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de Matos TRA, Palka APG, de Souza C, Fragoso SP, Pavoni DP. Detection of avian reovirus (ARV) by ELISA based on recombinant σB, σC and σNS full-length proteins and protein fragments. J Med Microbiol 2024; 73. [PMID: 38935078 DOI: 10.1099/jmm.0.001836] [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: 06/28/2024] Open
Abstract
Introduction. Avian reovirus (ARV) is associated with arthritis/tenosynovitis and malabsorption syndrome in chickens. The σC and σB proteins, both exposed to the virus capsid, are highly immunogenic and could form the basis for diagnostic devices designed to assess the immunological status of the flock.Gap Statement. Commercial ARV ELISAs cannot distinguish between vaccinated and infected animals and might not detect circulating ARV strains.Aim. We aimed to develop a customized test to detect the circulating field ARV strains as well as distinguish between vaccinated and unvaccinated animals.Methodology. We developed ELISA assays based on recombinant (r) σB, σC and the nonstructural protein σNS and tested them using antisera of vaccinated and unvaccinated chickens as well as negative controls. Fragments of σB and σC proteins were also used to study regions that could be further exploited in diagnostic tests.Results. Vaccinated and unvaccinated birds were positive by commercial ELISA, with no difference in optical density values. In contrast, samples of unvaccinated animals showed lower absorbance in the rσB and rσC ELISA tests and higher absorbance in the rσNS ELISA test than the vaccinated animals. Negative control samples were negative in all tests. Fragmentation of σB and σC proteins showed that some regions can differentiate between vaccinated and unvaccinated animals. For example, σB amino acids 128-179 (σB-F4) and σC amino acids 121-165 (σC-F4) exhibited 85 and 95% positivity among samples of vaccinated animals but only 5% and zero positivity among samples of unvaccinated animals, respectively.Conclusion. These data suggest that unvaccinated birds might have been exposed to field strains of ARV. The reduction in absorbance in the recombinant tests possibly reflects an increased specificity of our test since unvaccinated samples showed less cross-reactivity with the vaccine proteins immobilized on ELISAs. The discrepant results obtained with the protein fragment tests between vaccinated and unvaccinated animals are discussed in light of the diversity between ARV strains.
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Affiliation(s)
- Tatiana Reichert Assunção de Matos
- Fundação Oswaldo Cruz, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba/PR, Brazil
- Programa de Pós-graduação em Biociências e Biotecnologia, Fundação Oswaldo Cruz, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba/PR, Brazil
| | - Ana Paula Gori Palka
- Fundação Oswaldo Cruz, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba/PR, Brazil
- Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Paraná/UFPR, Curitiba/PR, Brazil
- Instituto de Tecnologia do Paraná/Tecpar, Curitiba/PR, Brazil
| | - Claudemir de Souza
- Fundação Oswaldo Cruz, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba/PR, Brazil
- Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Paraná/UFPR, Curitiba/PR, Brazil
| | - Stenio Perdigão Fragoso
- Fundação Oswaldo Cruz, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba/PR, Brazil
- Programa de Pós-graduação em Biociências e Biotecnologia, Fundação Oswaldo Cruz, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba/PR, Brazil
| | - Daniela Parada Pavoni
- Fundação Oswaldo Cruz, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba/PR, Brazil
- Programa de Pós-graduação em Biociências e Biotecnologia, Fundação Oswaldo Cruz, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba/PR, Brazil
- Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Paraná/UFPR, Curitiba/PR, Brazil
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Zhao B, Hu L, Kaundal S, Neetu N, Lee CH, Somoulay X, Sankaran B, Taylor GM, Dermody TS, Venkataram Prasad BV. Structure of orthoreovirus RNA chaperone σNS, a component of viral replication factories. Nat Commun 2024; 15:2460. [PMID: 38503747 PMCID: PMC10950856 DOI: 10.1038/s41467-024-46627-8] [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: 08/25/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024] Open
Abstract
The mammalian orthoreovirus (reovirus) σNS protein is required for formation of replication compartments that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of a σNS mutant that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure shows that dimers interact with each other using N-terminal arms to form a helical assembly resembling WT σNS filaments in complex with RNA observed using cryo-EM. The interior of the helical assembly is of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same site as the N-terminal arm. This finding suggests that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS, which is supported by the structure of σNS lacking an N-terminal arm. We further observed that σNS has RNA chaperone activity likely essential for presenting mRNA to the viral polymerase for genome replication. This activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.
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Affiliation(s)
- Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Soni Kaundal
- Verna and Marrs Mclean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Neetu Neetu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Christopher H Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburg, PA, USA
| | - Xayathed Somoulay
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburg, PA, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA, USA
| | - Gwen M Taylor
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburg, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA
| | - Terence S Dermody
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA.
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburg, PA, USA.
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA.
| | - B V Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Verna and Marrs Mclean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
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Dhar D, Mehanovic S, Moss W, Miller CL. Sequences at gene segment termini inclusive of untranslated regions and partial open reading frames play a critical role in mammalian orthoreovirus S gene packaging. PLoS Pathog 2024; 20:e1012037. [PMID: 38394338 PMCID: PMC10917250 DOI: 10.1371/journal.ppat.1012037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Mammalian orthoreovirus (MRV) is a prototypic member of the Spinareoviridae family and has ten double-stranded RNA segments. One copy of each segment must be faithfully packaged into the mature virion, and prior literature suggests that nucleotides (nts) at the terminal ends of each gene likely facilitate their packaging. However, little is known about the precise packaging sequences required or how the packaging process is coordinated. Using a novel approach, we have determined that 200 nts at each terminus, inclusive of untranslated regions (UTR) and parts of the open reading frame (ORF), are sufficient for packaging S gene segments (S1-S4) individually and together into replicating virus. Further, we mapped the minimal sequences required for packaging the S1 gene segment into a replicating virus to 25 5' nts and 50 3' nts. The S1 UTRs, while not sufficient, were necessary for efficient packaging, as mutations of the 5' or 3' UTRs led to a complete loss of virus recovery. Using a second novel assay, we determined that 50 5' nts and 50 3' nts of S1 are sufficient to package a non-viral gene segment into MRV. The 5' and 3' termini of the S1 gene are predicted to form a panhandle structure and specific mutations within the stem of the predicted panhandle region led to a significant decrease in viral recovery. Additionally, mutation of six nts that are conserved across the three major serotypes of MRV that are predicted to form an unpaired loop in the S1 3' UTR, led to a complete loss of viral recovery. Overall, our data provide strong experimental proof that MRV packaging signals lie at the terminal ends of the S gene segments and offer support that the sequence requirements for efficient packaging of the S1 segment include a predicted panhandle structure and specific sequences within an unpaired loop in the 3' UTR.
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Affiliation(s)
- Debarpan Dhar
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Samir Mehanovic
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Walter Moss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Cathy L. Miller
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
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Zhao B, Hu L, Kuandal S, Neetu N, Lee C, Somoulay X, Sankaran B, Taylor GM, Dermody TS, Prasad BVV. Structure of Orthoreovirus RNA Chaperone σNS, a Component of Viral Replication Factories. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551319. [PMID: 37577609 PMCID: PMC10418060 DOI: 10.1101/2023.07.31.551319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The reovirus σNS RNA-binding protein is required for formation of intracellular compartments during viral infection that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of an R6A mutant of σNS that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure of selenomethionine-substituted σNS-R6A reveals that the mutant protein forms a stable antiparallel dimer, with each subunit having a well-folded central core and a projecting N-terminal arm. The dimers interact with each other by inserting the N-terminal arms into a hydrophobic pocket of the neighboring dimers on either side to form a helical assembly that resembles filaments of WT σNS in complex with RNA observed using cryo-EM. The interior of the crystallographic helical assembly is positively charged and of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same hydrophobic pocket as the N-terminal arm, as demonstrated in the crystal structure of σNS-R6A in complex with bile acid, suggesting that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS. This idea is supported by the structure of σNS lacking the N-terminal arm. We discovered that σNS displays RNA helix destabilizing and annealing activities, likely essential for presenting mRNA to the viral RNA-dependent RNA polymerase for genome replication. The RNA chaperone activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.
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Durinova E, Mojzes P, Bily T, Franta Z, Fessl T, Borodavka A, Tuma R. Shedding light on reovirus assembly-Multimodal imaging of viral factories. Adv Virus Res 2023; 116:173-213. [PMID: 37524481 DOI: 10.1016/bs.aivir.2023.06.002] [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: 08/02/2023]
Abstract
Avian (ortho)reovirus (ARV), which belongs to Reoviridae family, is a major domestic fowl pathogen and is the causative agent of viral tenosynovitis and chronic respiratory disease in chicken. ARV replicates within cytoplasmic inclusions, so-called viral factories, that form by phase separation and thus belong to a wider class of biological condensates. Here, we evaluate different optical imaging methods that have been developed or adapted to follow formation, fluidity and composition of viral factories and compare them with the complementary structural information obtained by well-established transmission electron microscopy and electron tomography. The molecular and cellular biology aspects for setting up and following virus infection in cells by imaging are described first. We then demonstrate that a wide-field version of fluorescence recovery after photobleaching is an effective tool to measure fluidity of mobile viral factories. A new technique, holotomographic phase microscopy, is then used for imaging of viral factory formation in live cells in three dimensions. Confocal Raman microscopy of infected cells provides "chemical" contrast for label-free segmentation of images and addresses important questions about biomolecular concentrations within viral factories and other biological condensates. Optical imaging is complemented by electron microscopy and tomography which supply higher resolution structural detail, including visualization of individual virions within the three-dimensional cellular context.
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Affiliation(s)
- Eva Durinova
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Peter Mojzes
- Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Tomas Bily
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Zdenek Franta
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Roman Tuma
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.
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6
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Dhar D, Mehanovic S, Moss W, Miller CL. Sequences at gene segment termini inclusive of untranslated regions and partial open reading frames play a critical role in mammalian orthoreovirus S gene packaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542362. [PMID: 37292944 PMCID: PMC10245979 DOI: 10.1101/2023.05.25.542362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mammalian orthoreovirus (MRV) is a prototypic member of the Spinareoviridae family and has ten double-stranded RNA segments. One copy of each segment must be faithfully packaged into the mature virion, and prior literature suggests that nucleotides (nts) at the terminal ends of each gene likely facilitate their packaging. However, little is known about the precise packaging sequences required or how the packaging process is coordinated. Using a novel approach, we have determined that 200 nts at each terminus, inclusive of untranslated regions (UTR) and parts of the open reading frame (ORF), are sufficient for packaging each S gene segment (S1-S4) individually and together into replicating virus. Further, we mapped the minimal sequences required for packaging the S1 gene segment to 25 5' nts and 50 3' nts. The S1 UTRs alone are not sufficient, but are necessary for packaging, as mutations of the 5' or 3' UTRs led to a complete loss of virus recovery. Using a second novel assay, we determined that 50 5'nts and 50 3' nts of S1 are sufficient to package a non-viral gene segment into MRV. The 5' and 3' termini of the S1 gene are predicted to form a panhandle structure and specific mutations within the predicted stem of the panhandle region led to a significant decrease in viral recovery. Additionally, mutation of six nts that are conserved in the three major serotypes of MRV and are predicted to form an unpaired loop in the S1 3'UTR, led to a complete loss of viral recovery. Overall, our data provide strong experimental proof that MRV packaging signals lie at the terminal ends of the S gene segments and offer support that the sequence requirements for efficient packaging of the S1 segment include a predicted panhandle structure and specific sequences within an unpaired loop in the 3' UTR.
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A Fijivirus Major Viroplasm Protein Shows RNA-Stimulated ATPase Activity by Adopting Pentameric and Hexameric Assemblies of Dimers. mBio 2023; 14:e0002323. [PMID: 36786587 PMCID: PMC10128069 DOI: 10.1128/mbio.00023-23] [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: 02/15/2023] Open
Abstract
Fijiviruses replicate and package their genomes within viroplasms in a process involving RNA-RNA and RNA-protein interactions. Here, we demonstrate that the 24 C-terminal residues (C-arm) of the P9-1 major viroplasm protein of the mal de Río Cuarto virus (MRCV) are required for its multimerization and the formation of viroplasm-like structures. Using an integrative structural approach, the C-arm was found to be dispensable for P9-1 dimer assembly but essential for the formation of pentamers and hexamers of dimers (decamers and dodecamers), which favored RNA binding. Although both P9-1 and P9-1ΔC-arm catalyzed ATP with similar activities, an RNA-stimulated ATPase activity was only detected in the full-length protein, indicating a C-arm-mediated interaction between the ATP catalytic site and the allosteric RNA binding sites in the (do)decameric assemblies. A stronger preference to bind phosphate moieties in the decamer was predicted, suggesting that the allosteric modulation of ATPase activity by RNA is favored in this structural conformation. Our work reveals the structural versatility of a fijivirus major viroplasm protein and provides clues to its mechanism of action. IMPORTANCE The mal de Río Cuarto virus (MRCV) causes an important maize disease in Argentina. MRCV replicates in several species of Gramineae plants and planthopper vectors. The viral factories, also called viroplasms, have been studied in detail in animal reovirids. This work reveals that a major viroplasm protein of MRCV forms previously unidentified structural arrangements and provides evidence that it may simultaneously adopt two distinct quaternary assemblies. Furthermore, our work uncovers an allosteric communication between the ATP and RNA binding sites that is favored in the multimeric arrangements. Our results contribute to the understanding of plant reovirids viroplasm structure and function and pave the way for the design of antiviral strategies for disease control.
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Gga-miR-30c-5p Suppresses Avian Reovirus (ARV) Replication by Inhibition of ARV-Induced Autophagy via Targeting ATG5. J Virol 2022; 96:e0075922. [PMID: 35867570 PMCID: PMC9327706 DOI: 10.1128/jvi.00759-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Avian reovirus (ARV) is an important poultry pathogen causing viral arthritis, chronic respiratory diseases, and retarded growth, leading to considerable economic losses to the poultry industry across the globe. Elucidation of the pathogenesis of ARV infection is crucial to guiding the development of novel vaccines or drugs for the effective control of these diseases.
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Huang W, Li JY, Wu YY, Liao TL, Nielsen BL, Liu HJ. p17-Modulated Hsp90/Cdc37 Complex Governs Oncolytic Avian Reovirus Replication by Chaperoning p17, Which Promotes Viral Protein Synthesis and Accumulation of Viral Proteins σC and σA in Viral Factories. J Virol 2022; 96:e0007422. [PMID: 35107368 PMCID: PMC8941905 DOI: 10.1128/jvi.00074-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/20/2022] Open
Abstract
In this work we have determined that heat shock protein 90 (Hsp90) is essential for avian reovirus (ARV) replication by chaperoning the ARV p17 protein. p17 modulates the formation of the Hsp90/Cdc37 complex by phosphorylation of Cdc37, and this chaperone machinery protects p17 from ubiquitin-proteasome degradation. Inhibition of the Hsp90/Cdc37 complex by inhibitors (17-N-allylamino-17-demethoxygeldanamycin 17-AGG, and celastrol) or short hairpin RNAs (shRNAs) significantly reduced expression levels of viral proteins and virus yield, suggesting that the Hsp90/Cdc37 chaperone complex functions in virus replication. The expression levels of p17 were decreased at the examined time points (2 to 7 h and 7 to 16 h) in 17-AAG-treated cells in a dose-dependent manner while the expression levels of viral proteins σA, σC, and σNS were decreased at the examined time point (7 to 16 h). Interestingly, the expression levels of σC, σA, and σNS proteins increased along with coexpression of p17 protein. p17 together with the Hsp90/Cdc37 complex does not increase viral genome replication but enhances viral protein stability, maturation, and virus production. Virus factories of ARV are composed of nonstructural proteins σNS and μNS. We found that the Hsp90/Cdc37 chaperone complex plays an important role in accumulation of the outer-capsid protein σC, inner core protein σA, and nonstructural protein σNS of ARV in viral factories. Depletion of Hsp90 inhibited σA, σC, and p17 proteins colocalized with σNS in viral factories. This study provides novel insights into p17-modulated formation of the Hsp90/Cdc37 chaperone complex governing virus replication via stabilization and maturation of viral proteins and accumulation of viral proteins in viral factories for virus assembly. IMPORTANCE Molecular mechanisms that control stabilization of ARV proteins and the intermolecular interactions among inclusion components remain largely unknown. Here, we show that the ARV p17 is an Hsp90 client protein. The Hsp90/Cdc37 chaperone complex is essential for ARV replication by protecting p17 chaperone from ubiquitin-proteasome degradation. p17 modulates the formation of Hsp90/Cdc37 complex by phosphorylation of Cdc37, and this chaperone machinery protects p17 from ubiquitin-proteasome degradation, suggesting a feedback loop between p17 and the Hsp90/Cdc37 chaperone complex. p17 together with the Hsp90/Cdc37 complex does not increase viral genome replication but enhances viral protein stability and virus production. Depletion of Hsp90 prevented viral proteins σA, σC, and p17 from colocalizing with σNS in viral factories. Our findings elucidate that the Hsp90/Cdc37 complex chaperones p17, which, in turn, promotes the synthesis of viral proteins σA, σC, and σNS and facilitates accumulation of the outer-capsid protein σC and inner core protein σA in viral factories for virus assembly.
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Affiliation(s)
- Wei‐Ru Huang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Jyun-Yi Li
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Ying Wu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Tsai-Ling Liao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Brent L. Nielsen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Hung-Jen Liu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
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Huang WR, Li JY, Liao TL, Yeh CM, Wang CY, Wen HW, Hu NJ, Wu YY, Hsu CY, Chang YK, Chang CD, Nielsen BL, Liu HJ. Molecular chaperone TRiC governs avian reovirus replication by protecting outer-capsid protein σC and inner core protein σA and non-structural protein σNS from ubiquitin- proteasome degradation. Vet Microbiol 2021; 264:109277. [PMID: 34826648 DOI: 10.1016/j.vetmic.2021.109277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/27/2021] [Accepted: 11/07/2021] [Indexed: 01/15/2023]
Abstract
Avian reoviruses (ARVs) are important pathogens that cause considerable economic losses in poultry farming. To date, host factors that control stabilization of ARV proteins remain largely unknown. In this work we determined that the eukaryotic chaperonin T-complex protein-1 (TCP-1) ring complex (TRiC) is essential for avian reovirus (ARV) replication by stabilizing outer-capsid protein σC, inner core protein σA, and the non-structural protein σNS of ARV. TriC serves as a chaperone of viral proteins and prevent their degradation via the ubiquitin-proteasome pathway. Furthermore, reciprocal co-immunoprecipitation assays confirmed the association of viral proteins (σA, σC, and σNS) with TRiC. Immunofluorescence staining indicated that the TRiC chaperonins (CCT2 and CCT5) are colocalized with viral proteins σC, σA, and σNS of ARV. In this study, inhibition of TRiC chaperonins (CCT2 and CCT5) by the inhibitor HSF1A or shRNAs significantly reduced expression levels of the σC, σA, and σNS proteins of ARV as well as virus yield, suggesting that the TRiC complex functions in stabilization of viral proteins and virus replication. This study provides novel insights into TRiC chaperonin governing virus replication via stabilization of outer-capsid protein σC, inner core protein σA, and the non-structural protein σNS of ARV.
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Affiliation(s)
- Wei-Ru Huang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan; The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Jyun-Yi Li
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan; The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Tsai-Ling Liao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan; Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan; Ph.D Program in Translational Medicine, National Chung Hsing University, Taichung, 402, Taiwan
| | - Chuan-Ming Yeh
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan; Bioproduction Reearch Institute, National Institute of Advanced Industrial Science and Technology, Tsukaba, Japan
| | - Chi-Young Wang
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan; Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Hsiao-Wei Wen
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Nien-Jen Hu
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Ying Wu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan; The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chao-Yu Hsu
- Ph.D Program in Translational Medicine, National Chung Hsing University, Taichung, 402, Taiwan; Division of Urology, Department of Surgery, Tung's Taichung MetroHarbor Hospital, Taichung, Taiwan
| | - Yu-Kang Chang
- Department of Medical Research, Tung's Taichung MetroHarbor Hospital, Taichung, Taiwan; Depertment of Nursing, Jen-Teh Junior College of Medicine and Management, Taiwan
| | - Ching-Dong Chang
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Brent L Nielsen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Hung-Jen Liu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan; The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan; Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan; Ph.D Program in Translational Medicine, National Chung Hsing University, Taichung, 402, Taiwan; Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.
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11
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Egaña-Labrin S, Jerry C, Roh HJ, da Silva AP, Corsiglia C, Crossley B, Rejmanek D, Gallardo RA. Avian Reoviruses of the Same Genotype Induce Different Pathology in Chickens. Avian Dis 2021; 65:530-540. [DOI: 10.1637/0005-2086-65.4.530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/13/2021] [Indexed: 11/05/2022]
Affiliation(s)
- S. Egaña-Labrin
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, 4008 VM3B, Davis, CA 95616
| | - C. Jerry
- California Animal Health and Food Safety Laboratory System, Turlock branch, University of California, Davis, 1550 N Soderquist Road, Turlock, CA 95380
| | - H. J. Roh
- CEVA Scientific Support and Investigation Unit (SSIU) and Science and Investigation Department (SID), CEVA Animal Health USA, 8930 Rosehill Road, Lenexa, KS 66215
| | - A. P. da Silva
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, 4008 VM3B, Davis, CA 95616
| | - C. Corsiglia
- Foster Farms, 14519 Collier Road, Delhi, CA 95315
| | - B. Crossley
- California Animal Health and Food Safety Laboratory System, Davis branch, University of California, Davis, 620 W Health Science Drive, Davis, CA 95616
| | - D. Rejmanek
- California Animal Health and Food Safety Laboratory System, Davis branch, University of California, Davis, 620 W Health Science Drive, Davis, CA 95616
| | - R. A. Gallardo
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, 4008 VM3B, Davis, CA 95616
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12
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Egaña-Labrin S, Jerry C, Roh HJ, da Silva AP, Corsiglia C, Crossley B, Rejmanek D, Gallardo RA. Avian Reoviruses of the Same Genotype Induce Different Pathology in Chickens. Avian Dis 2021. [DOI: 10.1637/0005-2086-65.4.529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- S. Egaña-Labrin
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, 4008 VM3B, Davis, CA 95616
| | - C. Jerry
- California Animal Health and Food Safety Laboratory System, Turlock branch, University of California, Davis, 1550 N Soderquist Road, Turlock, CA 95380
| | - H. J. Roh
- CEVA Scientific Support and Investigation Unit (SSIU) and Science and Investigation Department (SID), CEVA Animal Health USA, 8930 Rosehill Road, Lenexa, KS 66215
| | - A. P. da Silva
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, 4008 VM3B, Davis, CA 95616
| | - C. Corsiglia
- Foster Farms, 14519 Collier Road, Delhi, CA 95315
| | - B. Crossley
- California Animal Health and Food Safety Laboratory System, Davis branch, University of California, Davis, 620 W Health Science Drive, Davis, CA 95616
| | - D. Rejmanek
- California Animal Health and Food Safety Laboratory System, Davis branch, University of California, Davis, 620 W Health Science Drive, Davis, CA 95616
| | - R. A. Gallardo
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, 1089 Veterinary Medicine Drive, 4008 VM3B, Davis, CA 95616
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13
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Caddy S, Papa G, Borodavka A, Desselberger U. Rotavirus research: 2014-2020. Virus Res 2021; 304:198499. [PMID: 34224769 DOI: 10.1016/j.virusres.2021.198499] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 02/09/2023]
Abstract
Rotaviruses are major causes of acute gastroenteritis in infants and young children worldwide and also cause disease in the young of many other mammalian and of avian species. During the recent 5-6 years rotavirus research has benefitted in a major way from the establishment of plasmid only-based reverse genetics systems, the creation of human and other mammalian intestinal enteroids, and from the wide application of structural biology (cryo-electron microscopy, cryo-EM tomography) and complementary biophysical approaches. All of these have permitted to gain new insights into structure-function relationships of rotaviruses and their interactions with the host. This review follows different stages of the viral replication cycle and summarizes highlights of structure-function studies of rotavirus-encoded proteins (both structural and non-structural), molecular mechanisms of viral replication including involvement of cellular proteins and lipids, the spectrum of viral genomic and antigenic diversity, progress in understanding of innate and acquired immune responses, and further developments of prevention of rotavirus-associated disease.
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Affiliation(s)
- Sarah Caddy
- Cambridge Institute for Therapeutic Immunology and Infectious Disease Jeffery Cheah Biomedical Centre, Cambridge, CB2 0AW, UK.
| | - Guido Papa
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
| | - Ulrich Desselberger
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
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14
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Bravo JPK, Bartnik K, Venditti L, Acker J, Gail EH, Colyer A, Davidovich C, Lamb DC, Tuma R, Calabrese AN, Borodavka A. Structural basis of rotavirus RNA chaperone displacement and RNA annealing. Proc Natl Acad Sci U S A 2021; 118:e2100198118. [PMID: 34615715 PMCID: PMC8521686 DOI: 10.1073/pnas.2100198118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2021] [Indexed: 01/13/2023] Open
Abstract
Rotavirus genomes are distributed between 11 distinct RNA molecules, all of which must be selectively copackaged during virus assembly. This likely occurs through sequence-specific RNA interactions facilitated by the RNA chaperone NSP2. Here, we report that NSP2 autoregulates its chaperone activity through its C-terminal region (CTR) that promotes RNA-RNA interactions by limiting its helix-unwinding activity. Unexpectedly, structural proteomics data revealed that the CTR does not directly interact with RNA, while accelerating RNA release from NSP2. Cryo-electron microscopy reconstructions of an NSP2-RNA complex reveal a highly conserved acidic patch on the CTR, which is poised toward the bound RNA. Virus replication was abrogated by charge-disrupting mutations within the acidic patch but completely restored by charge-preserving mutations. Mechanistic similarities between NSP2 and the unrelated bacterial RNA chaperone Hfq suggest that accelerating RNA dissociation while promoting intermolecular RNA interactions may be a widespread strategy of RNA chaperone recycling.
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Affiliation(s)
- Jack P K Bravo
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Kira Bartnik
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich, Centre for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Luca Venditti
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Julia Acker
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Emma H Gail
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, European Molecular Biology Laboratory (EMBL) Australia, Clayton, VIC 3800, Australia
| | - Alice Colyer
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council (ARC) Centre of Excellence in Advanced Molecular Imaging, European Molecular Biology Laboratory (EMBL) Australia, Clayton, VIC 3800, Australia
| | - Don C Lamb
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich, Centre for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
- Faculty of Science, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom;
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich, Centre for Integrated Protein Science Munich, Ludwig Maximilian University of Munich, D-81377 Munich, Germany
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15
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Abstract
The function of the mammalian orthoreovirus (reovirus) σNS nonstructural protein is enigmatic. σNS is an RNA-binding protein that forms oligomers and enhances the stability of bound RNAs, but the mechanisms by which it contributes to reovirus replication are unknown. To determine the function of σNS-RNA binding in reovirus replication, we engineered σNS mutants deficient in RNA-binding capacity. We found that alanine substitutions of positively charged residues in a predicted RNA-binding domain decrease RNA-dependent oligomerization. To define steps in reovirus replication facilitated by the RNA-binding property of σNS, we established a complementation system in which wild-type or mutant forms of σNS could be tested for the capacity to overcome inhibition of σNS expression. Mutations in σNS that disrupt RNA binding also diminish viral replication and σNS distribution to viral factories. Moreover, viral mRNAs only incorporate into viral factories or factory-like structures (formed following expression of nonstructural protein μNS) when σNS is present and capable of binding RNA. Collectively, these findings indicate that σNS requires positively charged residues in a putative RNA-binding domain to recruit viral mRNAs to sites of viral replication and establish a function for σNS in reovirus replication.
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16
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Thoner TW, Ye X, Karijolich J, Ogden KM. Reovirus Low-Density Particles Package Cellular RNA. Viruses 2021; 13:v13061096. [PMID: 34201386 PMCID: PMC8228547 DOI: 10.3390/v13061096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/03/2021] [Indexed: 12/02/2022] Open
Abstract
Packaging of segmented, double-stranded RNA viral genomes requires coordination of viral proteins and RNA segments. For mammalian orthoreovirus (reovirus), evidence suggests either all ten or zero viral RNA segments are simultaneously packaged in a highly coordinated process hypothesized to exclude host RNA. Accordingly, reovirus generates genome-containing virions and “genomeless” top component particles. Whether reovirus virions or top component particles package host RNA is unknown. To gain insight into reovirus packaging potential and mechanisms, we employed next-generation RNA-sequencing to define the RNA content of enriched reovirus particles. Reovirus virions exclusively packaged viral double-stranded RNA. In contrast, reovirus top component particles contained similar proportions but reduced amounts of viral double-stranded RNA and were selectively enriched for numerous host RNA species, especially short, non-polyadenylated transcripts. Host RNA selection was not dependent on RNA abundance in the cell, and specifically enriched host RNAs varied for two reovirus strains and were not selected solely by the viral RNA polymerase. Collectively, these findings indicate that genome packaging into reovirus virions is exquisitely selective, while incorporation of host RNAs into top component particles is differentially selective and may contribute to or result from inefficient viral RNA packaging.
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Affiliation(s)
- Timothy W. Thoner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (T.W.T.J.); (X.Y.); (J.K.)
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (T.W.T.J.); (X.Y.); (J.K.)
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (T.W.T.J.); (X.Y.); (J.K.)
| | - Kristen M. Ogden
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (T.W.T.J.); (X.Y.); (J.K.)
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Correspondence:
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17
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Translation of the long-term fundamental studies on viral DNA packaging motors into nanotechnology and nanomedicine. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1103-1129. [DOI: 10.1007/s11427-020-1752-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023]
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18
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Hagen T, Malinowska AL, Lightfoot HL, Bigatti M, Hall J. Site-Specific Fluorophore Labeling of Guanosines in RNA G-Quadruplexes. ACS OMEGA 2019; 4:8472-8479. [PMID: 31459936 PMCID: PMC6648711 DOI: 10.1021/acsomega.9b00704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/24/2019] [Indexed: 05/08/2023]
Abstract
RNA G-quadruplexes are RNA secondary structures that are implicated in many cellular processes. Although conventional biophysical techniques are widely used for their in vitro characterization, more advanced methods are needed to study complex equilibria and the kinetics of their folding. We have developed a new Förster resonance energy-transfer-based method to detect the folding of RNA G-quadruplexes, which is enabled by labeling the 2'-positions of participating guanosines with fluorophores. Importantly, this does not interfere with the required anti conformation of the nucleobase in a quadruplex with parallel topology. Sequential click reactions on the solid phase and in solution using a stop-and-go strategy circumvented the issue of unselective cross-labeling. We exemplified the method on a series of sequences under different assay conditions. In contrast to the commonly used end-labeling approach, our internal labeling strategy would also allow the study of G-quadruplex formation in long functional RNAs.
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19
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Tenorio R, Fernández de Castro I, Knowlton JJ, Zamora PF, Sutherland DM, Risco C, Dermody TS. Function, Architecture, and Biogenesis of Reovirus Replication Neoorganelles. Viruses 2019; 11:v11030288. [PMID: 30901959 PMCID: PMC6466366 DOI: 10.3390/v11030288] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/17/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
Most viruses that replicate in the cytoplasm of host cells form neoorganelles that serve as sites of viral genome replication and particle assembly. These highly specialized structures concentrate viral proteins and nucleic acids, prevent the activation of cell-intrinsic defenses, and coordinate the release of progeny particles. Reoviruses are common pathogens of mammals that have been linked to celiac disease and show promise for oncolytic applications. These viruses form nonenveloped, double-shelled virions that contain ten segments of double-stranded RNA. Replication organelles in reovirus-infected cells are nucleated by viral nonstructural proteins µNS and σNS. Both proteins partition the endoplasmic reticulum to form the matrix of these structures. The resultant membranous webs likely serve to anchor viral RNA⁻protein complexes for the replication of the reovirus genome and the assembly of progeny virions. Ongoing studies of reovirus replication organelles will advance our knowledge about the strategies used by viruses to commandeer host biosynthetic pathways and may expose new targets for therapeutic intervention against diverse families of pathogenic viruses.
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Affiliation(s)
- Raquel Tenorio
- Cell Structure Laboratory, National Center for Biotechnology, CNB-CSIC, Cantoblanco Campus, 28049 Madrid, Spain.
| | - Isabel Fernández de Castro
- Cell Structure Laboratory, National Center for Biotechnology, CNB-CSIC, Cantoblanco Campus, 28049 Madrid, Spain.
| | - Jonathan J Knowlton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| | - Paula F Zamora
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Danica M Sutherland
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.
- Center for Microbial Pathogenesis, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.
| | - Cristina Risco
- Cell Structure Laboratory, National Center for Biotechnology, CNB-CSIC, Cantoblanco Campus, 28049 Madrid, Spain.
| | - Terence S Dermody
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.
- Center for Microbial Pathogenesis, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.
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20
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Borodavka A, Desselberger U, Patton JT. Genome packaging in multi-segmented dsRNA viruses: distinct mechanisms with similar outcomes. Curr Opin Virol 2018; 33:106-112. [PMID: 30145433 PMCID: PMC6289821 DOI: 10.1016/j.coviro.2018.08.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/20/2022]
Abstract
Segmented double-stranded (ds)RNA viruses share remarkable similarities in their replication strategy and capsid structure. During virus replication, positive-sense single-stranded (+)RNAs are packaged into procapsids, where they serve as templates for dsRNA synthesis, forming progeny particles containing a complete equimolar set of genome segments. How the +RNAs are recognized and stoichiometrically packaged remains uncertain. Whereas bacteriophages of the Cystoviridae family rely on specific RNA-protein interactions to select appropriate +RNAs for packaging, viruses of the Reoviridae instead rely on specific inter-molecular interactions between +RNAs that guide multi-segmented genome assembly. While these families use distinct mechanisms to direct +RNA packaging, both yield progeny particles with a complete set of genomic dsRNAs.
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Affiliation(s)
- Alexander Borodavka
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Ulrich Desselberger
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK
| | - John T Patton
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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21
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Detection of Novel duck reovirus (NDRV) using visual reverse transcription loop-mediated isothermal amplification (RT-LAMP). Sci Rep 2018; 8:14039. [PMID: 30232402 PMCID: PMC6145877 DOI: 10.1038/s41598-018-32473-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 08/30/2018] [Indexed: 01/06/2023] Open
Abstract
Here we present a visual reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detecting the gene encoding the σB major outer-capsid protein of novel duck reovirus (NDRV). A set of primers, composed of two outer primers, two inner primers and two loop primers, was designed based on the gene of interest. The LAMP reaction was conducted in a traditional laboratory water bath at 65 °C for 50 min. We compared the performance of calcein/Mn2+ and SYBR Green I dyes, as well as electrophoresis on agarose gel stained with GoldView nucleic acid dye to detect the RT-LAMP-amplified products and all assays could be employed to discriminate between positive and negative specimens in visible or UV light. Our data showed that there is no cross-reaction with other viruses and the RT-LAMP technique displayed high sensitivity for detecting NDRV with a minimal detection limit of 200 fg RNA input. This assay was more sensitive than conventional PCR in detecting NDRV both in natural and experimental infection. In conclusion, the RT-LAMP technique was remarkably sensitive, specific, rapid, simple and profitable for the identification of NDRV.
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22
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Bravo JPK, Borodavka A, Barth A, Calabrese AN, Mojzes P, Cockburn JJB, Lamb DC, Tuma R. Stability of local secondary structure determines selectivity of viral RNA chaperones. Nucleic Acids Res 2018; 46:7924-7937. [PMID: 29796667 PMCID: PMC6125681 DOI: 10.1093/nar/gky394] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/24/2018] [Accepted: 04/30/2018] [Indexed: 01/02/2023] Open
Abstract
To maintain genome integrity, segmented double-stranded RNA viruses of the Reoviridae family must accurately select and package a complete set of up to a dozen distinct genomic RNAs. It is thought that the high fidelity segmented genome assembly involves multiple sequence-specific RNA-RNA interactions between single-stranded RNA segment precursors. These are mediated by virus-encoded non-structural proteins with RNA chaperone-like activities, such as rotavirus (RV) NSP2 and avian reovirus σNS. Here, we compared the abilities of NSP2 and σNS to mediate sequence-specific interactions between RV genomic segment precursors. Despite their similar activities, NSP2 successfully promotes inter-segment association, while σNS fails to do so. To understand the mechanisms underlying such selectivity in promoting inter-molecular duplex formation, we compared RNA-binding and helix-unwinding activities of both proteins. We demonstrate that octameric NSP2 binds structured RNAs with high affinity, resulting in efficient intramolecular RNA helix disruption. Hexameric σNS oligomerizes into an octamer that binds two RNAs, yet it exhibits only limited RNA-unwinding activity compared to NSP2. Thus, the formation of intersegment RNA-RNA interactions is governed by both helix-unwinding capacity of the chaperones and stability of RNA structure. We propose that this protein-mediated RNA selection mechanism may underpin the high fidelity assembly of multi-segmented RNA genomes in Reoviridae.
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Affiliation(s)
- Jack P K Bravo
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Alexander Borodavka
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
- Department of Chemistry, Center for NanoScience (CeNS), Nanosystems Initiative Munich (NIM) and Centre for Integrated Protein Science Munich (CiPSM), Ludwig Maximilian University of Munich, Munich, Germany
| | - Anders Barth
- Department of Chemistry, Center for NanoScience (CeNS), Nanosystems Initiative Munich (NIM) and Centre for Integrated Protein Science Munich (CiPSM), Ludwig Maximilian University of Munich, Munich, Germany
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Peter Mojzes
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-12116 Prague 2, Czech Republic
| | - Joseph J B Cockburn
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Don C Lamb
- Department of Chemistry, Center for NanoScience (CeNS), Nanosystems Initiative Munich (NIM) and Centre for Integrated Protein Science Munich (CiPSM), Ludwig Maximilian University of Munich, Munich, Germany
| | - Roman Tuma
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
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23
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Reovirus Nonstructural Protein σNS Acts as an RNA Stability Factor Promoting Viral Genome Replication. J Virol 2018; 92:JVI.00563-18. [PMID: 29769334 DOI: 10.1128/jvi.00563-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/07/2018] [Indexed: 12/23/2022] Open
Abstract
Viral nonstructural proteins, which are not packaged into virions, are essential for the replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral replication and dissemination in the host. The reovirus nonstructural protein σNS is a single-stranded RNA (ssRNA)-binding protein that must be expressed in infected cells for production of viral progeny. However, the activities of σNS during individual steps of the reovirus replication cycle are poorly understood. We explored the function of σNS by disrupting its expression during infection using cells expressing a small interfering RNA (siRNA) targeting the σNS-encoding S3 gene and found that σNS is required for viral genome replication. Using complementary biochemical assays, we determined that σNS forms complexes with viral and nonviral RNAs. We also discovered, using in vitro and cell-based RNA degradation experiments, that σNS increases the RNA half-life. Cryo-electron microscopy revealed that σNS and ssRNAs organize into long, filamentous structures. Collectively, our findings indicate that σNS functions as an RNA-binding protein that increases the viral RNA half-life. These results suggest that σNS forms RNA-protein complexes in preparation for genome replication.IMPORTANCE Following infection, viruses synthesize nonstructural proteins that mediate viral replication and promote dissemination. Viruses from the family Reoviridae encode nonstructural proteins that are required for the formation of progeny viruses. Although nonstructural proteins of different viruses in the family Reoviridae diverge in primary sequence, they are functionally homologous and appear to facilitate conserved mechanisms of dsRNA virus replication. Using in vitro and cell culture approaches, we found that the mammalian reovirus nonstructural protein σNS binds and stabilizes viral RNA and is required for genome synthesis. This work contributes new knowledge about basic mechanisms of dsRNA virus replication and provides a foundation for future studies to determine how viruses in the family Reoviridae assort and replicate their genomes.
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24
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Borodavka A, Dykeman EC, Schrimpf W, Lamb DC. Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments. eLife 2017; 6:27453. [PMID: 28922109 PMCID: PMC5621836 DOI: 10.7554/elife.27453] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/03/2017] [Indexed: 01/06/2023] Open
Abstract
Segmented RNA viruses are ubiquitous pathogens, which include influenza viruses and rotaviruses. A major challenge in understanding their assembly is the combinatorial problem of a non-random selection of a full genomic set of distinct RNAs. This process involves complex RNA-RNA and protein-RNA interactions, which are often obscured by non-specific binding at concentrations approaching in vivo assembly conditions. Here, we present direct experimental evidence of sequence-specific inter-segment interactions between rotavirus RNAs, taking place in a complex RNA- and protein-rich milieu. We show that binding of the rotavirus-encoded non-structural protein NSP2 to viral ssRNAs results in the remodeling of RNA, which is conducive to formation of stable inter-segment contacts. To identify the sites of these interactions, we have developed an RNA-RNA SELEX approach for mapping the sequences involved in inter-segment base-pairing. Our findings elucidate the molecular basis underlying inter-segment interactions in rotaviruses, paving the way for delineating similar RNA-RNA interactions that govern assembly of other segmented RNA viruses. Rotavirus is a highly infectious virus that affects children worldwide, causing severe diarrhoea. Despite the introduction of several highly effective vaccines, more than 200,000 children still die from rotavirus each year. There are currently no drugs that can combat this disease once a child has been infected. Viruses carry the instructions that determine their properties and behavior in molecules of DNA or RNA. Unlike many other viruses, which typically have a single molecule of DNA or RNA, rotavirus has 11 distinct “RNA segments”. After invading a cell the virus begins to replicate itself. During replication, the RNA segments (which consist of two strands of RNA paired together) are copied many times. It is not clear how rotaviruses ‘count’ up to 11 so that each new virus acquires a single copy of each segment. Previous biochemical and structural studies of rotavirus replication suggest that selecting 11 distinct RNA segments must involve the RNAs forming complex interactions with proteins and other RNA molecules. Using a highly sensitive fluorescence-based approach, termed fluorescence cross-correlation spectroscopy, Borodavka et al. now present direct experimental evidence of interactions between the RNA segments that occur via single strands of the rotavirus RNA. These RNA-RNA interactions require the binding of a rotavirus protein NSP2 to the RNA strands, which results in the remodeling of the RNA; this remodeling is required to form stable contacts between different RNA segments. Furthermore, a new experimental approach (called RNA-RNA SELEX) developed by Borodavka et al. identified the parts of the RNA segments that may take part in these interactions. The results presented by Borodavka et al. pave the way for identifying the RNA-RNA interactions that govern how other segmented RNA viruses can package their genetic material. Further work to uncover the entire RNA interaction network in rotaviruses would also accelerate the design of new vaccines and may help us to develop antiviral drugs to treat infections.
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Affiliation(s)
- Alexander Borodavka
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom.,Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilian University of Munich, Munich, Germany
| | - Eric C Dykeman
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom.,Department of Mathematics, University of York, York, United Kingdom.,Department of Biology, University of York, York, United Kingdom
| | - Waldemar Schrimpf
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilian University of Munich, Munich, Germany
| | - Don C Lamb
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilian University of Munich, Munich, Germany
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Borodavka A, Singaram SW, Stockley PG, Gelbart WM, Ben-Shaul A, Tuma R. Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures. Biophys J 2016; 111:2077-2085. [PMID: 27851933 PMCID: PMC5113152 DOI: 10.1016/j.bpj.2016.10.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/25/2016] [Accepted: 10/11/2016] [Indexed: 12/26/2022] Open
Abstract
Long RNA molecules are at the core of gene regulation across all kingdoms of life, while also serving as genomes in RNA viruses. Few studies have addressed the basic physical properties of long single-stranded RNAs. Long RNAs with nonrepeating sequences usually adopt highly ramified secondary structures and are better described as branched polymers. To test whether a branched polymer model can estimate the overall sizes of large RNAs, we employed fluorescence correlation spectroscopy to examine the hydrodynamic radii of a broad spectrum of biologically important RNAs, ranging from viral genomes to long noncoding regulatory RNAs. The relative sizes of long RNAs measured at low ionic strength correspond well to those predicted by two theoretical approaches that treat the effective branching associated with secondary structure formation-one employing the Kramers theorem for calculating radii of gyration, and the other featuring the metric of maximum ladder distance. Upon addition of multivalent cations, most RNAs are found to be compacted as compared with their original, low ionic-strength sizes. These results suggest that sizes of long RNA molecules are determined by the branching pattern of their secondary structures. We also experimentally validate the proposed computational approaches for estimating hydrodynamic radii of single-stranded RNAs, which use generic RNA structure prediction tools and thus can be universally applied to a wide range of long RNAs.
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Affiliation(s)
- Alexander Borodavka
- Faculty of Biological Sciences, Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Surendra W Singaram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California; The Institute of Chemistry and Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Peter G Stockley
- Faculty of Biological Sciences, Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - William M Gelbart
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Avinoam Ben-Shaul
- The Institute of Chemistry and Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Roman Tuma
- Faculty of Biological Sciences, Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.
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