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Potgieter RL, Mwangi PN, Mogotsi MT, Uwimana J, Mutesa L, Muganga N, Murenzi D, Tusiyenge L, Seheri ML, Steele AD, Mwenda JM, Nyaga MM. Genomic Analysis of Rwandan G9P[8] Rotavirus Strains Pre- and Post-RotaTeq ® Vaccine Reveals Significant Distinct Sub-Clustering in a Post-Vaccination Cohort. Viruses 2023; 15:2321. [PMID: 38140562 PMCID: PMC10747556 DOI: 10.3390/v15122321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Although the introduction of rotavirus vaccines has substantially contributed to the reduction in rotavirus morbidity and mortality, concerns persist about the re-emergence of variant strains that might alter vaccine effectiveness in the long term. The G9 strains re-emerged in Africa during the mid-1990s and have more recently become predominant in some countries, such as Ghana and Zambia. In Rwanda, during the 2011 to 2015 routine surveillance period, G9P[8] persisted during both the pre- and post-vaccine periods. The pre-vaccination cohort was based on the surveillance period of 2011 to 2012, and the post-vaccination cohort was based on the period of 2013 to 2015, excluding 2014. The RotaTeq® vaccine that was first introduced in Rwanda in 2012 is genotypically heterologous to Viral Protein 7 (VP7) G9. This study elucidated the whole genome of Rwandan G9P[8] rotavirus strains pre- and post-RotaTeq® vaccine introduction. Fecal samples from Rwandan children under the age of five years (pre-vaccine n = 23; post-vaccine n = 7), conventionally genotyped and identified as G9P[8], were included. Whole-genome sequencing was then performed using the Illumina® MiSeq platform. Phylogenetic analysis and pair-wise sequence analysis were performed using MEGA6 software. Distinct clustering of three post-vaccination study strains was observed in all 11 gene segments, compared to the other Rwandan G9P[8] study strains. Specific amino acid differences were identified across the gene segments of these three 2015 post-vaccine strains. Important amino acid differences were identified at position N242S in the VP7 genome segment of the three post-vaccine G9 strains compared to the other G9 strains. This substitution occurs at a neutralization epitope site and may slightly affect protein interaction at that position. These findings indicate that the Rwandan G9P[8] strains revealed a distinct sub-clustering pattern among post-vaccination study strains circulating in Rwanda, with changes at neutralization epitopes, which may play a role in neutralization escape from vaccine candidates. This emphasizes the need for continuous whole-genome surveillance to better understand the evolution and epidemiology of the G9P[8] strains post-vaccination.
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Affiliation(s)
- Robyn-Lee Potgieter
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (R.-L.P.); (P.N.M.); (M.T.M.)
| | - Peter N. Mwangi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (R.-L.P.); (P.N.M.); (M.T.M.)
| | - Milton T. Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (R.-L.P.); (P.N.M.); (M.T.M.)
| | - Jeannine Uwimana
- Department of Pediatrics, Kigali University Teaching Hospital, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 4285, Rwanda; (J.U.); (L.M.); (N.M.); (D.M.); (L.T.)
| | - Leon Mutesa
- Department of Pediatrics, Kigali University Teaching Hospital, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 4285, Rwanda; (J.U.); (L.M.); (N.M.); (D.M.); (L.T.)
- Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 4285, Rwanda
| | - Narcisse Muganga
- Department of Pediatrics, Kigali University Teaching Hospital, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 4285, Rwanda; (J.U.); (L.M.); (N.M.); (D.M.); (L.T.)
| | - Didier Murenzi
- Department of Pediatrics, Kigali University Teaching Hospital, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 4285, Rwanda; (J.U.); (L.M.); (N.M.); (D.M.); (L.T.)
| | - Lisine Tusiyenge
- Department of Pediatrics, Kigali University Teaching Hospital, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 4285, Rwanda; (J.U.); (L.M.); (N.M.); (D.M.); (L.T.)
| | - Mapaseka L. Seheri
- Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa; (M.L.S.); (A.D.S.)
| | - A. Duncan Steele
- Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa; (M.L.S.); (A.D.S.)
| | - Jason M. Mwenda
- World Health Organization, Regional Office for Africa, Brazzaville P.O. Box 06, Congo;
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (R.-L.P.); (P.N.M.); (M.T.M.)
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Lipid metabolism is involved in the association of rotavirus viroplasms with endoplasmic reticulum membranes. Virology 2022; 569:29-36. [DOI: 10.1016/j.virol.2022.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/21/2022]
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Abid N, Pietrucci D, Salemi M, Chillemi G. New Insights into the Effect of Residue Mutations on the Rotavirus VP1 Function Using Molecular Dynamic Simulations. J Chem Inf Model 2020; 60:5011-5025. [PMID: 32786703 DOI: 10.1021/acs.jcim.0c00475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rotavirus group A remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious questions. Thirteen VP1 structures with mutations mapping to the RNA entry site were analyzed using molecular dynamics simulations, and the results were combined with the experimental findings reported previously. The results revealed structural fluctuations in the protein-protein recognition sites and in the bottleneck of the RNA entry site that may affect the interaction of different proteins and delay the initiation of the viral replication, respectively. Altogether, the structural analysis of VP1 in the region crucial for the initiation of the viral replication, mainly the bottleneck site, may boost efforts to develop antivirals, as they might complement the available vaccines.
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Affiliation(s)
- Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, 5000 Monastir, Tunisia.,High Institute of Biotechnology of Sidi Thabet, Department of Biotechnology, University Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
| | - Daniele Pietrucci
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Marco Salemi
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Emerging Pathogens Institute, University of Florida, P.O. Box 100009, Gainesville, Florida 32610-3633, United States
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, Via Giovanni Amendola, 122/O, 70126 Bari, Italy
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Abstract
Because of their replication mode and segmented dsRNA genome, homologous recombination is assumed to be rare in the rotaviruses. We analyzed 23,627 complete rotavirus genome sequences available in the NCBI Virus Variation database, and found 109 instances of homologous recombination, at least eleven of which prevailed across multiple sequenced isolates. In one case, recombination may have generated a novel rotavirus VP1 lineage. We also found strong evidence for intergenotypic recombination in which more than one sequence strongly supported the same event, particularly between different genotypes of segment 9, which encodes the glycoprotein, VP7. The recombined regions of many putative recombinants showed amino acid substitutions differentiating them from their major and minor parents. This finding suggests that these recombination events were not overly deleterious, since presumably these recombinants proliferated long enough to acquire adaptive mutations in their recombined regions. Protein structural predictions indicated that, despite the sometimes substantial amino acid replacements resulting from recombination, the overall protein structures remained relatively unaffected. Notably, recombination junctions appear to occur nonrandomly with hot spots corresponding to secondary RNA structures, a pattern seen consistently across segments. In total, we found strong evidence for recombination in nine of eleven rotavirus A segments. Only segments 7 (NSP3) and 11 (NSP5) did not show strong evidence of recombination. Collectively, the results of our computational analyses suggest that, contrary to the prevailing sentiment, recombination may be a significant driver of rotavirus evolution and may influence circulating strain diversity.
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Affiliation(s)
- Irene Hoxie
- Biology Department, Queens College of The City University of New York, 65-30 Kissena Blvd, Queens, NY 11367, USA.,The Graduate Center of The City University of New York, Biology Program, 365 5th Ave, New York, NY 10016, USA
| | - John J Dennehy
- Biology Department, Queens College of The City University of New York, 65-30 Kissena Blvd, Queens, NY 11367, USA.,The Graduate Center of The City University of New York, Biology Program, 365 5th Ave, New York, NY 10016, USA
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The Guanine Nucleotide Exchange Factor GBF1 Participates in Rotavirus Replication. J Virol 2019; 93:JVI.01062-19. [PMID: 31270230 DOI: 10.1128/jvi.01062-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 01/06/2023] Open
Abstract
Cellular and viral factors participate in the replication cycle of rotavirus. We report that the guanine nucleotide exchange factor GBF1, which activates the small GTPase Arf1 to induce COPI transport processes, is required for rotavirus replication since knocking down GBF1 expression by RNA interference or inhibiting its activity by treatment with brefeldin A (BFA) or Golgicide A (GCA) significantly reduces the yield of infectious viral progeny. This reduction in virus yield was related to a block in virus assembly, since in the presence of either BFA or GCA, the assembly of infectious mature triple-layered virions was significantly prevented and only double-layered particles were detected. We report that the catalytic activity of GBF1, but not the activation of Arf1, is essential for the assembly of the outer capsid of rotavirus. We show that both BFA and GCA, as well as interfering with the synthesis of GBF1, alter the electrophoretic mobility of glycoproteins VP7 and NSP4 and block the trimerization of the virus surface protein VP7, a step required for its incorporation into virus particles. Although a posttranslational modification of VP7 (other than glycosylation) could be related to the lack of trimerization, we found that NSP4 might also be involved in this process, since knocking down its expression reduces VP7 trimerization. In support, recombinant VP7 protein overexpressed in transfected cells formed trimers only when cotransfected with NSP4.IMPORTANCE Rotavirus, a member of the family Reoviridae, is the major cause of severe diarrhea in children and young animals worldwide. Despite significant advances in the characterization of the biology of this virus, the mechanisms involved in morphogenesis of the virus particle are still poorly understood. In this work, we show that the guanine nucleotide exchange factor GBF1, relevant for COPI/Arf1-mediated cellular vesicular transport, participates in the replication cycle of the virus, influencing the correct processing of viral glycoproteins VP7 and NSP4 and the assembly of the virus surface proteins VP7 and VP4.
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Malik MS, Bjørgen H, Dhamotharan K, Wessel Ø, Koppang EO, Di Cicco E, Hansen EF, Dahle MK, Rimstad E. Erythroid Progenitor Cells in Atlantic Salmon ( Salmo salar) May Be Persistently and Productively Infected with Piscine Orthoreovirus (PRV). Viruses 2019; 11:E824. [PMID: 31491892 PMCID: PMC6784031 DOI: 10.3390/v11090824] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 12/13/2022] Open
Abstract
Piscine orthoreovirus (PRV-1) can cause heart and skeletal muscle inflammation (HSMI) in farmed Atlantic salmon (Salmo salar). The virus targets erythrocytes in the acute peak phase, followed by cardiomyocytes, before the infection subsides into persistence. The persistent phase is characterized by high level of viral RNA, but low level of viral protein. The origin and nature of persistent PRV-1 are not clear. Here, we analyzed for viral persistence and activity in various tissues and cell types in experimentally infected Atlantic salmon. Plasma contained PRV-1 genomic dsRNA throughout an 18-week long infection trial, indicating that viral particles are continuously produced and released. The highest level of PRV-1 RNA in the persistent phase was found in kidney. The level of PRV-1 ssRNA transcripts in kidney was significantly higher than that of blood cells in the persistent phase. In-situ hybridization assays confirmed that PRV-1 RNA was present in erythroid progenitor cells, erythrocytes, macrophages, melano-macrophages and in some additional un-characterized cells in kidney. These results show that PRV-1 establishes a productive, persistent infection in Atlantic salmon and that erythrocyte progenitor cells are PRV target cells.
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Affiliation(s)
- Muhammad Salman Malik
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0454 Oslo, Norway.
| | - Håvard Bjørgen
- Department of Basic Science and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0454 Oslo, Norway.
| | - Kannimuthu Dhamotharan
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0454 Oslo, Norway.
| | - Øystein Wessel
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0454 Oslo, Norway.
| | - Erling Olaf Koppang
- Department of Basic Science and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0454 Oslo, Norway.
| | - Emiliano Di Cicco
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada.
| | - Elisabeth F Hansen
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0454 Oslo, Norway.
| | - Maria K Dahle
- Department of Fish Health, Norwegian Veterinary Institute, 0454 Oslo, Norway
| | - Espen Rimstad
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0454 Oslo, Norway.
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Contreras-Treviño HI, Reyna-Rosas E, León-Rodríguez R, Ruiz-Ordaz BH, Dinkova TD, Cevallos AM, Padilla-Noriega L. Species A rotavirus NSP3 acquires its translation inhibitory function prior to stable dimer formation. PLoS One 2017; 12:e0181871. [PMID: 28738064 PMCID: PMC5524322 DOI: 10.1371/journal.pone.0181871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/07/2017] [Indexed: 11/18/2022] Open
Abstract
Species A rotavirus non-structural protein 3 (NSP3) is a translational regulator that inhibits or, under some conditions, enhances host cell translation. NSP3 binds to the translation initiation factor eIF4G1 and evicts poly-(A) binding protein (PABP) from eIF4G1, thus inhibiting translation of polyadenylated mRNAs, presumably by disrupting the effect of PABP bound to their 3’-ends. NSP3 has a long coiled-coil region involved in dimerization that includes a chaperone Hsp90-binding domain (HS90BD). We aimed to study the role in NSP3 dimerization of a segment of the coiled-coil region adjoining the HS90BD. We used a vaccinia virus system to express NSP3 with point mutations in conserved amino acids in the coiled-coil region and determined the effects of these mutations on translation by metabolic labeling of proteins as well as on accumulation of stable NSP3 dimers by non-dissociating Western blot, a method that separates stable NSP3 dimers from the monomer/dimerization intermediate forms of the protein. Four of five mutations reduced the total yield of NSP3 and the formation of stable dimers (W170A, K171E, R173E and R187E:K191E), whereas one mutation had the opposite effects (Y192A). Treatment with the proteasome inhibitor MG132 revealed that stable NSP3 dimers and monomers/dimerization intermediates are susceptible to proteasome degradation. Surprisingly, mutants severely impaired in the formation of stable dimers were still able to inhibit host cell translation, suggesting that NSP3 dimerization intermediates are functional. Our results demonstrate that rotavirus NSP3 acquires its function prior to stable dimer formation and remain as a proteasome target throughout dimerization.
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Affiliation(s)
- Hugo I. Contreras-Treviño
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Edgar Reyna-Rosas
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Renato León-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Blanca H. Ruiz-Ordaz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tzvetanka D. Dinkova
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana M. Cevallos
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis Padilla-Noriega
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- * E-mail:
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8
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Rotavirus Controls Activation of the 2'-5'-Oligoadenylate Synthetase/RNase L Pathway Using at Least Two Distinct Mechanisms. J Virol 2015; 89:12145-53. [PMID: 26401041 DOI: 10.1128/jvi.01874-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/17/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED The innate immune response is the first line of defense of the host cell against a viral infection. In turn, viruses have evolved a wide variety of strategies to hide from, and to directly antagonize, the host innate immune pathways. One of these pathways is the 2'-5'-oligoadenylate synthetase (OAS)/RNase L pathway. OAS is activated by double-stranded RNA (dsRNA) to produce 2'-5' oligoadenylates, which are the activators of RNase L; this enzyme degrades viral and cellular RNAs, restricting viral infection. It has been recently found that the carboxy-terminal domain (CTD) of rotavirus VP3 has a 2'-5'-phosphodiesterase (PDE) activity that is able to functionally substitute for the PDE activity of the mouse hepatitis virus ns2 protein. This particular phosphodiesterase cleaves the 2'-5'-phosphodiester bond of the oligoadenylates, antagonizing the OAS/RNase L pathway. However, whether this activity of VP3 is relevant during the replication cycle of rotavirus is not known. Here, we demonstrate that after rotavirus infection the OAS/RNase L complex becomes activated; however, the virus is able to control its activity using at least two distinct mechanisms. A virus-cell interaction that occurs during or before rotavirus endocytosis triggers a signal that prevents the early activation of RNase L, while later on the control is taken by the newly synthesized VP3. Cosilencing the expression of VP3 and RNase L in infected cells yields viral infectious particles at levels similar to those obtained in control infected cells, where no genes were silenced, suggesting that the capping activity of VP3 is not essential for the formation of infectious viral particles. IMPORTANCE Rotaviruses represent an important cause of severe gastroenteritis in the young of many animal species, including humans. In this work, we have found that the OAS/RNase L pathway is activated during rotavirus infection, but the virus uses two different strategies to prevent the deleterious effects of this innate immune response of the cell. Early during virus entry, the initial interactions of the viral particle with the cell result in the inhibition of RNase L activity during the first hours of the infection. Later on, once viral proteins are synthesized, the phosphodiesterase activity of VP3 degrades the cellular 2'-5'-oligoadenylates, which are potent activators of RNase L, preventing its activation. This work demonstrates that the OAS/RNase L pathway plays an important role during infection and that the phosphodiesterase activity of VP3 is relevant during the replication cycle of the virus.
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Boudreaux CE, Kelly DF, McDonald SM. Electron microscopic analysis of rotavirus assembly-replication intermediates. Virology 2015; 477:32-41. [PMID: 25635339 PMCID: PMC4359669 DOI: 10.1016/j.virol.2015.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/14/2014] [Accepted: 01/05/2015] [Indexed: 11/24/2022]
Abstract
Rotaviruses (RVs) replicate their segmented, double-stranded RNA genomes in tandem with early virion assembly. In this study, we sought to gain insight into the ultrastructure of RV assembly-replication intermediates (RIs) using transmission electron microscopy (EM). Specifically, we examined a replicase-competent, subcellular fraction that contains all known RV RIs. Three never-before-seen complexes were visualized in this fraction. Using in vitro reconstitution, we showed that ~15-nm doughnut-shaped proteins in strings were nonstructural protein 2 (NSP2) bound to viral RNA transcripts. Moreover, using immunoaffinity-capture EM, we revealed that ~20-nm pebble-shaped complexes contain the viral RNA polymerase (VP1) and RNA capping enzyme (VP3). Finally, using a gel purification method, we demonstrated that ~30–70-nm electron-dense, particle-shaped complexes represent replicase-competent core RIs, containing VP1, VP3, and NSP2 as well as capsid proteins VP2 and VP6. The results of this study raise new questions about the interactions among viral proteins and RNA during the concerted assembly-replicase process.
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Affiliation(s)
- Crystal E Boudreaux
- Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA, USA
| | - Deborah F Kelly
- Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA, USA
| | - Sarah M McDonald
- Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA, USA; Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, USA.
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10
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Gridley CL, Patton JT. Regulation of rotavirus polymerase activity by inner capsid proteins. Curr Opin Virol 2014; 9:31-8. [PMID: 25243800 DOI: 10.1016/j.coviro.2014.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 08/28/2014] [Accepted: 08/29/2014] [Indexed: 11/16/2022]
Abstract
Rotavirus, a cause of pediatric gastroenteritis, has a genome consisting of 11 segments of double-stranded (ds)RNA surrounded by a triple-layered protein capsid. The rotavirus RNA-dependent RNA polymerase, VP1, synthesizes both dsRNA and plus-strand RNA (+RNA) within subviral particles. Structural analyses of the rotavirus capsid and polymerase, combined with functional studies of purified capsid proteins, indicate that the inner capsid protein controls the initiation of RNA synthesis by VP1. Whether VP1 directs dsRNA versus +RNA synthesis may be regulated by the impact of the viral RNA capping enzyme on the position of the polymerase plug, a flexible element that inserts into one of the polymerase's RNA exit tunnels. This review discusses recent findings and ideas into the mechanisms used by rotavirus capsid proteins to control the activities of its viral polymerase and to coordinate RNA synthesis with the assembly of virus particles.
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Affiliation(s)
- Chelsea L Gridley
- Rotavirus Molecular Biology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, United States
| | - John T Patton
- Rotavirus Molecular Biology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, United States.
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11
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Li W, Zhang Y, Kao CC. The classic swine fever virus (CSFV) core protein can enhance de novo-initiated RNA synthesis by the CSFV polymerase NS5B. Virus Genes 2014; 49:106-15. [DOI: 10.1007/s11262-014-1080-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/23/2014] [Indexed: 12/28/2022]
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12
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Abstract
Capsid proteins are obligatory components of infectious virions. Their primary structural function is to protect viral genomes during entry and exit from host cells. Evidence suggests that these proteins can also modulate the activity and specificity of viral replication complexes. More recently, it has become apparent that they play critical roles at the virus–host interface. Here, we discuss how capsid proteins of RNA viruses interact with key host cell proteins and pathways to modulate cell physiology in order to benefit virus replication. Capsid–host cell interactions may also have implications for viral disease. Understanding how capsids regulate virus–host interactions may lead to the development of novel antiviral therapies based on targeting the activities of cellular proteins.
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Affiliation(s)
- Steven Willows
- Department of Cell Biology, University of Alberta, 5–14 Medical Sciences Building, Edmonton, T6G 2H7, Canada
| | - Shangmei Hou
- Department of Cell Biology, University of Alberta, 5–14 Medical Sciences Building, Edmonton, T6G 2H7, Canada
| | - Tom C Hobman
- Department of Li Ka Shing Institute of Virology, University of Alberta, 5–14 Medical Sciences Building, Edmonton, T6G 2H7, Canada
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Generation of genetically stable recombinant rotaviruses containing novel genome rearrangements and heterologous sequences by reverse genetics. J Virol 2013; 87:6211-20. [PMID: 23536662 DOI: 10.1128/jvi.00413-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The rotavirus (RV) genome consists of 11 segments of double-stranded RNA (dsRNA). Typically, each segment contains 5' and 3' untranslated regions (UTRs) that flank an open reading frame (ORF) encoding a single protein. RV variants with segments of atypical size owing to sequence rearrangements have been described. In many cases, the rearrangement originates from a partial head-to-tail sequence duplication that initiates after the stop codon of the ORF, leaving the protein product of the segment unaffected. To probe the limits of the RV genome to accommodate additional genetic sequence, we used reverse genetics to insert duplications (analogous to synthetic rearrangements) and heterologous sequences into the 3' UTR of the segment encoding NSP2 (gene 8). The approach allowed the recovery of recombinant RVs that contained sequence duplications (up to 200 bp) and heterologous sequences, including those for FLAG, the hepatitis C virus E2 epitope, and the internal ribosome entry site of cricket paralysis virus. The recombinant RVs grew to high titer (>10(7) PFU/ml) and remained genetically stable during serial passage. Despite their longer 3' UTRs, rearranged RNAs of recombinant RVs expressed wild-type levels of protein in vivo. Competitive growth experiments indicated that, unlike RV segments with naturally occurring sequence duplications, genetically engineered segments were less efficiently packaged into progeny viruses. Thus, features of naturally occurring rearranged segments, other than their increased length, contribute to their enhanced packaging phenotype. Our results define strategies for developing recombinant RVs as expression vectors, potentially leading to next-generation RV vaccines that induce protection against other infectious agents.
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Arnold MM, Sen A, Greenberg HB, Patton JT. The battle between rotavirus and its host for control of the interferon signaling pathway. PLoS Pathog 2013; 9:e1003064. [PMID: 23359266 PMCID: PMC3554623 DOI: 10.1371/journal.ppat.1003064] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Viral pathogens must overcome innate antiviral responses to replicate successfully in the host organism. Some of the mechanisms viruses use to interfere with antiviral responses in the infected cell include preventing detection of viral components, perturbing the function of transcription factors that initiate antiviral responses, and inhibiting downstream signal transduction. RNA viruses with small genomes and limited coding space often express multifunctional proteins that modulate several aspects of the normal host response to infection. One such virus, rotavirus, is an important pediatric pathogen that causes severe gastroenteritis, leading to ∼450,000 deaths globally each year. In this review, we discuss the nature of the innate antiviral responses triggered by rotavirus infection and the viral mechanisms for inhibiting these responses.
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Affiliation(s)
- Michelle M. Arnold
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Adrish Sen
- Department of Medicine and Microbiology and Immunology, Stanford University, Stanford, California, and VA Palo Alto Health Care System, Palo Alto, California, United States of America
| | - Harry B. Greenberg
- Department of Medicine and Microbiology and Immunology, Stanford University, Stanford, California, and VA Palo Alto Health Care System, Palo Alto, California, United States of America
| | - John T. Patton
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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15
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The infectious bursal disease virus RNA-binding VP3 polypeptide inhibits PKR-mediated apoptosis. PLoS One 2012; 7:e46768. [PMID: 23056444 PMCID: PMC3467284 DOI: 10.1371/journal.pone.0046768] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 09/05/2012] [Indexed: 01/07/2023] Open
Abstract
Infectious bursal disease virus (IBDV) is an avian pathogen responsible for an acute immunosuppressive disease that causes major losses to the poultry industry. Despite having a bipartite dsRNA genome, IBDV, as well as other members of the Birnaviridae family, possesses a single capsid layer formed by trimers of the VP2 capsid protein. The capsid encloses a ribonucleoprotein complex formed by the genome associated to the RNA-dependent RNA polymerase and the RNA-binding polypeptide VP3. A previous report evidenced that expression of the mature VP2 IBDV capsid polypeptide triggers a swift programmed cell death response in a wide variety of cell lines. The mechanism(s) underlying this effect remained unknown. Here, we show that VP2 expression in HeLa cells activates the double-stranded RNA (dsRNA)-dependent protein kinase (PKR), which in turn triggers the phosphorylation of the eukaryotic initiation factor 2α (eIF2α). This results in a strong blockade of protein synthesis and the activation of an apoptotic response which is efficiently blocked by coexpression of a dominant negative PKR polypeptide. Our results demonstrate that coexpression of the VP3 polypeptide precludes phosphorylation of both PKR and eIF2α and the onset of programmed cell death induced by VP2 expression. A mutation blocking the capacity of VP3 to bind dsRNA also abolishes its capacity to prevent PKR activation and apoptosis. Further experiments showed that VP3 functionally replaces the host-range vaccinia virus (VACV) E3 protein, thus allowing the E3 deficient VACV deletion mutant WRΔE3L to grow in non-permissive cell lines. According to results presented here, VP3 can be categorized along with other well characterized proteins such us VACV E3, avian reovirus sigmaA, and influenza virus NS1 as a virus-encoded dsRNA-binding polypeptide with antiapoptotic properties. Our results suggest that VP3 plays a central role in ensuring the viability of the IBDV replication cycle by preventing programmed cell death.
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16
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Rotavirus-host cell interactions: an arms race. Curr Opin Virol 2012; 2:389-98. [PMID: 22658208 DOI: 10.1016/j.coviro.2012.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 05/02/2012] [Accepted: 05/08/2012] [Indexed: 12/21/2022]
Abstract
As obligate parasites, viruses depend on the synthetic machinery of the cell to translate their proteins and on the cell's energy and building blocks to replicate their genomes. Cells respond to virus invasions by eliciting diverse responses to eliminate the incoming parasitic agents. In turn, to establish a successful infection, viruses have developed different strategies to take over the cellular metabolic machinery and to cope with the defense mechanisms of the cell. The characterization of this battle has allowed the discovery of the different elements that viruses and cells have developed in the attempt to overcome the enemy. Here some of the strategies used by rotaviruses to hijack the protein synthesis apparatus of the cell to ensure the translation of their mRNAs, and to deal with the cellular stress and antiviral responses will be reviewed.
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17
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Uetrecht C, Heck AJR. Modern biomolecular mass spectrometry and its role in studying virus structure, dynamics, and assembly. Angew Chem Int Ed Engl 2011; 50:8248-62. [PMID: 21793131 PMCID: PMC7159578 DOI: 10.1002/anie.201008120] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Indexed: 01/04/2023]
Abstract
Over a century since its development, the analytical technique of mass spectrometry is blooming more than ever, and applied in nearly all aspects of the natural and life sciences. In the last two decades mass spectrometry has also become amenable to the analysis of proteins and even intact protein complexes, and thus begun to make a significant impact in the field of structural biology. In this Review, we describe the emerging role of mass spectrometry, with its different technical facets, in structural biology, focusing especially on structural virology. We describe how mass spectrometry has evolved into a tool that can provide unique structural and functional information about viral-protein and protein-complex structure, conformation, assembly, and topology, extending to the direct analysis of intact virus capsids of several million Dalton in mass. Mass spectrometry is now used to address important questions in virology ranging from how viruses assemble to how they interact with their host.
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Affiliation(s)
- Charlotte Uetrecht
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht (The Netherlands)
- Netherlands Proteomics Centre (The Netherlands)
- Present address: Molecular Biophysics, Uppsala University, Uppsala (Sweden)
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht (The Netherlands)
- Netherlands Proteomics Centre (The Netherlands)
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18
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Uetrecht C, Heck AJR. Moderne biomolekulare Massenspektrometrie und ihre Bedeutung für die Erforschung der Struktur, der Dynamik und des Aufbaus von Viren. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008120] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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McDonald SM, Patton JT. Assortment and packaging of the segmented rotavirus genome. Trends Microbiol 2011; 19:136-44. [PMID: 21195621 PMCID: PMC3072067 DOI: 10.1016/j.tim.2010.12.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 11/19/2010] [Accepted: 12/01/2010] [Indexed: 12/13/2022]
Abstract
The rotavirus (RV) genome comprises 11 segments of double-stranded RNA (dsRNA) and is contained within a non-enveloped, icosahedral particle. During assembly, a highly coordinated selective packaging mechanism ensures that progeny RV virions contain one of each genome segment. Cis-acting signals thought to mediate assortment and packaging are associated with putative panhandle structures formed by base-pairing of the ends of RV plus-strand RNAs (+RNAs). Viral polymerases within assembling core particles convert the 11 distinct +RNAs to dsRNA genome segments. It remains unclear whether RV +RNAs are assorted before or during encapsidation, and the functions of viral proteins during these processes are not resolved. However, as reviewed here, recent insights gained from the study of RV and two other segmented RNA viruses, influenza A virus and bacteriophage Φ6, reveal potential mechanisms of RV assortment and packaging.
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Affiliation(s)
- Sarah M McDonald
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-8026, USA
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20
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Broquet AH, Hirata Y, McAllister CS, Kagnoff MF. RIG-I/MDA5/MAVS are required to signal a protective IFN response in rotavirus-infected intestinal epithelium. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2011; 186:1618-26. [PMID: 21187438 DOI: 10.4049/jimmunol.1002862] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Rotavirus is a dsRNA virus that infects epithelial cells that line the surface of the small intestine. It causes severe diarrheal illness in children and ∼500,000 deaths per year worldwide. We studied the mechanisms by which intestinal epithelial cells (IECs) sense rotavirus infection and signal IFN-β production, and investigated the importance of IFN-β production by IECs for controlling rotavirus production by intestinal epithelium and virus excretion in the feces. In contrast with most RNA viruses, which interact with either retinoic acid-inducible gene I (RIG-I) or melanoma differentiation-associated gene 5 (MDA5) inside cells, rotavirus was sensed by both RIG-I and MDA5, alone and in combination. Rotavirus did not signal IFN-β through either of the dsRNA sensors TLR3 or dsRNA-activated protein kinase (PKR). Silencing RIG-I or MDA5, or their common adaptor protein mitochondrial antiviral signaling protein (MAVS), significantly decreased IFN-β production and increased rotavirus titers in infected IECs. Overexpression of laboratory of genetics and physiology 2, a RIG-I-like receptor that interacts with viral RNA but lacks the caspase activation and recruitment domains required for signaling through MAVS, significantly decreased IFN-β production and increased rotavirus titers in infected IECs. Rotavirus-infected mice lacking MAVS, but not those lacking TLR3, TRIF, or PKR, produced significantly less IFN-β and increased amounts of virus in the intestinal epithelium, and shed increased quantities of virus in the feces. We conclude that RIG-I or MDA5 signaling through MAVS is required for the activation of IFN-β production by rotavirus-infected IECs and has a functionally important role in determining the magnitude of rotavirus replication in the intestinal epithelium.
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MESH Headings
- Adaptor Proteins, Signal Transducing/deficiency
- Adaptor Proteins, Signal Transducing/physiology
- Animals
- Cell Line
- Chlorocebus aethiops
- DEAD Box Protein 58
- DEAD-box RNA Helicases/deficiency
- DEAD-box RNA Helicases/physiology
- HT29 Cells
- Humans
- Interferon-Induced Helicase, IFIH1
- Interferon-beta/biosynthesis
- Interferon-beta/physiology
- Intestinal Mucosa/enzymology
- Intestinal Mucosa/immunology
- Intestinal Mucosa/virology
- Membrane Proteins/deficiency
- Membrane Proteins/physiology
- Mice
- Mice, 129 Strain
- Mice, Inbred C57BL
- Mice, Knockout
- Nerve Tissue Proteins/deficiency
- Nerve Tissue Proteins/physiology
- RNA Helicases/genetics
- RNA Helicases/physiology
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- Receptors, Cell Surface
- Receptors, Immunologic
- Response Elements/immunology
- Rotavirus/genetics
- Rotavirus/immunology
- Signal Transduction/genetics
- Signal Transduction/immunology
- Virus Replication/genetics
- Virus Replication/immunology
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Affiliation(s)
- Alexis H Broquet
- Laboratory of Mucosal Immunology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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21
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Residues of the rotavirus RNA-dependent RNA polymerase template entry tunnel that mediate RNA recognition and genome replication. J Virol 2010; 85:1958-69. [PMID: 21147920 DOI: 10.1128/jvi.01689-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To replicate its segmented, double-stranded RNA (dsRNA) genome, the rotavirus RNA-dependent RNA polymerase, VP1, must recognize viral plus-strand RNAs (+RNAs) and guide them into the catalytic center. VP1 binds to the conserved 3' end of rotavirus +RNAs via both sequence-dependent and sequence-independent contacts. Sequence-dependent contacts permit recognition of viral +RNAs and specify an autoinhibited positioning of the template within the catalytic site. However, the contributions to dsRNA synthesis of sequence-dependent and sequence-independent VP1-RNA interactions remain unclear. To analyze the importance of VP1 residues that interact with +RNA on genome replication, we engineered mutant VP1 proteins and assayed their capacity to synthesize dsRNA in vitro. Our results showed that, individually, mutation of residues that interact specifically with RNA bases did not diminish replication levels. However, simultaneous mutations led to significantly lower levels of dsRNA product, presumably due to impaired recruitment of +RNA templates. In contrast, point mutations of sequence-independent RNA contact residues led to severely diminished replication, likely as a result of improper positioning of templates at the catalytic site. A noteworthy exception was a K419A mutation that enhanced the initiation capacity and product elongation rate of VP1. The specific chemistry of Lys419 and its position at a narrow region of the template entry tunnel appear to contribute to its capacity to moderate replication. Together, our findings suggest that distinct classes of VP1 residues interact with +RNA to mediate template recognition and dsRNA synthesis yet function in concert to promote viral RNA replication at appropriate times and rates.
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22
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Characterization of viroplasm formation during the early stages of rotavirus infection. Virol J 2010; 7:350. [PMID: 21114853 PMCID: PMC3009706 DOI: 10.1186/1743-422x-7-350] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 11/29/2010] [Indexed: 12/29/2022] Open
Abstract
Background During rotavirus replication cycle, electron-dense cytoplasmic inclusions named viroplasms are formed, and two non-structural proteins, NSP2 and NSP5, have been shown to localize in these membrane-free structures. In these inclusions, replication of dsRNA and packaging of pre-virion particles occur. Despite the importance of viroplasms in the replication cycle of rotavirus, the information regarding their formation, and the possible sites of their nucleation during the early stages of infection is scarce. Here, we analyzed the formation of viroplasms after infection of MA104 cells with the rotavirus strain RRV, using different multiplicities of infection (MOI), and different times post-infection. The possibility that viroplasms formation is nucleated by the entering viral particles was investigated using fluorescently labeled purified rotavirus particles. Results The immunofluorescent detection of viroplasms, using antibodies specific to NSP2 showed that both the number and size of viroplasms increased during infection, and depend on the MOI used. Small-size viroplasms predominated independently of the MOI or time post-infection, although at MOI's of 2.5 and 10 the proportion of larger viroplasms increased. Purified RRV particles were successfully labeled with the Cy5 mono reactive dye, without decrease in virus infectivity, and the labeled viruses were clearly observed by confocal microscope. PAGE gel analysis showed that most viral proteins were labeled; including the intermediate capsid protein VP6. Only 2 out of 117 Cy5-labeled virus particles colocalized with newly formed viroplasms at 4 hours post-infection. Conclusions The results presented in this work suggest that during rotavirus infection the number and size of viroplasm increases in an MOI-dependent manner. The Cy5 in vitro labeled virus particles were not found to colocalize with newly formed viroplasms, suggesting that they are not involved in viroplasm nucleation.
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23
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Abstract
Experiments in cell-free systems have demonstrated that the VP5 cleavage fragment of the rotavirus spike protein, VP4, undergoes a foldback rearrangement that translocates three clustered hydrophobic loops from one end of the molecule to the other. This conformational change resembles the foldback rearrangements of enveloped virus fusion proteins. By recoating rotavirus subviral particles with recombinant VP4 and VP7, we tested the effects on cell entry of substituting hydrophilic for hydrophobic residues in the clustered VP5 loops. Several of these mutations decreased the infectivity of recoated particles without preventing either recoating or folding back. In particular, the V391D mutant had a diminished capacity to interact with liposomes when triggered to fold back by serial protease digestion in solution, and particles recoated with this mutant VP4 were 10,000-fold less infectious than particles recoated with wild-type VP4. Particles with V391D mutant VP4 attached normally to cells and internalized efficiently, but they failed in the permeabilization step that allows coentry of the toxin alpha-sarcin. These findings indicate that the hydrophobicity of the VP5 apex is required for membrane disruption during rotavirus cell entry.
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24
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Guglielmi KM, McDonald SM, Patton JT. Mechanism of intraparticle synthesis of the rotavirus double-stranded RNA genome. J Biol Chem 2010; 285:18123-8. [PMID: 20351108 DOI: 10.1074/jbc.r110.117671] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rotaviruses perform the remarkable tasks of transcribing and replicating 11 distinct double-stranded RNA genome segments within the confines of a subviral particle. Multiple viral polymerases are tethered to the interior of a particle, each dedicated to a solitary genome segment but acting in synchrony to synthesize RNA. Although the rotavirus polymerase specifically recognizes RNA templates in the absence of other proteins, its enzymatic activity is contingent upon interaction with the viral capsid. This intraparticle strategy of RNA synthesis helps orchestrate the concerted packaging and replication of the viral genome. Here, we review our current understanding of rotavirus RNA synthetic mechanisms.
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Affiliation(s)
- Kristen M Guglielmi
- Laboratory of Infectious Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892, USA
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25
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Contin R, Arnoldi F, Campagna M, Burrone OR. Rotavirus NSP5 orchestrates recruitment of viroplasmic proteins. J Gen Virol 2010; 91:1782-93. [PMID: 20200190 DOI: 10.1099/vir.0.019133-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rotavirus genome replication and the first steps of virus morphogenesis take place in cytoplasmic viral factories, called viroplasms, containing four structural (VP1, VP2, VP3 and VP6) and two non-structural (NSP2 and NSP5) proteins. NSP2 and NSP5 have been shown to be essential for viroplasm formation and, when co-expressed in uninfected cells, to form viroplasm-like structures (VLS). In the present work, VLS formation was shown upon co-expression of NSP5 with the core protein VP2 despite the absence of NSP2, indicating a central role for NSP5 in VLS assembly. Since VP2 and NSP2 also induce NSP5 hyperphosphorylation, the possible correlation between VLS formation and the NSP5 phosphorylation status was investigated without evidence of a direct link. In VLS induced by NSP2, the polymerase VP1 was recruited, while the middle layer protein VP6 was not, forming instead tubular structures. On the other hand, VLS induced by VP2 were able to recruit both VP1 and VP6. More importantly, in VLS formed when NSP5 was expressed with both inducers, all viroplasmic proteins were found co-localized, resembling their distribution in viroplasms. Our results suggest a key role for NSP5 in architectural assembly of viroplasms and in recruitment of viroplasmic proteins. A new role for VP2 as an inducer of viroplasms and of NSP5 hyperphosphorylation is also described. These data may contribute to the understanding of rotavirus morphogenesis.
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Affiliation(s)
- R Contin
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
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26
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Abstract
Rotavirus group A G12 genotypes were detected in 3 (1.5%) of 198 stool samples positive for human rotavirus. G12P[6] was present in 2 samples, and a mixed G3G12P[8] was found in 1 sample. Phylogenetic analysis of complete open reading frames of all 11 genomic RNA segments proved their Wa-like genogroup affiliation.
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Affiliation(s)
- Corinna Pietsch
- Institute of Virology, Leipzig University, Leipzig, Germany.
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27
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McDonald SM, Tao YJ, Patton JT. The ins and outs of four-tunneled Reoviridae RNA-dependent RNA polymerases. Curr Opin Struct Biol 2009; 19:775-82. [PMID: 19914820 DOI: 10.1016/j.sbi.2009.10.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 10/14/2009] [Accepted: 10/15/2009] [Indexed: 12/29/2022]
Abstract
RNA-dependent RNA polymerases (RdRps) of the segmented double-stranded (ds) RNA viruses of the Reoviridae family exhibit distinguishing structural elements, enabling the enzymes to function within the confines of a proteinaceous core particle. These globular, cage-like polymerases are traversed by four well-defined tunnels, which not only allow template RNAs, nucleotides, and divalent cations to access the interior catalytic site, but also provide two distinct exit conduits for RNA templates and products--one leading out of the core and the other back inside the core. Although Reoviridae RdRps are intrinsically capable of binding template, their catalytic activities are tightly regulated by interactions with core shell proteins. This intra-particle mechanism of RNA synthesis coordinates genome packaging with replication during the infectious cycle.
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Affiliation(s)
- Sarah M McDonald
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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28
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Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM. Proc Natl Acad Sci U S A 2009; 106:10644-8. [PMID: 19487668 DOI: 10.1073/pnas.0904024106] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rotaviruses, major causes of childhood gastroenteritis, are nonenveloped, icosahedral particles with double-strand RNA genomes. By the use of electron cryomicroscopy and single-particle reconstruction, we have visualized a rotavirus particle comprising the inner capsid coated with the trimeric outer-layer protein, VP7, at a resolution (4 A) comparable with that of X-ray crystallography. We have traced the VP7 polypeptide chain, including parts not seen in its X-ray crystal structure. The 3 well-ordered, 30-residue, N-terminal "arms" of each VP7 trimer grip the underlying trimer of VP6, an inner-capsid protein. Structural differences between free and particle-bound VP7 and between free and VP7-coated inner capsids may regulate mRNA transcription and release. The Ca(2+)-stabilized VP7 intratrimer contact region, which presents important neutralizing epitopes, is unaltered upon capsid binding.
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29
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Shared and group-specific features of the rotavirus RNA polymerase reveal potential determinants of gene reassortment restriction. J Virol 2009; 83:6135-48. [PMID: 19357162 DOI: 10.1128/jvi.00409-09] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rotaviruses (RVs) are nonenveloped, 11-segmented, double-stranded RNA viruses that are major pathogens associated with acute gastroenteritis. Group A, B, and C RVs have been isolated from humans; however, intergroup gene reassortment does not occur for reasons that remain unclear. This restriction might reflect the failure of the viral RNA-dependent RNA polymerase (RdRp; VP1) to recognize and replicate the RNA of a different group. To address this possibility, we contrasted the sequences, structures, and functions of RdRps belonging to RV groups A, B, and C (A-VP1, B-VP1, and C-VP1, respectively). We found that conserved amino acid residues are located within the hollow center of VP1 near the active site, whereas variable, group-specific residues are mostly surface exposed. By creating a three-dimensional homology model of C-VP1 with the A-VP1 crystallographic data, we provide evidence that these RV RdRps are nearly identical in their tertiary folds and that they have the same RNA template recognition mechanism that differs from that of B-VP1. Consistent with the structural data, recombinant A-VP1 and C-VP1 are capable of replicating one another's RNA templates in vitro. Nonetheless, the activity of both RdRps is strictly dependent upon the presence of cognate RV core shell protein A-VP2 or C-VP2, respectively. Together, the results of this study provide unprecedented insight into the structure and function of RV RdRps and support the notion that VP1 interactions may influence the emergence of reassortant viral strains.
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30
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Abstract
Studies on the molecular biology of rotavirus, the major etiologic agent of gastroenteritis in infants and young children worldwide, have so far led to a large but not exhaustive knowledge of the mechanisms by which rotavirus replicates in the host cell. While the role of rotavirus structural proteins in the replication cycle is well defined, the functions of nonstructural proteins remain poorly understood. Recent experiments of RNA interference have clearly indicated the phases of the replication cycle for which the nonstructural proteins are essentially required. In addition, biochemical studies of their interactions with other viral proteins, together with immunofluorescence experiments on cells expressing recombinant proteins in different combinations, are providing new indications of their functions. This article contains a critical collection of the most recent achievements and the current hypotheses about the roles of nonstructural proteins in virus replication.
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Affiliation(s)
- Francesca Arnoldi
- International Centre for Genetic Engineering & Biotechnology (ICGEB), Padriciano 99, 34012 Trieste, Italy
| | - Oscar R Burrone
- International Centre for Genetic Engineering & Biotechnology (ICGEB), Padriciano 99, 34012 Trieste, Italy
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31
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Abstract
In this issue of Structure, Lu et al. (2008) report results of structural and functional analysis of rotavirus RNA-dependent RNA polymerase, VP1. Based on their analyses of VP1 in RNA free and bound forms, the authors propose a mechanism for coordinated genome packaging and replication.
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32
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Alam MM, Kobayashi N, Ishino M, Nagashima S, Paul SK, Chawla-Sarkar M, Krishnan T, Naik TN. Identical rearrangement of NSP3 genes found in three independently isolated virus clones derived from mixed infection and multiple passages of Rotaviruses. Arch Virol 2007; 153:555-9. [PMID: 18092125 DOI: 10.1007/s00705-007-0004-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Accepted: 11/07/2007] [Indexed: 10/22/2022]
Abstract
Three rotavirus variants with a rearranged RNA segment derived from the NSP3 gene were isolated in three independent experiments of coinfection and multiple passages of simian rotavirus strain SA11 and single-VP7-gene- or NSP1-gene-substitution reassortants having genetic background of SA11. Sequence analysis indicated that the three rearranged NSP3 genes had almost identical sequences and genomic structures organized by partial duplication of the open reading frame in a head-to-tail orientation following the termination codon. The junction site of the original NSP3 gene (first copy) and the duplicated portion (second copy) was identical among the three rearranged genes, while a direct repeat, i.e., a homologous sequence between the first copy and second template for duplication, typically located at the junction site, was not detected. However, short similar sequences were present at the end of the first copy and beginning of the second copy. These findings suggest that rearrangement of the NSP3 gene may occur at a certain preferential site which is related to sequence similarity between 3'-untranslated region and a region near the 5'-end of ORF.
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Affiliation(s)
- M M Alam
- Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
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33
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Small C, Barro M, Brown TL, Patton JT. Genome heterogeneity of SA11 rotavirus due to reassortment with "O" agent. Virology 2007; 359:415-24. [PMID: 17059839 PMCID: PMC1925260 DOI: 10.1016/j.virol.2006.09.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 08/17/2006] [Accepted: 09/08/2006] [Indexed: 01/09/2023]
Abstract
Derivatives of the rotavirus SA11-H96 strain, isolated in 1958 from an overtly healthy vervet monkey, have been used extensively to probe the viral life cycle. To gain insight into the phenotypic and genotypic differences among SA11 isolates, we sequenced the segmented double-stranded RNA genomes of SA11-H96 (P5B[2]:G3), two SA11-4F-like viruses (P6[1]:G3), two SA11-4F-like viruses with gene 5 rearrangements, and relevant segments of SA11 temperature-sensitive mutants and the "O" (Offal) agent (P6[1]:G8), a rotavirus isolated in 1965 from abattoir waste. This analysis indicates that the only complete genomic sequence previously reported for SA11 (Both) is instead that of a reassortant, originating like the SA11-4F-like viruses, from the introduction of an "O" agent gene into the SA11 genetic background. These results, combined with identification of mutations that correlate with altered growth properties and ts phenotype, emphasize the importance of considering segment origin and sequence variation in interpreting experimental outcomes with SA11 strains.
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Affiliation(s)
- Catie Small
- Laboratory of Infectious Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892‐8026, USA
| | - Mario Barro
- Laboratory of Infectious Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892‐8026, USA
| | - Thomas L. Brown
- Laboratory of Infectious Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892‐8026, USA
| | - John T. Patton
- Laboratory of Infectious Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892‐8026, USA
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