenza virus, measles virus, Ebola virus, and rabies virus. Although these viruses differ widely in their pathogenic properties, they are united by each having a genome consisting of a single strand of negative-sense RNA. Consistent with their shared genome structure, the nsNSVs have evolved similar ways to transcribe their genome into mRNAs and replicate it to produce new genomes. Importantly, both mRNA transcription and genome replication are performed by a single virus-encoded polymerase. A fundamental and intriguing question is: how does the nsNSV polymerase commit to being either an mRNA transcriptase or a replicase? The polymerase must become committed to one process or the other either before it interacts with the genome template or in its initial interactions with the promoter sequence at the 3´ end of the genomic RNA. This review examines the biochemical, molecular biology, and structural biology data regarding the first steps of transcription and RNA replication that have been gathered over several decades for different families of nsNSVs. These findings are discussed in relation to possible models that could explain how an nsNSV polymerase initiates and commits to either transcription or genome replication.
Collapse
Affiliation(s)
- Victoria A Kleiner
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| |
Collapse
|
2
|
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.
Collapse
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;
| |
Collapse
|
3
|
Lara-Hernandez I, Muñoz-Escalante JC, Bernal-Silva S, Noyola DE, Wong-Chew RM, Comas-García A, Comas-Garcia M. Ultrastructural and Functional Characterization of Mitochondrial Dynamics Induced by Human Respiratory Syncytial Virus Infection in HEp-2 Cells. Viruses 2023; 15:1518. [PMID: 37515204 PMCID: PMC10386036 DOI: 10.3390/v15071518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Human respiratory syncytial virus (hRSV) is the leading cause of acute lower respiratory tract infections in children under five years of age and older adults worldwide. During hRSV infection, host cells undergo changes in endomembrane organelles, including mitochondria. This organelle is responsible for energy production in the cell and plays an important role in the antiviral response. The present study focuses on characterizing the ultrastructural and functional changes during hRSV infection using thin-section transmission electron microscopy and RT-qPCR. Here we report that hRSV infection alters mitochondrial morphodynamics by regulating the expression of key genes in the antiviral response process, such as Mfn1, VDAC2, and PINK1. Our results suggest that hRSV alters mitochondrial morphology during infection, producing a mitochondrial phenotype with shortened cristae, swollen matrix, and damaged membrane. We also observed that hRSV infection modulates the expression of the aforementioned genes, possibly as an evasion mechanism in the face of cellular antiviral response. Taken together, these results advance our knowledge of the ultrastructural alterations associated with hRSV infection and might guide future therapeutic efforts to develop effective antiviral drugs for hRSV treatment.
Collapse
Affiliation(s)
- Ignacio Lara-Hernandez
- High-Resolution Microscopy Section, Center for Research in Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Juan Carlos Muñoz-Escalante
- Center for Research in Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
- Department of Microbiology, School of Medicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Sofía Bernal-Silva
- Department of Microbiology, School of Medicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
- Genomic Medicine Section, Center for Research in Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Daniel E Noyola
- Center for Research in Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
- Department of Microbiology, School of Medicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Rosa María Wong-Chew
- Research Division, School of Medicine, National Autonomous University of Mexico, Mexico City 04360, Mexico
| | - Andreu Comas-García
- Department of Microbiology, School of Medicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Mauricio Comas-Garcia
- High-Resolution Microscopy Section, Center for Research in Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
- Science Department, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
- Molecular and Translation Medicine Section, Center for Research in Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
| |
Collapse
|
4
|
Cressey TN, Shareef AM, Kleiner VA, Noton SL, Byrne PO, McLellan JS, Mühlberger E, Fearns R. Distinctive features of the respiratory syncytial virus priming loop compared to other non-segmented negative strand RNA viruses. PLoS Pathog 2022; 18:e1010451. [PMID: 35731802 PMCID: PMC9255747 DOI: 10.1371/journal.ppat.1010451] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/05/2022] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
De novo initiation by viral RNA-dependent RNA polymerases often requires a polymerase priming residue, located within a priming loop, to stabilize the initiating NTPs. Polymerase structures from three different non-segmented negative strand RNA virus (nsNSV) families revealed putative priming loops in different conformations, and an aromatic priming residue has been identified in the rhabdovirus polymerase. In a previous study of the respiratory syncytial virus (RSV) polymerase, we found that Tyr1276, the L protein aromatic amino acid residue that most closely aligns with the rhabdovirus priming residue, is not required for RNA synthesis but two nearby residues, Pro1261 and Trp1262, were required. In this study, we examined the roles of Pro1261 and Trp1262 in RNA synthesis initiation. Biochemical studies showed that substitution of Pro1261 inhibited RNA synthesis initiation without inhibiting back-priming, indicating a defect in initiation. Biochemical and minigenome experiments showed that the initiation defect incurred by a P1261A substitution could be rescued by factors that would be expected to increase the stability of the initiation complex, specifically increased NTP concentration, manganese, and a more efficient promoter sequence. These findings indicate that Pro1261 of the RSV L protein plays a role in initiation, most likely in stabilizing the initiation complex. However, we found that substitution of the corresponding proline residue in a filovirus polymerase had no effect on RNA synthesis initiation or elongation. These results indicate that despite similarities between the nsNSV polymerases, there are differences in the features required for RNA synthesis initiation. RSV has a significant impact on human health. It is the major cause of respiratory disease in infants and exerts a significant toll on the elderly and immunocompromised. RSV is a member of the Mononegavirales, the non-segmented, negative strand RNA viruses (nsNSVs). Like other viruses in this order, RSV encodes an RNA dependent RNA polymerase, which is responsible for transcribing and replicating the viral genome. Due to its essential role during the viral replication cycle, the polymerase is a promising candidate target for antiviral inhibitors and so a greater understanding of the mechanistic basis of its activities could aid antiviral drug development. In this study, we identified an amino acid residue within the RSV polymerase that appears to stabilize the RNA synthesis initiation complex and showed that it plays a role in both transcription and RNA replication. However, the corresponding residue in a different nsNSV polymerase does not appear to play a similar role. This work reveals a key feature of the RSV polymerase but identifies differences with the polymerases of other related viruses.
Collapse
Affiliation(s)
- Tessa N. Cressey
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Afzaal M. Shareef
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Victoria A. Kleiner
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Patrick O. Byrne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
5
|
In Vitro Primer-Based RNA Elongation and Promoter Fine Mapping of the Respiratory Syncytial Virus. J Virol 2020; 95:JVI.01897-20. [PMID: 33028717 PMCID: PMC7737744 DOI: 10.1128/jvi.01897-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 11/20/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a nonsegmented negative-sense (NNS) RNA virus and shares a similar RNA synthesis strategy with other members of NNS RNA viruses, such as measles, rabies virus, and Ebola virus. RSV RNA synthesis is catalyzed by a multifunctional RNA-dependent RNA polymerase (RdRP), which is composed of a large (L) protein that catalyzes three distinct enzymatic functions and an essential coenzyme phosphoprotein (P). Here, we successfully prepared highly pure, full-length, wild-type and mutant RSV polymerase (L-P) complexes. We demonstrated that the RSV polymerase could carry out both de novo and primer-based RNA synthesis. We defined the minimal length of the RNA template for in vitro de novo RNA synthesis using the purified RSV polymerase as 8 nucleotides (nt), shorter than previously reported. We showed that the RSV polymerase catalyzed primer-dependent RNA elongation with different lengths of primers on both short (10-nt) and long (25-nt) RNA templates. We compared the sequence specificity of different viral promoters and identified positions 3, 5, and 8 of the promoter sequence as essential to the in vitro RSV polymerase activity, consistent with the results previously mapped with the in vivo minigenome assay. Overall, these findings agree well with those of previous biochemical studies and extend our understanding of the promoter sequence and the mechanism of RSV RNA synthesis.IMPORTANCE As a major human pathogen, RSV affects 3.4 million children worldwide annually. However, no effective antivirals or vaccines are available. An in-depth mechanistic understanding of the RSV RNA synthesis machinery remains a high priority among the NNS RNA viruses. There is a strong public health need for research on this virus, due to major fundamental gaps in our understanding of NNS RNA virus replication. As the key enzyme executing transcription and replication of the virus, the RSV RdRP is a logical target for novel antiviral drugs. Therefore, exploring the primer-dependent RNA elongation extends our mechanistic understanding of the RSV RNA synthesis. Further fine mapping of the promoter sequence paves the way to better understand the function and structure of the RSV polymerase.
Collapse
|
6
|
Bach S, Biedenkopf N, Grünweller A, Becker S, Hartmann RK. Hexamer phasing governs transcription initiation in the 3'-leader of Ebola virus. RNA (NEW YORK, N.Y.) 2020; 26:439-453. [PMID: 31924730 PMCID: PMC7075260 DOI: 10.1261/rna.073718.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/08/2020] [Indexed: 05/05/2023]
Abstract
The genomic, bipartite replication promoter of Ebola virus (EBOV) consists of elements 1 (PE1) and 2 (PE2). PE1 (55 nt at the 3'-terminus) is separated from PE2 (harboring eight 3'-UN5 hexamers) by the transcription start sequence (TSS) of the first nucleoprotein (NP) gene plus a spacer sequence. Insertions or deletions in the spacer were reported to support genome replication if comprising 6 or 12, but not 1/2/3/5/9 nt. This gave rise to the formulation of the "rule of 6" for the EBOV replication promoter. Here, we studied the impact of such hexamer phasing on viral transcription using a series of replication-competent and -deficient monocistronic minigenomes, in which the spacer of the NP gene was mutated or replaced with that of internal EBOV genes and mutated variants thereof. Beyond reporter gene assays, we conducted qRT-PCR to determine the levels of mRNA, genomic and antigenomic RNA. We demonstrate that hexamer phasing is also essential for viral transcription, that UN5 hexamer periodicity extends into PE1 and that the spacer region can be expanded by 48 nt without losses of transcriptional activity. Making the UN5 hexamer phasing continuous between PE1 and PE2 enhanced the efficiency of transcription and replication. We show that the 2 nt preceding the TSS are essential for transcription. We further propose a role for UN5 hexamer phasing in positioning NP during initiation of RNA synthesis, or in dissociation/reassociation of NP from the template RNA strand while threading the RNA through the active site of the elongating polymerase during replication and transcription.
Collapse
Affiliation(s)
- Simone Bach
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Nadine Biedenkopf
- Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Arnold Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Stephan Becker
- Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| |
Collapse
|
7
|
Cressey TN, Noton SL, Nagendra K, Braun MR, Fearns R. Mechanism for de novo initiation at two sites in the respiratory syncytial virus promoter. Nucleic Acids Res 2019; 46:6785-6796. [PMID: 29873775 PMCID: PMC6061868 DOI: 10.1093/nar/gky480] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/17/2018] [Indexed: 12/18/2022] Open
Abstract
The respiratory syncytial virus (RSV) RNA dependent RNA polymerase (RdRp) initiates two RNA synthesis processes from the viral promoter: genome replication from position 1U and mRNA transcription from position 3C. Here, we examined the mechanism by which a single promoter can direct initiation from two sites. We show that initiation at 1U and 3C occurred independently of each other, and that the same RdRp was capable of precisely selecting the two sites. The RdRp preferred to initiate at 3C, but initiation site selection could be modulated by the relative concentrations of ATP versus GTP. Analysis of template mutations indicated that the RdRp could bind ATP and CTP, or GTP, independently of template nucleotides. The data suggest a model in which innate affinity of the RdRp for particular NTPs, coupled with a repeating element within the promoter, allows precise initiation of replication at 1U or transcription at 3C.
Collapse
Affiliation(s)
- Tessa N Cressey
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sarah L Noton
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Kartikeya Nagendra
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Molly R Braun
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| |
Collapse
|
8
|
Ebolavirus polymerase uses an unconventional genome replication mechanism. Proc Natl Acad Sci U S A 2019; 116:8535-8543. [PMID: 30962389 DOI: 10.1073/pnas.1815745116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Most nonsegmented negative strand (NNS) RNA virus genomes have complementary 3' and 5' terminal nucleotides because the promoters at the 3' ends of the genomes and antigenomes are almost identical to each other. However, according to published sequences, both ends of ebolavirus genomes show a high degree of variability, and the 3' and 5' terminal nucleotides are not complementary. If correct, this would distinguish the ebolaviruses from other NNS RNA viruses. Therefore, we investigated the terminal genomic and antigenomic nucleotides of three different ebolavirus species, Ebola (EBOV), Sudan, and Reston viruses. Whereas the 5' ends of ebolavirus RNAs are highly conserved with the sequence ACAGG-5', the 3' termini are variable and are typically 3'-GCCUGU, ACCUGU, or CCUGU. A small fraction of analyzed RNAs had extended 3' ends. The majority of 3' terminal sequences are consistent with a mechanism of nucleotide addition by hairpin formation and back-priming. Using single-round replicating EBOV minigenomes, we investigated the effect of the 3' terminal nucleotide on viral replication and found that the EBOV polymerase initiates replication opposite the 3'-CCUGU motif regardless of the identity of the 3' terminal nucleotide(s) and of the position of this motif relative to the 3' end. Deletion or mutation of the first residue of the 3'-CCUGU motif completely abolished replication initiation, suggesting a crucial role of this nucleotide in directing initiation. Together, our data show that ebolaviruses have evolved a unique replication strategy among NNS RNA viruses resulting in 3' overhangs. This could be a mechanism to avoid antiviral recognition.
Collapse
|
9
|
Noton SL, Tremaglio CZ, Fearns R. Killing two birds with one stone: How the respiratory syncytial virus polymerase initiates transcription and replication. PLoS Pathog 2019; 15:e1007548. [PMID: 30817806 PMCID: PMC6394897 DOI: 10.1371/journal.ppat.1007548] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Chadene Z. Tremaglio
- Department of Biology, University of Saint Joseph, West Hartford, Connecticut, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
10
|
Braun MR, Deflubé LR, Noton SL, Mawhorter ME, Tremaglio CZ, Fearns R. RNA elongation by respiratory syncytial virus polymerase is calibrated by conserved region V. PLoS Pathog 2017; 13:e1006803. [PMID: 29281742 PMCID: PMC5760109 DOI: 10.1371/journal.ppat.1006803] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 01/09/2018] [Accepted: 12/11/2017] [Indexed: 02/06/2023] Open
Abstract
The large polymerase subunit (L) of non-segmented negative strand RNA viruses transcribes viral mRNAs and replicates the viral genome. Studies with VSV have shown that conserved region V (CRV) of the L protein is part of the capping domain. However, CRV folds over and protrudes into the polymerization domain, suggesting that it might also have a role in RNA synthesis. In this study, the role of respiratory syncytial virus (RSV) CRV was evaluated using single amino acid substitutions and a small molecule inhibitor called BI-D. Effects were analyzed using cell-based minigenome and in vitro biochemical assays. Several amino acid substitutions inhibited production of capped, full-length mRNA and instead resulted in accumulation of short transcripts of approximately 40 nucleotides in length, confirming that RSV CRV has a role in capping. In addition, all six variants tested were either partially or completely defective in RNA replication. This was due to an inability of the polymerase to efficiently elongate the RNA within the promoter region. BI-D also inhibited transcription and replication. In this case, polymerase elongation activity within the promoter region was enhanced, such that the small RNA transcribed from the promoter was not released and instead was elongated past the first gene start signal. This was accompanied by a decrease in mRNA initiation at the first gene start signal and accumulation of aberrant RNAs of varying length. Thus, in addition to its function in mRNA capping, conserved region V modulates the elongation properties of the polymerase to enable productive transcription and replication to occur.
Collapse
MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Antiviral Agents/pharmacology
- Cell Line
- Conserved Sequence
- Drug Discovery
- Genes, Viral
- Humans
- Models, Molecular
- Promoter Regions, Genetic
- RNA Caps/genetics
- RNA Caps/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/genetics
- RNA-Dependent RNA Polymerase/metabolism
- Respiratory Syncytial Virus Infections/drug therapy
- Respiratory Syncytial Virus Infections/virology
- Respiratory Syncytial Virus, Human/genetics
- Respiratory Syncytial Virus, Human/metabolism
- Respiratory Syncytial Virus, Human/pathogenicity
- Transcription Elongation, Genetic
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/metabolism
Collapse
Affiliation(s)
- Molly R. Braun
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Laure R. Deflubé
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Michael E. Mawhorter
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Chadene Z. Tremaglio
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States of America
- * E-mail:
| |
Collapse
|
11
|
Respiratory Syncytial Virus: Infection, Detection, and New Options for Prevention and Treatment. Clin Microbiol Rev 2017; 30:277-319. [PMID: 27903593 DOI: 10.1128/cmr.00010-16] [Citation(s) in RCA: 342] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Respiratory syncytial virus (RSV) infection is a significant cause of hospitalization of children in North America and one of the leading causes of death of infants less than 1 year of age worldwide, second only to malaria. Despite its global impact on human health, there are relatively few therapeutic options available to prevent or treat RSV infection. Paradoxically, there is a very large volume of information that is constantly being refined on RSV replication, the mechanisms of RSV-induced pathology, and community transmission. Compounding the burden of acute RSV infections is the exacerbation of preexisting chronic airway diseases and the chronic sequelae of RSV infection. A mechanistic link is even starting to emerge between asthma and those who suffer severe RSV infection early in childhood. In this article, we discuss developments in the understanding of RSV replication, pathogenesis, diagnostics, and therapeutics. We attempt to reconcile the large body of information on RSV and why after many clinical trials there is still no efficacious RSV vaccine and few therapeutics.
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Fearns R, Deval J. New antiviral approaches for respiratory syncytial virus and other mononegaviruses: Inhibiting the RNA polymerase. Antiviral Res 2016; 134:63-76. [PMID: 27575793 DOI: 10.1016/j.antiviral.2016.08.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/27/2016] [Accepted: 08/07/2016] [Indexed: 11/16/2022]
Abstract
Worldwide, respiratory syncytial virus (RSV) causes severe disease in infants, the elderly, and immunocompromised people. No vaccine or effective antiviral treatment is available. RSV is a member of the non-segmented, negative-strand (NNS) group of RNA viruses and relies on its RNA-dependent RNA polymerase to transcribe and replicate its genome. Because of its essential nature and unique properties, the RSV polymerase has proven to be a good target for antiviral drugs, with one compound, ALS-8176, having already achieved clinical proof-of-concept efficacy in a human challenge study. In this article, we first provide an overview of the role of the RSV polymerase in viral mRNA transcription and genome replication. We then review past and current approaches to inhibiting the RSV polymerase, including use of nucleoside analogs and non-nucleoside inhibitors. Finally, we consider polymerase inhibitors that hold promise for treating infections with other NNS RNA viruses, including measles and Ebola.
Collapse
Affiliation(s)
- Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA.
| | - Jerome Deval
- Alios BioPharma, Inc., Part of the Janssen Pharmaceutical Companies, South San Francisco, CA, USA.
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Initiation and regulation of paramyxovirus transcription and replication. Virology 2015; 479-480:545-54. [PMID: 25683441 DOI: 10.1016/j.virol.2015.01.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/04/2015] [Indexed: 12/18/2022]
Abstract
The paramyxovirus family has a genome consisting of a single strand of negative sense RNA. This genome acts as a template for two distinct processes: transcription to generate subgenomic, capped and polyadenylated mRNAs, and genome replication. These viruses only encode one polymerase. Thus, an intriguing question is, how does the viral polymerase initiate and become committed to either transcription or replication? By answering this we can begin to understand how these two processes are regulated. In this review article, we present recent findings from studies on the paramyxovirus, respiratory syncytial virus, which show how its polymerase is able to initiate transcription and replication from a single promoter. We discuss how these findings apply to other paramyxoviruses. Then, we examine how trans-acting proteins and promoter secondary structure might serve to regulate transcription and replication during different phases of the paramyxovirus replication cycle.
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
Respiratory syncytial virus polymerase can initiate transcription from position 3 of the leader promoter. J Virol 2013; 87:3196-207. [PMID: 23283954 DOI: 10.1128/jvi.02862-12] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mechanisms by which the respiratory syncytial virus (RSV) RNA-dependent RNA polymerase (RdRp) initiates mRNA transcription and RNA replication are poorly understood. A previous study, using an RSV minigenome, suggested that the leader (Le) promoter region at the 3' end of the genome has two initiation sites, one at position +1, opposite the 3' terminal nucleotide of the genome, and a second site at position +3, at a sequence that closely resembles the gene start (GS) signal of the RSV L gene. In this study, we show that the +3 initiation site of the Le is utilized with apparently high frequency in RSV-infected cells and yields small RNA transcripts that are heterogeneous in length but mostly approximately 25 nucleotides (nt) long. Experiments with an in vitro assay in which RSV RNA synthesis was reconstituted using purified RdRp and an RNA oligonucleotide showed that nt 1 to 14 of the Le promoter were sufficient to signal initiation from +3 and that the RdRp could access the +3 initiation site without prior initiation at +1. In a minigenome assay, nucleotide substitutions within the Le to increase its similarity to a GS signal resulted in more-efficient elongation of the RNA initiated from position +3 and a reduction in RNA initiated from the NS1 gene start signal at +45. Taken together, these data suggest a new model for initiation of sequential transcription of the RSV genes, whereby the RdRp initiates the process from a gene start-like sequence at position +3 of the Le.
Collapse
|
18
|
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.
Collapse
|
19
|
Noton SL, Deflubé LR, Tremaglio CZ, Fearns R. The respiratory syncytial virus polymerase has multiple RNA synthesis activities at the promoter. PLoS Pathog 2012; 8:e1002980. [PMID: 23093940 PMCID: PMC3475672 DOI: 10.1371/journal.ppat.1002980] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 09/06/2012] [Indexed: 12/21/2022] Open
Abstract
Respiratory syncytial virus (RSV) is an RNA virus in the Family Paramyxoviridae. Here, the activities performed by the RSV polymerase when it encounters the viral antigenomic promoter were examined. RSV RNA synthesis was reconstituted in vitro using recombinant, isolated polymerase and an RNA oligonucleotide template representing nucleotides 1–25 of the trailer complement (TrC) promoter. The RSV polymerase was found to have two RNA synthesis activities, initiating RNA synthesis from the +3 site on the promoter, and adding a specific sequence of nucleotides to the 3′ end of the TrC RNA using a back-priming mechanism. Examination of viral RNA isolated from RSV infected cells identified RNAs initiated at the +3 site on the TrC promoter, in addition to the expected +1 site, and showed that a significant proportion of antigenome RNAs contained specific nucleotide additions at the 3′ end, demonstrating that the observations made in vitro reflected events that occur during RSV infection. Analysis of the impact of the 3′ terminal extension on promoter activity indicated that it can inhibit RNA synthesis initiation. These findings indicate that RSV polymerase-promoter interactions are more complex than previously thought and suggest that there might be sophisticated mechanisms for regulating promoter activity during infection. Respiratory syncytial virus (RSV) is a major pathogen of infants with the potential to cause severe respiratory disease. RSV has an RNA genome and one approach to developing a drug against this virus is to gain a greater understanding of the mechanisms used by the viral polymerase to generate new RNA. In this study we developed a novel assay for examining how the RSV polymerase interacts with a specific promoter sequence at the end of an RNA template, and performed analysis of RSV RNA produced in infected cells to confirm the findings. Our experiments showed that the behavior of the polymerase on the promoter was surprisingly complex. We found that not only could the polymerase initiate synthesis of progeny genome RNA from an initiation site at the end of the template, but it could also generate another small RNA from a second initiation site. In addition, we showed that the polymerase could add additional RNA sequence to the template promoter, which affected its ability to initiate RNA synthesis. These findings extend our understanding of the functions of the promoter, and suggest a mechanism by which RNA synthesis from the promoter is regulated.
Collapse
Affiliation(s)
- Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Laure R. Deflubé
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Chadene Z. Tremaglio
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
20
|
Noton SL, Fearns R. The first two nucleotides of the respiratory syncytial virus antigenome RNA replication product can be selected independently of the promoter terminus. RNA (NEW YORK, N.Y.) 2011; 17:1895-1906. [PMID: 21878549 PMCID: PMC3185921 DOI: 10.1261/rna.2813411] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/31/2011] [Indexed: 05/31/2023]
Abstract
There is limited knowledge regarding how the RNA-dependent RNA polymerases of the nonsegmented negative-strand RNA viruses initiate genome replication. In a previous study of respiratory syncytial virus (RSV) RNA replication, we found evidence that the polymerase could select the 5'-ATP residue of the genome RNA independently of the 3' nucleotide of the template. To investigate if a similar mechanism is used during antigenome synthesis, a study of initiation from the RSV leader (Le) promoter was performed using an intracellular minigenome assay in which RNA replication was restricted to a single step, so that the products examined were derived only from input mutant templates. Templates in which Le nucleotides 1U, or 1U and 2G, were deleted directed efficient replication, and in both cases, the replication products were initiated at the wild-type position, at position -1 or -2 relative to the template, respectively. Sequence analysis of the RNA products showed that they contained ATP and CTP at the -1 and -2 positions, respectively, thus restoring the mini-antigenome RNA to wild-type sequence. These data indicate that the RSV polymerase is able to select the first two nucleotides of the antigenome and initiate at the correct position, even if the 3'-terminal two nucleotides of the template are missing. Substitution of positions +1 and +2 of the template reduced RNA replication and resulted in increased initiation at positions +3 and +5. Together these data suggest a model for how the RSV polymerase initiates antigenome synthesis.
Collapse
Affiliation(s)
- Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| |
Collapse
|
21
|
Kumaria R, Iyer LR, Hibberd ML, Simões EAF, Sugrue RJ. Whole genome characterization of non-tissue culture adapted HRSV strains in severely infected children. Virol J 2011; 8:372. [PMID: 21794174 PMCID: PMC3166936 DOI: 10.1186/1743-422x-8-372] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 07/28/2011] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Human respiratory syncytial virus (HRSV) is the most important virus causing lower respiratory infection in young children. The complete genetic characterization of RSV clinical strains is a prerequisite for understanding HRSV infection in the clinical context. Current information about the genetic structure of the HRSV genome has largely been obtained using tissue culture adapted viruses. During tissue culture adaptation genetic changes can be introduced into the virus genome, which may obscure subtle variations in the genetic structure of different RSV strains. METHODS In this study we describe a novel Sanger sequencing strategy which allowed the complete genetic characterisation of 14 clinical HRSV strains. The viruses were sequenced directly in the nasal washes of severely hospitalized children, and without prior passage of the viruses in tissue culture. RESULTS The analysis of nucleotide sequences suggested that vRNA length is a variable factor among primary strains, while the phylogenetic analysis suggests selective pressure for change. The G gene showed the greatest sequence variation (2-6.4%), while small hydrophobic protein and matrix genes were completely conserved across all clinical strains studied. A number of sequence changes in the F, L, M2-1 and M2-2 genes were observed that have not been described in laboratory isolates. The gene junction regions showed more sequence variability, and in particular the intergenic regions showed a highest level of sequence variation. Although the clinical strains grew slower than the HRSVA2 virus isolate in tissue culture, the HRSVA2 isolate and clinical strains formed similar virus structures such as virus filaments and inclusion bodies in infected cells; supporting the clinical relevance of these virus structures. CONCLUSION This is the first report to describe the complete genetic characterization of HRSV clinical strains that have been sequenced directly from clinical material. The presence of novel substitutions and deletions in the vRNA of clinical strains emphasize the importance of genomic characterization of non-tissue culture adapted primary strains.
Collapse
Affiliation(s)
- Rajni Kumaria
- Singapore-MIT Alliance for Research and Technology, Centre for Life Sciences, #05-06M, 28 Medical Drive, 117456, Singapore
| | - Laxmi Ravi Iyer
- Division of Molecular and Cell biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 639798, Singapore
| | - Martin L Hibberd
- Singapore-MIT Alliance for Research and Technology, Centre for Life Sciences, #05-06M, 28 Medical Drive, 117456, Singapore
- Genome Institute of Singapore, #02-01, Genome Building, 60 Biopolis Street, 138672, Singapore
| | - Eric AF Simões
- University of Colorado, Denver and The Division of Infectious Diseases, The Children's Hospital, 13123 East 16th Avenue, Aurora, CO 80045, USA
| | - Richard J Sugrue
- Singapore-MIT Alliance for Research and Technology, Centre for Life Sciences, #05-06M, 28 Medical Drive, 117456, Singapore
- Division of Molecular and Cell biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 639798, Singapore
| |
Collapse
|
22
|
Hanley LL, McGivern DR, Teng MN, Djang R, Collins PL, Fearns R. Roles of the respiratory syncytial virus trailer region: effects of mutations on genome production and stress granule formation. Virology 2010; 406:241-52. [PMID: 20701943 DOI: 10.1016/j.virol.2010.07.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 05/03/2010] [Accepted: 07/02/2010] [Indexed: 12/16/2022]
Abstract
The 5' extragenic trailer region of respiratory syncytial virus (RSV) is known to be necessary for genome replication, but is more than three times the length of the 3' leader replication promoter, raising the possibility that trailer might play an additional role in viral replication. To examine this, mutant recombinant viruses were constructed in which the trailer region was truncated or substituted with leader-complement sequence. This analysis showed that the complete trailer increased promoter activity, facilitating genome production and viral multiplication. In addition, trailer-containing viruses did not induce stress granules, whereas the leader-complement virus mutant did, resulting in poor multi-cycle viral growth. These data demonstrate that although the RSV trailer does not contain a unique essential sequence, it augments virus growth by enabling optimal genome production. In addition, a sequence at the 5' terminal end of the trailer region allows RSV to subvert stress granule formation.
Collapse
Affiliation(s)
- Laura L Hanley
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | | | | | | | | | | |
Collapse
|
23
|
Walter CT, Barr JN. Bunyamwera virus can repair both insertions and deletions during RNA replication. RNA (NEW YORK, N.Y.) 2010; 16:1138-45. [PMID: 20430858 PMCID: PMC2874166 DOI: 10.1261/rna.1962010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 03/16/2010] [Indexed: 05/29/2023]
Abstract
The genomic termini of RNA viruses contain essential cis-acting signals for such diverse functions as packaging, genome translation, mRNA transcription, and RNA replication, and thus preservation of their sequence integrity is critical for virus viability. Sequence alteration can arise due to cellular mechanisms that add or remove nucleotides from terminal regions, or, alternatively, from introduction of sequence errors through nucleotide misincorporation by the error-prone viral RNA-dependent RNA polymerase (RdRp). To preserve template function, many RNA viruses utilize repair mechanisms to prevent accumulation of terminal alterations. Here we show that Bunyamwera virus (BUNV), the prototype of the Bunyaviridae family of segmented negative-sense RNA viruses, also can repair its genomic termini. When an intact nontranslated region (NTR) was added to the anti-genomic 3' end, it was precisely removed, to restore both length and RNA synthesis function of the wild-type template. Furthermore, when nucleotides were removed from the anti-genome 3' end, and replaced with a duplicate and intact NTR, both the external NTR were removed, and the missing nucleotides were restored, thus, indicating that the BUNV RdRp can both remove and add nucleotides to the template. We show that the mechanism for repair of terminal extensions is likely that of internal entry of the viral RdRp during genome synthesis. Possible mechanisms for repair of terminal deletions are discussed.
Collapse
Affiliation(s)
- Cheryl T Walter
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | | |
Collapse
|
24
|
Evidence that the polymerase of respiratory syncytial virus initiates RNA replication in a nontemplated fashion. Proc Natl Acad Sci U S A 2010; 107:10226-31. [PMID: 20479224 DOI: 10.1073/pnas.0913065107] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
RNA virus polymerases must initiate replicative RNA synthesis with extremely high accuracy to maintain their genome termini and to avoid generating defective genomes. For the single-stranded negative-sense RNA viruses, it is not known how this accuracy is achieved. To investigate this question, mutations were introduced into the 3' terminal base of a respiratory syncytial virus (RSV) template, and the RNA products were examined to determine the impact of the mutation. To perform the assay, RNA replication was reconstituted using a modified minireplicon system in which replication was limited to a single step. Importantly, this system allowed analysis of RSV RNA generated intracellularly, but from a defined template that was not subject to selection by replication. Sequence analysis of RNA products generated from templates containing 1U-C and 1U-A substitutions showed that, in both cases, replication products were initiated with a nontemplated, WT A residue, rather than a templated G or U residue, indicating that the polymerase selects the terminal NTP independently of the template. Examination of a template in which the position 1 nucleotide was deleted supported these findings. This mutant directed efficient replication at approximately 60% of WT levels, and its product was found to be initiated at the WT position (-1 relative to the template) with a WT A residue. These findings show that the RSV replicase selects ATP and initiates at the correct position, independently of the first nucleotide of the template, suggesting a mechanism by which highly accurate replication initiation is achieved.
Collapse
|
25
|
Curran J, Kolakofsky D. Nonsegmented negative-strand RNA virus RNA synthesis in vivo. Virology 2008; 371:227-30. [PMID: 18177685 DOI: 10.1016/j.virol.2007.11.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 11/16/2007] [Indexed: 12/16/2022]
|
26
|
Cordey S, Roux L. Further characterization of a paramyxovirus transcription initiation signal: search for required nucleotides upstream and importance of the N phase context. J Gen Virol 2007; 88:1555-1564. [PMID: 17412986 DOI: 10.1099/vir.0.82701-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Paramyxovirus genomes contain a linear array of five to ten genes sequentially transcribed by the viral RNA polymerase. mRNA synthesis initiates at a nucleotide signal (gs1) within the genomic promoter located at the genome 3' end. To gain information about the mechanism involved in transcription initiation, a search was carried out for upstream nucleotides required for gs1 and the effects of the gs1 nucleocapsid protein (N) phase context on transcription regulation were determined. For both purposes, tandem promoter mini-genomes carrying a transcription signal ectopically positioned downstream of a replication-only signal were used. The requirement for hygromycin resistance gene expression was used in an attempt to select essential nucleotides within randomized stretches of nucleotides. Nucleotide insertions or deletions were also made on either side of the transcription signal to change its original N phase context in the five remaining possibilities and GFP expression from these modified signals was assessed. Cell cultures resistant to hygromycin treatment were readily obtained following amplification of mini-genomes harbouring randomized sequences. However, selected nucleotides upstream of gs1 could not be identified under conditions where nucleotides within gs1 were selected. In contrast, it was observed that changing the gs1 N phase context progressively decreased transcription by five- to tenfold. These results are discussed in relation to two different mechanisms of transcription initiation.
Collapse
Affiliation(s)
- Samuel Cordey
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| | - Laurent Roux
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| |
Collapse
|
27
|
Magoffin DE, Mackenzie JS, Wang LF. Genetic analysis of J-virus and Beilong virus using minireplicons. Virology 2007; 364:103-11. [PMID: 17397895 DOI: 10.1016/j.virol.2007.01.045] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 01/02/2007] [Accepted: 01/31/2007] [Indexed: 11/16/2022]
Abstract
J-virus (JPV), isolated from wild mice in Australia, and Beilong virus (BeiPV), originally isolated from human mesangial cells in China and subsequently detected in rat mesangial cells, represent a new group of paramyxoviruses which have exceptionally large genomes (>19 kb) and contain more than six transcriptional units. In this study, minireplicons were employed to assess the taxonomic status of JPV and BeiPV. Our results demonstrated that, whilst the genome replication machineries of JPV and BeiPV can be interchanged, they were not functional when exchanged with that of Nipah virus. These studies indicate that JPV and BeiPV are closely related to each other and support the classification of these two viruses into a separate genus. In addition, the minireplicons were also used to demonstrate that these large-genome viruses also comply with the 'rule of six' and that over-expression of the C protein has a detrimental effect on minigenome replication.
Collapse
Affiliation(s)
- Danielle E Magoffin
- CSIRO Livestock Industries, CSIRO Australian Animal Health Laboratory, PO Bag 24, Geelong, Victoria 3220, Australia
| | | | | |
Collapse
|
28
|
Plattet P, Strahle L, le Mercier P, Hausmann S, Garcin D, Kolakofsky D. Sendai virus RNA polymerase scanning for mRNA start sites at gene junctions. Virology 2007; 362:411-20. [PMID: 17300823 DOI: 10.1016/j.virol.2006.12.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Revised: 12/07/2006] [Accepted: 12/21/2006] [Indexed: 11/18/2022]
Abstract
Mini-genomes expressing two reporter genes and a variable gene junction were used to study Sendai virus RNA polymerase (RdRp) scanning for the mRNA start signal of the downstream gene (gs2). We found that RdRp could scan the template efficiently as long as the initiating uridylate of gs2 (3' UCCCnnUUUC) was preceded by the conserved intergenic region (3' GAA) and the last 3 uridylates of the upstream gene end signal (ge1; 3' AUUCUUUUU). The end of the leader sequence (3' CUAAAA, which precedes gs1) could also be used for gene2 expression, but this sequence was considerably less efficient. Increasing the distance between ge1 and gs2 (up to 200 nt) led to the progressive loss of gene2 expression, in which half of gene2 expression was lost for each 70 nucleotides of intervening sequence. Beyond 200 nt, gene2 expression was lost more slowly. Our results suggest that there may be two populations of RdRp that scan at gene junctions, which can be distinguished by the efficiency with which they can scan the genome template for gs.
Collapse
Affiliation(s)
- Philippe Plattet
- Department of Microbiology and Molecular Medicine, University of Geneva School of Medicine, C.M.U., 1211 Geneva, Switzerland
| | | | | | | | | | | |
Collapse
|
29
|
Bailey D, Chard LS, Dash P, Barrett T, Banyard AC. Reverse genetics for peste-des-petits-ruminants virus (PPRV): Promoter and protein specificities. Virus Res 2007; 126:250-5. [PMID: 17350130 DOI: 10.1016/j.virusres.2007.01.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 01/16/2007] [Accepted: 01/21/2007] [Indexed: 11/26/2022]
Abstract
Peste-des-petits-ruminants virus (PPRV) (family Paramyxoviridae, genus Morbillivirus) causes an acute febrile illness in sheep and goats resulting in significant morbidity and mortality in infected herds. The paramyxoviruses all have negative sense, non-segmented RNA genomes and their host range and pathogenic determinants have been extensively studied using reverse genetics. This technology also enables a more rational approach to be taken with respect to vaccine design. In order to initiate this type of work for PPRV we constructed a PPRV minigenome and studied its expression in transfected cells. As for other morbilliviruses, the minimum requirements for minigenome rescue were shown to be the cis-acting elements of the genome (GP) and antigenome (AGP) promoters as well as the three trans-acting helper proteins N (nucleocapsid), P (phosphoprotein) and L (large polymerase). Homologous PPRV helper proteins were compared to their heterologous analogues from the closely related rinderpest virus (RPV) and heterologous minigenome rescue was found to be a much less efficient process. By engineering two GP/AGP chimeric minigenomes we also identified differences between the two viruses in the specific interactions between the promoters and the transcriptase/replicase complexes. The PPRV minigenome was also shown not to strictly comply with the "rule of six"in vitro.
Collapse
Affiliation(s)
- Dalan Bailey
- Institute for Animal Health, Pirbright Laboratory, Ash Road, Woking, Surrey GU24 ONF, United Kingdom.
| | | | | | | | | |
Collapse
|
30
|
Tran TL, Castagné N, Bhella D, Varela PF, Bernard J, Chilmonczyk S, Berkenkamp S, Benhamo V, Grznarova K, Grosclaude J, Nespoulos C, Rey FA, Eléouët JF. The nine C-terminal amino acids of the respiratory syncytial virus protein P are necessary and sufficient for binding to ribonucleoprotein complexes in which six ribonucleotides are contacted per N protein protomer. J Gen Virol 2007; 88:196-206. [PMID: 17170452 DOI: 10.1099/vir.0.82282-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The respiratory syncytial virus (RSV) phosphoprotein (P) is a major polymerase co-factor that interacts with both the large polymerase fragment (L) and the nucleoprotein (N). The N-binding domain of RSV P has been investigated by co-expression of RSV P and N proteins in Escherichia coli. Pull-down assays performed with a series of truncated forms of P fused to glutathione S-transferase (GST) revealed that the region comprising the last nine C-terminal amino acid residues of P (233-DNDLSLEDF-241) is sufficient for efficient binding to N. Site-directed mutagenesis shows that the last four residues of this peptide are crucial for binding and must be present at the end of a flexible C-terminal tail. The presence of the P oligomerization domain (residues 100-160) was an important stabilizing factor for the interaction. The tetrameric full-length P fused to GST was able to pull down both helical and ring structures, whereas a monomeric C-terminal fragment of P (residues 161-241) fused to GST pulled down exclusively RNA-N rings. Electron-microscopy analysis of the purified rings showed the presence of two types of complex: undecamers (11N) and decamers (10N). Mass-spectrometry analysis of the RNA extracted from rings after RNase A treatment showed two peaks of 22,900 and 24,820 Da, corresponding to a mean RNA length of 67 and 73 bases, respectively. These results suggest strongly that each N subunit contacts 6 nt, with an extra three or four bases further protected from nuclease digestion by the ring structure at both the 5' and 3' ends.
Collapse
Affiliation(s)
- Thi-Lan Tran
- Unité de Virologie et Immunologie Moléculaires, INRA, 78350 Jouy-en-Josas, France
| | - Nathalie Castagné
- Unité de Virologie et Immunologie Moléculaires, INRA, 78350 Jouy-en-Josas, France
| | - David Bhella
- Medical Research Council Virology Unit, Church Street, Glasgow G11 5JR, UK
| | - Paloma F Varela
- Laboratoire de Virologie Moléculaire et Structurale, UMR 2472-1157 CNRS-INRA and IFR 115, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Julie Bernard
- Unité de Virologie et Immunologie Moléculaires, INRA, 78350 Jouy-en-Josas, France
| | - Stefan Chilmonczyk
- Unité de Virologie et Immunologie Moléculaires, INRA, 78350 Jouy-en-Josas, France
| | - Stefan Berkenkamp
- Institute of Medical Physics and Biophysics, Westfälische Wilhelms-Universität, Münster, Germany
| | - Vanessa Benhamo
- Unité de Virologie et Immunologie Moléculaires, INRA, 78350 Jouy-en-Josas, France
| | - Katarina Grznarova
- Unité de Virologie et Immunologie Moléculaires, INRA, 78350 Jouy-en-Josas, France
| | - Jeanne Grosclaude
- Unité de Virologie et Immunologie Moléculaires, INRA, 78350 Jouy-en-Josas, France
| | - Claude Nespoulos
- Unité de Biochimie et Structure des Protéines, INRA, 78350 Jouy-en-Josas, France
| | - Felix A Rey
- Laboratoire de Virologie Moléculaire et Structurale, UMR 2472-1157 CNRS-INRA and IFR 115, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | | |
Collapse
|
31
|
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.
Collapse
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
Collapse
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
| |
Collapse
|
32
|
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]
|