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Nichols SL, Haller C, Borodavka A, Esstman SM. Rotavirus NSP2: A Master Orchestrator of Early Viral Particle Assembly. Viruses 2024; 16:814. [PMID: 38932107 PMCID: PMC11209291 DOI: 10.3390/v16060814] [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: 04/18/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
Rotaviruses (RVs) are 11-segmented, double-stranded (ds) RNA viruses and important causes of acute gastroenteritis in humans and other animal species. Early RV particle assembly is a multi-step process that includes the assortment, packaging and replication of the 11 genome segments in close connection with capsid morphogenesis. This process occurs inside virally induced, cytosolic, membrane-less organelles called viroplasms. While many viral and cellular proteins play roles during early RV assembly, the octameric nonstructural protein 2 (NSP2) has emerged as a master orchestrator of this key stage of the viral replication cycle. NSP2 is critical for viroplasm biogenesis as well as for the selective RNA-RNA interactions that underpin the assortment of 11 viral genome segments. Moreover, NSP2's associated enzymatic activities might serve to maintain nucleotide pools for use during viral genome replication, a process that is concurrent with early particle assembly. The goal of this review article is to summarize the available data about the structures, functions and interactions of RV NSP2 while also drawing attention to important unanswered questions in the field.
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Affiliation(s)
- Sarah L. Nichols
- Department of Biology, Wake Forest University, Wake Downtown, 455 Vine Street, Winston-Salem, NC 27106, USA;
| | - Cyril Haller
- Department of Chemical Engineering and Biotechnology, Cambridge University, Philippa Fawcett Drive, Cambridge CB3 0AS, UK;
| | - Alexander Borodavka
- Department of Chemical Engineering and Biotechnology, Cambridge University, Philippa Fawcett Drive, Cambridge CB3 0AS, UK;
| | - Sarah M. Esstman
- Department of Biology, Wake Forest University, Wake Downtown, 455 Vine Street, Winston-Salem, NC 27106, USA;
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2
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Vetter J, Lee M, Eichwald C. The Role of the Host Cytoskeleton in the Formation and Dynamics of Rotavirus Viroplasms. Viruses 2024; 16:668. [PMID: 38793550 PMCID: PMC11125917 DOI: 10.3390/v16050668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Rotavirus (RV) replicates within viroplasms, membraneless electron-dense globular cytosolic inclusions with liquid-liquid phase properties. In these structures occur the virus transcription, replication, and packaging of the virus genome in newly assembled double-layered particles. The viroplasms are composed of virus proteins (NSP2, NSP5, NSP4, VP1, VP2, VP3, and VP6), single- and double-stranded virus RNAs, and host components such as microtubules, perilipin-1, and chaperonins. The formation, coalescence, maintenance, and perinuclear localization of viroplasms rely on their association with the cytoskeleton. A stabilized microtubule network involving microtubules and kinesin Eg5 and dynein molecular motors is associated with NSP5, NSP2, and VP2, facilitating dynamic processes such as viroplasm coalescence and perinuclear localization. Key post-translation modifications, particularly phosphorylation events of RV proteins NSP5 and NSP2, play pivotal roles in orchestrating these interactions. Actin filaments also contribute, triggering the formation of the viroplasms through the association of soluble cytosolic VP4 with actin and the molecular motor myosin. This review explores the evolving understanding of RV replication, emphasizing the host requirements essential for viroplasm formation and highlighting their dynamic interplay within the host cell.
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Affiliation(s)
| | | | - Catherine Eichwald
- Institute of Virology, University of Zurich, 8057 Zurich, Switzerland; (J.V.); (M.L.)
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3
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Vetter J, Papa G, Tobler K, Rodriguez JM, Kley M, Myers M, Wiesendanger M, Schraner EM, Luque D, Burrone OR, Fraefel C, Eichwald C. The recruitment of TRiC chaperonin in rotavirus viroplasms correlates with virus replication. mBio 2024; 15:e0049924. [PMID: 38470055 PMCID: PMC11005421 DOI: 10.1128/mbio.00499-24] [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: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Rotavirus (RV) replication takes place in the viroplasms, cytosolic inclusions that allow the synthesis of virus genome segments and their encapsidation in the core shell, followed by the addition of the second layer of the virion. The viroplasms are composed of several viral proteins, including NSP5, which serves as the main building block. Microtubules, lipid droplets, and miRNA-7 are among the host components recruited in viroplasms. We investigated the interaction between RV proteins and host components of the viroplasms by performing a pull-down assay of lysates from RV-infected cells expressing NSP5-BiolD2. Subsequent tandem mass spectrometry identified all eight subunits of the tailless complex polypeptide I ring complex (TRiC), a cellular chaperonin responsible for folding at least 10% of the cytosolic proteins. Our confirmed findings reveal that TRiC is brought into viroplasms and wraps around newly formed double-layered particles. Chemical inhibition of TRiC and silencing of its subunits drastically reduced virus progeny production. Through direct RNA sequencing, we show that TRiC is critical for RV replication by controlling dsRNA genome segment synthesis, particularly negative-sense single-stranded RNA. Importantly, cryo-electron microscopy analysis shows that TRiC inhibition results in defective virus particles lacking genome segments and polymerase complex (VP1/VP3). Moreover, TRiC associates with VP2 and NSP5 but not with VP1. Also, VP2 is shown to be essential for recruiting TRiC in viroplasms and preserving their globular morphology. This study highlights the essential role of TRiC in viroplasm formation and in facilitating virion assembly during the RV life cycle. IMPORTANCE The replication of rotavirus takes place in cytosolic inclusions termed viroplasms. In these inclusions, the distinct 11 double-stranded RNA genome segments are co-packaged to complete a genome in newly generated virus particles. In this study, we show for the first time that the tailless complex polypeptide I ring complex (TRiC), a cellular chaperonin responsible for the folding of at least 10% of the cytosolic proteins, is a component of viroplasms and is required for the synthesis of the viral negative-sense single-stranded RNA. Specifically, TRiC associates with NSP5 and VP2, the cofactor involved in RNA replication. Our study adds a new component to the current model of rotavirus replication, where TRiC is recruited to viroplasms to assist replication.
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Affiliation(s)
- Janine Vetter
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Guido Papa
- Molecular Immunology Lab, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Kurt Tobler
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Javier M. Rodriguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Cantoblanco, Madrid, Spain
| | - Manuel Kley
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Michael Myers
- Proteomics Lab, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Mahesa Wiesendanger
- Institute of Virology, University of Zurich, Zurich, Switzerland
- Institute of Veterinary Anatomy, University of Zurich, Zurich, Switzerland
| | - Elisabeth M. Schraner
- Institute of Virology, University of Zurich, Zurich, Switzerland
- Institute of Veterinary Anatomy, University of Zurich, Zurich, Switzerland
| | - Daniel Luque
- School of Biomedical Sciences, The University of New South Wales, Sydney, New South Wales, Australia
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, New South Wales, Australia
| | - Oscar R. Burrone
- Molecular Immunology Lab, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich, Switzerland
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4
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Chamera S, Wycisk K, Czarnocki-Cieciura M, Nowotny M. Cryo-EM structure of rotavirus B NSP2 reveals its unique tertiary architecture. J Virol 2024; 98:e0166023. [PMID: 38421167 PMCID: PMC10949507 DOI: 10.1128/jvi.01660-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Rotavirus (RV) NSP2 is a multifunctional RNA chaperone that exhibits numerous activities that are essential for replication and viral genome packaging. We performed an in silico analysis that highlighted a distant relationship of NSP2 from rotavirus B (RVB) to proteins from other human RVs. We solved a cryo-electron microscopy structure of RVB NSP2 that shows structural differences with corresponding proteins from other human RVs. Based on the structure, we identified amino acid residues that are involved in RNA interactions. Anisotropy titration experiments showed that these residues are important for nucleic acid binding. We also identified structural motifs that are conserved in all RV species. Collectively, our data complete the structural characterization of rotaviral NSP2 protein and demonstrate its structural diversity among RV species.IMPORTANCERotavirus B (RVB), also known as adult diarrhea rotavirus, has caused epidemics of severe diarrhea in China, India, and Bangladesh. Thousands of people are infected in a single RVB epidemic. However, information on this group of rotaviruses remains limited. As NSP2 is an essential protein in the viral life cycle, including its role in the formation of replication factories, it may be a target for future antiviral strategy against viruses with similar mechanisms.
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Affiliation(s)
- Sebastian Chamera
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Krzysztof Wycisk
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
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5
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Strauss S, Acker J, Papa G, Desirò D, Schueder F, Borodavka A, Jungmann R. Principles of RNA recruitment to viral ribonucleoprotein condensates in a segmented dsRNA virus. eLife 2023; 12:e68670. [PMID: 36700549 PMCID: PMC9925054 DOI: 10.7554/elife.68670] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 01/26/2023] [Indexed: 01/27/2023] Open
Abstract
Rotaviruses transcribe 11 distinct RNAs that must be co-packaged prior to their replication to make an infectious virion. During infection, nontranslating rotavirus transcripts accumulate in cytoplasmic protein-RNA granules known as viroplasms that support segmented genome assembly and replication via a poorly understood mechanism. Here, we analysed the RV transcriptome by combining DNA-barcoded smFISH of rotavirus-infected cells. Rotavirus RNA stoichiometry in viroplasms appears to be distinct from the cytoplasmic transcript distribution, with the largest transcript being the most enriched in viroplasms, suggesting a selective RNA enrichment mechanism. While all 11 types of transcripts accumulate in viroplasms, their stoichiometry significantly varied between individual viroplasms. Accumulation of transcripts requires the presence of 3' untranslated terminal regions and viroplasmic localisation of the viral polymerase VP1, consistent with the observed lack of polyadenylated transcripts in viroplasms. Our observations reveal similarities between viroplasms and other cytoplasmic RNP granules and identify viroplasmic proteins as drivers of viral RNA assembly during viroplasm formation.
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Affiliation(s)
| | - Julia Acker
- Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
| | - Guido Papa
- Molecular Immunology Laboratory, International Centre for Genetic Engineering and BiotechnologyTriesteItaly
| | - Daniel Desirò
- Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
| | - Florian Schueder
- Max Planck Institute of BiochemistryMunichGermany
- Department of Physics and Center for Nanoscience, Ludwig Maximilian UniversityMunichGermany
| | | | - Ralf Jungmann
- Max Planck Institute of BiochemistryMunichGermany
- Department of Physics and Center for Nanoscience, Ludwig Maximilian UniversityMunichGermany
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6
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Bravo JPK, Bartnik K, Venditti L, Acker J, Gail EH, Colyer A, Davidovich C, Lamb DC, Tuma R, Calabrese AN, Borodavka A. Structural basis of rotavirus RNA chaperone displacement and RNA annealing. Proc Natl Acad Sci U S A 2021; 118:e2100198118. [PMID: 34615715 PMCID: PMC8521686 DOI: 10.1073/pnas.2100198118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2021] [Indexed: 01/13/2023] Open
Abstract
Rotavirus genomes are distributed between 11 distinct RNA molecules, all of which must be selectively copackaged during virus assembly. This likely occurs through sequence-specific RNA interactions facilitated by the RNA chaperone NSP2. Here, we report that NSP2 autoregulates its chaperone activity through its C-terminal region (CTR) that promotes RNA-RNA interactions by limiting its helix-unwinding activity. Unexpectedly, structural proteomics data revealed that the CTR does not directly interact with RNA, while accelerating RNA release from NSP2. Cryo-electron microscopy reconstructions of an NSP2-RNA complex reveal a highly conserved acidic patch on the CTR, which is poised toward the bound RNA. Virus replication was abrogated by charge-disrupting mutations within the acidic patch but completely restored by charge-preserving mutations. Mechanistic similarities between NSP2 and the unrelated bacterial RNA chaperone Hfq suggest that accelerating RNA dissociation while promoting intermolecular RNA interactions may be a widespread strategy of RNA chaperone recycling.
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Affiliation(s)
- Jack P K Bravo
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Kira Bartnik
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich, Centre for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Luca Venditti
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Julia Acker
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Emma H Gail
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, European Molecular Biology Laboratory (EMBL) Australia, Clayton, VIC 3800, Australia
| | - Alice Colyer
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, European Molecular Biology Laboratory (EMBL) Australia, Clayton, VIC 3800, Australia
| | - Don C Lamb
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich, Centre for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
- Faculty of Science, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom;
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich, Centre for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, D-81377 Munich, Germany
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7
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Papa G, Borodavka A, Desselberger U. Viroplasms: Assembly and Functions of Rotavirus Replication Factories. Viruses 2021; 13:1349. [PMID: 34372555 PMCID: PMC8310052 DOI: 10.3390/v13071349] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023] Open
Abstract
Viroplasms are cytoplasmic, membraneless structures assembled in rotavirus (RV)-infected cells, which are intricately involved in viral replication. Two virus-encoded, non-structural proteins, NSP2 and NSP5, are the main drivers of viroplasm formation. The structures (as far as is known) and functions of these proteins are described. Recent studies using plasmid-only-based reverse genetics have significantly contributed to elucidation of the crucial roles of these proteins in RV replication. Thus, it has been recognized that viroplasms resemble liquid-like protein-RNA condensates that may be formed via liquid-liquid phase separation (LLPS) of NSP2 and NSP5 at the early stages of infection. Interactions between the RNA chaperone NSP2 and the multivalent, intrinsically disordered protein NSP5 result in their condensation (protein droplet formation), which plays a central role in viroplasm assembly. These droplets may provide a unique molecular environment for the establishment of inter-molecular contacts between the RV (+)ssRNA transcripts, followed by their assortment and equimolar packaging. Future efforts to improve our understanding of RV replication and genome assortment in viroplasms should focus on their complex molecular composition, which changes dynamically throughout the RV replication cycle, to support distinct stages of virion assembly.
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Affiliation(s)
- Guido Papa
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK;
| | | | - Ulrich Desselberger
- Department of Medicine, Addenbrooke’s Hospital, University of Cambridge, Cambridge CB2 0QQ, UK
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8
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Criglar JM, Crawford SE, Estes MK. Plasmid-based reverse genetics for probing phosphorylation-dependent viroplasm formation in rotaviruses. Virus Res 2020; 291:198193. [PMID: 33053412 DOI: 10.1016/j.virusres.2020.198193] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 01/15/2023]
Abstract
Rotavirus (RV) replication occurs in cytoplasmic compartments, known as viroplasms, that are composed of viral and cellular proteins. Viroplasm formation requires RV nonstructural proteins NSP2 and NSP5 and cellular lipid droplets (LDs); however, the mechanisms required for viroplasm assembly remain largely unknown. We previously identified two conformationally-distinct forms of NSP2 (dNSP2, vNSP2) found in RV-infected cells that interact differentially with hypo- and hyperphosphorylated NSP5, respectively, and indicate a coordinated phosphorylation-dependent mechanism regulating viroplasm assembly. We also reported that phosphorylation of dNSP2 on serine 313 by the cellular kinase CK1α triggers the localization of vNSP2 to sites of viroplasm assembly and its association with hyperphosphorylated NSP5. To directly evaluate the role of CK1α-mediated NSP2 phosphorylation on viroplasm formation, we used a recently published plasmid-based reverse genetics method to generate a recombinant rotavirus (rRV) with a phosphomimetic NSP2 mutation (rRV NSP2 S313D). The rRV NSP2 S313D virus is significantly delayed in viroplasm formation, virus replication, and interferes with wild type RV replication during co-infection. The rRV NSP2 S313A virus was not rescued. Taking advantage of the delay in viroplasm formation, the NSP2 S313D phosphomimetic mutant was used as a tool to observe very early events in viroplasm assembly. We show that (1) viroplasm assembly correlates with NSP5 hyperphosphorylation, and (2) that vNSP2 S313D co-localizes with RV-induced LDs without NSP5, suggesting that vNSP2 phospho-S313 is sufficient for interacting with LDs and may be the virus factor required for RV-induced LD formation. Further studies with the rRV NSP2 S313D virus are expected to reveal new aspects of viroplasm and LD initiation and assembly.
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Affiliation(s)
- Jeanette M Criglar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States; Department of Medicine, Divisions of Gastroenterology and Hepatology and Infectious Diseases, Baylor College of Medicine, Houston, TX 77030, United States.
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9
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Criglar JM, Crawford SE, Zhao B, Smith HG, Stossi F, Estes MK. A Genetically Engineered Rotavirus NSP2 Phosphorylation Mutant Impaired in Viroplasm Formation and Replication Shows an Early Interaction between vNSP2 and Cellular Lipid Droplets. J Virol 2020; 94:e00972-20. [PMID: 32461314 PMCID: PMC7375380 DOI: 10.1128/jvi.00972-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/18/2022] Open
Abstract
Many RNA viruses replicate in cytoplasmic compartments (virus factories or viroplasms) composed of viral and cellular proteins, but the mechanisms required for their formation remain largely unknown. Rotavirus (RV) replication in viroplasms requires interactions between virus nonstructural proteins NSP2 and NSP5, which are associated with components of lipid droplets (LDs). We previously identified two forms of NSP2 in RV-infected cells, a cytoplasmically dispersed form (dNSP2) and a viroplasm-specific form (vNSP2), which interact with hypophosphorylated and hyperphosphorylated NSP5, respectively, indicating that a coordinated phosphorylation cascade controls viroplasm assembly. The cellular kinase CK1α phosphorylates NSP2 on serine 313, triggering the localization of vNSP2 to sites of viroplasm assembly and its association with hyperphosphorylated NSP5. Using reverse genetics, we generated a rotavirus with a phosphomimetic NSP2 (S313D) mutation to directly evaluate the role of CK1α NSP2 phosphorylation in viroplasm formation. Recombinant rotavirus NSP2 S313D (rRV NSP2 S313D) is significantly delayed in viroplasm formation and in virus replication and interferes with wild-type RV replication in coinfection. Taking advantage of the delay in viroplasm formation, the NSP2 phosphomimetic mutant was used as a tool to observe very early events in viroplasm assembly. We show that (i) viroplasm assembly correlates with NSP5 hyperphosphorylation and (ii) vNSP2 S313D colocalizes with RV-induced LDs without NSP5, suggesting that vNSP2 phospho-S313 is sufficient for interacting with LDs and may be the virus factor required for RV-induced LD formation. Further studies with the rRV NSP2 S313D virus are expected to reveal new aspects of viroplasm and LD initiation and assembly.IMPORTANCE Reverse genetics was used to generate a recombinant rotavirus with a single phosphomimetic mutation in nonstructural protein 2 (NSP2 S313D) that exhibits delayed viroplasm formation, delayed replication, and an interfering phenotype during coinfection with wild-type rotavirus, indicating the importance of this amino acid during virus replication. Exploiting the delay in viroplasm assembly, we found that viroplasm-associated NSP2 colocalizes with rotavirus-induced lipid droplets prior to the accumulation of other rotavirus proteins that are required for viroplasm formation and that NSP5 hyperphosphorylation is required for viroplasm assembly. These data suggest that NSP2 phospho-S313 is sufficient for interaction with lipid droplets and may be the virus factor that induces lipid droplet biogenesis in rotavirus-infected cells. Lipid droplets are cellular organelles critical for the replication of many viral and bacterial pathogens, and thus, understanding the mechanism of NSP2-mediated viroplasm/lipid droplet initiation and interaction will lead to new insights into this important host-pathogen interaction.
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Affiliation(s)
- Jeanette M Criglar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Hunter G Smith
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Integrated Microscopy Core, Baylor College of Medicine, Houston, Texas, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Division of Infectious Diseases, Baylor College of Medicine, Houston, Texas, USA
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10
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Kumar D, Singh A, Kumar P, Uversky VN, Rao CD, Giri R. Understanding the penetrance of intrinsic protein disorder in rotavirus proteome. Int J Biol Macromol 2020; 144:892-908. [PMID: 31739058 PMCID: PMC7112477 DOI: 10.1016/j.ijbiomac.2019.09.166] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/09/2019] [Accepted: 09/20/2019] [Indexed: 01/03/2023]
Abstract
Rotavirus is a major cause of severe acute gastroenteritis in the infants and young children. The past decade has evidenced the role of intrinsically disordered proteins/regions (IDPs)/(IDPRs) in viral and other diseases. In general, (IDPs)/(IDPRs) are considered as dynamic conformational ensembles that devoid of a specific 3D structure, being associated with various important biological phenomena. Viruses utilize IDPs/IDPRs to survive in harsh environments, to evade the host immune system, and to highjack and manipulate host cellular proteins. The role of IDPs/IDPRs in Rotavirus biology and pathogenicity are not assessed so far, therefore, we have designed this study to deeply look at the penetrance of intrinsic disorder in rotavirus proteome consisting 12 proteins encoded by 11 segments of viral genome. Also, for all human rotaviral proteins, we have deciphered molecular recognition features (MoRFs), which are disorder based binding sites in proteins. Our study shows the wide spread of intrinsic disorder in several rotavirus proteins, primarily the nonstructural proteins NSP3, NSP4, and NSP5 that are involved in viral replication, translation, viroplasm formation and/or maturation. This study may serve as a primer for understanding the role of IDPs/MoRFs in rotavirus biology, design of alternative therapeutic strategies, and development of disorder-based drugs.
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Affiliation(s)
- Deepak Kumar
- Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh 175005, India
| | - Ankur Singh
- Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh 175005, India
| | - Prateek Kumar
- Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh 175005, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - C Durga Rao
- SRM University, AP - Amaravati, Neerukonda, Mangalagiri Mandal Guntur District, Mangalagiri, Andhra Pradesh 522502, India.
| | - Rajanish Giri
- Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh 175005, India; BioX Center, Indian Institute of Technology Mandi, Himachal Pradesh, India.
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11
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Abid N, Chillemi G, Salemi M. Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach. Genes (Basel) 2019; 11:genes11010028. [PMID: 31878331 PMCID: PMC7016848 DOI: 10.3390/genes11010028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 12/10/2019] [Accepted: 12/19/2019] [Indexed: 01/12/2023] Open
Abstract
Rotavirus 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 question. The distribution of unusual genotypes subject to viral fitness is influenced by interactions among viral proteins. The present work aimed at analyzing the genetic constellation and the coevolution of rotavirus coding genes for the available rotavirus genotypes. Seventy-two full genome sequences of different genetic constellations were analyzed using a genetic algorithm. The results revealed an extensive genome-wide covariance network among the 12 viral proteins. Altogether, the emergence of new genotypes represents a challenge to the outcome and success of vaccination and the coevolutionary analysis of rotavirus proteins may boost efforts to better understand the interaction networks of proteins during viral replication/transcription.
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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, Monastir 5000, Tunisia
- High Institute of Biotechnology of Sidi Thabet, Department of Biotechnology, University Manouba, BP-66, Ariana-Tunis 2020, Tunisia
- Correspondence: or ; Tel.: +216-92–974-000
| | - 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
| | - Marco Salemi
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Emerging Pathogens Institute, P.O. Box 100009, Gainesville, FL 32610-3633, USA;
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12
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Phosphorylation cascade regulates the formation and maturation of rotaviral replication factories. Proc Natl Acad Sci U S A 2018; 115:E12015-E12023. [PMID: 30509975 DOI: 10.1073/pnas.1717944115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The rotavirus (RV) genome is replicated and packaged into virus progeny in cytoplasmic inclusions called viroplasms, which require interactions between RV nonstructural proteins NSP2 and NSP5. How viroplasms form remains unknown. We previously found two forms of NSP2 in RV-infected cells: a cytoplasmically dispersed dNSP2, which interacts with hypophosphorylated NSP5; and a viroplasm-specific vNSP2, which interacts with hyperphosphorylated NSP5. Other studies report that CK1α, a ubiquitous cellular kinase, hyperphosphorylates NSP5, but requires NSP2 for reasons that are unclear. Here we show that silencing CK1α in cells before RV infection resulted in (i) >90% decrease in RV replication, (ii) disrupted vNSP2 and NSP5 interaction, (iii) dispersion of vNSP2 throughout the cytoplasm, and (iv) reduced vNSP2 protein levels. Together, these data indicate that CK1α directly affects NSP2. Accordingly, an in vitro kinase assay showed that CK1α phosphorylates serine 313 of NSP2 and triggers NSP2 octamers to form a lattice structure as demonstrated by crystallographic analysis. Additionally, a dual-specificity autokinase activity for NSP2 was identified and confirmed by mass spectrometry. Together, our studies show that phosphorylation of NSP2 involving CK1α controls viroplasm assembly. Considering that CK1α plays a role in the replication of other RNA viruses, similar phosphorylation-dependent mechanisms may exist for other virus pathogens that require cytoplasmic virus factories for replication.
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13
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Cowley D, Pavlic D, Bogdanovic-Sakran N, Boniface K, Kirkwood CD, Bines JE. Serological responses to rotavirus NSP2 following administration of RV3-BB human neonatal rotavirus vaccine. Hum Vaccin Immunother 2018; 14:2082-2087. [PMID: 29688121 PMCID: PMC6149983 DOI: 10.1080/21645515.2018.1467202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Serum rotavirus IgA responses are an imperfect non-mechanistic correlate of protection, and the lack of an accurate serological marker is a challenge to the development of new rotavirus vaccines. Serological responses to rotavirus NSP2 occur following wild-type infection; however, it is unknown if serological responses to NSP2 occur following administration of rotavirus vaccines. The phase IIa immunogenicity trial of RV3-BB provided an opportunity to investigate the serological responses to NSP2 following vaccination. Healthy, full-term babies (n = 96) were previously recruited as part of a phase IIa safety and immunogenicity trial in Dunedin, New Zealand between January 2012 and April 2014. Participants received three doses of oral RV3-BB vaccine with the first dose given at 0–5 days after birth (neonatal schedule), or the first dose given at about 8 weeks after birth (infant schedule), or to receive placebo (placebo schedule). Serum IgA and IgG antibody responses to total RV3-BB and NSP2 protein (RV3-BB) were assessed using ELISA. Despite significant serum IgA response against total RV3-BB, we were unable to demonstrate a significant serological response to NSP2 in participants receiving RV3-BB when compared to placebo. Heterotypic antibodies against multiple NSP2 genotypes were detected following RV3-BB vaccination. Our data demonstrates that while serological responses to NSP2 were detectable in a subset of participants, it is a less useful marker when compared to total rotavirus serum IgA response.
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Affiliation(s)
- Daniel Cowley
- a Enteric Virus Group, Murdoch Children's Research Institute , Parkville , VIC , Australia.,b Rotavirus Program, Murdoch Children's Research Institute , Parkville , VIC , Australia.,c Department of Paediatrics , The University of Melbourne , Parkville , VIC , Australia
| | - Daniel Pavlic
- a Enteric Virus Group, Murdoch Children's Research Institute , Parkville , VIC , Australia.,b Rotavirus Program, Murdoch Children's Research Institute , Parkville , VIC , Australia
| | - Nada Bogdanovic-Sakran
- a Enteric Virus Group, Murdoch Children's Research Institute , Parkville , VIC , Australia.,b Rotavirus Program, Murdoch Children's Research Institute , Parkville , VIC , Australia
| | - Karen Boniface
- a Enteric Virus Group, Murdoch Children's Research Institute , Parkville , VIC , Australia.,b Rotavirus Program, Murdoch Children's Research Institute , Parkville , VIC , Australia
| | - Carl D Kirkwood
- a Enteric Virus Group, Murdoch Children's Research Institute , Parkville , VIC , Australia.,b Rotavirus Program, Murdoch Children's Research Institute , Parkville , VIC , Australia.,c Department of Paediatrics , The University of Melbourne , Parkville , VIC , Australia
| | - Julie E Bines
- a Enteric Virus Group, Murdoch Children's Research Institute , Parkville , VIC , Australia.,b Rotavirus Program, Murdoch Children's Research Institute , Parkville , VIC , Australia.,c Department of Paediatrics , The University of Melbourne , Parkville , VIC , Australia.,d Department of Gastroenterology and Clinical Nutrition , Royal Children's Hospital , Parkville , Victoria , Australia
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14
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Single-Particle Detection of Transcription following Rotavirus Entry. J Virol 2017; 91:JVI.00651-17. [PMID: 28701394 PMCID: PMC5571246 DOI: 10.1128/jvi.00651-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 06/29/2017] [Indexed: 12/25/2022] Open
Abstract
Infectious rotavirus particles are triple-layered, icosahedral assemblies. The outer layer proteins, VP4 (cleaved to VP8* and VP5*) and VP7, surround a transcriptionally competent, double-layer particle (DLP), which they deliver into the cytosol. During entry of rhesus rotavirus, VP8* interacts with cell surface gangliosides, allowing engulfment into a membrane vesicle by a clathrin-independent process. Escape into the cytosol and outer-layer shedding depend on interaction of a hydrophobic surface on VP5* with the membrane bilayer and on a large-scale conformational change. We report here experiments that detect the fate of released DLPs and their efficiency in initiating RNA synthesis. By replacing the outer layer with fluorescently tagged, recombinant proteins and also tagging the DLP, we distinguished particles that have lost their outer layer and entered the cytosol (uncoated) from those still within membrane vesicles. We used fluorescent in situ hybridization with probes for nascent transcripts to determine how soon after uncoating transcription began and what fraction of the uncoated particles were active in initiating RNA synthesis. We detected RNA synthesis by uncoated particles as early as 15 min after adding virus. The uncoating efficiency was 20 to 50%; of the uncoated particles, about 10 to 15% synthesized detectable RNA. In the format of our experiments, about 10% of the added particles attached to the cell surface, giving an overall ratio of added particles to RNA-synthesizing particles of between 250:1 and 500:1, in good agreement with the ratio of particles to focus-forming units determined by infectivity assays. Thus, RNA synthesis by even a single, uncoated particle can initiate infection in a cell.IMPORTANCE The pathways by which a virus enters a cell transform its packaged genome into an active one. Contemporary fluorescence microscopy can detect individual virus particles as they enter cells, allowing us to map their multistep entry pathways. Rotaviruses, like most viruses that lack membranes of their own, disrupt or perforate the intracellular, membrane-enclosed compartment into which they become engulfed following attachment to a cell surface, in order to gain access to the cell interior. The properties of rotavirus particles make it possible to determine molecular mechanisms for these entry steps. In the work described here, we have asked the following question: what fraction of the rotavirus particles that penetrate into the cell make new viral RNA? We find that of the cell-attached particles, between 20 and 50% ultimately penetrate, and of these, about 10% make RNA. RNA synthesis by even a single virus particle can initiate a productive infection.
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15
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Abstract
RNAs are functionally diverse macromolecules whose proper functions rely strictly upon their correct tertiary structures. However, because of their high structural flexibility, correct folding of RNAs is challenging and slow. Therefore, cells and viruses encode a variety of RNA remodeling proteins, including helicases and RNA chaperones. In RNA viruses, these proteins are believed to play pivotal roles in all the processes involving viral RNAs during the life cycle. RNA helicases have been studied extensively for decades, whereas RNA chaperones, particularly virus-encoded RNA chaperones, are often overlooked. This review describes the activities of RNA chaperones encoded by RNA viruses, particularly the ones identified and characterized in recent years, and the functions of these proteins in different steps of viral life cycles, and presents an overview of this unique group of proteins.
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Affiliation(s)
- Jie Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hongjie Xia
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qi Qian
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xi Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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16
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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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17
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Lahon A, Ingle VC, Birade HS, Raut CG, Chitambar SD. Molecular characterization of group B rotavirus circulating in pigs from India: identification of a strain bearing a novel VP7 genotype, G21. Vet Microbiol 2014; 174:342-352. [PMID: 25465661 DOI: 10.1016/j.vetmic.2014.10.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 09/27/2014] [Accepted: 10/14/2014] [Indexed: 12/12/2022]
Abstract
The occurrence of group B rotavirus (RVB) infections in pigs has been reported from different parts of world. However, such infection in the pig population maintained in Indian farms has not been investigated as yet. A total of 187 faecal specimens were collected from pigs reared in different pig farms/pigsties located in western and northern regions of India and tested for the presence of porcine RVB by amplification of the NSP2 gene using conventional RT-PCR. Nine specimens (4.8%) were shown to contain RVB RNA. N2 and N4 genotypes of NSP2 gene were detected in three and six RVB strains respectively. VP7 (G-type) and NSP5 (H-type) genes of selected six RVB strains were characterized to identify the genotypes. Multiple G (G7, G19 and G20) and H (H4 and H5) genotypes detected in the RVB strains indicated circulation of heterogeneous population of RVB strains in pigs of India. Additionally, one strain was proposed to belong to a novel RVB genotype designated as G21 on account of <80% identity of VP7 gene sequence with its counterpart in RVB strains from 20 established genotypes. Deduced amino acid sequence of VP7 gene also displayed the presence of seven unique substitutions in the strain. The study reports for the first time the occurrence of RVB infections in Indian pig herds and provides important epidemiological data useful for better understanding of ecology and evolution of porcine RVBs.
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Affiliation(s)
- Anismrita Lahon
- Enteric Viruses Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India
| | - Vijay C Ingle
- Department of Veterinary Microbiology and Animal Biotechnology, Nagpur Veterinary College, Nagpur 400006, India
| | - Hemant S Birade
- Department of Animal Reproduction, Gynaecology & Obstetrics, Krantisinh Nana Patil College of Veterinary Science, Shirwal, Satara 412801, India
| | | | - Shobha D Chitambar
- Enteric Viruses Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune 411001, India.
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18
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Desselberger U. Rotaviruses. Virus Res 2014; 190:75-96. [DOI: 10.1016/j.virusres.2014.06.016] [Citation(s) in RCA: 240] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/26/2014] [Accepted: 06/26/2014] [Indexed: 01/12/2023]
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19
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Yang J, Cheng Z, Zhang S, Xiong W, Xia H, Qiu Y, Wang Z, Wu F, Qin CF, Yin L, Hu Y, Zhou X. A cypovirus VP5 displays the RNA chaperone-like activity that destabilizes RNA helices and accelerates strand annealing. Nucleic Acids Res 2013; 42:2538-54. [PMID: 24319147 PMCID: PMC3936753 DOI: 10.1093/nar/gkt1256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For double-stranded RNA (dsRNA) viruses in the family Reoviridae, their inner capsids function as the machinery for viral RNA (vRNA) replication. Unlike other multishelled reoviruses, cypovirus has a single-layered capsid, thereby representing a simplified model for studying vRNA replication of reoviruses. VP5 is one of the three major cypovirus capsid proteins and functions as a clamp protein to stabilize cypovirus capsid. Here, we expressed VP5 from type 5 Helicoverpa armigera cypovirus (HaCPV-5) in a eukaryotic system and determined that this VP5 possesses RNA chaperone-like activity, which destabilizes RNA helices and accelerates strand annealing independent of ATP. Our further characterization of VP5 revealed that its helix-destabilizing activity is RNA specific, lacks directionality and could be inhibited by divalent ions, such as Mg(2+), Mn(2+), Ca(2+) or Zn(2+), to varying degrees. Furthermore, we found that HaCPV-5 VP5 facilitates the replication initiation of an alternative polymerase (i.e. reverse transcriptase) through a panhandle-structured RNA template, which mimics the 5'-3' cyclization of cypoviral positive-stranded RNA. Given that the replication of negative-stranded vRNA on the positive-stranded vRNA template necessitates the dissociation of the 5'-3' panhandle, the RNA chaperone activity of VP5 may play a direct role in the initiation of reoviral dsRNA synthesis.
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Affiliation(s)
- Jie Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China and Department of Biochemistry, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
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20
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A novel form of rotavirus NSP2 and phosphorylation-dependent NSP2-NSP5 interactions are associated with viroplasm assembly. J Virol 2013; 88:786-98. [PMID: 24198401 DOI: 10.1128/jvi.03022-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Rotavirus (RV) replication occurs in cytoplasmic inclusions called viroplasms whose formation requires the interactions of RV proteins NSP2 and NSP5; however, the specific role(s) of NSP2 in viroplasm assembly remains largely unknown. To study viroplasm formation in the context of infection, we characterized two new monoclonal antibodies (MAbs) specific for NSP2. These MAbs show high-affinity binding to NSP2 and differentially recognize distinct pools of NSP2 in RV-infected cells; a previously unrecognized cytoplasmically dispersed NSP2 (dNSP2) is detected by an N-terminal binding MAb, and previously known viroplasmic NSP2 (vNSP2) is detected by a C-terminal binding MAb. Kinetic experiments in RV-infected cells demonstrate that dNSP2 is associated with NSP5 in nascent viroplasms that lack vNSP2. As viroplasms mature, dNSP2 remains in viroplasms, and the amount of diffuse cytoplasmic dNSP2 increases. vNSP2 is detected in increasing amounts later in infection in the maturing viroplasm, suggesting a conversion of dNSP2 into vNSP2. Immunoprecipitation experiments and reciprocal Western blot analysis confirm that there are two different forms of NSP2 that assemble in complexes with NSP5, VP1, VP2, and tubulin. dNSP2 associates with hypophosphorylated NSP5 and acetylated tubulin, which is correlated with stabilized microtubules, while vNSP2 associates with hyperphosphorylated NSP5. Mass spectroscopy analysis of NSP2 complexes immunoprecipitated from RV-infected cell lysates show both forms of NSP2 are phosphorylated, with a greater proportion of vNSP2 being phosphorylated compared to dNSP2. Together, these data suggest that dNSP2 interacts with viral proteins, including hypophosphorylated NSP5, to initiate viroplasm formation, while viroplasm maturation includes phosphorylation of NSP5 and vNSP2.
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21
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Desselberger U, Richards J, Tchertanov L, Lepault J, Lever A, Burrone O, Cohen J. Further characterisation of rotavirus cores: Ss(+)RNAs can be packaged in vitro but packaging lacks sequence specificity. Virus Res 2013; 178:252-63. [PMID: 24091366 PMCID: PMC3854842 DOI: 10.1016/j.virusres.2013.09.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/12/2013] [Accepted: 09/23/2013] [Indexed: 12/15/2022]
Abstract
Rotavirus (RV) cores were released from double-layered particles (DLPs) by high concentrations of CaCl2, purified and 'opened' by treatment with EDTA or EGTA. Under appropriate in vitro conditions DLPs have been shown to have transcriptase and 'open cores' replicase activity. Furthermore, it has been demonstrated that transcriptase activity and infectivity of native cores can be restored by transcapsidation with VP6, VP7 and VP4. The missing link for particle reconstitution in vitro has been the manipulation of 'open cores' to become functionally active cores again. The experiments described here were undertaken with the aim of exploring packaging of RV RNAs into opened cores in vitro. Rotavirus cores were opened by approximately 200μM EGTA, leading to the release of genomic dsRNA. Conversely, RV cores were found to be stable in the presence of minimum concentrations of Ca(2+), Mg(2+), spermidine(3+) and cobalthexamine(3+) of between 40 and 300 μM. Aggregates of purified cores were resolved in the presence of 0.3mM deoxycholate (minimum concentration). Core shells opened with EGTA were reconstituted by the addition of di- or trivalent cations within 2 min of the opening procedure. Addition of purified, baculovirus recombinant-expressed VP6 to native and reconstituted cores led to the formation of DLPs or DLP-like particles, which upon transfection into MA104 cells were infectious. The rescued infectivity likely originated in part from unopened and in part from reconstituted cores. Radiolabelled RV (+) ssRNAs could be packaged into reconstituted cores and DLPs, as indicated by resistance to RNase I digestion. The packaging reaction was, however, not RV RNA sequence-specific, since unrelated ssRNAs, such as those transcribed from HIV-2 cDNAs, were also packaged. The kinetics of packaging of homologous and heterologous RNAs were similar, as evidenced by competitive packaging assays. None of the packaged in vitro engineered RNA segments has so far been rescued into infectious virus.
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Affiliation(s)
- Ulrich Desselberger
- Virologie Moléculaire et Structurale, UMR 2472 du CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette Cédex, France; Molecular Immunology Group, International Centre for Genetic Engineering, Trieste, Italy; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
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22
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Viroplasm protein P9-1 of Rice black-streaked dwarf virus preferentially binds to single-stranded RNA in its octamer form, and the central interior structure formed by this octamer constitutes the major RNA binding site. J Virol 2013; 87:12885-99. [PMID: 24067964 DOI: 10.1128/jvi.02264-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The P9-1 protein of Rice black-streaked dwarf virus (RBSDV) is an essential part of the viroplasm. However, little is known about its nature or biological function in the viroplasm. In this study, the structure and function of P9-1 were analyzed for in vitro binding to nucleic acids. We found that the P9-1 protein preferentially bound to single-stranded versus double-stranded nucleic acids; however, the protein displayed no preference for RBSDV versus non-RBSDV single-stranded ssRNA (ssRNA). A gel mobility shift assay revealed that the RNA gradually shifted as increasing amounts of P9-1 were added, suggesting that multiple subunits of P9-1 bind to ssRNA. By using discontinuous blue native gel and chromatography analysis, we found that the P9-1 protein was capable of forming dimers, tetramers, and octamers. Strikingly, we demonstrated that P9-1 preferentially bound to ssRNA in the octamer, rather than the dimer, form. Deletion of the C-terminal arm resulted in P9-1 no longer forming octamers; consequently, the deletion mutant protein bound to ssRNA with significantly lower affinity and with fewer copies bound per ssRNA. Alanine substitution analysis revealed that electropositive amino acids among residues 25 to 44 are important for RNA binding and map to the central interior structure that was formed only by P9-1 octamers. Collectively, our findings provide novel insights into the structure and function of RBSDV viroplasm protein P9-1 binding to RNA.
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23
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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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24
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Campagna M, Marcos-Villar L, Arnoldi F, de la Cruz-Herrera CF, Gallego P, González-Santamaría J, González D, Lopitz-Otsoa F, Rodriguez MS, Burrone OR, Rivas C. Rotavirus viroplasm proteins interact with the cellular SUMOylation system: implications for viroplasm-like structure formation. J Virol 2013; 87:807-17. [PMID: 23115286 PMCID: PMC3554093 DOI: 10.1128/jvi.01578-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/25/2012] [Indexed: 01/27/2023] Open
Abstract
Posttranslational modification by SUMO provides functional flexibility to target proteins. Viruses interact extensively with the cellular SUMO modification system in order to improve their replication, and there are numerous examples of viral proteins that are SUMOylated. However, thus far the relevance of SUMOylation for rotavirus replication remains unexplored. In this study, we report that SUMOylation positively regulates rotavirus replication and viral protein production. We show that SUMO can be covalently conjugated to the viroplasm proteins VP1, VP2, NSP2, VP6, and NSP5. In addition, VP1, VP2, and NSP2 can also interact with SUMO in a noncovalent manner. We observed that an NSP5 SUMOylation mutant protein retains most of its activities, such as its interaction with VP1 and NSP2, the formation of viroplasm-like structures after the coexpression with NSP2, and the ability to complement in trans the lack of NSP5 in infected cells. However, this mutant is characterized by a high degree of phosphorylation and is impaired in the formation of viroplasm-like structures when coexpressed with VP2. These results reveal for the first time a positive role for SUMO modification in rotavirus replication, describe the SUMOylation of several viroplasm resident rotavirus proteins, and demonstrate a requirement for NSP5 SUMOylation in the production of viroplasm-like structures.
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Affiliation(s)
| | | | - Francesca Arnoldi
- Dipartimento Universitario Clinico di Scienze Mediche, Chirurgiche e della Salute, University of Trieste, Trieste, Italy
| | | | - Pedro Gallego
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | | | | | | | - Manuel S. Rodriguez
- Proteomics Unit, CIC bioGUNE, CIBERehd, Derio, Spain
- Ubiquitylation and Cancer Molecular Biology laboratory, Inbiomed, San Sebastian-Donostia, Gipuzkoa, Spain
| | - Oscar R. Burrone
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Carmen Rivas
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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Crystallographic Analysis of Rotavirus NSP2-RNA Complex Reveals Specific Recognition of 5' GG Sequence for RTPase Activity. J Virol 2012; 86:10547-57. [PMID: 22811529 PMCID: PMC3457270 DOI: 10.1128/jvi.01201-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Rotavirus nonstructural protein NSP2, a functional octamer, is critical for the formation of viroplasms, which are exclusive sites for replication and packaging of the segmented double-stranded RNA (dsRNA) rotavirus genome. As a component of replication intermediates, NSP2 is also implicated in various replication-related activities. In addition to sequence-independent single-stranded RNA-binding and helix-destabilizing activities, NSP2 exhibits monomer-associated nucleoside and 5' RNA triphosphatase (NTPase/RTPase) activities that are mediated by a conserved H225 residue within a narrow enzymatic cleft. Lack of a 5' γ-phosphate is a common feature of the negative-strand RNA [(-)RNA] of the packaged dsRNA segments in rotavirus. Strikingly, all (-)RNAs (of group A rotaviruses) have a 5' GG dinucleotide sequence. As the only rotavirus protein with 5' RTPase activity, NSP2 is implicated in the removal of the γ-phosphate from the rotavirus (-)RNA. To understand how NSP2, despite its sequence-independent RNA-binding property, recognizes (-)RNA to hydrolyze the γ-phosphate within the catalytic cleft, we determined a crystal structure of NSP2 in complex with the 5' consensus sequence of minus-strand rotavirus RNA. Our studies show that the 5' GG of the bound oligoribonucleotide interacts extensively with highly conserved residues in the NSP2 enzymatic cleft. Although these residues provide GG-specific interactions, surface plasmon resonance studies suggest that the C-terminal helix and other basic residues outside the enzymatic cleft account for sequence-independent RNA binding of NSP2. A novel observation from our studies, which may have implications in viroplasm formation, is that the C-terminal helix of NSP2 exhibits two distinct conformations and engages in domain-swapping interactions, which result in the formation of NSP2 octamer chains.
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Repeated circulation over 6years of intergenogroup mono-reassortant G2P[4] rotavirus strains with genotype N1 of the NSP2 gene. INFECTION GENETICS AND EVOLUTION 2012; 12:1202-12. [DOI: 10.1016/j.meegid.2012.04.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Revised: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 11/18/2022]
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Hu L, Crawford SE, Hyser JM, Estes MK, Prasad BVV. Rotavirus non-structural proteins: structure and function. Curr Opin Virol 2012; 2:380-8. [PMID: 22789743 DOI: 10.1016/j.coviro.2012.06.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 06/13/2012] [Accepted: 06/13/2012] [Indexed: 10/28/2022]
Abstract
The replication of rotavirus is a complex process that is orchestrated by an exquisite interplay between the rotavirus non-structural and structural proteins. Subsequent to particle entry and genome transcription, the non-structural proteins coordinate and regulate viral mRNA translation and the formation of electron-dense viroplasms that serve as exclusive compartments for genome replication, genome encapsidation and capsid assembly. In addition, non-structural proteins are involved in antagonizing the antiviral host response and in subverting important cellular processes to enable successful virus replication. Although far from complete, new structural studies, together with functional studies, provide substantial insight into how the non-structural proteins coordinate rotavirus replication. This brief review highlights our current knowledge of the structure-function relationships of the rotavirus non-structural proteins, as well as fascinating questions that remain to be understood.
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Affiliation(s)
- Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
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Selection and evolutionary analysis in the nonstructural protein NSP2 of rotavirus A. INFECTION GENETICS AND EVOLUTION 2012; 12:1355-61. [PMID: 22610044 DOI: 10.1016/j.meegid.2012.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 05/07/2012] [Accepted: 05/09/2012] [Indexed: 01/03/2023]
Abstract
Rotavirus A is the leading cause of acute gastroenteritis in infants and young children worldwide. The nonstructural protein 2 (NSP2) plays essential roles in the replication cycle of rotavirus and may play a role in protective immunity against rotavirus disease. Using a Bayesian approach, we measured the mutation rate of genotype N1 NSP2 gene sequences. The N1 genotype is the main NSP2 genotype associated with rotavirus strains causing severe disease, and was found to have a high mutation rate (8.7 × 10(-4) substitutions/site/year) in comparison to the rotavirus VP4 gene and rates of mutation in other RNA viruses. NSP2 has traditionally been considered as a conserved rotavirus protein and selection analysis indicated that the NSP2 protein was under strong negative selection, suggesting that most nucleotide substitutions were synonymous. This conservation is likely a result of functional constraints of NSP2 in the rotavirus replication cycle. Four sites of positive selection were identified; two of these (positions 249 and 255) were located in a previously characterised antibody binding epitope. The remaining sites were not located in known functional regions, and the reason for variation at these sites remains to be elucidated.
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Suzuki T, Soma J, Kuga K, Miyazaki A, Tsunemitsu H. Sequence and phylogenetic analyses of nonstructural protein 2 genes of species B porcine rotaviruses detected in Japan during 2001–2009. Virus Res 2012; 165:46-51. [DOI: 10.1016/j.virusres.2012.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/20/2011] [Accepted: 01/01/2012] [Indexed: 01/10/2023]
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Arnold MM, Brownback CS, Taraporewala ZF, Patton JT. Rotavirus variant replicates efficiently although encoding an aberrant NSP3 that fails to induce nuclear localization of poly(A)-binding protein. J Gen Virol 2012; 93:1483-1494. [PMID: 22442114 DOI: 10.1099/vir.0.041830-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The rotavirus (RV) non-structural protein NSP3 forms a dimer that has binding domains for the translation initiation factor eIF4G and for a conserved 3'-terminal sequence of viral mRNAs. Through these activities, NSP3 has been proposed to promote viral mRNA translation by directing circularization of viral polysomes. In addition, by disrupting interactions between eIF4G and the poly(A)-binding protein (PABP), NSP3 has been suggested to inhibit translation of host polyadenylated mRNAs and to stimulate relocalization of PABP from the cytoplasm to the nucleus. Herein, we report the isolation and characterization of SA11-4Fg7re, an SA11-4F RV derivative that contains a large sequence duplication initiating within the genome segment (gene 7) encoding NSP3. Our analysis showed that mutant NSP3 (NSP3m) encoded by SA11-4Fg7re is almost twice the size of the wild-type protein and retains the capacity to dimerize. However, in comparison to wild-type NSP3, NSP3m has a decreased capacity to interact with eIF4G and to suppress the translation of polyadenylated mRNAs. In addition, NSP3m fails to induce the nuclear accumulation of PABP in infected cells. Despite the defective activities of NSP3m, the levels of viral protein and progeny virus produced in SA11-4Fg7re- and SA11-4F-infected cells were indistinguishable. Collectively, these data are consistent with a role for NSP3 in suppressing host protein synthesis through antagonism of PABP activity, but also suggest that NSP3 functions may have little or no impact on the efficiency of virus replication in widely used RV-permissive cell lines.
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Affiliation(s)
- Michelle M Arnold
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive MSC 8026, Room 6314, Bethesda, MD 20892-8026, USA
| | - Catie Small Brownback
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive MSC 8026, Room 6314, Bethesda, MD 20892-8026, USA
| | - Zenobia F Taraporewala
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive MSC 8026, Room 6314, Bethesda, MD 20892-8026, USA
| | - John T Patton
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive MSC 8026, Room 6314, Bethesda, MD 20892-8026, USA
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Assembly of Large Icosahedral Double-Stranded RNA Viruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:379-402. [DOI: 10.1007/978-1-4614-0980-9_17] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Decroly E, Ferron F, Lescar J, Canard B. Conventional and unconventional mechanisms for capping viral mRNA. Nat Rev Microbiol 2011; 10:51-65. [PMID: 22138959 PMCID: PMC7097100 DOI: 10.1038/nrmicro2675] [Citation(s) in RCA: 328] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
mRNAs are protected at their 5′ ends by a cap structure consisting of an N7-methylated GTP molecule linked to the first transcribed nucleotide by a 5′–5′ triphosphate bond. The cap structure is essential for RNA splicing, export and stability, and allows the ribosomal complex to recognize mRNAs and ensure their efficient translation. Uncapped RNA molecules are degraded in cytoplasmic granular compartments called processing bodies and may be detected as 'non-self' by the host cell, triggering antiviral innate immune responses through the production of interferons. Conventional RNA capping (that is, of mRNAs from the host cell and from DNA viruses) requires hydrolysis of the 5′ γ-phosphate of RNA by an RNA triphosphatase, transfer of a GMP molecule onto the 5′-end of RNA by a guanylyltransferase, and methylation of this guanosine by an (guanine-N7)-methyltransferase. Subsequent methylations on the first and second transcribed nucleotides by (nucleoside-2′-O)-methyltransferases form cap-1 and cap-2 structures. Viruses have evolved highly diverse capping mechanisms to acquire cap structures using their own or cellular capping machineries, or by stealing cap structures from cellular mRNAs. Virally encoded RNA-capping machineries are diverse in terms of their genetic components, protein domain organization, enzyme structures, and reaction mechanisms and pathways, making viral RNA capping an attractive target for antiviral-drug design.
Capping the 5′ end of eukaryotic mRNAs with a 7-methylguanosine moiety enables efficient splicing, nuclear export and translation of mRNAs, and also limits their degradation by cellular exonucleases. Here, Canard and colleagues describe how viruses synthesize their own mRNA cap structures or steal them from host mRNAs, allowing efficient synthesis of viral proteins and avoidance of host innate immune responses. In the eukaryotic cell, capping of mRNA 5′ ends is an essential structural modification that allows efficient mRNA translation, directs pre-mRNA splicing and mRNA export from the nucleus, limits mRNA degradation by cellular 5′–3′ exonucleases and allows recognition of foreign RNAs (including viral transcripts) as 'non-self'. However, viruses have evolved mechanisms to protect their RNA 5′ ends with either a covalently attached peptide or a cap moiety (7-methyl-Gppp, in which p is a phosphate group) that is indistinguishable from cellular mRNA cap structures. Viral RNA caps can be stolen from cellular mRNAs or synthesized using either a host- or virus-encoded capping apparatus, and these capping assemblies exhibit a wide diversity in organization, structure and mechanism. Here, we review the strategies used by viruses of eukaryotic cells to produce functional mRNA 5′-caps and escape innate immunity.
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Affiliation(s)
- Etienne Decroly
- Centre National de Recherche Scientifique and Aix-Marseille Université, UMR 6098, Architecture et Fonction des Macromolécules Biologiques, 163 avenue de Luminy, 13288 Marseille cedex 09, France
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Crystallographic analysis reveals octamerization of viroplasm matrix protein P9-1 of Rice black streaked dwarf virus. J Virol 2011; 86:746-56. [PMID: 22072761 DOI: 10.1128/jvi.00826-11] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The P9-1 protein of Rice black streaked dwarf virus accumulates in viroplasm inclusions, which are structures that appear to play an important role in viral morphogenesis and are commonly found in viruses in the family Reoviridae. Crystallographic analysis of P9-1 revealed structural features that allow the protein to form dimers via hydrophobic interactions. Each dimer has carboxy-terminal regions, resembling arms, that extend to neighboring dimers, thereby uniting sets of four dimers via lateral hydrophobic interactions, to yield cylindrical octamers. The importance of these regions for the formation of viroplasm-like inclusions was confirmed by the absence of such inclusions when P9-1 was expressed without its carboxy-terminal arm. The octamers are vertically elongated cylinders resembling the structures formed by NSP2 of rotavirus, even though there are no significant similarities between the respective primary and secondary structures of the two proteins. Our results suggest that an octameric structure with an internal pore might be important for the functioning of the respective proteins in the events that occur in the viroplasm, which might include viral morphogenesis.
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Akita F, Miyazaki N, Hibino H, Shimizu T, Higashiura A, Uehara-Ichiki T, Sasaya T, Tsukihara T, Nakagawa A, Iwasaki K, Omura T. Viroplasm matrix protein Pns9 from rice gall dwarf virus forms an octameric cylindrical structure. J Gen Virol 2011; 92:2214-2221. [DOI: 10.1099/vir.0.032524-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The non-structural Pns9 protein of rice gall dwarf virus (RGDV) accumulates in viroplasm inclusions, which are structures that appear to play an important role in viral morphogenesis and are commonly found in host cells infected by viruses in the family Reoviridae. Immunofluorescence and immunoelectron microscopy of RGDV-infected vector cells in monolayers, using antibodies against Pns9 of RGDV and expression of Pns9 in Spodoptera frugiperda cells, demonstrated that Pns9 is the minimal viral factor necessary for formation of viroplasm inclusion during infection by RGDV. When Pns9 in solution was observed under a conventional electron microscope, it appeared as ring-like aggregates of approximately 100 Å in diameter. Cryo-electron microscopic analysis of these aggregates revealed cylinders of octameric Pns9, whose dimensions were similar to those observed under the conventional electron microscope. Octamerization of Pns9 in solution was confirmed by the results of size-exclusion chromatography. Among proteins of viruses that belong to the family Reoviridae whose three-dimensional structures are available, a matrix protein of the viroplasm of rotavirus, NSP2, forms similar octamers, an observation that suggests similar roles for Pns9 and NSP2 in morphogenesis in animal-infecting and in plant-infecting reoviruses.
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Affiliation(s)
- Fusamichi Akita
- National Agricultural Research Center, 3-1-1 Kan-nondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Naoyuki Miyazaki
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroyuki Hibino
- National Agricultural Research Center, 3-1-1 Kan-nondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Takumi Shimizu
- National Agricultural Research Center, 3-1-1 Kan-nondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Akifumi Higashiura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tamaki Uehara-Ichiki
- National Agricultural Research Center, 3-1-1 Kan-nondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Takahide Sasaya
- National Agricultural Research Center, 3-1-1 Kan-nondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Tomitake Tsukihara
- Department of Life Science, University of Hyogo, 3-2-1 Koto, Kamighori, Akoh, Hyogo 678-1297, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kenji Iwasaki
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshihiro Omura
- National Agricultural Research Center, 3-1-1 Kan-nondai, Tsukuba, Ibaraki 305-8666, Japan
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Donker NC, Foley M, Tamvakis DC, Bishop R, Kirkwood CD. Identification of an antibody-binding epitope on the rotavirus A non-structural protein NSP2 using phage display analysis. J Gen Virol 2011; 92:2374-2382. [PMID: 21697352 DOI: 10.1099/vir.0.032599-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The non-structural protein 2 (NSP2) of rotavirus has important roles in rotavirus replication associated with RNA binding, hydrolysis of NTPs and RNA, and helix destabilizing properties. A cell-culture assay using an NSP2-specific mAb and polyclonal antiserum to block virus replication showed a 73 and 96 % reduction in the amount of virus produced during replication, respectively. Phage display technology was used to identify the antibody-binding region on the NSP2 protein with the motif (244)T-(Y/F)-Ø-Ø-Ø-X-K-Ø-G(252), where Ø is a hydrophilic residue and X is any amino acid. This region was mapped to the three-dimensional NSP2 crystal structure to visualize the epitope. Analysis revealed identity to a region on NSP2 that mapped to a site exposed on the surface of the protein, which could possibly interfere with a functionally important region of the protein. Antibody binding to this region could disrupt the essential roles of NSP2, such as the formation of viroplasms with NSP5 or the interaction with viral RNA, thereby indicating a possible mechanism for the observed inhibition of virus replication. Genetic analysis of the putative binding region of NSP2 revealed a high level of conservation, suggesting that the region is under strict control.
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Affiliation(s)
- Nicole C Donker
- Department of Microbiology, La Trobe University, Bundoora, Victoria 3083, Australia
- Enteric Virus Group, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Michael Foley
- Department of Biochemistry, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Debra C Tamvakis
- Department of Biochemistry, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Ruth Bishop
- Enteric Virus Group, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Carl D Kirkwood
- Department of Microbiology, La Trobe University, Bundoora, Victoria 3083, Australia
- Enteric Virus Group, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
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Donker NC, Boniface K, Kirkwood CD. Phylogenetic analysis of rotavirus A NSP2 gene sequences and evidence of intragenic recombination. INFECTION GENETICS AND EVOLUTION 2011; 11:1602-7. [PMID: 21689784 DOI: 10.1016/j.meegid.2011.05.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 05/19/2011] [Accepted: 05/27/2011] [Indexed: 11/17/2022]
Abstract
The rotavirus non-structural protein NSP2 is one of the earliest and most abundant viral proteins produced during infection. This protein has multiple essential roles in the replication cycle involving RNA binding, viroplasm formation, helicase and can hydrolyse the γ-phosphate of RNA and NTPs acting as an RTPase and NTPase. In studying sequences from rotavirus strains isolated in Australia between 1984 and 2009, the NSP2 gene was seen to be highly conserved and clustered with defined NSP2 genotypes N1 and N2 according to the full genome based rotavirus classification system. Phylogenetic analysis indicated that NSP2 gene sequences isolated from Australian rotavirus strains formed four distinct lineages. Temporal variation was observed in several clusters during the 26 year period, with lineage D identified throughout the entire study period and lineage A only detected since 1999. Phylogenetic analysis and dendrograms identified NSP2 genes that exhibited reassortment between different virus VP7 genotypes, as well as a sequence from a human strain that grouped closely with the NSP2 genes of bovine rotavirus strains. This study also identified a sequence that fell between lineages and exhibited evidence of recombination, the first time that intergenic recombination has been detected in a NSP2 gene sequence. This study increases the understanding of the evolution mechanisms of NSP2 in view of improved vaccine design.
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Affiliation(s)
- Nicole C Donker
- Enteric Virus Group, Murdoch Childrens Research Institute, Royal Childrens Hospital, Parkville, Victoria 3052, Australia.
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37
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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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Wang Q, Tao T, Zhang Y, Wu W, Li D, Yu J, Han C. Rice black-streaked dwarf virus P6 self-interacts to form punctate, viroplasm-like structures in the cytoplasm and recruits viroplasm-associated protein P9-1. Virol J 2011; 8:24. [PMID: 21241517 PMCID: PMC3032713 DOI: 10.1186/1743-422x-8-24] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 01/18/2011] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Rice black-streaked dwarf virus (RBSDV), a member of the genus Fijivirus within the family Reoviridae, can infect several graminaceous plant species including rice, maize and wheat, and is transmitted by planthoppers. Although several RBSDV proteins have been studied in detail, functions of the nonstructural protein P6 are still largely unknown. RESULTS In the current study, we employed yeast two-hybrid assays, bimolecular fluorescence complementation and subcellular localization experiments to show that P6 can self-interact to form punctate, cytoplasmic viroplasm-like structures (VLS) when expressed alone in plant cells. The region from residues 395 to 659 is necessary for P6 self-interaction, whereas two polypeptides (residues 580-620 and 615-655) are involved in the subcellular localization of P6. Furthermore, P6 strongly interacts with the viroplasm-associated protein P9-1 and recruits P9-1 to localize in VLS. The P6 395-659 region is also important for the P6-P9-1 interaction, and deleting any region of P9-1 abolishes this heterologous interaction. CONCLUSIONS RBSDV P6 protein has an intrinsic ability to self-interact and forms VLS without other RBSDV proteins or RNAs. P6 recruits P9-1 to VLS by direct protein-protein interaction. This is the first report on the functionality of RBSDV P6 protein. P6 may be involved in the process of viroplasm nucleation and virus morphogenesis.
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Affiliation(s)
- Qian Wang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, P. R. China
| | - Tao Tao
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, P. R. China
| | - Yanjing Zhang
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, P. R. China
| | - Wenqi Wu
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, P. R. China
| | - Dawei Li
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, P. R. China
| | - Jialin Yu
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, P. R. China
| | - Chenggui Han
- State Key Laboratory for Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, P. R. China
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Dual selection mechanisms drive efficient single-gene reverse genetics for rotavirus. Proc Natl Acad Sci U S A 2010; 107:18652-7. [PMID: 20937889 DOI: 10.1073/pnas.1011948107] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Current methods for engineering the segmented double-stranded RNA genome of rotavirus (RV) are limited by inefficient recovery of the recombinant virus. In an effort to expand the utility of RV reverse genetics, we developed a method to recover recombinant viruses in which independent selection strategies are used to engineer single-gene replacements. We coupled a mutant SA11 RV encoding a temperature-sensitive (ts) defect in the NSP2 protein with RNAi-mediated degradation of NSP2 mRNAs to isolate a virus containing a single recombinant gene that evades both selection mechanisms. Recovery is rapid and simple; after two rounds of selective passage the recombinant virus reaches titers of ≥10(4) pfu/mL. We used this reverse genetics method to generate a panel of viruses with chimeric NSP2 genes. For one of the chimeric viruses, the introduced NSP2 sequence was obtained from a pathogenic, noncultivated human RV isolate, demonstrating that this reverse genetics system can be used to study the molecular biology of circulating RVs. Combining characterized RV ts mutants and validated siRNA targets should permit the extension of this "two-hit" reverse genetics methodology to other RV genes. Furthermore, application of a dual selection strategy to previously reported reverse genetics methods for RV may enhance the efficiency of recombinant virus recovery.
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Butan C, Tucker P. Insights into the role of the non-structural protein 2 (NS2) in Bluetongue virus morphogenesis. Virus Res 2010; 151:109-17. [DOI: 10.1016/j.virusres.2010.05.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2010] [Revised: 05/25/2010] [Accepted: 05/27/2010] [Indexed: 10/19/2022]
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Maroniche GA, Mongelli VC, Peralta AV, Distéfano AJ, Llauger G, Taboga OA, Hopp EH, del Vas M. Functional and biochemical properties of Mal de Río Cuarto virus (Fijivirus, Reoviridae) P9-1 viroplasm protein show further similarities to animal reovirus counterparts. Virus Res 2010; 152:96-103. [PMID: 20600394 DOI: 10.1016/j.virusres.2010.06.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 06/14/2010] [Indexed: 10/19/2022]
Abstract
Mal de Río Cuarto virus (MRCV) is a plant virus of the genus Fijivirus within the family Reoviridae that infects several monocotyledonous species and is transmitted by planthoppers in a persistent and propagative manner. Other members of the family replicate in viral inclusion bodies (VIBs) termed viroplasms that are formed in the cytoplasm of infected plant and insect cells. In this study, the protein coded by the first ORF of MRCV segment S9 (P9-1) was shown to establish cytoplasmic inclusion bodies resembling viroplasms after transfection of Spodoptera frugiperda insect cells. In accordance, MRCV P9-1 self-associates giving rise to high molecular weight complexes when expressed in bacteria. Strong self-interaction was also evidenced by yeast two-hybrid assays. Furthermore, biochemical characterization showed that MRCV P9-1 bound single stranded RNA and had ATPase activity. Finally, the MRCV P9-1 region required for the formation of VIB-like structures was mapped to the protein carboxy-terminal half. This extensive functional and biochemical characterization of MRCV P9-1 revealed further similarities between plant and animal reovirus viroplasm proteins.
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Affiliation(s)
- Guillermo A Maroniche
- Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria, Las Cabañas y Los Reseros s/n., Hurlingham, Buenos Aires, Argentina
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Sequestration of free tubulin molecules by the viral protein NSP2 induces microtubule depolymerization during rotavirus infection. J Virol 2009; 84:2522-32. [PMID: 20032187 DOI: 10.1128/jvi.01883-09] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Microtubules, components of the cell cytoskeleton, play a central role in cellular trafficking. Here we show that rotavirus infection leads to a remodeling of the microtubule network together with the formation of tubulin granules. While most microtubules surrounding the nucleus depolymerize, others appear packed at the cell periphery. In microtubule depolymerization areas, tubulin granules are observed; they colocalize with viroplasms, viral compartments formed by interactions between rotavirus proteins NSP2 and NSP5. With purified proteins, we show that tubulin directly interacts in vitro with NSP2 but not with NSP5. The binding of NSP2 to tubulin is independent of its phosphatase activity. The comparison of three-dimensional (3-D) reconstructions of NSP2 octamers alone or associated with tubulin reveals electron densities in the positively charged grooves of NSP2 that we attribute to tubulin. Site-directed mutagenesis of NSP2 and competition assays between RNA and tubulin for NSP2 binding confirm that tubulin binds to these charged grooves of NSP2. Although the tubulin position within NSP2 grooves cannot be precisely determined, the tubulin C-terminal H12 alpha-helix could be involved in the interaction. NSP2 overexpression and rotavirus infection produce similar effects on the microtubule network. NSP2 depolymerizes microtubules and leads to tubulin granule formation. Our results demonstrate that tubulin is a viroplasm component and reveal an original mechanism. Tubulin sequestration by NSP2 induces microtubule depolymerization. This depolymerization probably reroutes the cell machinery by inhibiting trafficking and functions potentially involved in defenses to viral infections.
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Maes P, Matthijnssens J, Rahman M, Van Ranst M. RotaC: a web-based tool for the complete genome classification of group A rotaviruses. BMC Microbiol 2009; 9:238. [PMID: 19930627 PMCID: PMC2785824 DOI: 10.1186/1471-2180-9-238] [Citation(s) in RCA: 345] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 11/23/2009] [Indexed: 01/31/2023] Open
Abstract
Background Group A rotaviruses are the most common cause of severe diarrhea in infants and children worldwide and continue to have a major global impact on childhood morbidity and mortality. In recent years, considerable research efforts have been devoted to the development of two new live, orally administered vaccines. Although both vaccines have proven to confer a good protection against severe rotavirus gastroenteritis, these vaccines will have to be screened and may have to be updated regularly to reflect temporal and spatial genotype fluctuations. In this matter, the genetic characterization of circulating and new emerging rotavirus strains will need to be compulsory and accurate. An extended classification system for rotaviruses in which all the 11 genomic RNA segments are used, has been proposed recently. The use of this classification system will help to elucidate the role of gene reassortments in the generation of genetic diversity, host range restriction, co-segregation of certain gene segments, and in adaptation to a new host species. Results Here we present a web-based tool that can be used for fast rotavirus genotype differentiation of all 11 group A rotavirus gene segments according to the new guidelines proposed by the Rotavirus Classification Working Group (RCWG). Conclusion With the increasing sequencing efforts that are being conducted around the world to unravel complete rotavirus genomes of human and animal origin, this tool will be of great help to analyze and correctly classify the large amount of new data. The web-based tool is freely available at http://rotac.regatools.be.
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Affiliation(s)
- Piet Maes
- Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B3000 Leuven, Belgium.
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44
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Multimerization of hepatitis delta antigen is a critical determinant of RNA binding specificity. J Virol 2009; 84:1406-13. [PMID: 19923178 DOI: 10.1128/jvi.01723-09] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Hepatitis delta virus (HDV) RNA forms an unbranched rod structure that is associated with hepatitis delta antigen (HDAg) in cells replicating HDV. Previous in vitro binding experiments using bacterially expressed HDAg showed that the formation of a minimal ribonucleoprotein complex requires an HDV unbranched rod RNA of at least about 300 nucleotides (nt) and suggested that HDAg binds the RNA as a multimer of fixed size. The present study specifically examines the role of HDAg multimerization in the formation of the HDV ribonucleoprotein complex (RNP). Disruption of HDAg multimerization by site-directed mutagenesis was found to profoundly alter the nature of RNP formation. Mutant HDAg proteins defective for multimerization exhibited neither the 300-nt RNA size requirement for binding nor specificity for the unbranched rod structure. The results unambiguously demonstrate that HDAg binds HDV RNA as a multimer and that the HDAg multimer is formed prior to binding the RNA. RNP formation was found to be temperature dependent, which is consistent with conformational changes occurring on binding. Finally, analysis of RNPs constructed with unbranched rod RNAs successively longer than the minimum length indicated that multimeric binding is not limited to the first HDAg bound and that a minimum RNA length of between 604 and 714 nt is required for binding of a second multimer. The results confirm the previous proposal that HDAg binds as a large multimer and demonstrate that the multimer is a critical determinant of the structure of the HDV RNP.
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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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Kirkwood CD, Boniface K, Richardson S, Taraporewala ZF, Patton JT, Bishop RF. Non-structural protein NSP2 induces heterotypic antibody responses during primary rotavirus infection and reinfection in children. J Med Virol 2008; 80:1090-8. [PMID: 18428132 DOI: 10.1002/jmv.21160] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Rotaviruses are the single most important causes of severe acute diarrhoea in children worldwide. Despite success in developing vaccines, there is still a lack of knowledge about many components of the immune response, particularly those to non-structural proteins. This study established radioimmunoprecipitation (RIP) assays using labeled G1P[8], G2P[4], and G4P[6] human rotaviruses to examine the spectrum and duration of rotavirus antibodies in sera collected sequentially for 18-36 months from 27 children after hospitalization for primary rotavirus gastroenteritis. Five children experienced rotavirus re-infections. Primary responses detected to non-structural protein NSP2 declined to baseline after 100-150 days. Responses were heterotypic between NSP2 of G1P[8] and G4P[8] rotaviruses. Re-infections after 465-786 days boosted antibody levels to NSP2of both serotypes, together with the appearance of anti-NSP2 to G2P[4], even though there was no evidence of infection with this serotype. We developed an enzyme-immunoassay to measure sequential levels of anti-NSP2 IgG and IgA, using recombinant (heterotypic) NSP2 derived from SA11 (G3P[2]). Anti-NSP2 IgG and IgA were detected in sera from 23/23 (100%) and 18/24 (75%) of children after primary infection, declined to baseline after 100-150 days, were boosted after rotavirus re-infections, and again declined to baseline 150 days later. Anti-NSP2 IgA was also detected after primary infection, in duodenal juice from 14/16 (87%), and faecal extract from 11/19 (57%) of children. Sequential estimation of anti-NSP2 EIA levels in sera could be a sensitive index of rotavirus infection and re-infection. The potential of anti-NSP2 to limit viral replication after re-infection deserves further study.
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Affiliation(s)
- Carl D Kirkwood
- Enteric Virus Research Group, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Australia.
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Bar-Magen T, Spencer E, Patton JT. An ATPase activity associated with the rotavirus phosphoprotein NSP5. Virology 2007; 369:389-99. [PMID: 17825341 PMCID: PMC2702534 DOI: 10.1016/j.virol.2007.07.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2007] [Revised: 07/04/2007] [Accepted: 07/25/2007] [Indexed: 02/02/2023]
Abstract
Interactions between NSP5 and NSP2 drive the formation of viroplasms, sites of genome replication and packaging in rotavirus-infected cells. The serine-threonine-rich NSP5 transitions between hypo- and hyper-phosphorylated isomers during the replication cycle. In this study, we determined that purified recombinant NSP5 has a Mg2+-dependent ATP-specific triphosphatase activity that generates free ADP and Pi (Vmax of 19.33 fmol of product/min/pmol of enzyme). The ATPase activity was correlated with low levels of NSP5 phosphorylation, suggestive of a possible link between ATP hydrolysis and an NSP5 autokinase activity. Mutagenesis showed that the critical residue (Ser67) needed for NSP5 hyperphosphorylation by cellular casein kinase-like enzymes has no role in the ATPase or autokinase activities of NSP5. Through its NDP kinase activity, the NSP2 octamer may support NSP5 phosphorylation by creating a constant source of ATP molecules for the autokinase activity of NSP5 and for cellular kinases associated with NSP5.
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Affiliation(s)
- Tamara Bar-Magen
- Laboratorio de Virologia, Facultad de Quimica y Biologia, Universidad de Santiago, Santauthor: Laboratory of Infectious Diseases, NIAID, National, Institutes of Health, 50 South Drive, MSC 8026, Room 6314, Bethesda, MD 20892-8026, USA, Phone: (301) 594-1615, Fax: (301) 496-8312,
| | - Eugenio Spencer
- Laboratorio de Virologia, Facultad de Quimica y Biologia, Universidad de Santiago, Santauthor: Laboratory of Infectious Diseases, NIAID, National, Institutes of Health, 50 South Drive, MSC 8026, Room 6314, Bethesda, MD 20892-8026, USA, Phone: (301) 594-1615, Fax: (301) 496-8312,
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Kumar M, Jayaram H, Vasquez-Del Carpio R, Jiang X, Taraporewala ZF, Jacobson RH, Patton JT, Prasad BVV. Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals a nucleoside diphosphate kinase-like activity. J Virol 2007; 81:12272-84. [PMID: 17804496 PMCID: PMC2168982 DOI: 10.1128/jvi.00984-07] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rotavirus, the major pathogen of infantile gastroenteritis, carries a nonstructural protein, NSP2, essential for viroplasm formation and genome replication/packaging. In addition to RNA-binding and helix-destabilizing properties, NSP2 exhibits nucleoside triphosphatase activity. A conserved histidine (H225) functions as the catalytic residue for this enzymatic activity, and mutation of this residue abrogates genomic double-stranded RNA synthesis without affecting viroplasm formation. To understand the structural basis of the phosphatase activity of NSP2, we performed crystallographic analyses of native NSP2 and a functionally defective H225A mutant in the presence of nucleotides. These studies showed that nucleotides bind inside a cleft between the two domains of NSP2 in a region that exhibits structural similarity to ubiquitous cellular HIT (histidine triad) proteins. Only minor conformational alterations were observed in the cleft upon nucleotide binding and hydrolysis. This hydrolysis involved the formation of a stable phosphohistidine intermediate. These observations, reminiscent of cellular nucleoside diphosphate (NDP) kinases, prompted us to investigate whether NSP2 exhibits phosphoryl-transfer activity. Bioluminometric assay showed that NSP2 exhibits an NDP kinase-like activity that transfers the bound phosphate to NDPs. However, NSP2 is distinct from the highly conserved cellular NDP kinases in both its structure and catalytic mechanism, thus making NSP2 a potential target for antiviral drug design. With structural similarities to HIT proteins, which are not known to exhibit NDP kinase activity, NSP2 represents a unique example among structure-activity relationships. The newly observed phosphoryl-transfer activity of NSP2 may be utilized for homeostasis of nucleotide pools in viroplasms during genome replication.
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Affiliation(s)
- Mukesh Kumar
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Fritz D, Stefanovic B. RNA-binding protein RBMS3 is expressed in activated hepatic stellate cells and liver fibrosis and increases expression of transcription factor Prx1. J Mol Biol 2007; 371:585-95. [PMID: 17586524 PMCID: PMC1976254 DOI: 10.1016/j.jmb.2007.06.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 06/04/2007] [Accepted: 06/05/2007] [Indexed: 12/01/2022]
Abstract
Hepatic stellate cells (HSCs) are mesenchymal cells of the liver, activation of which is responsible for excessive synthesis of extracellular matrix, including type I collagen, and development of liver fibrosis. The activation of HSCs is driven by transcription factors and pair-related homeobox transcription factor Prx1 was identified as one of the transcription factors involved in this process, because transcription of collagen alpha1(I) gene is stimulated by Prx1 in HSCs and in the liver. Here, we show that expression of the RNA-binding protein RBMS3 is upregulated in the activation of HSCs and fibrotic livers. Immunoprecipitation followed by differential display identified Prx1 mRNA as one of the mRNAs interacting with RBMS3. The RBMS3 sequence-specific binding site was mapped to 60 nt located 1946 nt 3' of the stop codon of Prx1 mRNA. Ectopic expression of RBMS3 in quiescent HSCs, which express trace amounts of type I collagen, increased expression of Prx1 mRNA and collagen alpha1(I) mRNA. Expression of reporter Prx1 mRNA containing the RBMS3 binding site was higher than the mRNA lacking this site. Over-expression of RBMS3 further increased the steady-state level of the reporter mRNA-containing RBMS3 binding site, but had no effect on the mRNA lacking this site. Binding of RBMS3 to the Prx1 3' UTR increased the half-life of this mRNA, resulting in increased protein synthesis. These results suggest that RBMS3, by binding Prx1 mRNA in a sequence-specific manner, controls Prx1 expression and indirectly collagen synthesis. This is the first description of the function of RBMS3, as a key regulator of profibrotic potential of HSCs, representing a novel mechanism by which activated HSCs contribute to liver fibrosis.
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Affiliation(s)
- Dillon Fritz
- Department of Biomedical Science, College of Medicine, Florida State University, Tallahassee, FL 32306-4300, USA
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Su YP, Shien JH, Liu HJ, Yin HS, Lee LH. Avian reovirus core protein μA expressed in Escherichia coli possesses both NTPase and RTPase activities. J Gen Virol 2007; 88:1797-1805. [PMID: 17485541 DOI: 10.1099/vir.0.82592-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of the amino acid sequence of core protein μA of avian reovirus has indicated that it may share similar functions to protein μ2 of mammalian reovirus. Since μ2 displayed both nucleotide triphosphatase (NTPase) and RNA triphosphatase (RTPase) activities, the purified recombinant μA ( μA) was designed and used to test these activities. μA was thus expressed in bacteria with a 4.5 kDa fusion peptide and six His tags at its N terminus. Results indicated that μA possessed NTPase activity that enabled the protein to hydrolyse theβ–γphosphoanhydride bond of all four NTPs, since NDPs were the only radiolabelled products observed. The substrate preference was ATP>CTP>GTP>UTP, based on the estimatedkcatvalues. Alanine substitutions for lysines 408 and 412 (K408A/K412A) in a putative nucleotide-binding site of μA abolished NTPase activity, further suggesting that NTPase activity is attributable to protein μA. The activity of μA is dependent on the divalent cations Mg2+or Mn2+, but not Ca2+or Zn2+. Optimal NTPase activity of μA was achieved between pH 5.5 and 6.0. In addition, μA enzymic activity increased with temperature up to 40 °C and was almost totally inhibited at temperatures higher than 55 °C. Tests of phosphate release from RNA substrates with μA or K408A/K412A μA indicated that μA, but not K408A/K412A μA, displayed RTPase activity. The results suggested that both NTPase and RTPase activities of μA might be carried out at the same active site, and that protein μA could play important roles during viral RNA synthesis.
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Affiliation(s)
- Yu Pin Su
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Jui Huang Shien
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Hung Jen Liu
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
| | - Hsien Sheng Yin
- Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Long Huw Lee
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung 402, Taiwan
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