1
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Gonnin L, Richard CA, Gutsche I, Chevret D, Troussier J, Vasseur JJ, Debart F, Eléouët JF, Galloux M. Importance of RNA length for in vitro encapsidation by the nucleoprotein of human Respiratory Syncytial Virus. J Biol Chem 2022; 298:102337. [PMID: 35931116 PMCID: PMC9436823 DOI: 10.1016/j.jbc.2022.102337] [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] [Received: 04/23/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/29/2022] Open
Abstract
Respiratory syncytial virus has a negative-sense single-stranded RNA genome constitutively encapsidated by the viral nucleoprotein N, forming a helical nucleocapsid which is the template for viral transcription and replication by the viral polymerase L. Recruitment of L onto the nucleocapsid depends on the viral phosphoprotein P, which is an essential L cofactor. A prerequisite for genome and antigenome encapsidation is the presence of the monomeric, RNA-free, neosynthesized N protein, named N0. Stabilization of N0 depends on the binding of the N-terminal residues of P to its surface, which prevents N oligomerization. However, the mechanism involved in the transition from N0-P to nucleocapsid assembly, and thus in the specificity of viral genome encapsidation, is still unknown. Furthermore, the specific role of N oligomerization and RNA in the morphogenesis of viral factories, where viral transcription and replication occur, have not been elucidated although the interaction between P and N complexed to RNA has been shown to be responsible for this process. Here, using a chimeric protein comprising N and the first 40 N-terminal residues of P, we succeeded in purifying a recombinant N0-like protein competent for RNA encapsidation in vitro. Our results showed the importance of RNA length for stable encapsidation and revealed that the nature of the 5′ end of RNA does not explain the specificity of encapsidation. Finally, we showed that RNA encapsidation is crucial for the in vitro reconstitution of pseudo-viral factories. Together, our findings provide insight into respiratory syncytial virus viral genome encapsidation specificity.
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Affiliation(s)
- Lorène Gonnin
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | - Irina Gutsche
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Didier Chevret
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Joris Troussier
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | | | - Françoise Debart
- IBMM, Université de Montpellier, ENSCM, CNRS, UMR 5247, Montpellier, France
| | | | - Marie Galloux
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France.
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2
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Slović A, Košutić-Gulija T, Forčić D, Šantak M, Jagušić M, Jurković M, Pali D, Ivančić-Jelečki J. Population Variability Generated during Rescue Process and Passaging of Recombinant Mumps Viruses. Viruses 2021; 13:2550. [PMID: 34960819 PMCID: PMC8707793 DOI: 10.3390/v13122550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Recombinant mumps viruses (MuVs) based on established vaccine strains represent attractive vector candidates as they have known track records for high efficacy and the viral genome does not integrate in the host cells. We developed a rescue system based on the consensus sequence of the L-Zagreb vaccine and generated seven different recombinant MuVs by (a) insertion of one or two additional transcription units (ATUs), (b) lengthening of a noncoding region to the extent that the longest noncoding region in MuV genome is created, or (c) replacement of original L-Zagreb sequences with sequences rich in CG and AT dinucleotides. All viruses were successfully rescued and faithfully matched sequences of input plasmids. In primary rescued stocks, low percentages of heterogeneous positions were found (maximum 0.12%) and substitutions were predominantly obtained in minor variants, with maximally four substitutions seen in consensus. ATUs did not accumulate more mutations than the natural MuV genes. Six substitutions characteristic for recombinant viruses generated in our system were defined, as they repetitively occurred during rescue processes. In subsequent passaging of primary rescue stocks in Vero cells, different inconsistencies within quasispecies structures were observed. In order to assure that unwanted mutations did not emerge and accumulate, sub-consensus variability should be closely monitored. As we show for Pro408Leu mutation in L gene and a stop codon in one of ATUs, positively selected variants can rise to frequencies over 85% in only few passages.
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Affiliation(s)
- Anamarija Slović
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (A.S.); (T.K.-G.); (D.F.); (M.J.); (M.J.); (D.P.)
| | - Tanja Košutić-Gulija
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (A.S.); (T.K.-G.); (D.F.); (M.J.); (M.J.); (D.P.)
| | - Dubravko Forčić
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (A.S.); (T.K.-G.); (D.F.); (M.J.); (M.J.); (D.P.)
| | - Maja Šantak
- Ruđer Bošković Institute, 10000 Zagreb, Croatia;
| | - Maja Jagušić
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (A.S.); (T.K.-G.); (D.F.); (M.J.); (M.J.); (D.P.)
| | - Mirna Jurković
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (A.S.); (T.K.-G.); (D.F.); (M.J.); (M.J.); (D.P.)
| | - Dorotea Pali
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (A.S.); (T.K.-G.); (D.F.); (M.J.); (M.J.); (D.P.)
| | - Jelena Ivančić-Jelečki
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (A.S.); (T.K.-G.); (D.F.); (M.J.); (M.J.); (D.P.)
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3
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Ogonczyk Makowska D, Hamelin MÈ, Boivin G. Engineering of Live Chimeric Vaccines against Human Metapneumovirus. Pathogens 2020; 9:E135. [PMID: 32093057 PMCID: PMC7168645 DOI: 10.3390/pathogens9020135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 02/07/2023] Open
Abstract
Human metapneumovirus (HMPV) is an important human pathogen that, along with respiratory syncytial virus (RSV), is a major cause of respiratory tract infections in young infants. Development of an effective vaccine against Pneumoviruses has proven to be particularly difficult; despite over 50 years of research in this field, no vaccine against HMPV or RSV is currently available. Recombinant chimeric viruses expressing antigens of other viruses can be generated by reverse genetics and used for simultaneous immunization against more than one pathogen. This approach can result in the development of promising vaccine candidates against HMPV, and several studies have indeed validated viral vectors expressing HMPV antigens. In this review, we summarize current efforts in generating recombinant chimeric vaccines against HMPV, and we discuss their potential optimization based on the correspondence with RSV studies.
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Affiliation(s)
| | | | - Guy Boivin
- Centre de Recherche en Infectiologie of the Centre Hospitalier Universitaire de Québec and Université Laval, Québec, QC G1V 4G2, Canada; (D.O.M.); (M.-È.H.)
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4
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Gao Y, Cao D, Ahn HM, Swain A, Hill S, Ogilvie C, Kurien M, Rahmatullah T, Liang B. In vitro trackable assembly of RNA-specific nucleocapsids of the respiratory syncytial virus. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49942-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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5
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Gao Y, Cao D, Ahn HM, Swain A, Hill S, Ogilvie C, Kurien M, Rahmatullah T, Liang B. In vitro trackable assembly of RNA-specific nucleocapsids of the respiratory syncytial virus. J Biol Chem 2019; 295:883-895. [PMID: 31822560 PMCID: PMC6970927 DOI: 10.1074/jbc.ra119.011602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/26/2019] [Indexed: 12/25/2022] Open
Abstract
The templates for transcription and replication by respiratory syncytial virus (RSV) polymerase are helical nucleocapsids (NCs), formed by viral RNAs that are encapsidated by the nucleoprotein (N). Proper NC assembly is vital for RSV polymerase to engage the RNA template for RNA synthesis. Previous studies of NCs or nucleocapsid-like particles (NCLPs) from RSV and other nonsegmented negative-sense RNA viruses have provided insights into the overall NC architecture. However, in these studies, the RNAs were either random cellular RNAs or average viral genomic RNAs. An in-depth mechanistic understanding of NCs has been hampered by lack of an in vitro assay that can track NC or NCLP assembly. Here we established a protocol to obtain RNA-free N protein (N0) and successfully demonstrated the utility of a new assay for tracking assembly of N with RNA oligonucleotides into NCLPs. We discovered that the efficiency of the NCLP (N–RNA) assembly depends on the length and sequence of the RNA incorporated into NCLPs. This work provides a framework to generate purified N0 and incorporate it with RNA into NCLPs in a controllable manner. We anticipate that our assay for in vitro trackable assembly of RSV-specific nucleocapsids may enable in-depth mechanistic analyses of this process.
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Affiliation(s)
- Yunrong Gao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Dongdong Cao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Hyunjun Max Ahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Anshuman Swain
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Shaylan Hill
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Claire Ogilvie
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Matthew Kurien
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Taha Rahmatullah
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
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6
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Sun Y, Kim EJ, Felt SA, Taylor LJ, Agarwal D, Grant GR, López CB. A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes. PLoS Pathog 2019; 15:e1007707. [PMID: 30995283 PMCID: PMC6504078 DOI: 10.1371/journal.ppat.1007707] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/07/2019] [Accepted: 03/15/2019] [Indexed: 01/12/2023] Open
Abstract
Defective viral genomes of the copy-back type (cbDVGs) are the primary initiators of the antiviral immune response during infection with respiratory syncytial virus (RSV) both in vitro and in vivo. However, the mechanism governing cbDVG generation remains unknown, thereby limiting our ability to manipulate cbDVG content in order to modulate the host response to infection. Here we report a specific genomic signal that mediates the generation of a subset of RSV cbDVG species. Using a customized bioinformatics tool, we identified regions in the RSV genome frequently used to generate cbDVGs during infection. We then created a minigenome system to validate the function of one of these sequences and to determine if specific nucleotides were essential for cbDVG generation at that position. Further, we created a recombinant virus unable to produce a subset of cbDVGs due to mutations introduced in this sequence. The identified sequence was also found as a site for cbDVG generation during natural RSV infections, and common cbDVGs originated at this sequence were found among samples from various infected patients. These data demonstrate that sequences encoded in the viral genome determine the location of cbDVG formation and, therefore, the generation of cbDVGs is not a stochastic process. These findings open the possibility of genetically manipulating cbDVG formation to modulate infection outcome.
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Affiliation(s)
- Yan Sun
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Eun Ji Kim
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sébastien A. Felt
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Louis J. Taylor
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Divyansh Agarwal
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Gregory R. Grant
- Institute of Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Carolina B. López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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7
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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.
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8
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Molouki A, Peeters B. Rescue of recombinant Newcastle disease virus: a short history of how it all started. Arch Virol 2017; 162:1845-1854. [PMID: 28316014 DOI: 10.1007/s00705-017-3308-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 02/16/2017] [Indexed: 01/24/2023]
Abstract
Reverse genetics of viruses has come a long way, and many recombinant viruses have been generated since the first successful "rescues" were reported in the late 1970s. Recombinant Newcastle disease virus (rNDV), a non-segmented negative-sense RNA virus (NSNSV), was first rescued in 1999 using a reverse genetics approach similar to that reported for other recombinant viruses of the order Mononegavirales a few years before. The route from an original NDV isolate to the generation of its recombinant counterpart requires many steps that have to be sequentially and carefully completed. Background knowledge of each of these steps is essential because it allows one to make the best choices for fulfilling the specific requirements of the final recombinant virus. We have previously reviewed the latest strategies in cloning the NDV full-length cDNA into transcription vectors and the use of different RNA polymerase systems for the generation of viral RNA from plasmid DNA. In this article, we review a number of discoveries on the mechanism of transcription and replication of NDV, including a brief history behind the discovery of its RNP complex. This includes the generation of artificial and functional RNP constructs, in combination with the smart use of available knowledge and technologies that ultimately resulted in rescue of the first rNDV.
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Affiliation(s)
- Aidin Molouki
- Department of Avian Disease Research and Diagnostic, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.
| | - Ben Peeters
- Department of Virology, Wageningen Bioveterinary Research, PO Box 65, 8200 AB, Lelystad, The Netherlands
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9
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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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10
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Evidence that a polyhexameric genome length is preferred, but not strictly required, for efficient mumps virus replication. Virology 2016; 493:173-88. [PMID: 27058764 DOI: 10.1016/j.virol.2016.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/22/2016] [Accepted: 03/24/2016] [Indexed: 11/22/2022]
Abstract
Mumps virus (MuV) is postulated to adhere to the "rule of six" for efficient replication. To examine the requirement for MuV, minigenomes of nonpolyhexameric length (6n-1 and 6n+1) were analyzed. Expression of the reporter gene CAT was significantly reduced with minigenomes of nonpolyhexameric length compared to the wild type 6n genome, and reduction was more pronounced for the 6n-1 than for the 6n+1 minigenome. That 6n-1 genomes are impacted by nonconformance with the rule of six to a greater degree as compared to 6n+1 genomes was also suggested with MuV derived from cDNA coding for 6n+1 or 6n-1 genomes. While viruses recovered from 6n+1 cDNAs maintained a nonpolyhexameric genome length over multiple replication cycles, viruses rescued from the 6n-1 cDNAs acquired length correcting mutations rapidly following rescue. Our data indicate that polyhexameric genomes are the preferred template for the MuV RNA polymerase, but that this requirement is not absolute.
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11
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Russell CJ, Hurwitz JL. Sendai virus as a backbone for vaccines against RSV and other human paramyxoviruses. Expert Rev Vaccines 2015; 15:189-200. [PMID: 26648515 DOI: 10.1586/14760584.2016.1114418] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human paramyxoviruses are the etiological agents for life-threatening respiratory virus infections of infants and young children. These viruses, including respiratory syncytial virus (RSV), the human parainfluenza viruses (hPIV1-4) and human metapneumovirus (hMPV), are responsible for millions of serious lower respiratory tract infections each year worldwide. There are currently no standard treatments and no licensed vaccines for any of these pathogens. Here we review research with which Sendai virus, a mouse parainfluenza virus type 1, is being advanced as a Jennerian vaccine for hPIV1 and as a backbone for RSV, hMPV and other hPIV vaccines for children.
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Affiliation(s)
- Charles J Russell
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA.,b Department of Microbiology, Immunology and Biochemistry , University of Tennessee Health Science Center , Memphis , TN , USA
| | - Julia L Hurwitz
- a Department of Infectious Diseases , St. Jude Children's Research Hospital , Memphis , TN , USA.,b Department of Microbiology, Immunology and Biochemistry , University of Tennessee Health Science Center , Memphis , TN , USA
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12
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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.
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13
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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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14
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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.
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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:
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15
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Bayon JCL, Lina B, Rosa-Calatrava M, Boivin G. Recent developments with live-attenuated recombinant paramyxovirus vaccines. Rev Med Virol 2012; 23:15-34. [DOI: 10.1002/rmv.1717] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/14/2012] [Accepted: 03/22/2012] [Indexed: 12/30/2022]
Affiliation(s)
- Jean-Christophe Le Bayon
- Laboratoire de Virologie et Pathologie Humaine, VirPath EMR 4610/Equipe VirCell, Université de Lyon; Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Faculté de médecine RTH Laennec; Lyon France
- Research Center in Infectious Diseases; CHUQ-CHUL and Université Laval; Québec City QC Canada
| | - Bruno Lina
- Laboratoire de Virologie et Pathologie Humaine, VirPath EMR 4610/Equipe VirCell, Université de Lyon; Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Faculté de médecine RTH Laennec; Lyon France
- Laboratoire de Virologie, Centre de Biologie et de Pathologie Est; Hospices Civils de Lyon; Lyon Bron Cedex France
| | - Manuel Rosa-Calatrava
- Laboratoire de Virologie et Pathologie Humaine, VirPath EMR 4610/Equipe VirCell, Université de Lyon; Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Faculté de médecine RTH Laennec; Lyon France
| | - Guy Boivin
- Research Center in Infectious Diseases; CHUQ-CHUL and Université Laval; Québec City QC Canada
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16
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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.
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17
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Samuel AS, Paldurai A, Kumar S, Collins PL, Samal SK. Complete genome sequence of avian paramyxovirus (APMV) serotype 5 completes the analysis of nine APMV serotypes and reveals the longest APMV genome. PLoS One 2010; 5:e9269. [PMID: 20174645 PMCID: PMC2822847 DOI: 10.1371/journal.pone.0009269] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 01/27/2010] [Indexed: 01/08/2023] Open
Abstract
Background Avian paramyxoviruses (APMV) consist of nine known serotypes. The genomes of representatives of all APMV serotypes except APMV type 5 have recently been fully sequenced. Here, we report the complete genome sequence of the APMV-5 prototype strain budgerigar/Kunitachi/74. Methodology/Principal Findings APMV-5 Kunitachi virus is unusual in that it lacks a virion hemagglutinin and does not grow in the allantoic cavity of embryonated chicken eggs. However, the virus grew in the amniotic cavity of embryonated chicken eggs and in twelve different established cell lines and two primary cell cultures. The genome is 17,262 nucleotides (nt) long, which is the longest among members of genus Avulavirus, and encodes six non-overlapping genes in the order of 3′N-P/V/W-M-F-HN-L-5′ with intergenic regions of 4–57 nt. The genome length follows the ‘rule of six’ and contains a 55-nt leader sequence at the 3′end and a 552 nt trailer sequence at the 5′ end. The phosphoprotein (P) gene contains a conserved RNA editing site and is predicted to encode P, V, and W proteins. The cleavage site of the F protein (G-K-R-K-K-R↓F) conforms to the cleavage site motif of the ubiquitous cellular protease furin. Consistent with this, exogenous protease was not required for virus replication in vitro. However, the intracerebral pathogenicity index of APMV-5 strain Kunitachi in one-day-old chicks was found to be zero, indicating that the virus is avirulent for chickens despite the presence of a polybasic F cleavage site. Conclusions/Significance Phylogenetic analysis of the sequences of the APVM-5 genome and proteins versus those of the other APMV serotypes showed that APMV-5 is more closely related to APMV-6 than to the other APMVs. Furthermore, these comparisons provided evidence of extensive genome-wide divergence that supports the classification of the APMVs into nine separate serotypes. The structure of the F cleavage site does not appear to be a reliable indicator of virulence among APMV serotypes 2–9. The availability of sequence information for all known APMV serotypes will facilitate studies in epidemiology and vaccinology.
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Affiliation(s)
- Arthur S Samuel
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, United States of America.
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18
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Kumar S, Nayak B, Samuel AS, Xiao S, Collins PL, Samal SK. Complete genome sequence of avian paramyxovirus-3 strain Wisconsin: evidence for the existence of subgroups within the serotype. Virus Res 2010; 149:78-85. [PMID: 20079781 DOI: 10.1016/j.virusres.2009.12.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 12/29/2009] [Accepted: 12/31/2009] [Indexed: 12/27/2022]
Abstract
The complete consensus genome sequence was determined for avian paramyxovirus (APMV) serotype 3 strain Wisconsin. The genome is 16,182 nucleotides (nt) in length, consisting of six non-overlapping genes in the order of 3'-N-P/V/W-M-F-HN-L-5', with a 55-nt leader at its 3' end and a 681-nt trailer at its 5' end. Comparison of the APMV-3 strain Wisconsin nt and the aggregate predicted amino acid (aa) sequences with those of APMV-3 strain Netherlands revealed 67% and 78%, identity, respectively. The nt and aa sequence identities between the two APMV-3 strains were lower than between the two antigenic subgroups of human respiratory syncytial virus (81% and 88% identity, respectively) and the two subgroups of human metapeumovirus (80% and 90% identity, respectively). Reciprocal cross-hemagglutination inhibition and cross-neutralization assays using post-infection sera from chickens indicated that strains Wisconsin and Netherlands are highly related antigenically, with only a 2- to 4-fold difference in antibody reactivity between the homologous and heterologous strains. Taken together, our results indicate that the two APMV-3 strains represent a single serotype with two subgroups that differ substantially based on nt and aa sequences, but with only a modest antigenic difference.
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Affiliation(s)
- Sachin Kumar
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
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19
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Xiao S, Paldurai A, Nayak B, Subbiah M, Collins PL, Samal SK. Complete genome sequence of avian paramyxovirus type 7 (strain Tennessee) and comparison with other paramyxoviruses. Virus Res 2009; 145:80-91. [PMID: 19540277 PMCID: PMC3292215 DOI: 10.1016/j.virusres.2009.06.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2009] [Revised: 06/04/2009] [Accepted: 06/05/2009] [Indexed: 11/22/2022]
Abstract
The complete genome sequence of avian paramyxovirus serotype 7 (APMV-7) prototype strain dove/Tennessee/4/75 was determined. The genome size is 15,480 nucleotides (nt) long and follows the "rule of six". The genome contains six non-overlapping genes in the order of 3'-N-P/V/W-M-F-HN-L-5'. The 3'-leader and 5'-trailer sequences of the genome are 55 and 127nt long, respectively. The first 12nt of the leader and trailer sequences are complementary to each other. The viral genes are flanked by highly conserved gene-start (GS) and gene-end (GE) transcription signals, and in addition the 3'-leader sequence contains a sequence ((35)AAUUAUUUUUU(45)) that is identical to the GE signal present at two of the genes. The genes are separated by intergenic sequences (IGS) ranging between 11 and 70nt. The phosphoprotein (P) gene contains a conserved RNA editing site (3'-UUUUUCCC-5') presumed to be involved in the production of V and W proteins. The viral fusion (F) protein has a single basic amino acid at the putative cleavage site ((101)TLPSSR [see formula in text] F(107)); however, the virus did not require exogenous protease for in vitro replication. The virus grew in only a few established cell lines, indicating a restricted host range. Sequence alignment and phylogenetic analysis of the predicted amino acid sequence of APMV-7 proteins with the cognate proteins of the viruses of all five genera of the family Paramyxoviridae showed that APMV-7 is more closely related to APMV-2, -6, -8 than to APMV-1, -3, -4 and -9. The mean death time in embryonated chicken eggs was found to be more than 144h, indicating APMV-7 to be avirulent for chickens.
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Affiliation(s)
- Sa Xiao
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Anandan Paldurai
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Baibaswata Nayak
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Madhuri Subbiah
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
| | - Peter L. Collins
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, USA
| | - Siba K Samal
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, USA
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20
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Paldurai A, Subbiah M, Kumar S, Collins PL, Samal SK. Complete genome sequences of avian paramyxovirus type 8 strains goose/Delaware/1053/76 and pintail/Wakuya/20/78. Virus Res 2009; 142:144-53. [PMID: 19341613 DOI: 10.1016/j.virusres.2009.02.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 02/03/2009] [Accepted: 02/05/2009] [Indexed: 11/24/2022]
Abstract
Complete consensus genome sequences were determined for avian paramyxovirus type 8 (APMV-8) strains goose/Delaware/1053/76 (prototype strain) and pintail/Wakuya/20/78. The genome of each strain is 15,342 nucleotides (nt) long, which follows the "rule of six". The genome consists of six genes in the order of 3'-N-P/V/W-M-F-HN-L-5'. The genes are flanked on either side by conserved transcription start and stop signals, and have intergenic regions ranging from 1 to 30nt. The genome contains a 55nt leader region at the 3'-end and a 171nt trailer region at the 5'-end. Comparison of sequences of strains Delaware and Wakuya showed nucleotide identity of 96.8% at the genome level and amino acid identities of 99.3%, 96.5%, 98.6%, 99.4%, 98.6% and 99.1% for the predicted N, P, M, F, HN and L proteins, respectively. Both strains grew in embryonated chicken eggs and in primary chicken embryo kidney cells, and 293T cells. Both strains contained only a single basic residue at the cleavage activation site of the F protein and their efficiency of replication in vitro depended on and was augmented by, the presence of exogenous protease in most cell lines. Sequence alignment and phylogenic analysis of the predicted amino acid sequence of APMV-8 strain Delaware proteins with the cognate proteins of other available APMV serotypes showed that APMV-8 is more closely related to APMV-2 and -6 than to APMV-1, -3 and -4.
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Affiliation(s)
- Anandan Paldurai
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
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21
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Samuel AS, Kumar S, Madhuri S, Collins PL, Samal SK. Complete sequence of the genome of avian paramyxovirus type 9 and comparison with other paramyxoviruses. Virus Res 2009; 142:10-8. [PMID: 19185593 DOI: 10.1016/j.virusres.2008.12.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 12/22/2008] [Accepted: 12/24/2008] [Indexed: 11/17/2022]
Abstract
The complete genome consensus sequence was determined for avian paramyxovirus (APMV) serotype 9 prototype strain PMV-9/domestic Duck/New York/22/78. The genome is 15,438 nucleotides (nt) long and encodes six non-overlapping genes in the order of 3'-N-P/V/W-M-F-HN-L-5' with intergenic regions of 0-30 nt. The genome length follows the "rule of six" and contains a 55-nt leader sequence at the 3' end and a 47-nt trailer sequence at the 5' end. The cleavage site of the F protein is I-R-E-G-R-I downward arrowF, which does not conform to the conventional cleavage site of the ubiquitous cellular protease furin. The virus required exogenous protease for in vitro replication and grew only in a few established cell lines, indicating a restricted host range. Alignment and phylogenetic analysis of the predicted amino acid sequences of APMV-9 proteins with the cognate proteins of viruses of all five genera of family Paramyxoviridae showed that APMV-9 is more closely related to APMV-1 than to other APMVs. The mean death time in embryonated chicken eggs was found to be more than 120h, indicating APMV-9 to be avirulent for chickens.
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Affiliation(s)
- Arthur S Samuel
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, MD 20742, USA
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22
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Nayak B, Kumar S, Collins PL, Samal SK. Molecular characterization and complete genome sequence of avian paramyxovirus type 4 prototype strain duck/Hong Kong/D3/75. Virol J 2008; 5:124. [PMID: 18937854 PMCID: PMC2577636 DOI: 10.1186/1743-422x-5-124] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 10/20/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Avian paramyxoviruses (APMVs) are frequently isolated from domestic and wild birds throughout the world. All APMVs, except avian metapneumovirus, are classified in the genus Avulavirus of the family Paramyxoviridae. At present, the APMVs of genus Avulavirus are divided into nine serological types (APMV 1-9). Newcastle disease virus represents APMV-1 and is the most characterized among all APMV types. Very little is known about the molecular characteristics and pathogenicity of APMV 2-9. RESULTS As a first step towards understanding the molecular genetics and pathogenicity of APMV-4, we have sequenced the complete genome of APMV-4 strain duck/Hong Kong/D3/75 and determined its pathogenicity in embryonated chicken eggs. The genome of APMV-4 is 15,054 nucleotides (nt) in length, which is consistent with the "rule of six". The genome contains six non-overlapping genes in the order 3'-N-P/V-M-F-HN-L-5'. The genes are flanked on either side by highly conserved transcription start and stop signals and have intergenic sequences varying in length from 9 to 42 nt. The genome contains a 55 nt leader region at 3' end. The 5' trailer region is 17 nt, which is the shortest in the family Paramyxoviridae. Analysis of mRNAs transcribed from the P gene showed that 35% of the transcripts were edited by insertion of one non-templated G residue at an editing site leading to production of V mRNAs. No message was detected that contained insertion of two non-templated G residues, indicating that the W mRNAs are inefficiently produced in APMV-4 infected cells. The cleavage site of the F protein (DIPQR downward arrowF) does not conform to the preferred cleavage site of the ubiquitous intracellular protease furin. However, exogenous proteases were not required for the growth of APMV-4 in cell culture, indicating that the cleavage does not depend on a furin site. CONCLUSION Phylogenic analysis of the nucleotide sequences of viruses of all five genera of the family Paramyxoviridae showed that APMV-4 is more closely related to the APMVs than to other paramyxoviruses, reinforcing the classification of all APMVs in the genus Avulavirus of the family Paramyxoviridae.
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Affiliation(s)
- Baibaswata Nayak
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland, USA.
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Complete genome sequence of avian paramyxovirus type 3 reveals an unusually long trailer region. Virus Res 2008; 137:189-97. [PMID: 18691616 DOI: 10.1016/j.virusres.2008.07.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 07/05/2008] [Accepted: 07/07/2008] [Indexed: 12/27/2022]
Abstract
The complete genome sequence was determined for prototype parakeet/Netherlands/449/75 strain of avian paramyxovirus (APMV) serotype 3. The genome is 16,272 nucleotides (nt) in length, consisting of six non-overlapping genes in the order of 3'-N-P/V/W-M-F-HN-L-5', with intergenic regions of 31-63nt. APMV-3 genome follows the "rule of six" and is the largest among the avian paramyxoviruses reported to date, with a trailer region of 707nt, the longest in the family Paramyxoviridae. The cleavage site of F protein, A-R-P-R-G-R downward arrowL, does not conform to the preferred cleavage site of the ubiquitous cellular protease furin. Therefore, exogenous protease was needed for replication in vitro. Alignment and phylogenetic analysis of the predicted amino acid sequences of strain Netherlands proteins with the cognate proteins of viruses of all of the five genera of family Paramyxoviridae showed that APMV-3 strain Netherlands is more closely related to APMV-1 than APMV-6.
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Subbiah M, Xiao S, Collins PL, Samal SK. Complete sequence of the genome of avian paramyxovirus type 2 (strain Yucaipa) and comparison with other paramyxoviruses. Virus Res 2008; 137:40-8. [PMID: 18603323 DOI: 10.1016/j.virusres.2008.05.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 05/21/2008] [Accepted: 05/23/2008] [Indexed: 10/21/2022]
Abstract
The complete RNA genome sequence of avian paramyxovirus (APMV) serotype 2, strain Yucaipa isolated from chicken has been determined. With genome size of 14,904 nucleotides (nt), strain Yucaipa is consistent with the "rule of six" and is the smallest virus reported to date among the members of subfamily Paramyxovirinae. The genome contains six non-overlapping genes in the order 3'-N-P/V-M-F-HN-L-5'. The genes are flanked on either side by highly conserved transcription start and stop signals and have intergenic sequences varying in length from 3 to 23nt. The genome contains a 55nt leader sequence at 3' end and a 154nt trailer sequence at 5' end. Alignment and phylogenetic analysis of the predicted amino acid sequences of strain Yucaipa proteins with the cognate proteins of viruses of all of the five genera of family Paramyxoviridae showed that APMV-2 strain Yucaipa is more closely related to APMV-6 than APMV-1.
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Affiliation(s)
- Madhuri Subbiah
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD 20742 USA
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25
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Hoffman MA, Thorson LM, Vickman JE, Anderson JS, May NA, Schweitzer MN. Roles of human parainfluenza virus type 3 bases 13 to 78 in replication and transcription: identification of an additional replication promoter element and evidence for internal transcription initiation. J Virol 2007; 80:5388-96. [PMID: 16699019 PMCID: PMC1472146 DOI: 10.1128/jvi.00204-06] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genomic promoter of human parainfluenza virus type 3 (HPIV3) contains multiple cis-elements controlling transcription and replication. Previous work showed that regions 1 to 12 and 79 to 96 were critical in promoting replication of an HPIV3 minireplicon, while the intergenic sequence and N gene start signal (IS/Ngs, bases 49 to 61) were important for transcription. Because these data were collected primarily using point mutations, not every base from position 1 to 96 was analyzed, and some important control elements may have been missed. To clarify the role of bases 13 to 78 in transcription and replication, a series of mutations were made which collectively scanned this entire region. Mutation of bases 13 to 28 resulted in markedly decreased HPIV3 minireplicon replication, indicating these bases constitute an additional cis-element involved in the synthesis of the HPIV3 antigenomic RNA. The position dependence of the IS/Ngs was also examined. Analysis of mutants in which the IS/Ngs was shifted 5' or 3' showed that this segment could be moved without significantly disrupting transcription initiation. Additional mutants which contained two successive IS/Ngs segments were created to test whether the polymerase accessed the gene start signal by proceeding along the template 3' to 5' or by binding internally at the gene start signal. Based on analysis of the double gene start mutants, we propose a model of internal transcription initiation in which the polymerase enters the template at approximately the location of the natural N gene start but then scans the template bidirectionally to find a gene start signal and initiate transcription.
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Affiliation(s)
- Michael A Hoffman
- Department of Microbiology, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, USA.
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26
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Abstract
Pneumovirus infection remains a significant problem for both human and veterinary medicine. Both avian pneumovirus (aMPV, Turkey rhinotracheitis virus) and human metapneumovirus (hMPV) are pathogens of birds and humans, which are associated with respiratory tract infections. Based on their different genomic organization and low level of nucleotide (nt) and amino acid (aa) identity with paramyxoviruses in the genus Pneumovirus, aMPV and hMPV have been classified into a new genus referred to as Metapneumovirus. The advancement of our understanding of pneumovirus biology and pathogenesis of pneumovirus disease in specific natural hosts can provide us with strategies for vaccine formulations and combined antiviral and immunomodulatory therapies.
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Affiliation(s)
- Shobha Broor
- Department of Microbiology, All India Institute of Medical Sciences Hospital, New Delhi, India.
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27
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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.
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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
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28
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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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29
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Cowton VM, Fearns R. Evidence that the respiratory syncytial virus polymerase is recruited to nucleotides 1 to 11 at the 3' end of the nucleocapsid and can scan to access internal signals. J Virol 2005; 79:11311-22. [PMID: 16103183 PMCID: PMC1193587 DOI: 10.1128/jvi.79.17.11311-11322.2005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 3'-terminal end of the respiratory syncytial virus genomic RNA contains a 44-nucleotide leader (Le) region adjoining the gene start signal of the first gene. Previous mapping studies demonstrated that there is a promoter located at the 3' end of Le, which can signal initiation of antigenome synthesis. The aim of this study was to investigate the role of the 3' terminus of the RNA template in (i) promoter recognition and (ii) determining the initiation site for antigenome synthesis. A panel of minigenomes containing additional sequence at the 3' end of the Le were analyzed for their ability to direct antigenome and mRNA synthesis. Minigenomes containing heterologous extensions of 6 nucleotides or more were unable to support efficient RNA synthesis. However, the activity of a minigenome with a 56-nucleotide extension could be restored by insertion of Le nucleotides 1 to 11 or 1 to 13 at the 3' end, indicating that these nucleotides, in conjunction with the 3' terminus, are sufficient to recruit polymerase to the template. Northern blot and 5' rapid amplification of cDNA ends analysis of antigenome RNA indicated that antigenome initiation occurred at the first position of Le, irrespective of the terminal extension. This finding demonstrates that the 3' terminus of the RNA is not necessary for determining the antigenome initiation site. Data are presented which suggest that following recruitment to a promoter at the 3' end of Le, the polymerase is able to scan and respond to a promoter signal embedded within the RNA template.
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Affiliation(s)
- Vanessa M Cowton
- Division of Pathology and Neuroscience, University of Dundee, UK
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30
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Weik M, Enterlein S, Schlenz K, Mühlberger E. The Ebola virus genomic replication promoter is bipartite and follows the rule of six. J Virol 2005; 79:10660-71. [PMID: 16051858 PMCID: PMC1182658 DOI: 10.1128/jvi.79.16.10660-10671.2005] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work we investigated the cis-acting signals involved in replication of Ebola virus (EBOV) genomic RNA. A set of mingenomes with mutant 3' ends were generated and used in a reconstituted replication and transcription system. Our results suggest that the EBOV genomic replication promoter is bipartite, consisting of a first element located within the leader region of the genome and a second, downstream element separated by a spacer region. While proper spacing of the two promoter elements is a prerequisite for replication, the nucleotide sequence of the spacer is not important. Replication activity was only observed when six or a multiple of six nucleotides were deleted or inserted, while all other changes in length abolished replication completely. These data indicate that the EBOV replication promoter obeys the rule of six, although the genome length is not divisible by six. The second promoter element is located in the 3' nontranslated region of the first gene and consists of eight UN5 hexamer repeats, where N is any nucleotide. However, three consecutive hexamers, which could be located anywhere within the promoter element, were sufficient to support replication as long as the hexameric phase was preserved. By using chemical modification assays, we could demonstrate that nucleotides 5 to 44 of the EBOV leader are involved in the formation of a stable secondary structure. Formation of the RNA stem-loop occurred independently of the presence of the trailer, indicating that a panhandle structure is not formed between the 3' and 5' ends.
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Affiliation(s)
- Michael Weik
- Department of Virology, Philipps University Marburg, Robert-Koch-Str.17, 35037 Marburg, Germany
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31
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Kolakofsky D, Roux L, Garcin D, Ruigrok RWH. Paramyxovirus mRNA editing, the "rule of six" and error catastrophe: a hypothesis. J Gen Virol 2005; 86:1869-1877. [PMID: 15958664 DOI: 10.1099/vir.0.80986-0] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The order Mononegavirales includes three virus families that replicate in the cytoplasm: the Paramyxoviridae, composed of two subfamilies, the Paramyxovirinae and Pneumovirinae, the Rhabdoviridae and the Filoviridae. These viruses, also called non-segmented negative-strand RNA viruses (NNV), contain five to ten tandemly linked genes, which are separated by conserved junctional sequences that act as mRNA start and poly(A)/stop sites. For the NNV, downstream mRNA synthesis depends on termination of the upstream mRNA, and all NNV RNA-dependent RNA polymerases reiteratively copy ("stutter" on) a short run of template uridylates during transcription to polyadenylate and terminate their mRNAs. The RNA-dependent RNA polymerase of a subset of the NNV, all members of the Paramyxovirinae, also stutter in a very controlled fashion to edit their phosphoprotein gene mRNA, and Ebola virus, a filovirus, carries out a related process on its glycoprotein mRNA. Remarkably, all viruses that edit their phosphoprotein mRNA are also governed by the "rule of six", i.e. their genomes must be of polyhexameric length (6n+0) to replicate efficiently. Why these two seemingly unrelated processes are so tightly linked in the Paramyxovirinae has been an enigma. This paper will review what is presently known about these two processes that are unique to viruses of this subfamily, and will discuss whether this enigmatic linkage could be due to the phenomenon of RNA virus error catastrophe.
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Affiliation(s)
- Daniel Kolakofsky
- Department of Microbiology and Molecular Medicine, Université de Genève, Geneva, Switzerland
| | - Laurent Roux
- Department of Microbiology and Molecular Medicine, Université de Genève, Geneva, Switzerland
| | - Dominique Garcin
- Department of Microbiology and Molecular Medicine, Université de Genève, Geneva, Switzerland
| | - Rob W H Ruigrok
- Laboratoire de Virologie Moléculaire et Structurale, FRE 2854 CNRS-Université Joseph Fourier, Grenoble, France
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32
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Govindarajan D, Samal SK. Analysis of the complete genome sequence of avian metapneumovirus subgroup C indicates that it possesses the longest genome among metapneumoviruses. Virus Genes 2005; 30:331-3. [PMID: 15830150 DOI: 10.1007/s11262-005-6775-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Accepted: 10/24/2004] [Indexed: 10/25/2022]
Affiliation(s)
- Dhanasekaran Govindarajan
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, 8075 Greenmead Drive, College Park, MD 20742, USA
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33
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Marcos F, Ferreira L, Cros J, Park MS, Nakaya T, García-Sastre A, Villar E. Mapping of the RNA promoter of Newcastle disease virus. Virology 2005; 331:396-406. [PMID: 15629782 DOI: 10.1016/j.virol.2004.10.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2004] [Revised: 08/25/2004] [Accepted: 10/25/2004] [Indexed: 11/18/2022]
Abstract
The RNA promoters of the genome and antigenome of Newcastle disease virus (NDV) were studied by mutational analysis of their 3' terminal ends. Similarly to other paramyxoviruses, NDV RNA replication follows the rule of six, and the genomic and antigenomic promoters require two discontinuous regions: conserved region I (first 18 nucleotides) and conserved region II (nucleotides 73-90). Proper spacing between those regions and the phase of six in region II is critical for efficient RNA promoter activity. As expected, the gene start signal at the 3' end of the NDV genome was required for mRNA transcription, but not for RNA replication. Surprisingly, mutation of the polyadenylation signal in the 5' end did not affect gene expression transcription. Although the conserved region I of NDV (avulavirus) promoter appears to be more similar to that of Sendai virus (SeV) (respirovirus), conserved region II is analogous to that of rubulaviruses.
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Affiliation(s)
- Fernando Marcos
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Plaza Doctores de la Reina s/n, Edificio Departamental, lab. 108. Salamanca 37007, Spain
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34
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McGivern DR, Collins PL, Fearns R. Identification of internal sequences in the 3' leader region of human respiratory syncytial virus that enhance transcription and confer replication processivity. J Virol 2005; 79:2449-60. [PMID: 15681446 PMCID: PMC546581 DOI: 10.1128/jvi.79.4.2449-2460.2005] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2004] [Accepted: 09/23/2004] [Indexed: 11/20/2022] Open
Abstract
Previous studies of respiratory syncytial virus have shown that the 44-nucleotide (nt) leader (Le) region is sufficient to initiate RNA replication, producing antigenome RNA, and that the Le and adjoining gene start (GS) signal of the first gene are sufficient to initiate transcription, producing mRNA. A cis-acting element necessary for both transcription and replication was mapped within the first 11 nt at the 3' end of Le. In the present study the remainder of the Le region was mapped to identify sequences important for transcription and replication. A series of minigenomes with mutant Le sequences was generated, and their ability to direct transcription and replication was determined by Northern blot analysis, which examined full-length antigenome and mRNA, and by primer extension analysis, which examined antigenome and mRNA initiation. With regard to transcription, nt 36 to 43, located immediately upstream of the GS signal, were found to be necessary for optimal levels of mRNA synthesis, although the GS signal in conjunction with the 3'-terminal region of Le was sufficient to direct accurate mRNA synthesis initiation. With regard to replication, the first 15 nt of Le were found to be sufficient to direct initiation of antigenome synthesis, but nt 16 to 34 were required in addition for efficient encapsidation and production of full-length antigenome. Analysis of transcripts produced from di- and tricistronic minigenomes indicated that a significant proportion of abortive replicases continue RNA synthesis to the end of the first gene and then continue in a transcription mode along the remainder of the genome.
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Affiliation(s)
- David R McGivern
- Division of Pathology and Neuroscience, University of Dundee Medical School, Ninewells Hospital, Dundee DD1 9SY, UK
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35
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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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36
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Abstract
"Reverse genetics" or de novo synthesis of nonsegmented negative-sense RNA viruses (Mononegavirales) from cloned cDNA has become a reliable technique to study this group of medically important viruses. Since the first generation of a negative-sense RNA virus entirely from cDNA in 1994, reverse genetics systems have been established for members of most genera of the Rhabdo-, Paramyxo-, and Filoviridae families. These systems are based on intracellular transcription of viral full-length RNAs and simultaneous expression of viral proteins required to form the typical viral ribonucleoprotein complex (RNP). These systems are powerful tools to study all aspects of the virus life cycle as well as the roles of virus proteins in virus-host interplay and pathogenicity. In addition, recombinant viruses can be designed to have specific properties that make them attractive as biotechnological tools and live vaccines.
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Affiliation(s)
- K K Conzelmann
- Max von Pettenkofer-Institut and Genzentrum, Ludwig-Maximilians-Universität München, Munich, Germany.
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37
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Whelan SPJ, Barr JN, Wertz GW. Transcription and replication of nonsegmented negative-strand RNA viruses. Curr Top Microbiol Immunol 2004; 283:61-119. [PMID: 15298168 DOI: 10.1007/978-3-662-06099-5_3] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The nonsegmented negative-strand (NNS) RNA viruses of the order Mononegavirales include a wide variety of human, animal, and plant pathogens. The NNS RNA genomes of these viruses are templates for two distinct RNA synthetic processes: transcription to generate mRNAs and replication of the genome via production of a positive-sense antigenome that acts as template to generate progeny negative-strand genomes. The four virus families within the Mononegavirales all express the information encoded in their genomes by transcription of discrete subgenomic mRNAs. The key feature of transcriptional control in the NNS RNA viruses is entry of the virus-encoded RNA-dependent RNA polymerase at a single 3' proximal site followed by obligatory sequential transcription of the linear array of genes. Levels of gene expression are primarily regulated by position of each gene relative to the single promoter and also by cis-acting sequences located at the beginning and end of each gene and at the intergenic junctions. Obligatory sequential transcription dictates that termination of each upstream gene is required for initiation of downstream genes. Therefore, termination is a means to regulate expression of individual genes within the framework of a single transcriptional promoter. By engineering either whole virus genomes or subgenomic replicon derivatives, elements important for signaling transcript initiation, 5' end modification, 3' end polyadenylation, and transcription termination have been identified. Although the diverse families of NNS RNA virus use different sequences to control these processes, transcriptional termination is a common theme in controlling gene expression and overall transcriptional regulation is key in controlling the outcome of viral infection. The latest models for control of replication and transcription are discussed.
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Affiliation(s)
- S P J Whelan
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
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38
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Keller MA, Parks GD. Positive- and negative-acting signals combine to determine differential RNA replication from the paramyxovirus simian virus 5 genomic and antigenomic promoters. Virology 2003; 306:347-58. [PMID: 12642107 DOI: 10.1016/s0042-6822(02)00071-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The cis-acting signals found at the 3' ends of the genomic and antigenomic RNAs are a major factor determining the level of paramyxovirus RNA replication from each promoter. Using a minigenome system that reconstitutes SV5 RNA synthesis from cDNA-derived components, we show here that the genomic promoter (GP) for the paramyxovirus SV5 directs RNA replication approximately 14-fold lower than that seen from the antigenomic promoter (AGP). The goal of this study was to identify cis-acting signals responsible for differential levels of RNA replication from the SV5 GP and AGP. We have previously shown that the SV5 AGP contains three sequence-dependent elements (CRI, CRII, and Region III) that are separated by sequence-independent spacer regions. Minigenomes containing chimeric promoters were constructed to test the hypothesis that transfer of discrete cis-acting AGP elements to the GP could confer higher replication properties to the GP. Minigenomes containing a substitution of the AGP CRI, CRII, or Region III elements alone in place of the corresponding GP sequences did not show enhanced levels of RNA replication. However, transfer of both the AGP 3' terminal CRI and Region III elements into the corresponding sites of the GP led to a minigenome which replicated to approximately 40% of the levels seen with the AGP. This enhanced RNA replication from the GP was further increased up to AGP levels by also including the intervening AGP segment (bases 20-50) located between CRI and Region III. Importantly, transfer of nonviral sequences in place of GP bases 20-50 also increased RNA replication to levels approaching that of the AGP, but only in the context of the AGP CRI and Region III substitutions. These data indicate that differential levels of RNA replication from the SV5 GP and AGP are due to a combination of positive-acting signals in the AGP (CRI and Region III) and a negative-acting signal in the GP (bases 20-50). Possible functions for the SV5 promoter elements in determining RNA replication levels are proposed.
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Affiliation(s)
- Michael A Keller
- Department of Microbiology and Immunology, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157-1064, USA
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39
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Neumann G, Whitt MA, Kawaoka Y. A decade after the generation of a negative-sense RNA virus from cloned cDNA - what have we learned? J Gen Virol 2002; 83:2635-2662. [PMID: 12388800 DOI: 10.1099/0022-1317-83-11-2635] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Since the first generation of a negative-sense RNA virus entirely from cloned cDNA in 1994, similar reverse genetics systems have been established for members of most genera of the Rhabdo- and Paramyxoviridae families, as well as for Ebola virus (Filoviridae). The generation of segmented negative-sense RNA viruses was technically more challenging and has lagged behind the recovery of nonsegmented viruses, primarily because of the difficulty of providing more than one genomic RNA segment. A member of the Bunyaviridae family (whose genome is composed of three RNA segments) was first generated from cloned cDNA in 1996, followed in 1999 by the production of influenza virus, which contains eight RNA segments. Thus, reverse genetics, or the de novo synthesis of negative-sense RNA viruses from cloned cDNA, has become a reliable laboratory method that can be used to study this large group of medically and economically important viruses. It provides a powerful tool for dissecting the virus life cycle, virus assembly, the role of viral proteins in pathogenicity and the interplay of viral proteins with components of the host cell immune response. Finally, reverse genetics has opened the way to develop live attenuated virus vaccines and vaccine vectors.
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Affiliation(s)
- Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Drive West, Madison, WI 53706, USA1
| | - Michael A Whitt
- Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, TN, USA2
| | - Yoshihiro Kawaoka
- CREST, Japan Science and Technology Corporation, Japan4
- Institute of Medical Science, University of Tokyo, Tokyo, Japan3
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Drive West, Madison, WI 53706, USA1
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40
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Iseni F, Baudin F, Garcin D, Marq JB, Ruigrok RWH, Kolakofsky D. Chemical modification of nucleotide bases and mRNA editing depend on hexamer or nucleoprotein phase in Sendai virus nucleocapsids. RNA (NEW YORK, N.Y.) 2002; 8:1056-1067. [PMID: 12212849 PMCID: PMC1370316 DOI: 10.1017/s1355838202029977] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The minus-strand genome of Sendai virus is an assembly of the nucleocapsid protein (N) and RNA, in which each N subunit is associated with precisely 6 nt. Only genomes that are a multiple of 6 nt long replicate efficiently or are found naturally, and their replication promoters contain sequence elements with hexamer repeats. Paramyxoviruses that are governed by this hexamer rule also edit their P gene mRNA during its synthesis, by G insertions, via a controlled form of viral RNA polymerase "stuttering" (pseudo-templated transcription). This stuttering is directed by a cis-acting sequence (3' UNN UUUUUU CCC), whose hexamer phase is conserved within each virus group. To determine whether the hexamer phase of a given nucleotide sequence within nucleocapsids affected its sensitivity to chemical modification, and whether hexamer phase of the mRNA editing site was important for the editing process, we prepared a matched set of viruses in which a model editing site was displaced 1 nt at a time relative to the genome ends. The relative abilities of these Sendai viruses to edit their mRNAs in cell culture infections were examined, and the ability of DMS to chemically modify the nucleotides of this cis-acting signal within resting viral nucleocapsids was also studied. Cytidines at hexamer phases 1 and 6 were the most accessible to chemical modification, whereas mRNA editing was most extensive when the stutter-site C was in positions 2 to 5. Apparently, the N subunit imprints the nucleotide sequence it is associated with, and affects both the initiation of viral RNA synthesis and mRNA editing. The N-subunit assembly thus appears to superimpose another code upon the genetic code.
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Affiliation(s)
- Frédéric Iseni
- Department of Genetics and Microbiology, University of Geneva School of Medicine, Centre Médicale Universitaire, Switzerland
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41
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Bhella D, Ralph A, Murphy LB, Yeo RP. Significant differences in nucleocapsid morphology within the Paramyxoviridae. J Gen Virol 2002; 83:1831-1839. [PMID: 12124447 DOI: 10.1099/0022-1317-83-8-1831] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleocapsid (N) proteins from representative viruses of three genera within the Paramyxoviridae were expressed in insect cells using recombinant baculoviruses. RNA-containing structures, which appear morphologically identical to viral nucleocapsids, were isolated and subsequently imaged under a transmission electron microscope. Analysis of these images revealed marked differences in nucleocapsid morphology among the genera investigated, most notably between viruses of the Paramyxovirinae and the Pneumovirinae subfamilies. Helical pitch measurements were made, revealing that measles virus (MV, a Morbillivirus within the subfamily Paramyxovirinae) N protein produces helices that adopt multiple conformations with varying degrees of flexibility, while that of the Rubulavirus simian virus type 5 (SV5, subfamily Paramyxovirinae) produces more rigid structures with a less heterogeneous pitch distribution. Nucleocapsids produced by respiratory syncytial virus (RSV, subfamily Pneumovirinae) appear significantly narrower than those of MV and SV5 and have a longer pitch than the most extended form of MV. In addition to helical nucleocapsids, ring structures were also produced, image analysis of which has demonstrated that rings assembled from MV N protein consist of 13 subunits. This is consistent with previous reports that Sendai virus nucleocapsids have 13.07 subunits per turn. It was determined, however, that SV5 subnucleocapsid rings have 14 subunits, while rings derived from the radically different RSV nucleocapsid have been found to contain predominantly 10 subunits.
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Affiliation(s)
- David Bhella
- Medical Research Council Virology Unit, Church Street, Glasgow G11 5JR, UK1
| | - Adam Ralph
- Medical Research Council Virology Unit, Church Street, Glasgow G11 5JR, UK1
| | - Lindsay B Murphy
- Medical Research Council Virology Unit, Church Street, Glasgow G11 5JR, UK1
| | - Robert P Yeo
- Medical Research Council Virology Unit, Church Street, Glasgow G11 5JR, UK1
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42
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Yunus AS, Khattar SK, Collins PL, Samal SK. Rescue of bovine respiratory syncytial virus from cloned cDNA: entire genome sequence of BRSV strain A51908. Virus Genes 2002; 23:157-64. [PMID: 11724268 DOI: 10.1023/a:1011888019966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Infectious bovine respiratory syncytial virus (BRSV) was produced by intracellular co-expression of five plasmid borne cDNAs, each under the control of a T7 RNA polymerase promoter. These separately encoded a full-length, genetically-marked copy of BRSV antigenome along with either BRSV or human respiratory syncytial virus (HRSV) support plasmids, which express N, P, L and M2-1 proteins. HEp2 cells were used in transfection and recombinant vaccinia virus (MVA-T7) provided T7 RNA polymerase to drive the transcription. The recovery of recombinant BRSV (rBRSV) was confirmed by immunological staining of plaques, restriction enzyme digestion and nucleotide sequencing of PCR fragments carrying the genetic markers from the rescued virus. The rBRSV was indistinguishable from its parental wild-type virus in its growth characteristics in cell culture. The present work has completed the entire genome sequence of BRSV strain A51908 (15,140 nt) and has also identified changes in sequence and growth characteristics in cell culture from the original BRSV strain A51908 laboratory isolate.
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Affiliation(s)
- A S Yunus
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park 20742, USA
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43
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Fearns R, Peeples ME, Collins PL. Mapping the transcription and replication promoters of respiratory syncytial virus. J Virol 2002; 76:1663-72. [PMID: 11799161 PMCID: PMC135899 DOI: 10.1128/jvi.76.4.1663-1672.2002] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An important, unresolved issue in mononegavirus biology is whether or not transcription is initiated by the same promoter as RNA replication. In this study, residues important for respiratory syncytial virus (RSV) transcription and RNA replication were identified by subjecting the first 26 nucleotides of genome RNA to saturation mutagenesis. This analysis was performed using a genome analog that allowed transcription and RNA replication to be dissociated from each other and monitored as independent events in an intracellular assay. This analysis showed that nucleotides 3C, 5C, 8U, 9U, 10U, and 11U were important for transcription and RNA replication. Additional nucleotides (1U, 2G, 6U, and 7U) were important for RNA replication, but not transcription. At position 4, G versus C or U augmented transcription and decreased replication, showing that the naturally occurring assignments in the genomic (4G) and antigenomic (4U) promoters are optimal for transcription and RNA replication, respectively. These data show that RSV transcription and RNA replication each involve a cis-acting signal at the very 3" end of the genome. This signal appears to contain a minimum, common element that functions in both transcription and RNA replication, defined by those substitutions that had similar effects on the two processes. Apart from these common nucleotides, other positions were involved in RNA replication but not transcription or had different effects on the two processes. This indicates that the promoters for transcription and replication involve overlapping sets of nucleotides at the very 3" end of the genome and provides evidence that the nucleotide preferences for the two processes are not identical.
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Affiliation(s)
- Rachel Fearns
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0720, USA
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44
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Abstract
The "rule of six" stipulates that the Paramyxovirus RNA polymerase efficiently replicates only viral genomes counting 6n + 0 nucleotides. Because the nucleocapsid proteins (N) interact with 6 nucleotides, an exact nucleotide-N match at the RNA 3'-OH end (3'-OH congruence) may be required for recognition of an active replication promoter. Alternatively, assuming that the six positions for the interaction of N with the nucleotides are not equivalent, the nucleotide position relative to N may be critical (N phase context). The replication abilities of various minireplicons, designed so that the 3'-OH congruence could be discriminated from the N phase context, were studied. The results strongly suggest that the application of the rule of six depends on the recognition of nucleotides positioned in the proper N phase context.
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Affiliation(s)
- D Vulliémoz
- Department of Genetics and Microbiology, University of Geneva Medical School, CMU, CH-1211 Geneva 4, Switzerland
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45
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Keller MA, Murphy SK, Parks GD. RNA replication from the simian virus 5 antigenomic promoter requires three sequence-dependent elements separated by sequence-independent spacer regions. J Virol 2001; 75:3993-8. [PMID: 11264390 PMCID: PMC114892 DOI: 10.1128/jvi.75.8.3993-3998.2001] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have previously shown for the paramyxovirus simian virus 5 (SV5) that a functional promoter for RNA replication requires proper spacing between two discontinuous elements: a 19-base segment at the 3' terminus (conserved region I [CRI]) and an 18-base internal region (CRII) that is contained within the coding region of the L protein gene. In the work described here, we have used a reverse-genetics system to determine if the 53-base segment between CRI and CRII contains additional sequence-specific signals required for optimal replication or if this segment functions solely as a sequence-independent spacer region. A series of copyback defective interfering minigenome analogs were constructed to contain substitutions of nonviral sequences in place of bases 21 to 72 of the antigenomic promoter, and the relative level of RNA replication was measured by Northern blot analysis. The results from our mutational analysis indicate that in addition to CRI and CRII, optimal replication from the SV5 antigenomic promoter requires a third sequence-dependent element located 51 to 66 bases from the 3' end of the RNA. Minigenome RNA replication was not affected by changes in the either the position of this element in relation to CRI and CRII or the predicted hexamer phase of NP encapsidation. Thus, optimal RNA replication from the SV5 antigenomic promoter requires three sequence-dependent elements, CRI, CRII and bases 51 to 66.
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Affiliation(s)
- M A Keller
- Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157-1064, USA
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Fearns R, Collins PL, Peeples ME. Functional analysis of the genomic and antigenomic promoters of human respiratory syncytial virus. J Virol 2000; 74:6006-14. [PMID: 10846082 PMCID: PMC112097 DOI: 10.1128/jvi.74.13.6006-6014.2000] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The promoters involved in transcription and RNA replication by respiratory syncytial virus (RSV) were examined by using a plasmid-based minireplicon system. The 3' ends of the genome and antigenome, which, respectively, contain the 44-nucleotide (nt) leader (Le) and 155-nt trailer-complement (TrC) regions, should each contain a promoter for RNA replication. The 3' genome end also should have the promoter for transcription. Substitution for the Le with various lengths of TrC demonstrated that the 3'-terminal 36 nt of TrC are sufficient for extensive (but not maximal) replication and that when juxtaposed with a transcription gene-start (GS) signal, this sequence was also able to direct transcription. It was also shown that the region of Le immediately preceding the GS signal of the first gene could be deleted with either no effect or with a slight decrease in transcription initiation. Thus, the TrC is competent to direct transcription even though it does not do so in nature, and the partial sequence identity it shares with the 3' end of the genome likely represents the important elements of a conserved promoter active in both replication and transcription. Increasing the length of the introduced TrC sequence incrementally to 147 nt resulted in a fourfold increase in replication and a nearly complete inhibition of transcription. These two effects were unrelated, implying that transcription and replication are not interconvertible processes mediated by a common polymerase, but rather are independent processes. The increase in replication was specific to the TrC sequence, implying the presence of a nonessential, replication-enhancing cis-acting element. In contrast, the inhibitory effect on transcription was due solely to the altered spacing between the 3' end of the genome and GS signal, which implies that the transcriptase recognizes the first GS signal as a promoter element. Neither the enhancement of replication nor the inhibition of transcription was due to increased base-pairing potential between the 3' and 5' ends. The relative strengths of the Le and TrC promoters for directing RNA synthesis were compared and found to be very similar. Thus, these findings highlighted a high degree of functional similarity between the RSV antigenomic and genomic promoters, but provided a further distinction between promoter requirements for transcription and replication.
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Affiliation(s)
- R Fearns
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892-0720, USA
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47
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Hoffman MA, Banerjee AK. Precise mapping of the replication and transcription promoters of human parainfluenza virus type 3. Virology 2000; 269:201-11. [PMID: 10725212 DOI: 10.1006/viro.2000.0223] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The terminal RNA regions of the genomic and antigenomic RNAs of the paramyxoviruses and rhabdoviruses are known to contain sequences essential for directing RNA replication and transcription. The 3' terminus (leader region) of the negative-sense, genomic RNA of the rhabdoviruses and paramyxoviruses is known as the leader (Le) promoter and directs synthesis of positive-sense replication and transcription products. The 3' terminus of the antigenome is termed the trailer complementary (TrC) promoter and directs the synthesis of genomic RNA. By creating mutations in the corresponding regions of an HPIV3 minireplicon in which the viral protein coding sequences were replaced by the luciferase gene, we were able to precisely define the elements of the leader promoter involved in directing positive-strand replication of HPIV3. Nucleotides 1 through 12 (from the terminus) formed a domain critical for replication. The region from nucleotides 13 through 55 was important but not crucial for replication, while G residues at positions 79, 85, and 91 comprised another domain critical for replication. It was also shown that the TrC promoter is similar, though not identical, to the Le promoter. Nucleotides 1 through 12 of the TrC promoter were critical for synthesis of genomic RNA, though specific positions behaved differently from the corresponding positions of the Le promoter. While many of these mutations could not be analyzed for transcription because they completely abrogated genomic RNA synthesis (the template for transcription), we were surprised to find that no mutations in the leader promoter which decreased replication had any significant effect on transcription. However, mutations in the intergenic sequence and gene start signal following the leader and preceding the luciferase message severely decreased transcription, but not replication.
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MESH Headings
- Base Sequence
- Gene Expression Regulation, Viral/genetics
- Genes, Reporter/genetics
- Genome, Viral
- HeLa Cells
- Humans
- Mutation/genetics
- Parainfluenza Virus 3, Human/genetics
- Physical Chromosome Mapping
- Promoter Regions, Genetic/genetics
- RNA, Complementary/analysis
- RNA, Complementary/biosynthesis
- RNA, Complementary/genetics
- RNA, Messenger/analysis
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Viral/analysis
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- Replication Origin/genetics
- Replicon
- Sequence Alignment
- Templates, Genetic
- Transcription, Genetic/genetics
- Transfection
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Affiliation(s)
- M A Hoffman
- Department of Virology, Lerner Research Institute, Cleveland, OH 44195, USA
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48
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Peeples ME, Collins PL. Mutations in the 5' trailer region of a respiratory syncytial virus minigenome which limit RNA replication to one step. J Virol 2000; 74:146-55. [PMID: 10590101 PMCID: PMC111523 DOI: 10.1128/jvi.74.1.146-155.2000] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 3' termini of the genomic and antigenomic RNAs of human respiratory syncytial virus (RSV) are identical at 10 of the first 11 nucleotide positions and 21 of the first 26 positions. These conserved 3'-terminal sequences are thought to contain the genomic and antigenomic promoters. Furthermore, the complement of each conserved sequence (i.e., the 5' end of the RNA it encodes) might contain an encapsidation signal. Using an RSV minigenome system, we individually mutated each of the last seven nucleotides in the 5' trailer region of the genome. We analyzed effects of these mutations on encapsidation of the T7 polymerase-transcribed negative-sense genome, its ability to function as a template for RSV-driven synthesis of positive-sense antigenome and mRNA, and the ability of this antigenome to be encapsidated and to function as template for the synthesis of more genome. As a technical complication, mutations in the last five nucleotides of the trailer region were found to affect the efficiency of the adjoining T7 promoter over more than a 10-fold range, even though three nonviral G residues had been included between the core promoter and the trailer to maximize the efficiency of promoter activity. This was controlled in all experiments by monitoring the levels of total and encapsidated genome. The efficiency of encapsidation of the T7 polymerase-transcribed genome was not affected by any of the trailer mutations. Furthermore, neither the efficiency of positive-sense RNA synthesis from the genome nor the efficiency of encapsidation of the encoded antigenome was affected by the mutations. However, nucleotide substitution at positions 2, 3, 6, or 7 relative to the 5' end of the trailer blocked the production of progeny genome, whereas substitution at positions 1 and 5 allowed a low level of genome production and substitutions at position 4 were tolerated. Position 4 is the only one of the seven positions examined that is not conserved between the 3' ends of genomic and antigenomic RNA. The mutations that blocked the synthesis of progeny genome thus limited RNA replication to one step, namely, the synthesis and encapsidation of antigenome. Restoration of terminal complementarity for one of the trailer mutants by making a compensatory mutation in the leader region did not restore synthesis of genomic RNA, confirming that its loss was not due to reduced terminal complementarity. Interestingly, this leader mutation appeared to prevent antigenome synthesis with only a slight effect on mRNA synthesis, apparently providing a dissociation between these two synthetic activities. Genomes in which the terminal 24 or 325 nucleotides of the trailer have been deleted were competent for encapsidation and the synthesis of mRNA and antigenomic RNA, further confirming that terminal complementarity was not required for these functions.
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Affiliation(s)
- M E Peeples
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0720, USA
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Abstract
Molecular studies on the replication of paramyxoviruses have undergone a revolution in recent years due to the development of techniques that permit the manipulation of their genomes as cDNA. This has led to new information on the structure-function organization of the viral proteins involved in genome expression, as well as dissection of the cis-acting template sequences that regulate transcription and replication. Studies using recombinant viruses have also provided new insights into the role of the accessory proteins (V, C, M1/M2) in both for virus growth in cultured cells and pathogenesis in animals.
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Affiliation(s)
- J Curran
- Department of Genetics and Microbiology, University of Geneva Medical School (CMU), Switzerland
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50
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Collins PL, Whitehead SS, Bukreyev A, Fearns R, Teng MN, Juhasz K, Chanock RM, Murphy BR. Rational design of live-attenuated recombinant vaccine virus for human respiratory syncytial virus by reverse genetics. Adv Virus Res 1999; 54:423-51. [PMID: 10547682 DOI: 10.1016/s0065-3527(08)60374-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
RSV is a major cause of pediatric respiratory tract disease worldwide, but a vaccine is not yet available. It is now possible to prepare live infectious RSV completely from cDNA. This provides a method for introducing defined mutations into infectious virus, making possible the rational design of a live-attenuated vaccine virus for intranasal administration. This is particularly important for RSV, for which achieving the appropriate balance between attenuation and immunogenicity by conventional methods has proven elusive. We took advantage of the existence of a panel of biologically derived vaccine candidate viruses that were incompletely attenuated but well characterized biologically. The mutations in these viruses were identified by sequence analysis and characterized by insertion into recombinant virus, thereby providing a menu of known attenuating mutations. These included a series of amino acid point mutations, mostly in the L polymerase, and a nucleotide substitution in a transcription gene-start signal, a cis-acting RNA element. The second source of mutations was from experimental mutational analysis of recombinant virus and involves deletion of the NS1, NS2, or SH gene. We have reconstructed a previously tested, biologically derived attenuated virus, cpts248/404, in recombinant form and are now proceeding to introduce additional mutations from the menu to achieve stepwise increases in attenuation. The ability to modify the attenuation phenotype incrementally in a directed manner should result in an appropriate vaccine virus.
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Affiliation(s)
- P L Collins
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892-0720, USA
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