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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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2
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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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3
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Carpenter M, Kopanke J, Lee J, Rodgers C, Reed K, Sherman TJ, Graham B, Cohnstaedt LW, Wilson WC, Stenglein M, Mayo C. Evaluating Temperature Effects on Bluetongue Virus Serotype 10 and 17 Coinfection in Culicoides sonorensis. Int J Mol Sci 2024; 25:3063. [PMID: 38474308 PMCID: PMC10932384 DOI: 10.3390/ijms25053063] [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: 12/01/2023] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Bluetongue virus (BTV) is a segmented, double-stranded RNA virus transmitted by Culicoides midges that infects ruminants. As global temperatures increase and geographical ranges of midges expand, there is increased potential for BTV outbreaks from incursions of novel serotypes into endemic regions. However, an understanding of the effect of temperature on reassortment is lacking. The objectives of this study were to compare how temperature affected Culicoides survival, virogenesis, and reassortment in Culicoides sonorensis coinfected with two BTV serotypes. Midges were fed blood meals containing BTV-10, BTV-17, or BTV serotype 10 and 17 and maintained at 20 °C, 25 °C, or 30 °C. Midge survival was assessed, and pools of midges were collected every other day to evaluate virogenesis of BTV via qRT-PCR. Additional pools of coinfected midges were collected for BTV plaque isolation. The genotypes of plaques were determined using next-generation sequencing. Warmer temperatures impacted traits related to vector competence in offsetting ways: BTV replicated faster in midges at warmer temperatures, but midges did not survive as long. Overall, plaques with BTV-17 genotype dominated, but BTV-10 was detected in some plaques, suggesting parental strain fitness may play a role in reassortment outcomes. Temperature adds an important dimension to host-pathogen interactions with implications for transmission and evolution.
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Affiliation(s)
- Molly Carpenter
- Department of Microbiology, Immunology and Pathology, Colorado State University, 1601 Campus Delivery, Fort Collins, CO 80526, USA; (M.C.); (J.L.); (C.R.); (B.G.); (M.S.)
| | - Jennifer Kopanke
- Department of Comparative Medicine, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Justin Lee
- Department of Microbiology, Immunology and Pathology, Colorado State University, 1601 Campus Delivery, Fort Collins, CO 80526, USA; (M.C.); (J.L.); (C.R.); (B.G.); (M.S.)
| | - Case Rodgers
- Department of Microbiology, Immunology and Pathology, Colorado State University, 1601 Campus Delivery, Fort Collins, CO 80526, USA; (M.C.); (J.L.); (C.R.); (B.G.); (M.S.)
| | - Kirsten Reed
- Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Tyler J. Sherman
- Diagnostic Medicine Center, Colorado State University, 2450 Gillette Drive, Fort Collins, CO 80526, USA;
| | - Barbara Graham
- Department of Microbiology, Immunology and Pathology, Colorado State University, 1601 Campus Delivery, Fort Collins, CO 80526, USA; (M.C.); (J.L.); (C.R.); (B.G.); (M.S.)
| | - Lee W. Cohnstaedt
- Foreign Arthropod-Borne Animal Diseases Research Unit, The National Bio and Agro-Defense Facility, USDA Agricultural Research Service, P.O. Box 1807, Manhattan, KS 66505, USA; (L.W.C.); (W.C.W.)
| | - William C. Wilson
- Foreign Arthropod-Borne Animal Diseases Research Unit, The National Bio and Agro-Defense Facility, USDA Agricultural Research Service, P.O. Box 1807, Manhattan, KS 66505, USA; (L.W.C.); (W.C.W.)
| | - Mark Stenglein
- Department of Microbiology, Immunology and Pathology, Colorado State University, 1601 Campus Delivery, Fort Collins, CO 80526, USA; (M.C.); (J.L.); (C.R.); (B.G.); (M.S.)
| | - Christie Mayo
- Department of Microbiology, Immunology and Pathology, Colorado State University, 1601 Campus Delivery, Fort Collins, CO 80526, USA; (M.C.); (J.L.); (C.R.); (B.G.); (M.S.)
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4
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Anderson ML, Sullivan OM, Nichols SL, Kaylor L, Kelly DF, McDonald Esstman S. Rotavirus core shell protein sites that regulate intra-particle polymerase activity. J Virol 2023; 97:e0086023. [PMID: 37830817 PMCID: PMC10617381 DOI: 10.1128/jvi.00860-23] [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: 06/06/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Rotaviruses are important causes of severe gastroenteritis in young children. A characteristic feature of rotaviruses is that they copy ribonucleic acid (RNA) inside of the viral particle. In fact, the viral polymerase (VP1) only functions when it is connected to the viral inner core shell protein (VP2). Here, we employed a biochemical assay to identify which sites of VP2 are critical for regulating VP1 activity. Specifically, we engineered VP2 proteins to contain amino acid changes at structurally defined sites and assayed them for their capacity to support VP1 function in a test tube. Through this work, we were able to identify several VP2 residues that appeared to regulate the activity of the polymerase, positively and negatively. These results are important because they help explain how rotavirus synthesizes its RNA while inside of particles and they identify targets for the future rational design of drugs to prevent rotavirus disease.
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Affiliation(s)
| | - Owen M. Sullivan
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Sarah L. Nichols
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Liam Kaylor
- Department of Biomedical Engineering, State University, University Park, Pennsylvania, USA
| | - Deborah F. Kelly
- Department of Biomedical Engineering, State University, University Park, Pennsylvania, USA
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Zhang Q, Gao Y, Baker ML, Liu S, Jia X, Xu H, He J, Kaelber JT, Weng S, Jiang W. The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization. PLoS Pathog 2023; 19:e1011341. [PMID: 37083840 PMCID: PMC10155992 DOI: 10.1371/journal.ppat.1011341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/03/2023] [Accepted: 04/02/2023] [Indexed: 04/22/2023] Open
Abstract
Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell and carry out genome replication and transcription inside the virion. Several cryo-electron microscopy (cryo-EM) structures of reoviruses with 9, 10 or 11 segmented dsRNA genomes have revealed insights into genome arrangement and transcription. However, the structure and genome arrangement of 12-segmented Reovirales members remain poorly understood. Using cryo-EM, we determined the structure of mud crab reovirus (MCRV), a 12-segmented dsRNA virus that is a putative member of Reovirales in the non-turreted Sedoreoviridae family, to near-atomic resolutions with icosahedral symmetry (3.1 Å) and without imposing icosahedral symmetry (3.4 Å). These structures revealed the organization of the major capsid proteins in two layers: an outer T = 13 layer consisting of VP12 trimers and unique VP11 clamps, and an inner T = 1 layer consisting of VP3 dimers. Additionally, ten RNA dependent RNA polymerases (RdRp) were well resolved just below the VP3 layer but were offset from the 5-fold axes and arranged with D5 symmetry, which has not previously been seen in other members of Reovirales. The N-termini of VP3 were shown to adopt four unique conformations; two of which anchor the RdRps, while the other two conformations are likely involved in genome organization and capsid stability. Taken together, these structures provide a new level of understanding for capsid stabilization and genome organization of segmented dsRNA viruses.
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Affiliation(s)
- Qinfen Zhang
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanzhu Gao
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at the University of Texas Health Science Center, Houston, Texas, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shanshan Liu
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xudong Jia
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Haidong Xu
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Shaoping Weng
- State key lab for biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
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6
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Kopanke J, Carpenter M, Lee J, Reed K, Rodgers C, Burton M, Lovett K, Westrich JA, McNulty E, McDermott E, Barbera C, Cavany S, Rohr JR, Perkins TA, Mathiason CK, Stenglein M, Mayo C. Bluetongue Research at a Crossroads: Modern Genomics Tools Can Pave the Way to New Insights. Annu Rev Anim Biosci 2022; 10:303-324. [PMID: 35167317 DOI: 10.1146/annurev-animal-051721-023724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bluetongue virus (BTV) is an arthropod-borne, segmented double-stranded RNA virus that can cause severe disease in both wild and domestic ruminants. BTV evolves via several key mechanisms, including the accumulation of mutations over time and the reassortment of genome segments.Additionally, BTV must maintain fitness in two disparate hosts, the insect vector and the ruminant. The specific features of viral adaptation in each host that permit host-switching are poorly characterized. Limited field studies and experimental work have alluded to the presence of these phenomena at work, but our understanding of the factors that drive or constrain BTV's genetic diversification remains incomplete. Current research leveraging novel approaches and whole genome sequencing applications promises to improve our understanding of BTV's evolution, ultimately contributing to the development of better predictive models and management strategies to reduce future impacts of bluetongue epizootics.
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Affiliation(s)
- Jennifer Kopanke
- Office of the Campus Veterinarian, Washington State University, Spokane, Washington, USA;
| | - Molly Carpenter
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Justin Lee
- Genomic Sequencing Laboratory, Centers for Disease Control and Prevention, Atlanta, Georgia, USA;
| | - Kirsten Reed
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Case Rodgers
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Mollie Burton
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Kierra Lovett
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Joseph A Westrich
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Erin McNulty
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Emily McDermott
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, Arkansas, USA;
| | - Carly Barbera
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - Sean Cavany
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - Jason R Rohr
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; , , ,
| | - Candace K Mathiason
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Mark Stenglein
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
| | - Christie Mayo
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA; , , , , , , , , ,
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Liu H, Cheng L. Viral Capsid and Polymerase in Reoviridae. Subcell Biochem 2022; 99:525-552. [PMID: 36151388 DOI: 10.1007/978-3-031-00793-4_17] [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] [Indexed: 06/16/2023]
Abstract
The members of the family Reoviridae (reoviruses) consist of 9-12 discrete double-stranded RNA (dsRNA) segments enclosed by single, double, or triple capsid layers. The outer capsid proteins of reoviruses exhibit the highest diversity in both sequence and structural organization. By contrast, the conserved RNA-dependent RNA polymerase (RdRp) structure in the conserved innermost shell in all reoviruses suggests that they share common transcriptional regulatory mechanisms. After reoviruses are delivered into the cytoplasm of a host cell, their inner capsid particles (ICPs) remain intact and serve as a stable nanoscale machine for RNA transcription and capping performed using enzymes in ICPs. Advances in cryo-electron microscopy have enabled the reconstruction at near-atomic resolution of not only the icosahedral capsid, including capping enzymes, but also the nonicosahedrally distributed complexes of RdRps within the capsid at different transcriptional stages. These near-atomic resolution structures allow us to visualize highly coordinated structural changes in the related enzymes, genomic RNA, and capsid protein during reovirus transcription. In addition, reoviruses encode their own enzymes for nascent RNA capping before RNA releasing from their ICPs.
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Affiliation(s)
- Hongrong Liu
- Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China.
| | - Lingpeng Cheng
- Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China.
- School of Life Sciences, Tsinghua University, Beijing, China.
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8
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Abstract
The RNA-dependent RNA polymerase (RdRp) of all known double-stranded RNA viruses is located within the viral particle and is responsible for the transcription and replication of the viral genome. Through an RT-PCR assay, we determined that purified virions, in vitro translated RdRp proteins, and purified recombinant RdRp proteins of partitiviruses also have reverse transcriptase (RT) function. We show that partitivirus RdRps 1) synthesized DNA from homologous and heterologous dsRNA templates; 2) are active using both ssRNA and dsRNA templates; and 3) are active at lower temperatures compared to an optimal reaction temperature of commercial RT enzymes. This finding poses an intriguing question: why do partitiviruses, with dsRNA genomes, have a polymerase with RT functions? In comparison, 3Dpol, the RdRp of poliovirus, did not show any RT activity. Our findings lead us to propose a new evolutionary model for RNA viruses where the RdRp of dsRNA viruses could be the ancestor of RdRps.
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Affiliation(s)
- Mahtab Peyambari
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, PA, USA
| | | | - Marilyn J Roossinck
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, PA, USA
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9
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Chávez-Maya F, García-Espinosa G, López-Arellano ME, Padilla-Noriega L. Mutations in the VP2 gene of rotavirus associated with benzimidazole sensitivity. Virus Res 2020; 291:198189. [PMID: 33049307 DOI: 10.1016/j.virusres.2020.198189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/23/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022]
Abstract
Rotavirus species A (RVA) is the etiological agent of acute gastroenteritis in young individuals of various animal species, including humans. Vaccination has helped to reduce the impact of these viruses on humans and some species of domestic mammals, but they do not confer complete immunity, so antirotavirus agents are another important control option. In this study, millimolar concentrations of benzimidazole inhibited the replication of the Rhesus rotavirus (RRV) strain of RVA. Two mutants partially resistant to the inhibitory effect of benzimidazole were independently selected, and their genomes and those of their parental strains were fully sequenced. Most (7/11) mutations occurred in the gene that encodes the VP2 protein, and similarly most of the missense mutations (5/9), including the only one shared by the two mutants (G2,414 → R[G/A], D800 N), occurred in the VP2 gene. Our results identify the VP2 gene as the primary target affected by benzimidazole.
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Affiliation(s)
- Fernando Chávez-Maya
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Coyoacán 04510, Ciudad de México, Mexico.
| | - Gary García-Espinosa
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Coyoacán 04510, Ciudad de México, Mexico.
| | - María Eugenia López-Arellano
- Departamento de Helmintología, Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, INIFAP-México, Jiutepec 62550, Morelos, Mexico.
| | - Luis Padilla-Noriega
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, edificio A, primer piso, Coyoacán 04510, Ciudad de México, Mexico.
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10
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Conserved Rotavirus NSP5 and VP2 Domains Interact and Affect Viroplasm. J Virol 2020; 94:JVI.01965-19. [PMID: 31915278 DOI: 10.1128/jvi.01965-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/21/2019] [Indexed: 01/15/2023] Open
Abstract
One step of the life cycle common to all rotaviruses (RV) studied so far is the formation of viroplasms, membrane-less cytosolic inclusions providing a microenvironment for early morphogenesis and RNA replication. Viroplasm-like structures (VLS) are simplified viroplasm models consisting of complexes of nonstructural protein 5 (NSP5) with the RV core shell VP2 or NSP2. We identified and characterized the domains required for NSP5-VP2 interaction and VLS formation. VP2 mutations L124A, V865A, and I878A impaired both NSP5 hyperphosphorylation and NSP5/VP2 VLS formation. Moreover, NSP5-VP2 interaction does not depend on NSP5 hyperphosphorylation. The NSP5 tail region is required for VP2 interaction. Notably, VP2 L124A expression acts as a dominant-negative element by disrupting the formation of either VLS or viroplasms and blocking RNA synthesis. In silico analyses revealed that VP2 L124, V865, and I878 are conserved among RV species A to H. Detailed knowledge of the protein interaction interface required for viroplasm formation may facilitate the design of broad-spectrum antivirals to block RV replication.IMPORTANCE Alternative treatments to combat rotavirus infection are a requirement for susceptible communities where vaccines cannot be applied. This demand is urgent for newborn infants, immunocompromised patients, adults traveling to high-risk regions, and even for the livestock industry. Aside from structural and physiological divergences among RV species studied before now, all replicate within cytosolic inclusions termed viroplasms. These inclusions are composed of viral and cellular proteins and viral RNA. Viroplasm-like structures (VLS), composed of RV protein NSP5 with either NSP2 or VP2, are models for investigating viroplasms. In this study, we identified a conserved amino acid in the VP2 protein, L124, necessary for its interaction with NSP5 and the formation of both VLSs and viroplasms. As RV vaccines cover a narrow range of viral strains, the identification of VP2 L124 residue lays the foundations for the design of drugs that specifically block NSP5-VP2 interaction as a broad-spectrum RV antiviral.
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11
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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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12
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Ilca SL, Sun X, El Omari K, Kotecha A, de Haas F, DiMaio F, Grimes JM, Stuart DI, Poranen MM, Huiskonen JT. Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus. Nature 2019; 570:252-256. [DOI: 10.1038/s41586-019-1229-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 03/08/2019] [Indexed: 01/17/2023]
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13
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Ding K, Celma CC, Zhang X, Chang T, Shen W, Atanasov I, Roy P, Zhou ZH. In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release. Nat Commun 2019; 10:2216. [PMID: 31101900 PMCID: PMC6525196 DOI: 10.1038/s41467-019-10236-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/25/2019] [Indexed: 01/11/2023] Open
Abstract
Transcribing and replicating a double-stranded genome require protein modules to unwind, transcribe/replicate nucleic acid substrates, and release products. Here we present in situ cryo-electron microscopy structures of rotavirus dsRNA-dependent RNA polymerase (RdRp) in two states pertaining to transcription. In addition to the previously discovered universal "hand-shaped" polymerase core domain shared by DNA polymerases and telomerases, our results show the function of N- and C-terminal domains of RdRp: the former opens the genome duplex to isolate the template strand; the latter splits the emerging template-transcript hybrid, guides genome reannealing to form a transcription bubble, and opens a capsid shell protein (CSP) to release the transcript. These two "helicase" domains also extensively interact with CSP, which has a switchable N-terminal helix that, like cellular transcriptional factors, either inhibits or promotes RdRp activity. The in situ structures of RdRp, CSP, and RNA in action inform mechanisms of not only transcription, but also replication.
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Affiliation(s)
- Ke Ding
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Cristina C Celma
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Xing Zhang
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Thomas Chang
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Wesley Shen
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Ivo Atanasov
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Polly Roy
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Z Hong Zhou
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA.
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA.
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14
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Group A Rotavirus VP1 Polymerase and VP2 Core Shell Proteins: Intergenotypic Sequence Variation and In Vitro Functional Compatibility. J Virol 2019; 93:JVI.01642-18. [PMID: 30355692 DOI: 10.1128/jvi.01642-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/16/2018] [Indexed: 02/05/2023] Open
Abstract
Group A rotaviruses (RVAs) are classified according to a nucleotide sequence-based system that assigns a genotype to each of the 11 double-stranded RNA (dsRNA) genome segments. For the segment encoding the VP1 polymerase, 22 genotypes (R1 to R22) are defined with an 83% nucleotide identity cutoff value. For the segment encoding the VP2 core shell protein, which is a functional VP1-binding partner, 20 genotypes (C1 to C20) are defined with an 84% nucleotide identity cutoff value. However, the extent to which the VP1 and VP2 proteins encoded by these genotypes differ in their sequences or interactions has not been described. Here, we sought to (i) delineate the relationships and sites of variation for VP1 and VP2 proteins belonging to the known RVA genotypes and (ii) correlate intergenotypic sequence diversity with functional VP1-VP2 interaction(s) during dsRNA synthesis. Using bioinformatic approaches, we revealed which VP1 and VP2 genotypes encode divergent proteins and identified the positional locations of amino acid changes in the context of known structural domains/subdomains. We then employed an in vitro dsRNA synthesis assay to test whether genotype R1, R2, R4, and R7 VP1 polymerases could be enzymatically activated by genotype C1, C2, C4, C5, and C7 VP2 core shell proteins. Genotype combinations that were incompatible informed the rational design and in vitro testing of chimeric mutant VP1 and VP2 proteins. The results of this study connect VP1 and VP2 nucleotide-level diversity to protein-level diversity for the first time, and they provide new insights into regions/residues critical for VP1-VP2 interaction(s) during viral genome replication.IMPORTANCE Group A rotaviruses (RVAs) are widespread in nature, infecting numerous mammalian and avian hosts and causing severe gastroenteritis in human children. RVAs are classified using a system that assigns a genotype to each viral gene according to its nucleotide sequence. To date, 22 genotypes have been described for the gene encoding the viral polymerase (VP1), and 20 genotypes have been described for the gene encoding the core shell protein (VP2). Here, we analyzed if/how the VP1 and VP2 proteins encoded by the known RVA genotypes differ from each other in their sequences. We also used a biochemical approach to test whether the intergenotypic sequence differences influenced how VP1 and VP2 functionally engage each other to mediate RNA synthesis in a test tube. This work is important because it increases our understanding of RVA protein-level diversity and raises new ideas about the VP1-VP2 binding interface(s) that is important for viral replication.
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15
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Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly. Proc Natl Acad Sci U S A 2018; 115:7344-7349. [PMID: 29941585 DOI: 10.1073/pnas.1803885115] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together with other capsid proteins and genomic RNA. Here we report the near-atomic resolution structure of the RdRp protein VP2 in complex with its cofactor protein VP4 and genomic RNA within an aquareovirus capsid using 200-kV cryoelectron microscopy and symmetry-mismatch reconstruction. The structure of these capsid proteins enabled us to observe the elaborate nonicosahedral structure within the double-layered icosahedral capsid. Our structure shows that the RdRp complex is anchored at the inner surface of the capsid shell and interacts with genomic dsRNA and four of the five asymmetrically arranged N termini of the capsid shell proteins under the fivefold axis, implying roles for these N termini in virus assembly. The binding site of the RNA end at VP2 is different from the RNA cap binding site identified in the crystal structure of orthoreovirus RdRp λ3, although the structures of VP2 and λ3 are almost identical. A loop, which was thought to separate the RNA template and transcript, interacts with an apical domain of the capsid shell protein, suggesting a mechanism for regulating RdRp replication and transcription. A conserved nucleoside triphosphate binding site was localized in our RdRp cofactor protein VP4 structure, and interactions between the VP4 and the genomic RNA were identified.
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16
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Abstract
Most emerging and re-emerging human and animal viral diseases are associated with RNA viruses. All these pathogens, with the exception of retroviruses, encode a specialized enzyme called RNA-dependent RNA polymerase (RdRP), which catalyze phosphodiester-bond formation between ribonucleotides (NTPs) in an RNA template-dependent manner. These enzymes function either as single polypeptides or in complex with other viral or host components to transcribe and replicate the viral RNA genome. The structures of RdRPs and RdRP catalytic complexes, currently available for several members of (+) ssRNA, (-)ssRNA and dsRNA virus families, have provided high resolution snapshots of the functional steps underlying replication and transcription of viral RNA genomes and their regulatory mechanisms.
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Affiliation(s)
- Diego Ferrero
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Cristina Ferrer-Orta
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Núria Verdaguer
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain.
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17
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Yuan J, Zhang X, Shi H, Chen J, Han X, Wei P, Feng L. The interaction of Rotavirus A pig/China/NMTL/2008/G9P[23] VP6 with cellular beta-actin is required for optimal RV replication and infectivity. Vet Microbiol 2016; 197:111-121. [PMID: 27938672 DOI: 10.1016/j.vetmic.2016.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 10/22/2016] [Accepted: 11/09/2016] [Indexed: 11/16/2022]
Abstract
VP6 forms the intermediate layer of the rotavirus (RV) capsid, and it plays important roles after RV penetration and uncoating. These functions rely on its ability to interact with host cell proteins. To gain further insights into the role of VP6 in porcine RV (PoRV) infection, a glutathione S-transferase pull-down assay was utilized to find unknown cellular factors that interact with VP6. In this study, beta-actin, tropomyosin 1, and 40S ribosomal protein S16 were identified as interaction partners of VP6 by mass spectrometry and co-immunoprecipitation. The interaction with beta-actin was further studied. By immunoelectron microscopy, we observed VP6 proteins that labeled with colloidal gold localized on the actin microfilaments at the early stage of PoRV infection, we also found VP6 distributed in the ribosome, mitochondria, endoplasmic reticulum and nucleus in the infected cells. Actin binding protein spin-down assays verified PoRV double-layered particles (DLPs) bound to F-actin in vitro, but didn't have actin polymerization enhancement activity. After a small interfering RNA (siACTB) was used to knock down beta-actin expression, PoRV VP6 expression and the infection rates of newly synthesized virions releasing into culture supernatants decreased dramatically. Our results confirm and extend previous reports indicating that the interaction between PoRV VP6 and beta-actin plays vital roles in the PoRV lifecycle.
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Affiliation(s)
- Jing Yuan
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xin Zhang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Hongyan Shi
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jianfei Chen
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xiao Han
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Ping Wei
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China.
| | - Li Feng
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
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18
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Collier AM, Lyytinen OL, Guo YR, Toh Y, Poranen MM, Tao YJ. Initiation of RNA Polymerization and Polymerase Encapsidation by a Small dsRNA Virus. PLoS Pathog 2016; 12:e1005523. [PMID: 27078841 PMCID: PMC4831847 DOI: 10.1371/journal.ppat.1005523] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/03/2016] [Indexed: 01/07/2023] Open
Abstract
During the replication cycle of double-stranded (ds) RNA viruses, the viral RNA-dependent RNA polymerase (RdRP) replicates and transcribes the viral genome from within the viral capsid. How the RdRP molecules are packaged within the virion and how they function within the confines of an intact capsid are intriguing questions with answers that most likely vary across the different dsRNA virus families. In this study, we have determined a 2.4 Å resolution structure of an RdRP from the human picobirnavirus (hPBV). In addition to the conserved polymerase fold, the hPBV RdRP possesses a highly flexible 24 amino acid loop structure located near the C-terminus of the protein that is inserted into its active site. In vitro RNA polymerization assays and site-directed mutagenesis showed that: (1) the hPBV RdRP is fully active using both ssRNA and dsRNA templates; (2) the insertion loop likely functions as an assembly platform for the priming nucleotide to allow de novo initiation; (3) RNA transcription by the hPBV RdRP proceeds in a semi-conservative manner; and (4) the preference of virus-specific RNA during transcription is dictated by the lower melting temperature associated with the terminal sequences. Co-expression of the hPBV RdRP and the capsid protein (CP) indicated that, under the conditions used, the RdRP could not be incorporated into the recombinant capsids in the absence of the viral genome. Additionally, the hPBV RdRP exhibited higher affinity towards the conserved 5'-terminal sequence of the viral RNA, suggesting that the RdRP molecules may be encapsidated through their specific binding to the viral RNAs during assembly.
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Affiliation(s)
- Aaron M. Collier
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Outi L. Lyytinen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Yusong R. Guo
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Yukimatsu Toh
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Minna M. Poranen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail: (YJT); (MMP)
| | - Yizhi J. Tao
- Department of BioSciences, Rice University, Houston, Texas, United States of America
- * E-mail: (YJT); (MMP)
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19
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Zhang X, Ding K, Yu X, Chang W, Sun J, Zhou ZH. In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus. Nature 2015; 527:531-534. [PMID: 26503045 PMCID: PMC5086257 DOI: 10.1038/nature15767] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/07/2015] [Indexed: 01/15/2023]
Abstract
Viruses in the Reoviridae, like the triple-shelled human rotavirus and the single-shelled insect cytoplasmic polyhedrosis virus (CPV), all package a genome of segmented double-stranded RNAs (dsRNAs) inside the viral capsid and carry out endogenous messenger RNA synthesis through a transcriptional enzyme complex (TEC). By direct electron-counting cryoelectron microscopy and asymmetric reconstruction, we have determined the organization of the dsRNA genome inside quiescent CPV (q-CPV) and the in situ atomic structures of TEC within CPV in both quiescent and transcribing (t-CPV) states. We show that the ten segmented dsRNAs in CPV are organized with ten TECs in a specific, non-symmetric manner, with each dsRNA segment attached directly to a TEC. The TEC consists of two extensively interacting subunits: an RNA-dependent RNA polymerase (RdRP) and an NTPase VP4. We find that the bracelet domain of RdRP undergoes marked conformational change when q-CPV is converted to t-CPV, leading to formation of the RNA template entry channel and access to the polymerase active site. An amino-terminal helix from each of two subunits of the capsid shell protein (CSP) interacts with VP4 and RdRP. These findings establish the link between sensing of environmental cues by the external proteins and activation of endogenous RNA transcription by the TEC inside the virus.
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MESH Headings
- Capsid Proteins/chemistry
- Capsid Proteins/metabolism
- Capsid Proteins/ultrastructure
- Catalytic Domain
- Cryoelectron Microscopy
- Genome, Viral/genetics
- Models, Molecular
- Multienzyme Complexes/chemistry
- Multienzyme Complexes/metabolism
- Multienzyme Complexes/ultrastructure
- Nucleoside-Triphosphatase/metabolism
- Nucleoside-Triphosphatase/ultrastructure
- Protein Subunits/chemistry
- Protein Subunits/metabolism
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/ultrastructure
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/ultrastructure
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- RNA, Viral/ultrastructure
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/metabolism
- RNA-Dependent RNA Polymerase/ultrastructure
- Reoviridae/enzymology
- Reoviridae/genetics
- Reoviridae/ultrastructure
- Templates, Genetic
- Transcription, Genetic
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Affiliation(s)
- Xing Zhang
- California Nanosystems Institute, Los Angeles, CA 90095, USA
| | - Ke Ding
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Xuekui Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Winston Chang
- California Nanosystems Institute, Los Angeles, CA 90095, USA
| | - Jingchen Sun
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Z. Hong Zhou
- California Nanosystems Institute, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Bioengineering, University of California, Los Angeles, CA 90095, USA
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20
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Abstract
ABSTRACT Within the Paramyxoviridae family, Henipaviruses are the deadliest human pathogens. Nipah and Hendra viruses comprise the genus Henipavirus, zoonotic pathogens which cause encephalitis and respiratory disease in humans with mortality rates that can exceed 70%. Henipaviruses are the only Paramyxoviruses classified as biosafety level 4 pathogens due to their extreme pathogenicity, potential for bioterrorism and lack of available licensed vaccines or therapeutic modalities. Both viruses emerged from their natural reservoir, Asian fruit bats, during the last decade of the 20th century. They caused severe disease and mortality in humans, horses and swine. They also infected a number of other mammalian species. With significant progress in understanding the biology of these deadly pathogens, including the discovery of a Hendra virus vaccine and a potential neutralizing antibody, have we really won the war against the Henipavirus?
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21
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Gridley CL, Patton JT. Regulation of rotavirus polymerase activity by inner capsid proteins. Curr Opin Virol 2014; 9:31-8. [PMID: 25243800 DOI: 10.1016/j.coviro.2014.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 08/28/2014] [Accepted: 08/29/2014] [Indexed: 11/16/2022]
Abstract
Rotavirus, a cause of pediatric gastroenteritis, has a genome consisting of 11 segments of double-stranded (ds)RNA surrounded by a triple-layered protein capsid. The rotavirus RNA-dependent RNA polymerase, VP1, synthesizes both dsRNA and plus-strand RNA (+RNA) within subviral particles. Structural analyses of the rotavirus capsid and polymerase, combined with functional studies of purified capsid proteins, indicate that the inner capsid protein controls the initiation of RNA synthesis by VP1. Whether VP1 directs dsRNA versus +RNA synthesis may be regulated by the impact of the viral RNA capping enzyme on the position of the polymerase plug, a flexible element that inserts into one of the polymerase's RNA exit tunnels. This review discusses recent findings and ideas into the mechanisms used by rotavirus capsid proteins to control the activities of its viral polymerase and to coordinate RNA synthesis with the assembly of virus particles.
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Affiliation(s)
- Chelsea L Gridley
- Rotavirus Molecular Biology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, United States
| | - John T Patton
- Rotavirus Molecular Biology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, United States.
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22
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Abstract
UNLABELLED Replication and packaging of the rotavirus genome occur in cytoplasmic compartments called viroplasms, which form during virus infection. These processes are orchestrated by yet-to-be-understood complex networks of interactions involving nonstructural proteins (NSPs) 2, 5, and 6 and structural proteins (VPs) 1, 2, 3, and 6. The multifunctional enzyme NSP2, an octamer with RNA binding activity, is critical for viroplasm formation with its binding partner, NSP5, and for genome replication/packaging through its interactions with replicating RNA, the viral polymerase VP1, and the inner core protein VP2. Using isothermal calorimetry, biolayer interferometry, and peptide array screening, we examined the interactions between NSP2, VP1, VP2, NSP5, and NSP6. These studies provide the first evidence that NSP2 can directly bind to VP1, VP2, and NSP6, in addition to the previously known binding to NSP5. The interacting sites identified from reciprocal peptide arrays were found to be in close proximity to the RNA template entry and double-stranded RNA (dsRNA) exit tunnels of VP1 and near the catalytic cleft and RNA-binding grooves of NSP2; these sites are consistent with the proposed role of NSP2 in facilitating dsRNA synthesis by VP1. Peptide screening of VP2 identified NSP2-binding sites in the regions close to the intersubunit junctions, suggesting that NSP2 binding could be a regulatory mechanism for preventing the premature self-assembly of VP2. The binding sites on NSP2 for NSP6 were found to overlap that of VP1, and the NSP5-binding sites overlap those of VP2 and VP1, suggesting that interaction of these proteins with NSP2 is likely spatially and/or temporally regulated. IMPORTANCE Replication and packaging of the rotavirus genome occur in cytoplasmic compartments called viroplasms that form during virus infection and are orchestrated by complex networks of interactions involving nonstructural proteins (NSPs) and structural proteins (VPs). A multifunctional RNA-binding NSP2 octamer with nucleotidyl phosphatase activity is central to viroplasm formation and RNA replication. Here we provide the first evidence that NSP2 can directly bind to VP1, VP2, and NSP6, in addition to the previously known binding to NSP5. The interacting sites identified from peptide arrays are consistent with the proposed role of NSP2 in facilitating dsRNA synthesis by VP1 and also point to NSP2's possible role in preventing the premature self-assembly of VP2 cores. Our findings lead us to propose that the NSP2 octamer with multiple enzymatic activities is a principal regulator of viroplasm formation, recruitment of viral proteins into the viroplasms, and possibly genome replication.
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23
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Yan L, Liu H, Li X, Fang Q. The VP2 protein of grass carp reovirus (GCRV) expressed in a baculovirus exhibits RNA polymerase activity. Virol Sin 2014; 29:86-93. [PMID: 24643934 DOI: 10.1007/s12250-014-3366-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 01/03/2014] [Indexed: 10/25/2022] Open
Abstract
The double-shelled grass carp reovirus (GCRV) is capable of endogenous RNA transcription and processing. Genome sequence analysis has revealed that the protein VP2, encoded by gene segment 2 (S2), is the putative RNA-dependent RNA polymerase (RdRp). In previous work, we have ex-pressed the functional region of VP2 that is associated with RNA polymerase activity (denoted as rVP2(390-900)) in E. coli and have prepared a polyclonal antibody against VP2. To characterize the GCRV RNA polymerase, a recombinant full-length VP2 (rVP2) was first constructed and expressed in a baculovirus system, as a fusion protein with an attached His-tag. Immunofluorescence (IF) assays, together with immunoblot (IB) analyses from both expressed cell extracts and purified Histagged rVP2, showed that rVP2 was successfully expressed in Sf9 cells. Further characterization of the replicase activity showed that purified rVP2 and GCRV particles exhibited poly(C)-dependent poly(G) polymerase activity. The RNA enzymatic activity required the divalent cation Mg(2+), and was optimal at 28 °C. The results provide a foundation for further studies on the RNA polymerases of aquareoviruses during viral transcription and replication.
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Affiliation(s)
- Liming Yan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
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24
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The molecular biology of Bluetongue virus replication. Virus Res 2013; 182:5-20. [PMID: 24370866 DOI: 10.1016/j.virusres.2013.12.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 01/17/2023]
Abstract
The members of Orbivirus genus within the Reoviridae family are arthropod-borne viruses which are responsible for high morbidity and mortality in ruminants. Bluetongue virus (BTV) which causes disease in livestock (sheep, goat, cattle) has been in the forefront of molecular studies for the last three decades and now represents the best understood orbivirus at a molecular and structural level. The complex nature of the virion structure has been well characterised at high resolution along with the definition of the virus encoded enzymes required for RNA replication; the ordered assembly of the capsid shell as well as the protein and genome sequestration required for it; and the role of host proteins in virus entry and virus release. More recent developments of Reverse Genetics and Cell-Free Assembly systems have allowed integration of the accumulated structural and molecular knowledge to be tested at meticulous level, yielding higher insight into basic molecular virology, from which the rational design of safe efficacious vaccines has been possible. This article is centred on the molecular dissection of BTV with a view to understanding the role of each protein in the virus replication cycle. These areas are important in themselves for BTV replication but they also indicate the pathways that related viruses, which includes viruses that are pathogenic to man and animals, might also use providing an informed starting point for intervention or prevention.
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25
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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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26
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Hendra and Nipah infection: emerging paramyxoviruses. Virus Res 2013; 177:119-26. [PMID: 23954578 DOI: 10.1016/j.virusres.2013.08.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 12/22/2022]
Abstract
Since their first emergence in mid 1990s henipaviruses continued to re emerge in Australia and South East Asia almost every year. In total there has been more than 12 Nipah and 48 Hendra virus outbreaks reported in South East Asia and Australia, respectively. These outbreaks are associated with significant economic and health damages that most high risks countries (particularly in South East Asia) cannot bear the burden of such economical threats. Up until recently, there were no actual therapeutics available to treat or prevent these lethal infections. However, an international collaborative research has resulted in the identification of a potential equine Hendra vaccine capable of providing antibody protection against Hendra virus infections. Consequently, with the current findings and after nearly 2 decades since their first detection, are we there yet? This review recaps the chronicle of the henipavirus emergence and briefly evaluates potential anti-henipavirus vaccines and antivirals.
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Abstract
Capsid proteins are obligatory components of infectious virions. Their primary structural function is to protect viral genomes during entry and exit from host cells. Evidence suggests that these proteins can also modulate the activity and specificity of viral replication complexes. More recently, it has become apparent that they play critical roles at the virus–host interface. Here, we discuss how capsid proteins of RNA viruses interact with key host cell proteins and pathways to modulate cell physiology in order to benefit virus replication. Capsid–host cell interactions may also have implications for viral disease. Understanding how capsids regulate virus–host interactions may lead to the development of novel antiviral therapies based on targeting the activities of cellular proteins.
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Affiliation(s)
- Steven Willows
- Department of Cell Biology, University of Alberta, 5–14 Medical Sciences Building, Edmonton, T6G 2H7, Canada
| | - Shangmei Hou
- Department of Cell Biology, University of Alberta, 5–14 Medical Sciences Building, Edmonton, T6G 2H7, Canada
| | - Tom C Hobman
- Department of Li Ka Shing Institute of Virology, University of Alberta, 5–14 Medical Sciences Building, Edmonton, T6G 2H7, Canada
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McDonald SM. RNA synthetic mechanisms employed by diverse families of RNA viruses. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:351-67. [PMID: 23606593 PMCID: PMC7169773 DOI: 10.1002/wrna.1164] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
RNA viruses are ubiquitous in nature, infecting every known organism on the planet. These viruses can also be notorious human pathogens with significant medical and economic burdens. Central to the lifecycle of an RNA virus is the synthesis of new RNA molecules, a process that is mediated by specialized virally encoded enzymes called RNA‐dependent RNA polymerases (RdRps). RdRps directly catalyze phosphodiester bond formation between nucleoside triphosphates in an RNA‐templated manner. These enzymes are strikingly conserved in their structural and functional features, even among diverse RNA viruses belonging to different families. During host cell infection, the activities of viral RdRps are often regulated by viral cofactor proteins. Cofactors can modulate the type and timing of RNA synthesis by directly engaging the RdRp and/or by indirectly affecting its capacity to recognize template RNA. High‐resolution structures of RdRps as apoenzymes, bound to RNA templates, in the midst of catalysis, and/or interacting with regulatory cofactor proteins, have dramatically increased our understanding of viral RNA synthetic mechanisms. Combined with elegant biochemical studies, such structures are providing a scientific platform for the rational design of antiviral agents aimed at preventing and treating RNA virus‐induced diseases. WIREs RNA 2013, 4:351–367. doi: 10.1002/wrna.1164 This article is categorized under:
RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Sarah M McDonald
- Virginia Tech Carilion Research Institute and School of Medicine, Roanoke, VA, USA.
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Boudreaux CE, Vile DC, Gilmore BL, Tanner JR, Kelly DF, McDonald SM. Rotavirus core shell subdomains involved in polymerase encapsidation into virus-like particles. J Gen Virol 2013; 94:1818-1826. [PMID: 23596269 DOI: 10.1099/vir.0.052951-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The triple-layered rotavirus virion encases an 11-segmented, dsRNA genome and 11-12 copies of the viral polymerase (VP1). VP1 transcribes and replicates the genome while tethered beneath the VP2 core shell. Genome replication (i.e. minus-strand RNA synthesis) by VP1 occurs in association with core assembly. During this process, VP2 directly engages VP1, thereby (i) packaging the polymerase into a nascent core and (ii) triggering the enzyme to initiate minus-strand RNA synthesis on bound plus-strand RNA templates. Recent work has shed light on VP2 regions important for VP1 enzymic activity. In the current study, we sought to investigate VP2 subdomains involved in the encapsidation of VP1 into recombinant virus-like particles (VLPs), which are formed of VP2 and the middle layer virion protein (VP6). We showed that strain SA11 VLPs efficiently encapsidated SA11 VP1, but not the genetically divergent Bristol VP1. VLPs made with an SA11 VP2 mutant lacking residues 1-10 of the amino-terminal domain (NTD) were still able to encapsidate VP1; however, removal of the entire NTD (residues 1-102) completely abolished polymerase packaging. We also showed that a chimeric VP2 protein containing the NTD and dimer-forming subdomain of strain Bristol VP2 can efficiently encapsidate SA11 VP1. These results suggest that the VP2 NTD and dimer-forming subdomain play important, albeit non-specific, roles in both VP1 packaging and activation. When combined with previous work, the results of this study support the notion that the same VP2 regions that engage VP1 during activation are also involved in packaging the enzyme into the core.
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Affiliation(s)
| | - Donald C Vile
- Virginia Tech Carilion School of Medicine, Roanoke, VA, USA.,Virginia Tech Carilion Research Institute, Roanoke, VA, USA
| | | | | | - Deborah F Kelly
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Virginia Tech Carilion School of Medicine, Roanoke, VA, USA.,Virginia Tech Carilion Research Institute, Roanoke, VA, USA
| | - Sarah M McDonald
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, USA.,Virginia Tech Carilion School of Medicine, Roanoke, VA, USA.,Virginia Tech Carilion Research Institute, Roanoke, VA, USA
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30
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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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31
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Norovirus RNA synthesis is modulated by an interaction between the viral RNA-dependent RNA polymerase and the major capsid protein, VP1. J Virol 2012; 86:10138-49. [PMID: 22787222 DOI: 10.1128/jvi.01208-12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using a cell-based assay for RNA synthesis by the RNA-dependent RNA polymerase (RdRp) of noroviruses, we previously observed that VP1, the major structural protein of the human GII.4 norovirus, enhanced the GII.4 RdRp activity but not that of the related murine norovirus (MNV) or other unrelated RNA viruses (C. V. Subba-Reddy, I. Goodfellow, and C. C. Kao, J. Virol. 85:13027-13037, 2011). Here, we examine the mechanism of VP1 enhancement of RdRp activity and the mechanism of mouse norovirus replication. We determined that the GII.4 and MNV VP1 proteins can enhance cognate RdRp activities in a concentration-dependent manner. The VP1 proteins coimmunoprecipitated with their cognate RdRps. Coexpression of individual domains of VP1 with the viral RdRps showed that the VP1 shell domain (SD) was sufficient to enhance polymerase activity. Using SD chimeras from GII.4 and MNV, three loops connecting the central β-barrel structure were found to be responsible for the species-specific enhancement of RdRp activity. A differential scanning fluorimetry assay showed that recombinant SDs can bind to the purified RdRps in vitro. An MNV replicon with a frameshift mutation in open reading frame 2 (ORF2) that disrupts VP1 expression was defective for RNA replication, as quantified by luciferase reporter assay and real-time quantitative reverse transcription-PCR (qRT-PCR). Trans-complementation of VP1 or its SD significantly recovered the VP1 knockout MNV replicon replication, and the presence or absence of VP1 affected the kinetics of viral RNA synthesis. The results document a regulatory role for VP1 in the norovirus replication cycle, further highlighting the paradigm of viral structural proteins playing additional functional roles in the virus life cycle.
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32
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Structural insights into the coupling of virion assembly and rotavirus replication. Nat Rev Microbiol 2012; 10:165-77. [PMID: 22266782 DOI: 10.1038/nrmicro2673] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Viral replication is rapid and robust, but it is far from a chaotic process. Instead, successful production of infectious progeny requires that events occur in the correct place and at the correct time. Rotaviruses (segmented double-stranded RNA viruses of the Reoviridae family) seem to govern their replication through ordered disassembly and assembly of a triple-layered icosahedral capsid. In recent years, high-resolution structural data have provided unprecedented insight into these events. In this Review, we explore the current understanding of rotavirus replication and how it compares to replication of other Reoviridae family members.
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33
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Matsuo E, Roy P. Bluetongue virus VP1 polymerase activity in vitro: template dependency, dinucleotide priming and cap dependency. PLoS One 2011; 6:e27702. [PMID: 22110731 PMCID: PMC3216989 DOI: 10.1371/journal.pone.0027702] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 10/22/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Bluetongue virus (BTV) protein, VP1, is known to possess an intrinsic polymerase function, unlike rotavirus VP1, which requires the capsid protein VP2 for its catalytic activity. However, compared with the polymerases of other members of the Reoviridae family, BTV VP1 has not been characterized in detail. METHODS AND FINDINGS Using an in vitro polymerase assay system, we demonstrated that BTV VP1 could synthesize the ten dsRNAs simultaneously from BTV core-derived ssRNA templates in a single in vitro reaction as well as genomic dsRNA segments from rotavirus core-derived ssRNA templates that possess no sequence similarity with BTV. In contrast, dsRNAs were not synthesized from non-viral ssRNA templates by VP1, unless they were fused with specific BTV sequences. Further, we showed that synthesis of dsRNAs from capped ssRNA templates was significantly higher than that from uncapped ssRNA templates and the addition of dinucleotides enhanced activity as long as the last base of the dinucleotide complemented the 3' -terminal nucleotide of the ssRNA template. CONCLUSIONS We showed that the polymerase activity was stimulated by two different factors: cap structure, likely due to allosteric effect, and dinucleotides due to priming. Our results also suggested the possible presence of cis-acting elements shared by ssRNAs in the members of family Reoviridae.
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Affiliation(s)
- Eiko Matsuo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Polly Roy
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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34
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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: 87] [Impact Index Per Article: 6.7] [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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35
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Abstract
The innermost VP2 core shell of the triple-layered, icosahedral rotavirus particle surrounds the viral genome and RNA processing enzymes, including the RNA-dependent RNA polymerase (VP1). In addition to anchoring VP1 within the core, VP2 is also an essential cofactor that triggers the polymerase to initiate double-stranded RNA (dsRNA) synthesis using packaged plus-strand RNA templates. The VP2 requirement effectively couples packaging with genome replication and ensures that VP1 makes dsRNA only within an assembling previrion particle. However, the mechanism by which the rotavirus core shell protein activates the viral polymerase remains very poorly understood. In the current study, we sought to elucidate VP2 regions critical for VP1-mediated in vitro dsRNA synthesis. By comparing the functions of proteins from several different rotaviruses, we found that polymerase activation by the core shell protein is specific. Through truncation and chimera mutagenesis, we demonstrate that the VP2 amino terminus, which forms a decameric, internal hub underneath each 5-fold axis, plays an important but nonspecific role in VP1 activation. Our results indicate that the VP2 residues correlating with polymerase activation specificity are located on the inner face of the core shell, distinct from the amino terminus. Based on these findings, we predict that several regions of VP2 engage the polymerase during the concerted processes of rotavirus core assembly and genome replication.
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36
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Residues of the rotavirus RNA-dependent RNA polymerase template entry tunnel that mediate RNA recognition and genome replication. J Virol 2010; 85:1958-69. [PMID: 21147920 DOI: 10.1128/jvi.01689-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To replicate its segmented, double-stranded RNA (dsRNA) genome, the rotavirus RNA-dependent RNA polymerase, VP1, must recognize viral plus-strand RNAs (+RNAs) and guide them into the catalytic center. VP1 binds to the conserved 3' end of rotavirus +RNAs via both sequence-dependent and sequence-independent contacts. Sequence-dependent contacts permit recognition of viral +RNAs and specify an autoinhibited positioning of the template within the catalytic site. However, the contributions to dsRNA synthesis of sequence-dependent and sequence-independent VP1-RNA interactions remain unclear. To analyze the importance of VP1 residues that interact with +RNA on genome replication, we engineered mutant VP1 proteins and assayed their capacity to synthesize dsRNA in vitro. Our results showed that, individually, mutation of residues that interact specifically with RNA bases did not diminish replication levels. However, simultaneous mutations led to significantly lower levels of dsRNA product, presumably due to impaired recruitment of +RNA templates. In contrast, point mutations of sequence-independent RNA contact residues led to severely diminished replication, likely as a result of improper positioning of templates at the catalytic site. A noteworthy exception was a K419A mutation that enhanced the initiation capacity and product elongation rate of VP1. The specific chemistry of Lys419 and its position at a narrow region of the template entry tunnel appear to contribute to its capacity to moderate replication. Together, our findings suggest that distinct classes of VP1 residues interact with +RNA to mediate template recognition and dsRNA synthesis yet function in concert to promote viral RNA replication at appropriate times and rates.
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37
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Guglielmi KM, McDonald SM, Patton JT. Mechanism of intraparticle synthesis of the rotavirus double-stranded RNA genome. J Biol Chem 2010; 285:18123-8. [PMID: 20351108 DOI: 10.1074/jbc.r110.117671] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rotaviruses perform the remarkable tasks of transcribing and replicating 11 distinct double-stranded RNA genome segments within the confines of a subviral particle. Multiple viral polymerases are tethered to the interior of a particle, each dedicated to a solitary genome segment but acting in synchrony to synthesize RNA. Although the rotavirus polymerase specifically recognizes RNA templates in the absence of other proteins, its enzymatic activity is contingent upon interaction with the viral capsid. This intraparticle strategy of RNA synthesis helps orchestrate the concerted packaging and replication of the viral genome. Here, we review our current understanding of rotavirus RNA synthetic mechanisms.
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Affiliation(s)
- Kristen M Guglielmi
- Laboratory of Infectious Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892, USA
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38
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Arnold MM, Patton JT. Rotavirus antagonism of the innate immune response. Viruses 2009; 1:1035-56. [PMID: 21994581 PMCID: PMC3185539 DOI: 10.3390/v1031035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 11/05/2009] [Accepted: 11/20/2009] [Indexed: 12/17/2022] Open
Abstract
Rotavirus is a primary cause of severe dehydrating gastroenteritis in infants and young children. The virus is sensitive to the antiviral effects triggered by the interferon (IFN)-signaling pathway, an important component of the host cell innate immune response. To counteract these effects, rotavirus encodes a nonstructural protein (NSP1) that induces the degradation of proteins involved in regulating IFN expression, such as members of the IFN regulatory factor (IRF) family. In some instances, NSP1 also subverts IFN expression by causing the degradation of a component of the E3 ubiquitin ligase complex responsible for activating NF-κB. By antagonizing multiple components of the IFN-induction pathway, NSP1 aids viral spread and contributes to rotavirus pathogenesis.
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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; E-Mail:
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McDonald SM, Tao YJ, Patton JT. The ins and outs of four-tunneled Reoviridae RNA-dependent RNA polymerases. Curr Opin Struct Biol 2009; 19:775-82. [PMID: 19914820 DOI: 10.1016/j.sbi.2009.10.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 10/14/2009] [Accepted: 10/15/2009] [Indexed: 12/29/2022]
Abstract
RNA-dependent RNA polymerases (RdRps) of the segmented double-stranded (ds) RNA viruses of the Reoviridae family exhibit distinguishing structural elements, enabling the enzymes to function within the confines of a proteinaceous core particle. These globular, cage-like polymerases are traversed by four well-defined tunnels, which not only allow template RNAs, nucleotides, and divalent cations to access the interior catalytic site, but also provide two distinct exit conduits for RNA templates and products--one leading out of the core and the other back inside the core. Although Reoviridae RdRps are intrinsically capable of binding template, their catalytic activities are tightly regulated by interactions with core shell proteins. This intra-particle mechanism of RNA synthesis coordinates genome packaging with replication during the infectious cycle.
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Affiliation(s)
- Sarah M McDonald
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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Pan J, Lin L, Tao YJ. Self-guanylylation of birnavirus VP1 does not require an intact polymerase activity site. Virology 2009; 395:87-96. [PMID: 19801157 DOI: 10.1016/j.virol.2009.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Revised: 08/19/2009] [Accepted: 09/04/2009] [Indexed: 11/27/2022]
Abstract
Protein priming is an important mechanism that many viruses use to initiate genomic DNA or RNA synthesis. Birnaviruses are the only double-stranded (ds) RNA viruses that use protein priming. The viral-encoded VP1 of birnavirus functions as both a polymerase and a protein primer and is able to undergo self-guanylylation to acquire a covalently linked rGMP. By employing biochemical assays using recombinant proteins, we have shown that VP1 self-guanylylation does not require an RNA template but is dependent on divalent metal ions. VP1 reacts with all four types of rNTPs but strongly prefers rGTP. Unexpectedly, two fatal polymerase mutants D402A and E421Y, each having an essential catalytic residue mutated and unable to catalyze RNA synthesis, remain active in self-guanylylation. The guanylylation site was further mapped to the VP1 N-terminal domain. Our results support a mechanism in which VP1 self-guanylylation is catalyzed by a novel active site different from the polymerase active site.
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Affiliation(s)
- Junhua Pan
- Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street, Houston, TX 77005, USA
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41
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Analysis of the kinetics of transcription and replication of the rotavirus genome by RNA interference. J Virol 2009; 83:8819-31. [PMID: 19553303 DOI: 10.1128/jvi.02308-08] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Rotaviruses have a genome composed of 11 segments of double-stranded RNA (dsRNA) surrounded by three protein layers. The virus contains an RNA-dependent RNA polymerase that synthesizes RNA transcripts corresponding to all segments of the viral genome. These transcripts direct the synthesis of the viral proteins and also serve as templates for the synthesis of the complementary strand to form the dsRNA genome. In this work, we analyzed the kinetics of transcription and replication of the viral genome throughout the replication cycle of the virus using quantitative reverse transcription-PCR. The role of the proteins that form double-layered particles ([DLPs] VP1, VP2, VP3, and VP6) in replication and transcription of the viral genome was analyzed by silencing their expression in rotavirus-infected cells. All of them were shown to be essential for the replication of the dsRNA genome since in their absence there was little synthesis of viral mRNA and dsRNA. The characterization of the kinetics of RNA transcription and replication of the viral genome under conditions where these proteins were silenced provided direct evidence for a second round of transcription during the replication of the virus. Interestingly, despite the decrease in mRNA accumulation when any of the four proteins was silenced, the synthesis of viral proteins decreased when VP2 and VP6 were knocked down, whereas the absence of VP1 and VP3 did not have a severe impact on viral protein synthesis. Characterization of viral particle assembly in the absence of VP1 and VP3 showed that while the formation of triple-layered particles and DLPs was decreased, the amount of assembled lower-density particles, often referred to as empty particles, was not different from the amount in control-infected cells, suggesting that viral particles can assemble in the absence of either VP1 or VP3.
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42
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Shared and group-specific features of the rotavirus RNA polymerase reveal potential determinants of gene reassortment restriction. J Virol 2009; 83:6135-48. [PMID: 19357162 DOI: 10.1128/jvi.00409-09] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rotaviruses (RVs) are nonenveloped, 11-segmented, double-stranded RNA viruses that are major pathogens associated with acute gastroenteritis. Group A, B, and C RVs have been isolated from humans; however, intergroup gene reassortment does not occur for reasons that remain unclear. This restriction might reflect the failure of the viral RNA-dependent RNA polymerase (RdRp; VP1) to recognize and replicate the RNA of a different group. To address this possibility, we contrasted the sequences, structures, and functions of RdRps belonging to RV groups A, B, and C (A-VP1, B-VP1, and C-VP1, respectively). We found that conserved amino acid residues are located within the hollow center of VP1 near the active site, whereas variable, group-specific residues are mostly surface exposed. By creating a three-dimensional homology model of C-VP1 with the A-VP1 crystallographic data, we provide evidence that these RV RdRps are nearly identical in their tertiary folds and that they have the same RNA template recognition mechanism that differs from that of B-VP1. Consistent with the structural data, recombinant A-VP1 and C-VP1 are capable of replicating one another's RNA templates in vitro. Nonetheless, the activity of both RdRps is strictly dependent upon the presence of cognate RV core shell protein A-VP2 or C-VP2, respectively. Together, the results of this study provide unprecedented insight into the structure and function of RV RdRps and support the notion that VP1 interactions may influence the emergence of reassortant viral strains.
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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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Aljofan M, Saubern S, Meyer AG, Marsh G, Meers J, Mungall BA. Characteristics of Nipah virus and Hendra virus replication in different cell lines and their suitability for antiviral screening. Virus Res 2009; 142:92-9. [PMID: 19428741 DOI: 10.1016/j.virusres.2009.01.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 01/12/2009] [Accepted: 01/20/2009] [Indexed: 11/28/2022]
Abstract
We have recently described the development and validation of a high throughput screening assay suitable for henipavirus antiviral identification. While we are confident this assay is robust and effective, we wished to investigate assay performance in a range of alternative cell lines to determine if assay sensitivity and specificity could be improved. We evaluated ten different cell lines for their susceptibility to Hendra and Nipah virus infection and their sensitivity of detection of the effects of the broad spectrum antiviral, ribavirin and nine novel antivirals identified using our initial screening approach. Cell lines were grouped into three categories with respect to viral replication. Virus replicated best in Vero and BSR cells, followed by Hep-2, HeLa, BHK-21 and M17 cells. The lowest levels of RNA replication and viral protein expression were observed in BAEC, MMEC, A549 and ECV304 cells. Eight cell lines appeared to be similarly effective at discriminating the antiviral effects of ribavirin (<2.7-fold difference). The two cells lines most sensitive to the effect of ribavirin (ECV304 and BAEC) also displayed the lowest levels of viral replication while Vero cells were the least sensitive suggesting excess viral replication may limit drug efficacy and cell lines which limit viral replication may result in enhanced antiviral efficacy. However, there was no consistent trend observed with the other nine antivirals tested. While improvements in antiviral sensitivity in other cell lines may indicate an important role in future HTS assays, the slightly lower sensitivity to antiviral detection in Vero cells has inherent advantages in reducing the number of partially effective lead molecules identified during initial screens. Comparison of a panel of 54 novel antiviral compounds identified during routine screening of an in-house compound library in Vero, BHK-21 and BSR cells suggests no clear advantage of screening in either cell type.
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Affiliation(s)
- Mohamad Aljofan
- Australian Animal Health Laboratory, CSIRO Livestock Industries, Geelong, Australia
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Lu X, McDonald SM, Tortorici MA, Tao YJ, Vasquez-Del Carpio R, Nibert ML, Patton JT, Harrison SC. Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1. Structure 2009; 16:1678-88. [PMID: 19000820 DOI: 10.1016/j.str.2008.09.006] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 09/06/2008] [Accepted: 09/17/2008] [Indexed: 10/21/2022]
Abstract
Rotavirus RNA-dependent RNA polymerase VP1 catalyzes RNA synthesis within a subviral particle. This activity depends on core shell protein VP2. A conserved sequence at the 3' end of plus-strand RNA templates is important for polymerase association and genome replication. We have determined the structure of VP1 at 2.9 A resolution, as apoenzyme and in complex with RNA. The cage-like enzyme is similar to reovirus lambda3, with four tunnels leading to or from a central, catalytic cavity. A distinguishing characteristic of VP1 is specific recognition, by conserved features of the template-entry channel, of four bases, UGUG, in the conserved 3' sequence. Well-defined interactions with these bases position the RNA so that its 3' end overshoots the initiating register, producing a stable but catalytically inactive complex. We propose that specific 3' end recognition selects rotavirus RNA for packaging and that VP2 activates the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.
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Affiliation(s)
- Xiaohui Lu
- Laboratory of Molecular Medicine, Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
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46
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Sarin LP, Poranen MM, Lehti NM, Ravantti JJ, Koivunen MRL, Aalto AP, van Dijk AA, Stuart DI, Grimes JM, Bamford DH. Insights into the pre-initiation events of bacteriophage phi 6 RNA-dependent RNA polymerase: towards the assembly of a productive binary complex. Nucleic Acids Res 2009; 37:1182-92. [PMID: 19129226 PMCID: PMC2651803 DOI: 10.1093/nar/gkn1035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The RNA-dependent RNA polymerase (RdRP) of double-stranded RNA (dsRNA) viruses performs both RNA replication and transcription. In order to initiate RNA polymerization, viral RdRPs must be able to interact with the incoming 3′ terminus of the template and position it, so that a productive binary complex is formed. Structural studies have revealed that RdRPs of dsRNA viruses that lack helicases have electrostatically charged areas on the polymerase surface, which might facilitate such interactions. In this study, structure-based mutagenesis, enzymatic assays and molecular mapping of bacteriophage φ6 RdRP and its RNA were used to elucidate the roles of the negatively charged plough area on the polymerase surface, of the rim of the template tunnel and of the template specificity pocket that is key in the formation of the productive RNA-polymerase binary complex. The positively charged rim of the template tunnel has a significant role in the engagement of highly structured ssRNA molecules, whereas specific interactions further down in the template tunnel promote ssRNA entry to the catalytic site. Hence, we show that by aiding the formation of a stable binary complex with optimized RNA templates, the overall polymerization activity of the φ6 RdRP can be greatly enhanced.
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Affiliation(s)
- L Peter Sarin
- Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, Biocenter 2, Helsinki, Finland
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Group A human rotavirus genomics: evidence that gene constellations are influenced by viral protein interactions. J Virol 2008; 82:11106-16. [PMID: 18786998 DOI: 10.1128/jvi.01402-08] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Group A human rotaviruses (HRVs) are the major cause of severe viral gastroenteritis in infants and young children. To gain insight into the level of genetic variation among HRVs, we determined the genome sequences for 10 strains belonging to different VP7 serotypes (G types). The HRVs chosen for this study, D, DS-1, P, ST3, IAL28, Se584, 69M, WI61, A64, and L26, were isolated from infected persons and adapted to cell culture to use as serotype references. Our sequencing results revealed that most of the individual proteins from each HRV belong to one of three genotypes (1, 2, or 3) based on their similarities to proteins of genogroup strains (Wa, DS-1, or AU-1, respectively). Strains D, P, ST3, IAL28, and WI61 encode genotype 1 (Wa-like) proteins, whereas strains DS-1 and 69M encode genotype 2 (DS-1-like) proteins. Of the 10 HRVs sequenced, 3 of them (Se584, A64, and L26) encode proteins belonging to more than one genotype, indicating that they are intergenogroup reassortants. We used amino acid sequence alignments to identify residues that distinguish proteins belonging to HRV genotype 1, 2, or 3. These genotype-specific changes cluster in definitive regions within each viral protein, many of which are sites of known protein-protein interactions. For the intermediate viral capsid protein (VP6), the changes map onto the atomic structure at the VP2-VP6, VP4-VP6, and VP7-VP6 interfaces. The results of this study provide evidence that group A HRV gene constellations exist and may be influenced by interactions among viral proteins during replication.
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Abstract
Bluetongue is a vector-borne viral disease of ruminants that is endemic in tropical and subtropical countries. Since 1998 the virus has also appeared in Europe. Partly due to the seriousness of the disease, bluetongue virus (BTV), a member of genus Orbivirus within the family Reoviridae, has been a subject of intense molecular study for the last three decades and is now one of the best understood viruses at the molecular and structural levels. BTV is a complex non-enveloped virus with seven structural proteins arranged in two capsids and a genome of ten double-stranded (ds) RNA segments. Shortly after cell entry, the outer capsid is lost to release an inner capsid (the core) which synthesizes capped mRNAs from each genomic segment, extruding them into the cytoplasm. This requires the efficient co-ordination of a number of enzymes, including helicase, polymerase and RNA capping activities. This review will focus on our current understanding of these catalytic proteins as derived from the use of recombinant proteins, combined with functional assays and the in vitro reconstitution of the transcription/replication complex. In some cases, 3D structures have complemented this analysis to reveal the fine structural detail of these proteins. The combined activities of the core enzymes produce infectious transcripts necessary and sufficient to initiate BTV infection. Such infectious transcripts can now be synthesized wholly in vitro and, when introduced into cells by transfection, lead to the recovery of infectious virus. Future studies thus hold the possibility of analysing the consequence of mutation in a replicating virus system.
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Affiliation(s)
- Polly Roy
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Molecular characterization of a subgroup specificity associated with the rotavirus inner capsid protein VP2. J Virol 2008; 82:2752-64. [PMID: 18216104 DOI: 10.1128/jvi.02492-07] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Group A rotaviruses are classified into serotypes, based on the reactivity pattern of neutralizing antibodies to VP4 and VP7, as well as into subgroups (SGs), based on non-neutralizing antibodies directed against VP6. The inner capsid protein (VP2) has also been described as a SG antigen; however, little is known regarding the molecular determinants of VP2 SG specificity. In this study, we characterize VP2 SGs by correlating genetic markers with the immunoreactivity of the SG-specific monoclonal antibody (YO-60). Our results show that VP2 proteins similar in sequence to that of the prototypic human strain Wa are recognized by YO-60, classifying them as VP2 SG-II. In contrast, proteins not bound by YO-60 are similar to those of human strains DS-1 or AU-1 and represent VP2 SG-I. Using a mutagenesis approach, we identified residues that determine recognition by either YO-60 or the group A-specific VP2 monoclonal antibody (6E8). We found that YO-60 binds to a conformationally dependent epitope that includes Wa VP2 residue M328. The epitope for 6E8 is also contingent upon VP2 conformation and resides within a single region of the protein (Wa VP2 residues A440 to T530). Using a high-resolution structure of bovine rotavirus double-layered particles, we predicted these epitopes to be spatially distinct from each other and located on opposite surfaces of VP2. This study reveals the extent of genetic variation among group A rotavirus VP2 proteins and illuminates the molecular basis for a previously described SG specificity associated with the rotavirus inner capsid protein.
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50
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Rainsford EW, McCrae MA. Characterization of the NSP6 protein product of rotavirus gene 11. Virus Res 2007; 130:193-201. [PMID: 17658646 DOI: 10.1016/j.virusres.2007.06.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 05/25/2007] [Accepted: 06/11/2007] [Indexed: 11/20/2022]
Abstract
The 12kDa non-structural protein 6 (NSP6) is the least studied of the rotavirus proteins. In an attempt to further characterize this protein mono-specific antisera was generated using purified protein expressed in E. coli. Pulse/chase radio-labeling of virus infected cells was used to show that it is expressed at a steady but low rate throughout the virus replication cycle. In contrast to the other rotavirus non-structural proteins, NSP6 was found to have a high rate of turnover, being completely degraded within 2h of synthesis. NSP6 tagged with GFP was used to probe the intracellular distribution of the protein, perinuclear aggregates were observed in the cytoplasm of transfected cells. Following virus infection of these transfected cells the aggregates were seen to redistribute to the viroplasms. Consistent with its localization to the site of viral genome replication and packaging, NSP6 was found to be a sequence independent nucleic acid binding protein, with similar affinities for ssRNA and dsRNA.
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Affiliation(s)
- Edward W Rainsford
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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