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Kotaki T, Kanai Y, Onishi M, Minami S, Chen Z, Nouda R, Nurdin JA, Yamasaki M, Kobayashi T. Generation of single-round infectious rotavirus with a mutation in the intermediate capsid protein VP6. J Virol 2024:e0076224. [PMID: 38837379 DOI: 10.1128/jvi.00762-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024] Open
Abstract
Rotavirus causes severe diarrhea in infants. Although live attenuated rotavirus vaccines are available, vaccine-derived infections have been reported, which warrants development of next-generation rotavirus vaccines. A single-round infectious virus is a promising vaccine platform; however, this platform has not been studied extensively in the context of rotavirus. Here, we aimed to develop a single-round infectious rotavirus by impairing the function of the viral intermediate capsid protein VP6. Recombinant rotaviruses harboring mutations in VP6 were rescued using a reverse genetics system. Mutations were targeted at VP6 residues involved in virion assembly. Although the VP6-mutated rotavirus expressed viral proteins, it did not produce progeny virions in wild-type cells; however, the virus did produce progeny virions in VP6-expressing cells. This indicates that the VP6-mutated rotavirus is a single-round infectious rotavirus. Insertion of a foreign gene, and replacement of the VP7 gene segment with that of human rotavirus clinical isolates, was successful. No infectious virions were detected in mice infected with the single-round infectious rotavirus. Immunizing mice with the single-round infectious rotavirus induced neutralizing antibody titers as high as those induced by wild-type rotavirus. Taken together, the data suggest that this single-round infectious rotavirus has potential as a safe and effective rotavirus vaccine. This system is also applicable for generation of safe and orally administrable viral vectors.IMPORTANCERotavirus, a leading cause of acute gastroenteritis in infants, causes an annual estimated 128,500 infant deaths worldwide. Although live attenuated rotavirus vaccines are available, they are replicable and may cause vaccine-derived infections. Thus, development of safe and effective rotavirus vaccine is important. In this study, we report the development of a single-round infectious rotavirus that can replicate only in cells expressing viral VP6 protein. We demonstrated that (1) the single-round infectious rotavirus did not replicate in wild-type cells or in mice; (2) insertion of foreign genes and replacement of the outer capsid gene were possible; and (3) it was as immunogenic as the wild-type virus. Thus, the mutated virus shows promise as a next-generation rotavirus vaccine. The system is also applicable to orally administrable viral vectors, facilitating development of vaccines against other enteric pathogens.
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Affiliation(s)
- Tomohiro Kotaki
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yuta Kanai
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Megumi Onishi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shohei Minami
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Zelin Chen
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Ryotaro Nouda
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Jeffery A Nurdin
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Moeko Yamasaki
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takeshi Kobayashi
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Osaka, Japan
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Valusenko-Mehrkens R, Schilling-Loeffler K, Johne R, Falkenhagen A. VP4 Mutation Boosts Replication of Recombinant Human/Simian Rotavirus in Cell Culture. Viruses 2024; 16:565. [PMID: 38675907 PMCID: PMC11054354 DOI: 10.3390/v16040565] [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: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Rotavirus A (RVA) is the leading cause of diarrhea requiring hospitalization in children and causes over 100,000 annual deaths in Sub-Saharan Africa. In order to generate next-generation vaccines against African RVA genotypes, a reverse genetics system based on a simian rotavirus strain was utilized here to exchange the antigenic capsid proteins VP4, VP7 and VP6 with those of African human rotavirus field strains. One VP4/VP7/VP6 (genotypes G9-P[6]-I2) triple-reassortant was successfully rescued, but it replicated poorly in the first cell culture passages. However, the viral titer was enhanced upon further passaging. Whole genome sequencing of the passaged virus revealed a single point mutation (A797G), resulting in an amino acid exchange (E263G) in VP4. After introducing this mutation into the VP4-encoding plasmid, a VP4 mono-reassortant as well as the VP4/VP7/VP6 triple-reassortant replicated to high titers already in the first cell culture passage. However, the introduction of the same mutation into the VP4 of other human RVA strains did not improve the rescue of those reassortants, indicating strain specificity. The results show that specific point mutations in VP4 can substantially improve the rescue and replication of recombinant RVA reassortants in cell culture, which may be useful for the development of novel vaccine strains.
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Affiliation(s)
| | | | | | - Alexander Falkenhagen
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (R.V.-M.); (K.S.-L.); (R.J.)
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Carossino M, Vissani MA, Barrandeguy ME, Balasuriya UBR, Parreño V. Equine Rotavirus A under the One Health Lens: Potential Impacts on Public Health. Viruses 2024; 16:130. [PMID: 38257830 PMCID: PMC10819593 DOI: 10.3390/v16010130] [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: 12/15/2023] [Revised: 12/29/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Group A rotaviruses are a well-known cause of viral gastroenteritis in infants and children, as well as in many mammalian species and birds, affecting them at a young age. This group of viruses has a double-stranded, segmented RNA genome with high genetic diversity linked to point mutations, recombination, and, importantly, reassortment. While initial molecular investigations undertaken in the 1900s suggested host range restriction among group A rotaviruses based on the fact that different gene segments were distributed among different animal species, recent molecular surveillance and genome constellation genotyping studies conducted by the Rotavirus Classification Working Group (RCWG) have shown that animal rotaviruses serve as a source of diversification of human rotavirus A, highlighting their zoonotic potential. Rotaviruses occurring in various animal species have been linked with contributing genetic material to human rotaviruses, including horses, with the most recent identification of equine-like G3 rotavirus A infecting children. The goal of this article is to review relevant information related to rotavirus structure/genomic organization, epidemiology (with a focus on human and equine rotavirus A), evolution, inter-species transmission, and the potential zoonotic role of equine and other animal rotaviruses. Diagnostics, surveillance and the current status of human and livestock vaccines against RVA are also reviewed.
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Affiliation(s)
- Mariano Carossino
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Maria Aldana Vissani
- Escuela de Veterinaria, Facultad de Ciencias Agrarias y Veterinarias, Universidad del Salvador, Pilar, Buenos Aires B1630AHU, Argentina; (M.A.V.); (M.E.B.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Maria E. Barrandeguy
- Escuela de Veterinaria, Facultad de Ciencias Agrarias y Veterinarias, Universidad del Salvador, Pilar, Buenos Aires B1630AHU, Argentina; (M.A.V.); (M.E.B.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
| | - Udeni B. R. Balasuriya
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Viviana Parreño
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686LQF, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1033AAJ, Argentina
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Zhu D, Cao D, Zhang X. Virus structures revealed by advanced cryoelectron microscopy methods. Structure 2023; 31:1348-1359. [PMID: 37797619 DOI: 10.1016/j.str.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
Before the resolution revolution, cryoelectron microscopy (cryo-EM) single-particle analysis (SPA) already achieved resolutions beyond 4 Å for certain icosahedral viruses, enabling ab initio atomic model building of these viruses. As the only samples that achieved such high resolution at that time, cryo-EM method development was closely intertwined with the improvement of reconstructions of symmetrical viruses. Viral morphology exhibits significant diversity, ranging from small to large, uniform to non-uniform, and from containing single symmetry to multiple symmetries. Furthermore, viruses undergo conformational changes during their life cycle. Several methods, such as asymmetric reconstruction, Ewald sphere correction, cryoelectron tomography (cryo-ET), and sub-tomogram averaging (STA), have been developed and applied to determine virus structures in vivo and in vitro. This review outlines current advanced cryo-EM methods for high-resolution structure determination of viruses and summarizes accomplishments obtained with these approaches. Moreover, persisting challenges in comprehending virus structures are discussed and we propose potential solutions.
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Affiliation(s)
- Dongjie Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Asensio-Cob D, Rodríguez JM, Luque D. Rotavirus Particle Disassembly and Assembly In Vivo and In Vitro. Viruses 2023; 15:1750. [PMID: 37632092 PMCID: PMC10458742 DOI: 10.3390/v15081750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Rotaviruses (RVs) are non-enveloped multilayered dsRNA viruses that are major etiologic agents of diarrheal disease in humans and in the young in a large number of animal species. The viral particle is composed of three different protein layers that enclose the segmented dsRNA genome and the transcriptional complexes. Each layer defines a unique subparticle that is associated with a different phase of the replication cycle. Thus, while single- and double-layered particles are associated with the intracellular processes of selective packaging, genome replication, and transcription, the viral machinery necessary for entry is located in the third layer. This modular nature of its particle allows rotaviruses to control its replication cycle by the disassembly and assembly of its structural proteins. In this review, we examine the significant advances in structural, molecular, and cellular RV biology that have contributed during the last few years to illuminating the intricate details of the RV particle disassembly and assembly processes.
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Affiliation(s)
- Dunia Asensio-Cob
- Department of Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G0A4, Canada;
| | - Javier M. Rodríguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Daniel Luque
- Electron Microscopy Unit UCCT/ISCIII, 28220 Majadahonda, Spain
- School of Biomedical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052, Australia
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Carossino M, Balasuriya UBR, Thieulent CJ, Barrandeguy ME, Vissani MA, Parreño V. Quadruplex Real-Time TaqMan ® RT-qPCR Assay for Differentiation of Equine Group A and B Rotaviruses and Identification of Group A G3 and G14 Genotypes. Viruses 2023; 15:1626. [PMID: 37631969 PMCID: PMC10459720 DOI: 10.3390/v15081626] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Equine rotavirus A (ERVA) is the leading cause of diarrhea in foals, with G3P[12] and G14P[12] genotypes being the most prevalent. Recently, equine G3-like RVA was recognized as an emerging infection in children, and a group B equine rotavirus (ERVB) was identified as an emergent cause of foal diarrhea in the US. Thus, there is a need to adapt molecular diagnostic tools for improved detection and surveillance to identify emerging strains, understand their molecular epidemiology, and inform future vaccine development. We developed a quadruplex TaqMan® RT-qPCR assay for differentiation of ERVA and ERVB and simultaneous G-typing of ERVA strains, evaluated its analytical and clinical performance, and compared it to (1) a previously established ERVA triplex RT-qPCR assay and (2) standard RT-PCR assay and Sanger sequencing of PCR products. This quadruplex RT-qPCR assay demonstrated high sensitivity (>90%)/specificity (100%) for every target and high overall agreement (>96%). Comparison between the triplex and quadruplex assays revealed only a slightly higher sensitivity for the ERVA NSP3 target using the triplex format (p-value 0.008) while no significant differences were detected for other targets. This quadruplex RT-qPCR assay will significantly enhance rapid surveillance of both ERVA and ERVB circulating and emerging strains with potential for interspecies transmission.
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Affiliation(s)
- Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Udeni B. R. Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Côme J. Thieulent
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Maria E. Barrandeguy
- Escuela de Veterinaria, Universidad del Salvador, Buenos Aires B1630, Argentina; (M.E.B.); (M.A.V.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686, Argentina;
| | - Maria Aldana Vissani
- Escuela de Veterinaria, Universidad del Salvador, Buenos Aires B1630, Argentina; (M.E.B.); (M.A.V.)
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1425, Argentina
| | - Viviana Parreño
- Instituto de Virología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires B1686, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1425, Argentina
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Chari A, Stark H. Prospects and Limitations of High-Resolution Single-Particle Cryo-Electron Microscopy. Annu Rev Biophys 2023; 52:391-411. [PMID: 37159297 DOI: 10.1146/annurev-biophys-111622-091300] [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: 05/10/2023]
Abstract
Single particle cryo-electron microscopy (cryo-EM) has matured into a robust method for the determination of biological macromolecule structures in the past decade, complementing X-ray crystallography and nuclear magnetic resonance. Constant methodological improvements in both cryo-EM hardware and image processing software continue to contribute to an exponential growth in the number of structures solved annually. In this review, we provide a historical view of the many steps that were required to make cryo-EM a successful method for the determination of high-resolution protein complex structures. We further discuss aspects of cryo-EM methodology that are the greatest pitfalls challenging successful structure determination to date. Lastly, we highlight and propose potential future developments that would improve the method even further in the near future.
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Affiliation(s)
- Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany;
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Strain-Specific Interactions between the Viral Capsid Proteins VP4, VP7 and VP6 Influence Rescue of Rotavirus Reassortants by Reverse Genetics. Int J Mol Sci 2023; 24:ijms24065670. [PMID: 36982745 PMCID: PMC10054668 DOI: 10.3390/ijms24065670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Rotavirus A (RVA) genome segments can reassort upon co-infection of target cells with two different RVA strains. However, not all reassortants are viable, which limits the ability to generate customized viruses for basic and applied research. To gain insight into the factors that restrict reassortment, we utilized reverse genetics and tested the generation of simian RVA strain SA11 reassortants carrying the human RVA strain Wa capsid proteins VP4, VP7, and VP6 in all possible combinations. VP7-Wa, VP6-Wa, and VP7/VP6-Wa reassortants were effectively rescued, but the VP4-Wa, VP4/VP7-Wa, and VP4/VP6-Wa reassortants were not viable, suggesting a limiting effect of VP4-Wa. However, a VP4/VP7/VP6-Wa triple-reassortant was successfully generated, indicating that the presence of homologous VP7 and VP6 enabled the incorporation of VP4-Wa into the SA11 backbone. The replication kinetics of the triple-reassortant and its parent strain Wa were comparable, while the replication of all other rescued reassortants was similar to SA11. Analysis of the predicted structural protein interfaces identified amino acid residues, which might influence protein interactions. Restoring the natural VP4/VP7/VP6 interactions may therefore improve the rescue of RVA reassortants by reverse genetics, which could be useful for the development of next generation RVA vaccines.
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Rotavirus Infection and Genotyping in Yantai, Shandong Province, 2017-2019. Trop Med Infect Dis 2023; 8:tropicalmed8020101. [PMID: 36828517 PMCID: PMC9963496 DOI: 10.3390/tropicalmed8020101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/16/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
PURPOSE Rotavirus (RV) ranked first among infectious diarrhea-causing pathogens in Yantai from 2017 to 2019. This study investigated the seroserotypes of RV in Yantai, Shandong, from 2017 to 2019 to identify the dominant serotypes and explore the epidemic pattern, aiming to effectively reduce the infection rate, better guide vaccination, and help in epidemiological prevention and control. METHODS A total of 2227 human diarrhea samples were collected from 2017 to 2019 in Yantai. The VP7 (G serotype) and VP4 (P serotype) genes of 467 RV-positive samples were amplified using two-round nested reverse transcription-polymerase chain reaction for G/P genotyping. RESULTS The genotyping results of RV in Yantai from 2017 to 2019 revealed that G9 was the dominant serotype for all G serotypes, P[8] was the dominant serotype for all P serotypes, and G9P[8] was the dominant serotype for all G/P combinations. G9 serotype accounted for 60.84%, 95.65%, and 83.76% of the total RV samples collected in 2017, 2018, and 2019, respectively. P[8] accounted for 75.52%, 94.69%, and 88.89% of the RV-positive samples collected in 2017, 2018, and 2019, respectively. G9P[8] accounted for 60.84%, 94.69%, and 83.76% of the total RV samples collected in 2017, 2018, and 2019, respectively. Of the total 467 samples from 2017 to 2019, G2P[4] accounted for 3.64% (17/467), G3P[8] for 1.28% (6/467), and G1P[8] for 0.86% (4/467). CONCLUSION This study revealed the epidemiological characteristics of RV infection and the development pattern of dominant serotypes in Yantai in recent years, guiding the selection of RV vaccines. The prioritization of vaccines containing G9 serotype for infants in Yantai in recent years is recommended.
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Bakshi T, Pham D, Kaur R, Sun B. Hidden Relationships between N-Glycosylation and Disulfide Bonds in Individual Proteins. Int J Mol Sci 2022; 23:ijms23073742. [PMID: 35409101 PMCID: PMC8998389 DOI: 10.3390/ijms23073742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/04/2023] Open
Abstract
N-Glycosylation (NG) and disulfide bonds (DBs) are two prevalent co/post-translational modifications (PTMs) that are often conserved and coexist in membrane and secreted proteins involved in a large number of diseases. Both in the past and in recent times, the enzymes and chaperones regulating these PTMs have been constantly discovered to directly interact with each other or colocalize in the ER. However, beyond a few model proteins, how such cooperation affects N-glycan modification and disulfide bonding at selective sites in individual proteins is largely unknown. Here, we reviewed the literature to discover the current status in understanding the relationships between NG and DBs in individual proteins. Our results showed that more than 2700 human proteins carry both PTMs, and fewer than 2% of them have been investigated in the associations between NG and DBs. We summarized both these proteins with the reported relationships in the two PTMs and the tools used to discover the relationships. We hope that, by exposing this largely understudied field, more investigations can be encouraged to unveil the hidden relationships of NG and DBs in the majority of membranes and secreted proteins for pathophysiological understanding and biotherapeutic development.
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Affiliation(s)
- Tania Bakshi
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - David Pham
- Department of Computing Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - Raminderjeet Kaur
- Faculty of Health Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
| | - Bingyun Sun
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada;
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Correspondence:
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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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Himes B, Grigorieff N. Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation. IUCRJ 2021; 8:943-953. [PMID: 34804546 PMCID: PMC8562658 DOI: 10.1107/s2052252521008538] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Image simulation plays a central role in the development and practice of high-resolution electron microscopy, including transmission electron microscopy of frozen-hydrated specimens (cryo-EM). Simulating images with contrast that matches the contrast observed in experimental images remains challenging, especially for amorphous samples. Current state-of-the-art simulators apply post hoc scaling to approximate empirical solvent contrast, attenuated image intensity due to specimen thickness and amplitude contrast. This practice fails for images that require spatially variable scaling, e.g. simulations of a crowded or cellular environment. Modeling both the signal and the noise accurately is necessary to simulate images of biological specimens with contrast that is correct on an absolute scale. The 'frozen plasmon' method is introduced to explicitly model spatially variable inelastic scattering processes in cryo-EM specimens. This approach produces amplitude contrast that depends on the atomic composition of the specimen, reproduces the total inelastic mean free path as observed experimentally and allows for the incorporation of radiation damage in the simulation. These improvements are quantified using the matched filter concept to compare simulation and experiment. The frozen plasmon method, in combination with a new mathematical formulation for accurately sampling the tabulated atomic scattering potentials onto a Cartesian grid, is implemented in the open-source software package cisTEM.
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Affiliation(s)
- Benjamin Himes
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Nikolaus Grigorieff
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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Patra U, Mukhopadhyay U, Mukherjee A, Dutta S, Chawla-Sarkar M. Treading a HOSTile path: Mapping the dynamic landscape of host cell-rotavirus interactions to explore novel host-directed curative dimensions. Virulence 2021; 12:1022-1062. [PMID: 33818275 PMCID: PMC8023246 DOI: 10.1080/21505594.2021.1903198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Viruses are intracellular pathogens and are dependent on host cellular resources to carry out their cycles of perpetuation. Obtaining an integrative view of host-virus interaction is of utmost importance to understand the complex and dynamic interplay between viral components and host machineries. Besides its obvious scholarly significance, a comprehensive host-virus interaction profile also provides a platform where from host determinants of pro-viral and antiviral importance can be identified and further be subjected to therapeutic intervention. Therefore, adjunct to conventional methods of prophylactic vaccination and virus-directed antivirals, this host-targeted antiviral approach holds promising therapeutic potential. In this review, we present a comprehensive landscape of host cellular reprogramming in response to infection with rotavirus (RV) which causes profuse watery diarrhea in neonates and infants. In addition, an emphasis is given on how host determinants are either usurped or subverted by RV in course of infection and how therapeutic manipulation of specific host factors can effectively modulate the RV life cycle.
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Affiliation(s)
- Upayan Patra
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Urbi Mukhopadhyay
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Arpita Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
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Lestari FB, Vongpunsawad S, Wanlapakorn N, Poovorawan Y. Rotavirus infection in children in Southeast Asia 2008-2018: disease burden, genotype distribution, seasonality, and vaccination. J Biomed Sci 2020; 27:66. [PMID: 32438911 PMCID: PMC7239768 DOI: 10.1186/s12929-020-00649-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/27/2020] [Indexed: 01/30/2023] Open
Abstract
Background Rotaviruses (RVs) are recognized as a major cause of acute gastroenteritis (AGE) in infants and young children worldwide. Here we summarize the virology, disease burden, prevalence, distribution of genotypes and seasonality of RVs, and the current status of RV vaccination in Southeast Asia (Cambodia, Indonesia, Lao People’s Democratic Republic, Malaysia, Myanmar, Philippines, Singapore, Thailand, and Vietnam) from 2008 to 2018. Methods Rotavirus infection in Children in Southeast Asia countries was assessed using data from Pubmed and Google Scholars. Most countries in Southeast Asia have not yet introduced national RV vaccination programs. We exclude Brunei Darussalam, and Timor Leste because there were no eligible studies identified during that time. Results According to the 2008–2018 RV surveillance data for Southeast Asia, 40.78% of all diarrheal disease in children were caused by RV infection, which is still a major cause of morbidity and mortality in children under 5 years old in Southeast Asia. Mortality was inversely related to socioeconomic status. The most predominant genotype distribution of RV changed from G1P[8] and G2P[4] into the rare and unusual genotypes G3P[8], G8P[8], and G9P[8]. Although the predominat strain has changed, but the seasonality of RV infection remains unchanged. One of the best strategies for decreasing the global burden of the disease is the development and implementation of effective vaccines. Conclusions The most predominant genotype distribution of RV was changed time by time. Rotavirus vaccine is highly cost effective in Southeast Asian countries because the ratio between cost per disability-adjusted life years (DALY) averted and gross domestic product (GDP) per capita is less than one. These data are important for healthcare practitioners and officials to make appropriate policies and recommendations about RV vaccination.
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Affiliation(s)
- Fajar Budi Lestari
- Inter-Department of Biomedical Science, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand.,Department of Bioresources Technology and Veterinary, Vocational College, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Division of Academic Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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Novikova NA, Sashina TA, Epifanova NV, Kashnikov AU, Morozova OV. Long-term monitoring of G1P[8] rotaviruses circulating without vaccine pressure in Nizhny Novgorod, Russia, 1984-2019. Arch Virol 2020; 165:865-875. [DOI: 10.1007/s00705-020-04553-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/18/2020] [Indexed: 01/01/2023]
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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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Suzuki H. Rotavirus Replication: Gaps of Knowledge on Virus Entry and Morphogenesis. TOHOKU J EXP MED 2020; 248:285-296. [PMID: 31447474 DOI: 10.1620/tjem.248.285] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In 1973, rotaviruses A (RVAs) were discovered as major causative agents of acute gastroenteritis in infants and young children worldwide. The infectious RV virion is an icosahedral particle composed of three concentric protein layers surrounding the 11 double-stranded (dsRNA) segments. An in vitro replication system for RVs in permanent cell lines was developed in 1982 and expanded to replication in intestinal organoids in 2015. However, the details of rotavirus (RV) entry into cells and particle maturation mechanisms at the molecular level remain incompletely understood. Slowing down human RVA replication in cell culture on ice allowed morphological visualization of virus particle entry and the assembly of triple-layered particles (virion). Although RVAs are non-enveloped viruses, after virus attachment to the cell membrane, the virus enters the cell by perforating the plasma membrane by a fusion mechanism involving VP5* of the cleaved VP4 protein, as the alternative virus entry route besides the receptor-mediated endocytosis which is generally accepted. After assembling double-layered particles (DLPs) in viroplasm or cytoplasm, they appear to be connected with the endoplasmic reticulum (ER) membrane and become coated with outer capsid proteins (VP4 and VP7) in a coating process. The perforation of the ER membrane is caused by an unknown mechanism following interaction between non-structural protein 4 (NSP4) and the inner capsid protein VP6 of the DLPs. The coating process is closely related to the formation of a hetero-oligomeric complex (NSP4, VP4 and VP7). These lines of evidence suggest the existence of novel mechanisms of RV morphogenesis.
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Abstract
In vertebrates, immunoglobulins (Igs), commonly known as antibodies, play an integral role in the armamentarium of immune defense against various pathogens. After an antigenic challenge, antibodies are secreted by differentiated B cells called plasma cells. Antibodies have two predominant roles that involve specific binding to antigens to launch an immune response, along with activation of other components of the immune system to fight pathogens. The ability of immunoglobulins to fight against innumerable and diverse pathogens lies in their intrinsic ability to discriminate between different antigens. Due to this specificity and high affinity for their antigens, antibodies have been a valuable and indispensable tool in research, diagnostics and therapy. Although seemingly a simple maneuver, the association between an antibody and its antigen, to make an antigen-antibody complex, is comprised of myriads of non-covalent interactions. Amino acid residues on the antigen binding site, the epitope, and on the antibody binding site, the paratope, intimately contribute to the energetics needed for the antigen-antibody complex stability. Structural biology methods to study antigen-antibody complexes are extremely valuable tools to visualize antigen-antibody interactions in detail; this helps to elucidate the basis of molecular recognition between an antibody and its specific antigen. The main scope of this chapter is to discuss the structure and function of different classes of antibodies and the various aspects of antigen-antibody interactions including antigen-antibody interfaces-with a special focus on paratopes, complementarity determining regions (CDRs) and other non-CDR residues important for antigen binding and recognition. Herein, we also discuss methods used to study antigen-antibody complexes, antigen recognition by antibodies, types of antigens in complexes, and how antigen-antibody complexes play a role in modern day medicine and human health. Understanding the molecular basis of antigen binding and recognition by antibodies helps to facilitate the production of better and more potent antibodies for immunotherapy, vaccines and various other applications.
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Affiliation(s)
- A Brenda Kapingidza
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Krzysztof Kowal
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Department of Experimental Allergology and Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA.
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Abid N, Chillemi G, Salemi M. Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach. Genes (Basel) 2019; 11:genes11010028. [PMID: 31878331 PMCID: PMC7016848 DOI: 10.3390/genes11010028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 12/10/2019] [Accepted: 12/19/2019] [Indexed: 01/12/2023] Open
Abstract
Rotavirus remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious question. The distribution of unusual genotypes subject to viral fitness is influenced by interactions among viral proteins. The present work aimed at analyzing the genetic constellation and the coevolution of rotavirus coding genes for the available rotavirus genotypes. Seventy-two full genome sequences of different genetic constellations were analyzed using a genetic algorithm. The results revealed an extensive genome-wide covariance network among the 12 viral proteins. Altogether, the emergence of new genotypes represents a challenge to the outcome and success of vaccination and the coevolutionary analysis of rotavirus proteins may boost efforts to better understand the interaction networks of proteins during viral replication/transcription.
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Affiliation(s)
- Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, Monastir 5000, Tunisia
- High Institute of Biotechnology of Sidi Thabet, Department of Biotechnology, University Manouba, BP-66, Ariana-Tunis 2020, Tunisia
- Correspondence: or ; Tel.: +216-92–974-000
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest systems, DIBAF, University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy;
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, Via Giovanni Amendola, 122/O, 70126 Bari, Italy
| | - Marco Salemi
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Emerging Pathogens Institute, P.O. Box 100009, Gainesville, FL 32610-3633, USA;
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Cui T, Theuns S, Xie J, Nauwynck HJ. Porcine rotavirus mainly infects primary porcine enterocytes at the basolateral surface. Vet Res 2019; 50:110. [PMID: 31856906 PMCID: PMC6924034 DOI: 10.1186/s13567-019-0728-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/29/2019] [Indexed: 12/15/2022] Open
Abstract
Intestinal epithelium functions as a barrier to protect multicellular organisms from the outside world. It consists of epithelial cells closely connected by intercellular junctions, selective gates which control paracellular diffusion of solutes, ions and macromolecules across the epithelium and keep out pathogens. Rotavirus is one of the major enteric viruses causing severe diarrhea in humans and animals. It specifically infects the enterocytes on villi of small intestines. The polarity of rotavirus replication in their target enterocytes and the role of intestinal epithelial integrity were examined in the present study. Treatment with EGTA, a drug that chelates calcium and disrupts the intercellular junctions, (i) significantly enhanced the infection of rotavirus in primary enterocytes, (ii) increased the binding of rotavirus to enterocytes, but (iii) considerably blocked internalization of rotavirus. After internalization, rotavirus was resistant to EGTA treatment. To investigate the polarity of rotavirus infection, the primary enterocytes were cultured in a transwell system and infected with rotavirus at either the apical or the basolateral surface. Rotavirus preferentially infected enterocytes at the basolateral surface. Restriction of infection through apical inoculation was overcome by EGTA treatment. Overall, our findings demonstrate that integrity of the intestinal epithelium is crucial in the host's innate defense against rotavirus infection. In addition, the intercellular receptor is located basolaterally and disruption of intercellular junctions facilitates the binding of rotavirus to their receptor at the basolateral surface.
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Affiliation(s)
- Tingting Cui
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
| | - Sebastiaan Theuns
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Jiexiong Xie
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Hans J Nauwynck
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
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Cryo-EM Reveals Architectural Diversity in Active Rotavirus Particles. Comput Struct Biotechnol J 2019; 17:1178-1183. [PMID: 31467657 PMCID: PMC6710475 DOI: 10.1016/j.csbj.2019.07.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 12/04/2022] Open
Abstract
Rotavirus is a well-studied RNA virus that causes severe gastroenteritis in children. During viral entry, the outer layer of the virion is shed, creating a double-layered particle (DLP) that is competent to perform viral transcription (i.e., mRNA synthesis) and launch infection. While inactive forms of rotavirus DLPs have been structurally characterized in detail, information about the transcriptionally-active DLP remains limited. Here, we used cryo-Electron Microscopy (cryo-EM) and 3D image reconstructions to compare the structures of internal protein components in transcriptionally-active versus inactive DLPs. Our findings showed that transcriptionally-active DLPs gained internal order as mRNA synthesis unfolded, while inactive DLPs remained dynamically disordered. Regions of viral protein/RNA constituents were analyzed across two different axes of symmetry to provide a more comprehensive view of moving components. Taken together, our results bring forth a new view of active DLPs, which may enable future pharmacological strategies aimed at obliterating rotavirus transcription as a therapeutic approach.
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In situ Structure of Rotavirus VP1 RNA-Dependent RNA Polymerase. J Mol Biol 2019; 431:3124-3138. [PMID: 31233764 DOI: 10.1016/j.jmb.2019.06.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/07/2019] [Accepted: 06/14/2019] [Indexed: 02/03/2023]
Abstract
Rotaviruses, like other non-enveloped, double-strand RNA viruses, package an RNA-dependent RNA polymerase (RdRp) with each duplex of their segmented genomes. Rotavirus cell entry results in loss of an outer protein layer and delivery into the cytosol of an intact, inner capsid particle (the "double-layer particle," or DLP). The RdRp, designated VP1, is active inside the DLP; each VP1 achieves many rounds of mRNA transcription from its associated genome segment. Previous work has shown that one VP1 molecule lies close to each 5-fold axis of the icosahedrally symmetric DLP, just beneath the inner surface of its protein shell, embedded in tightly packed RNA. We have determined a high-resolution structure for the rotavirus VP1 RdRp in situ, by local reconstruction of density around individual 5-fold positions. We have analyzed intact virions ("triple-layer particles"), non-transcribing DLPs and transcribing DLPs. Outer layer dissociation enables the DLP to synthesize RNA, in vitro as well as in vivo, but appears not to induce any detectable structural change in the RdRp. Addition of NTPs, Mg2+, and S-adenosylmethionine, which allows active transcription, results in conformational rearrangements, in both VP1 and the DLP capsid shell protein, that allow a transcript to exit the polymerase and the particle. The position of VP1 (among the five symmetrically related alternatives) at one vertex does not correlate with its position at other vertices. This stochastic distribution of site occupancies limits long-range order in the 11-segment, double-strand RNA genome.
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Carossino M, Barrandeguy ME, Erol E, Li Y, Balasuriya UBR. Development and evaluation of a one-step multiplex real-time TaqMan ® RT-qPCR assay for the detection and genotyping of equine G3 and G14 rotaviruses in fecal samples. Virol J 2019; 16:49. [PMID: 31023319 PMCID: PMC6482509 DOI: 10.1186/s12985-019-1149-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 03/20/2019] [Indexed: 11/23/2022] Open
Abstract
Background Equine rotavirus A (ERVA) is the leading cause of diarrhea in neonatal foals and has a negative impact on equine breeding enterprises worldwide. Among ERVA strains infecting foals, the genotypes G3P[12] and G14P[12] are the most prevalent, while infections by strains with other genomic arrangements are infrequent. The identification of circulating strains of ERVA is critical for diagnostic and surveillance purposes, as well as to understand their molecular epidemiology. Current genotyping methods available for ERVA and rotaviruses affecting other animal species rely on Sanger sequencing and are significantly time-consuming, costly and labor intensive. Here, we developed the first one-step multiplex TaqMan® real-time reverse transcription polymerase chain reaction (RT-qPCR) assay targeting the NSP3 and VP7 genes of ERVA G3 and G14 genotypes for the rapid detection and G-typing directly from fecal specimens. Methods A one-step multiplex TaqMan® RT-qPCR assay targeting the NSP3 and VP7 genes of ERVA G3 and G14 genotypes was designed. The analytical sensitivity was assessed using serial dilutions of in vitro transcribed RNA containing the target sequences while the analytical specificity was determined using RNA and DNA derived from a panel of group A rotaviruses along with other equine viruses and bacteria. The clinical performance of this multiplex assay was evaluated using a panel of 177 fecal samples and compared to a VP7-specific standard RT-PCR assay and Sanger sequencing. Limits of detection (LOD), sensitivity, specificity, and agreement were determined. Results The multiplex G3 and G14 VP7 assays demonstrated high specificity and efficiency, with perfect linearity. A 100-fold difference in their analytical sensitivity was observed when compared to the singleplex assays; however, this difference did not have an impact on the clinical performance. Clinical performance of the multiplex RT-qPCR assay demonstrated that this assay had a high sensitivity/specificity for every target (100% for NSP3, > 90% for G3 VP7 and > 99% for G14 VP7, respectively) and high overall agreement (> 98%) compared to conventional RT-PCR and sequencing. Conclusions This new multiplex RT-qPCR assay constitutes a useful, very reliable tool that could significantly aid in the rapid detection and G-typing of ERVA strains circulating in the field.
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Affiliation(s)
- Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA.,Escuela de Veterinaria, Universidad del Salvador, Champagnat 1599, Ruta Panamericana km54.5 (B1630AHU), Pilar, Buenos Aires, Argentina
| | - Maria E Barrandeguy
- Escuela de Veterinaria, Universidad del Salvador, Champagnat 1599, Ruta Panamericana km54.5 (B1630AHU), Pilar, Buenos Aires, Argentina.,Instituto de Virología, CICVyA, INTA. Las Cabañas y Los Reseros s/n, (1712) Castelar, Buenos Aires, Argentina
| | - Erdal Erol
- Department of Veterinary Science, University of Kentucky Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY, USA
| | - Yanqiu Li
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Udeni B R Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA.
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Rodríguez JM, Luque D. Structural Insights into Rotavirus Entry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:45-68. [DOI: 10.1007/978-3-030-14741-9_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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Ogden KM, Tan Y, Akopov A, Stewart LS, McHenry R, Fonnesbeck CJ, Piya B, Carter MH, Fedorova NB, Halpin RA, Shilts MH, Edwards KM, Payne DC, Esona MD, Mijatovic-Rustempasic S, Chappell JD, Patton JT, Halasa NB, Das SR. Multiple Introductions and Antigenic Mismatch with Vaccines May Contribute to Increased Predominance of G12P[8] Rotaviruses in the United States. J Virol 2019; 93:e01476-18. [PMID: 30333170 PMCID: PMC6288334 DOI: 10.1128/jvi.01476-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
Rotavirus is the leading global cause of diarrheal mortality for unvaccinated children under 5 years of age. The outer capsid of rotavirus virions consists of VP7 and VP4 proteins, which determine viral G and P types, respectively, and are primary targets of neutralizing antibodies. Successful vaccination depends upon generating broadly protective immune responses following exposure to rotaviruses presenting a limited number of G- and P-type antigens. Vaccine introduction resulted in decreased rotavirus disease burden but also coincided with the emergence of uncommon G and P genotypes, including G12. To gain insight into the recent predominance of G12P[8] rotaviruses in the United States, we evaluated 142 complete rotavirus genome sequences and metadata from 151 clinical specimens collected in Nashville, TN, from 2011 to 2013 through the New Vaccine Surveillance Network. Circulating G12P[8] strains were found to share many segments with other locally circulating strains but to have distinct constellations. Phylogenetic analyses of G12 sequences and their geographic sources provided evidence for multiple separate introductions of G12 segments into Nashville, TN. Antigenic epitopes of VP7 proteins of G12P[8] strains circulating in Nashville, TN, differ markedly from those of vaccine strains. Fully vaccinated children were found to be infected with G12P[8] strains more frequently than with other rotavirus genotypes. Multiple introductions and significant antigenic mismatch may in part explain the recent predominance of G12P[8] strains in the United States and emphasize the need for continued monitoring of rotavirus vaccine efficacy against emerging rotavirus genotypes.IMPORTANCE Rotavirus is an important cause of childhood diarrheal disease worldwide. Two immunodominant proteins of rotavirus, VP7 and VP4, determine G and P genotypes, respectively. Recently, G12P[8] rotaviruses have become increasingly predominant. By analyzing rotavirus genome sequences from stool specimens obtained in Nashville, TN, from 2011 to 2013 and globally circulating rotaviruses, we found evidence of multiple introductions of G12 genes into the area. Based on sequence polymorphisms, VP7 proteins of these viruses are predicted to present themselves to the immune system very differently than those of vaccine strains. Many of the sick children with G12P[8] rotavirus in their diarrheal stools also were fully vaccinated. Our findings emphasize the need for continued monitoring of circulating rotaviruses and the effectiveness of the vaccines against strains with emerging G and P genotypes.
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Affiliation(s)
- Kristen M Ogden
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yi Tan
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- J. Craig Venter Institute, Rockville, Maryland, USA
| | - Asmik Akopov
- J. Craig Venter Institute, Rockville, Maryland, USA
| | - Laura S Stewart
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rendie McHenry
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Bhinnata Piya
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Maximilian H Carter
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | | | - Meghan H Shilts
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Daniel C Payne
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mathew D Esona
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John T Patton
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Natasha B Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Suman R Das
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- J. Craig Venter Institute, Rockville, Maryland, USA
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Jiménez-Zaragoza M, Yubero MP, Martín-Forero E, Castón JR, Reguera D, Luque D, de Pablo PJ, Rodríguez JM. Biophysical properties of single rotavirus particles account for the functions of protein shells in a multilayered virus. eLife 2018; 7:37295. [PMID: 30201094 PMCID: PMC6133545 DOI: 10.7554/elife.37295] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/01/2018] [Indexed: 12/27/2022] Open
Abstract
The functions performed by the concentric shells of multilayered dsRNA viruses require specific protein interactions that can be directly explored through their mechanical properties. We studied the stiffness, breaking force, critical strain and mechanical fatigue of individual Triple, Double and Single layered rotavirus (RV) particles. Our results, in combination with Finite Element simulations, demonstrate that the mechanics of the external layer provides the resistance needed to counteract the stringent conditions of extracellular media. Our experiments, in combination with electrostatic analyses, reveal a strong interaction between the two outer layers and how it is suppressed by the removal of calcium ions, a key step for transcription initiation. The intermediate layer presents weak hydrophobic interactions with the inner layer that allow the assembly and favor the conformational dynamics needed for transcription. Our work shows how the biophysical properties of the three shells are finely tuned to produce an infective RV virion.
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Affiliation(s)
- Manuel Jiménez-Zaragoza
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marina Pl Yubero
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Jose R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | - David Reguera
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain
| | - Daniel Luque
- Centro Nacional de Microbiología/ISCIII, Majadahonda, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain
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27
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Pal S, Ganesan K, Eswaran S. Chemical Crosslinking-Mass Spectrometry (CXL-MS) for Proteomics, Antibody-Drug Conjugates (ADCs) and Cryo-Electron Microscopy (cryo-EM). IUBMB Life 2018; 70:947-960. [DOI: 10.1002/iub.1916] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 06/06/2018] [Accepted: 06/27/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Shreya Pal
- Amity University Haryana; Manesar Haryana India
| | | | - Sambasivan Eswaran
- Regional Centre for Biotechnology (Established by DBT, Govt. of India under the auspices of UNESCO); NCR Biotech Science Cluster; Faridabad Haryana India
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28
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Carossino M, Barrandeguy ME, Li Y, Parreño V, Janes J, Loynachan AT, Balasuriya UBR. Detection, molecular characterization and phylogenetic analysis of G3P[12] and G14P[12] equine rotavirus strains co-circulating in central Kentucky. Virus Res 2018; 255:39-54. [PMID: 29864502 DOI: 10.1016/j.virusres.2018.05.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 11/18/2022]
Abstract
Equine rotavirus A (ERVA) is the leading cause of diarrhea in neonatal foals and a major health problem to the equine breeding industry worldwide. The G3P[12] and G14P[12] ERVA genotypes are the most prevalent in foals with diarrhea. Control and prevention strategies include vaccination of pregnant mares with an inactivated vaccine containing a prototype ERVA G3P[12] strain with limited and controversial field efficacy. Here, we performed the molecular characterization of ERVA strains circulating in central Kentucky using fecal samples collected during the 2017 foaling season. The data indicated for the first time that the G14P[12] genotype is predominant in this region in contrast to a previous serotyping study where only G3 genotype strains were reported. Overall, analysis of antigenic sites in the VP7 protein demonstrated the presence of several amino acid substitutions in the epitopes exposed on the surface including a non-conserved N-linked glycosylation site (D123N) in G14P[12] strains, while changes in antigenic sites of VP8* were minor. Also, we report the successful isolation of three ERVA G14P[12] strains which presented a high identity with other G14 strains from around the world. These may constitute ideal reference strains to comparatively study the molecular biology of G3 and G14 strains and perform vaccine efficacy studies following heterologous challenge in the future.
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Affiliation(s)
- Mariano Carossino
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA; Escuela de Veterinaria, Universidad del Salvador, Champagnat 1599, Ruta Panamericana km54.5 (B1630AHU), Pilar, Buenos Aires, Argentina
| | - Maria E Barrandeguy
- Instituto de Virología, CICVyA, INTA. Las Cabañas y Los Reseros s/n, 1712, Castelar, Buenos Aires, Argentina; Escuela de Veterinaria, Universidad del Salvador, Champagnat 1599, Ruta Panamericana km54.5 (B1630AHU), Pilar, Buenos Aires, Argentina
| | - Yanqiu Li
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Viviana Parreño
- Instituto de Virología, CICVyA, INTA. Las Cabañas y Los Reseros s/n, 1712, Castelar, Buenos Aires, Argentina
| | - Jennifer Janes
- University of Kentucky Veterinary Diagnostic Laboratory, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Alan T Loynachan
- University of Kentucky Veterinary Diagnostic Laboratory, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Udeni B R Balasuriya
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA.
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29
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Abstract
We have developed new open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cisTEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k – 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cisTEM is available for download from cistem.org.
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Affiliation(s)
- Timothy Grant
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Alexis Rohou
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
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30
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Mak J, de Marco A. Recent advances in retroviruses via cryo-electron microscopy. Retrovirology 2018; 15:23. [PMID: 29471854 PMCID: PMC5824478 DOI: 10.1186/s12977-018-0405-6] [Citation(s) in RCA: 4] [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: 09/17/2017] [Accepted: 02/14/2018] [Indexed: 12/14/2022] Open
Abstract
Cryo-electron microscopy has undergone a revolution in recent years and it has contributed significantly to a number of different areas in biological research. In this manuscript, we will describe some of the recent advancements in cryo-electron microscopy focussing on the advantages that this technique can bring rather than on the technology. We will then conclude discussing how the field of retrovirology has benefited from cryo-electron microscopy.
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Affiliation(s)
- Johnson Mak
- Institute for Glycomics, Griffith University Gold Coast, Southport, QLD, Australia
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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31
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Kondakova OA, Nikitin NA, Trifonova EA, Atabekov JG, Karpova OV. Rotavirus Vaccines: New Strategies and Approaches. ACTA ACUST UNITED AC 2018. [DOI: 10.3103/s0096392517040071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Ho PT, Reddy VS. Rapid increase of near atomic resolution virus capsid structures determined by cryo-electron microscopy. J Struct Biol 2018; 201:1-4. [DOI: 10.1016/j.jsb.2017.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/28/2017] [Accepted: 10/18/2017] [Indexed: 10/18/2022]
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33
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Single-Particle Detection of Transcription following Rotavirus Entry. J Virol 2017; 91:JVI.00651-17. [PMID: 28701394 PMCID: PMC5571246 DOI: 10.1128/jvi.00651-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 06/29/2017] [Indexed: 12/25/2022] Open
Abstract
Infectious rotavirus particles are triple-layered, icosahedral assemblies. The outer layer proteins, VP4 (cleaved to VP8* and VP5*) and VP7, surround a transcriptionally competent, double-layer particle (DLP), which they deliver into the cytosol. During entry of rhesus rotavirus, VP8* interacts with cell surface gangliosides, allowing engulfment into a membrane vesicle by a clathrin-independent process. Escape into the cytosol and outer-layer shedding depend on interaction of a hydrophobic surface on VP5* with the membrane bilayer and on a large-scale conformational change. We report here experiments that detect the fate of released DLPs and their efficiency in initiating RNA synthesis. By replacing the outer layer with fluorescently tagged, recombinant proteins and also tagging the DLP, we distinguished particles that have lost their outer layer and entered the cytosol (uncoated) from those still within membrane vesicles. We used fluorescent in situ hybridization with probes for nascent transcripts to determine how soon after uncoating transcription began and what fraction of the uncoated particles were active in initiating RNA synthesis. We detected RNA synthesis by uncoated particles as early as 15 min after adding virus. The uncoating efficiency was 20 to 50%; of the uncoated particles, about 10 to 15% synthesized detectable RNA. In the format of our experiments, about 10% of the added particles attached to the cell surface, giving an overall ratio of added particles to RNA-synthesizing particles of between 250:1 and 500:1, in good agreement with the ratio of particles to focus-forming units determined by infectivity assays. Thus, RNA synthesis by even a single, uncoated particle can initiate infection in a cell.IMPORTANCE The pathways by which a virus enters a cell transform its packaged genome into an active one. Contemporary fluorescence microscopy can detect individual virus particles as they enter cells, allowing us to map their multistep entry pathways. Rotaviruses, like most viruses that lack membranes of their own, disrupt or perforate the intracellular, membrane-enclosed compartment into which they become engulfed following attachment to a cell surface, in order to gain access to the cell interior. The properties of rotavirus particles make it possible to determine molecular mechanisms for these entry steps. In the work described here, we have asked the following question: what fraction of the rotavirus particles that penetrate into the cell make new viral RNA? We find that of the cell-attached particles, between 20 and 50% ultimately penetrate, and of these, about 10% make RNA. RNA synthesis by even a single virus particle can initiate a productive infection.
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34
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Doan YH, Suzuki Y, Fujii Y, Haga K, Fujimoto A, Takai-Todaka R, Someya Y, Nayak MK, Mukherjee A, Imamura D, Shinoda S, Chawla-Sarkar M, Katayama K. Complex reassortment events of unusual G9P[4] rotavirus strains in India between 2011 and 2013. INFECTION GENETICS AND EVOLUTION 2017; 54:417-428. [PMID: 28750901 DOI: 10.1016/j.meegid.2017.07.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 11/16/2022]
Abstract
Rotavirus A (RVA) is the predominant etiological agent of acute gastroenteritis in young children worldwide. Recently, unusual G9P[4] rotavirus strains emerged with high prevalence in many countries. Such intergenogroup reassortant strains highlight the ongoing spread of unusual rotavirus strains throughout Asia. This study was undertaken to determine the whole genome of eleven unusual G9P[4] strains detected in India during 2011-2013, and to compare them with other human and animal global RVAs to understand the exact origin of unusual G9P[4] circulating in India and other countries worldwide. Of these 11 RVAs, four G9P[4] strains were double-reassortants with the G9-VP7 and E6-NSP4 genes on a DS-1-like genetic backbone (G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2). The other strains showed a complex genetic constellation, likely derived from triple reassortment event with the G9-VP7, N1-NSP2 and E6-NSP4 on a DS-1-like genetic backbone (G9-P[4]-I2-R2-C2-M2-A2-N1-T2-E6-H2). Presumably, these unusual G9P[4] strains were generated after several reassortment events between the contemporary co-circulating human rotavirus strains. Moreover, the point mutation S291L at the interaction site between inner and outer capsid proteins of VP6 gene may be important in the rapid spread of this unusual strain. The complex reassortment events within the G9[4] strains may be related to the high prevalence of mixed infections in India as reported in this study and other previous studies.
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Affiliation(s)
- Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Japan
| | - Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kei Haga
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Japan
| | - Akira Fujimoto
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Japan
| | - Reiko Takai-Todaka
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Japan
| | - Yuichi Someya
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mukti K Nayak
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Anupam Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Daisuke Imamura
- Collaborative Research Center of Okayama University for Infectious Diseases, India
| | - Sumio Shinoda
- Collaborative Research Center of Okayama University for Infectious Diseases, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Japan.
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35
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Roy P. Bluetongue virus structure and assembly. Curr Opin Virol 2017; 24:115-123. [PMID: 28609677 DOI: 10.1016/j.coviro.2017.05.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 05/19/2017] [Accepted: 05/24/2017] [Indexed: 01/09/2023]
Abstract
Bluetongue virus (BTV) is an insect-vectored emerging pathogen of wild ruminants and livestock in many parts of the world. The virion particle is a complex structure of consecutive layers of protein surrounding a genome of ten double-stranded (ds) RNA segments. BTV has been studied as a model system for large, non-enveloped dsRNA viruses. Several new techniques have been applied to define the virus-encoded enzymes required for RNA replication to provide an order for the assembly of the capsid shell and the protein sequestration required for it. Further, a reconstituted in vitro system has defined the individual steps of the assembly and packaging of the genomic RNA. These findings illuminate BTV assembly and indicate the pathways that related viruses might use to provide an informed starting point for intervention or prevention.
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Affiliation(s)
- Polly Roy
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, UK.
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36
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Orlov I, Myasnikov AG, Andronov L, Natchiar SK, Khatter H, Beinsteiner B, Ménétret JF, Hazemann I, Mohideen K, Tazibt K, Tabaroni R, Kratzat H, Djabeur N, Bruxelles T, Raivoniaina F, Pompeo LD, Torchy M, Billas I, Urzhumtsev A, Klaholz BP. The integrative role of cryo electron microscopy in molecular and cellular structural biology. Biol Cell 2016; 109:81-93. [PMID: 27730650 DOI: 10.1111/boc.201600042] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 01/10/2023]
Abstract
After gradually moving away from preparation methods prone to artefacts such as plastic embedding and negative staining for cell sections and single particles, the field of cryo electron microscopy (cryo-EM) is now heading off at unprecedented speed towards high-resolution analysis of biological objects of various sizes. This 'revolution in resolution' is happening largely thanks to new developments of new-generation cameras used for recording the images in the cryo electron microscope which have much increased sensitivity being based on complementary metal oxide semiconductor devices. Combined with advanced image processing and 3D reconstruction, the cryo-EM analysis of nucleoprotein complexes can provide unprecedented insights at molecular and atomic levels and address regulatory mechanisms in the cell. These advances reinforce the integrative role of cryo-EM in synergy with other methods such as X-ray crystallography, fluorescence imaging or focussed-ion beam milling as exemplified here by some recent studies from our laboratory on ribosomes, viruses, chromatin and nuclear receptors. Such multi-scale and multi-resolution approaches allow integrating molecular and cellular levels when applied to purified or in situ macromolecular complexes, thus illustrating the trend of the field towards cellular structural biology.
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Affiliation(s)
- Igor Orlov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Alexander G Myasnikov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Leonid Andronov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Heena Khatter
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Brice Beinsteiner
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Jean-François Ménétret
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Kareem Mohideen
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Karima Tazibt
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Rachel Tabaroni
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Hanna Kratzat
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Nadia Djabeur
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Tatiana Bruxelles
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Finaritra Raivoniaina
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Lorenza di Pompeo
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Morgan Torchy
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Isabelle Billas
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Alexandre Urzhumtsev
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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37
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Molecular Docking and Aberration-Corrected STEM of Palladium Nanoparticles on Viral Templates. METALS 2016. [DOI: 10.3390/met6090200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Yonekura K, Maki-Yonekura S. Refinement of cryo-EM structures using scattering factors of charged atoms. J Appl Crystallogr 2016. [DOI: 10.1107/s1600576716011274] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
This paper reports a suitable treatment of electron scattering factors of charged atoms for refinement of atomic models against cryo-electron microscopy (cryo-EM) maps. The ScatCurve package developed here supports various curve models for parameterization of scattering factors and the parameter tables can be implemented in major refinement programs in structural biology. Partial charge values of charged amino acids in crystal structures were changed in small steps for refinement of the atomic models against electron diffraction data from three-dimensional crystals. By exploring a range of partial charges, the authors found the electrostatic setting that produces atomic models with improved statistics and better reflects experimental data. Structure refinement for single-particle analysis also benefits from the more accurate analysis and the programs could find wide use for model refinement against cryo-EM maps.
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Fusion of the mouse IgG1 Fc domain to the VHH fragment (ARP1) enhances protection in a mouse model of rotavirus. Sci Rep 2016; 6:30171. [PMID: 27439689 PMCID: PMC4954977 DOI: 10.1038/srep30171] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/28/2016] [Indexed: 11/15/2022] Open
Abstract
A variable fragment of a heavy chain antibody (VHH) directed against rotavirus, also referred to as anti-rotavirus protein 1 (ARP1), was shown to confer protection against rotavirus induced diarrhea in infant mouse model of rotavirus induced diarrhea. In this study, we have fused the mouse IgG1 Fc to ARP1 to improve the protective capacity of ARP1 by inducing an Fc-mediated effector function. We have shown that the Fc-ARP1 fusion protein confers significantly increased protection against rotavirus in a neonatal mouse model of rotavirus-induced diarrhea by reducing the prevalence, duration and severity of diarrhea and the viral load in the small intestines, suggesting that the Fc part of immunoglobulins may be engaged in Fc-mediated neutralization of rotavirus. Engineered conventional-like antibodies, by fusion of the Fc part of immunoglobulins to antigen-specific heavy-chain only VHH fragments, might be applied to novel antibody-based therapeutic approaches to enhance elimination of pathogens by activation of distinct effector signaling pathways.
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Do LP, Nakagomi T, Otaki H, Agbemabiese CA, Nakagomi O, Tsunemitsu H. Phylogenetic inference of the porcine Rotavirus A origin of the human G1 VP7 gene. INFECTION GENETICS AND EVOLUTION 2016; 40:205-213. [PMID: 26961591 DOI: 10.1016/j.meegid.2016.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 02/25/2016] [Accepted: 03/01/2016] [Indexed: 01/15/2023]
Abstract
Rotavirus A (RVA) is an important cause of acute gastroenteritis in children worldwide. The most common VP7 genotype of human RVA is G1, but G1 is rarely detected in porcine strains. To understand the evolutionary relationships between human and porcine G1 VP7 genes, we sequenced the VP7 genes of three Japanese G1 porcine strains; the first two (PRV2, S80B) were isolated in 1980 and the third (Kyusyu-14) was isolated in 2001. Then, we performed phylogenetic and in-silico structural analyses. All three VP7 sequences clustered into lineage VI, and the mean nucleotide sequence identity between any pair of porcine G1 VP7 sequences belonging to lineage VI was 91.9%. In contrast, the mean nucleotide sequence identity between any pair of human G1 VP7 sequences belonging to lineages I-V was 95.5%. While the mean nucleotide sequence identity between any pair of porcine lineage VI strain and human lineage I-V strain was 85.4%, the VP7 genes of PRV2 and a rare porcine-like human G1P[6] strain (AU19) were 98% identical, strengthening the porcine RVA origin of AU19. The phylogenetic tree suggests that human G1 VP7 genes originated from porcine G1 VP7 genes. The time of their most recent common ancestor was estimated to be 1948, and human and porcine RVA strains evolved along independent pathways. In-silico structural analyses identified 7 amino acid residues within the known neutralisation epitopes that show differences in electric charges and shape between different porcine and human G1 strains. When compared with much divergent porcine G1 VP7 lineages, monophyletic, less divergent human G1 VP7 lineages support the hypothesis that all human G1 VP7 genes included in this study originated from a rare event of a porcine RVA transmitting to humans that was followed by successful adaptation to the human host. By contrast, AU19 represents interspecies transmission that terminated in dead-end infection.
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Affiliation(s)
- Loan Phuong Do
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan; Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Toyoko Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan; Centre for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Hiroki Otaki
- Centre for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Chantal Ama Agbemabiese
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Osamu Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan; Centre for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
| | - Hiroshi Tsunemitsu
- Dairy Hygiene Research Division, Hokkaido Research Station, National Institute of Animal Health, Sapporo, Hokkaido, Japan
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41
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Miño S, Barrandeguy M, Parreño V, Parra GI. Genetic linkage of capsid protein-encoding RNA segments in group A equine rotaviruses. J Gen Virol 2016; 97:912-921. [PMID: 26758293 DOI: 10.1099/jgv.0.000397] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rotavirus virions are formed by three concentric protein layers that enclose the 11 dsRNA genome segments and the viral proteins VP1 and VP3. Interactions amongst the capsid proteins (VP2, VP6, VP7 and VP4) have been described to play a major role in viral fitness, whilst restricting the reassortment of the genomic segments during co-infection with different rotavirus strains. In this work we describe and characterize the linkage between VP6 and VP7 proteins based on structural and genomic analyses of group A rotavirus strains circulating in Argentinean horses. Strains with the VP7 genotype G3 showed a strong association with the VP6 genotype I6, whilst strains with G14 were associated with the I2 genotype. Most of the differences on the VP6 and VP7 proteins were observed in interactive regions between the two proteins, suggesting that VP6 : VP7 interactions may drive the co-evolution and co-segregation of their respective gene segments.
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Affiliation(s)
- Samuel Miño
- Instituto de Virología, CICVyA, INTA Castelar, Nicolás Repetto y De los Reseros s/n (CP 1816), Hurlingham, Buenos Aires, Argentina
| | - María Barrandeguy
- Instituto de Virología, CICVyA, INTA Castelar, Nicolás Repetto y De los Reseros s/n (CP 1816), Hurlingham, Buenos Aires, Argentina.,Escuela de Veterinaria, Universidad del Salvador, Champagnat 1599, Ruta Panamericana km54.5 (B1630AHU), Pilar, Buenos Aires, Argentina
| | - Viviana Parreño
- Instituto de Virología, CICVyA, INTA Castelar, Nicolás Repetto y De los Reseros s/n (CP 1816), Hurlingham, Buenos Aires, Argentina
| | - Gabriel I Parra
- Departamento de Biología Molecular y Genética, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay
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Eren E, Zamuda K, Patton JT. Modeling of the rotavirus group C capsid predicts a surface topology distinct from other rotavirus species. Virology 2016; 487:150-62. [PMID: 26524514 PMCID: PMC4679652 DOI: 10.1016/j.virol.2015.10.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 11/21/2022]
Abstract
Rotavirus C (RVC) causes sporadic gastroenteritis in adults and is an established enteric pathogen of swine. Because RVC strains grow poorly in cell culture, which hinders generation of virion-derived RVC triple-layered-particle (TLP) structures, we used the known Rotavirus A (RVA) capsid structure to model the human RVC (Bristol) capsid. Comparative analysis of RVA and RVC capsid proteins showed major differences at the VP7 layer, an important target region for vaccine development due to its antigenic properties. Our model predicted the presence of a surface extended loop in RVC, which could form a major antigenic site on the capsid. We analyzed variations in the glycosylation patterns among RV capsids and identified group specific conserved sites. In addition, our results showed a smaller RVC VP4 foot, which protrudes toward the intermediate VP6 layer, in comparison to that of RVA. Finally, our results showed major structural differences at the VP8* glycan recognition sites.
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Affiliation(s)
- Elif Eren
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Kimberly Zamuda
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John T Patton
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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44
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Ma Y. Identification of G and P genotype-specific motifs in the predicted VP7 and VP4 amino acid sequences. Virus Res 2015; 210:271-8. [PMID: 26321159 DOI: 10.1016/j.virusres.2015.08.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/22/2015] [Accepted: 08/24/2015] [Indexed: 10/23/2022]
Abstract
Equine rotavirus (ERV) strain L338 (G13P[18]) has a unique G and P genotype. However, the evolutionary relationship of L338 with other ERVs is still unknown. Here whole genome analysis of the L338 ERV strain was independently performed. Its genotype constellations were determined as G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11, confirming previous genotype assignments. The L338 strain only shared the P[18] and I6 genotypes with other ERVs. The nucleotide sequences of the other 9 RNA segments were different from those of cogent genes of all other group A rotavirus (RVA) strains including ERVs and formed unique phylogenetic lineages. The L338 evolutionary footprints were tentatively identified in both VP7 and VP4 amino acid sequences: two regions were found in VP7 and twelve in VP4. The conserved regions shared between L338 and other group A rotavirus strains (RVAs) indicated that L338 was more closely related genomically to animal and human RVAs other than ERVs, suggesting that L338 may not be an endogenous equine RV but have emerged as an interspecies reassortant with other RVA strains. Furthermore, genotype-specific motifs of all 27 G and 37 P types were identified in regions 7-1a (aa 91-100) of VP7 and regions 8-1 (aa146-151) and 8-3 (aa113-118 and 125-135) of VP4 (VP8*).
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Affiliation(s)
- Yongping Ma
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Yu Zhong District, Yi Xue Yuan Road #1, Chongqing 400016, China.
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45
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Passos DO, Lyumkis D. Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits. J Struct Biol 2015; 192:235-44. [PMID: 26470814 DOI: 10.1016/j.jsb.2015.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/29/2015] [Accepted: 10/01/2015] [Indexed: 11/17/2022]
Abstract
A single-particle cryoEM reconstruction of the large ribosomal subunit from Saccharomyces cerevisiae was obtained from a dataset of ∼75,000 particles. The gold-standard and frequency-limited approaches to single-particle refinement were each independently used to determine orientation parameters for the final reconstruction. Both approaches showed similar resolution curves and nominal resolution values for the 60S dataset, estimated at 2.9 Å. The amount of over-fitting present during frequency-limited refinement was quantitatively analyzed using the high-resolution phase-randomization test, and the results showed no apparent over-fitting. The number of asymmetric subunits required to reach specific resolutions was subsequently analyzed by refining subsets of the data in an ab initio manner. With our data collection and processing strategies, sub-nanometer resolution was obtained with ∼200 asymmetric subunits (or, equivalently for the ribosomal subunit, particles). Resolutions of 5.6 Å, 4.5 Å, and 3.8 Å were reached with ∼1000, ∼1600, and ∼5000 asymmetric subunits, respectively. At these resolutions, one would expect to detect alpha-helical pitch, separation of beta-strands, and separation of Cα atoms, respectively. Using this map, together with strategies for ab initio model building and model refinement, we built a region of the ribosomal protein eL6, which was missing in previous models of the yeast ribosome. The relevance for more routine high-resolution structure determination is discussed.
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Affiliation(s)
- Dario Oliveira Passos
- Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Dmitry Lyumkis
- Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, United States.
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Abstract
Until only a few years ago, single-particle electron cryo-microscopy (cryo-EM) was usually not the first choice for many structural biologists due to its limited resolution in the range of nanometer to subnanometer. Now, this method rivals X-ray crystallography in terms of resolution and can be used to determine atomic structures of macromolecules that are either refractory to crystallization or difficult to crystallize in specific functional states. In this review, I discuss the recent breakthroughs in both hardware and software that transformed cryo-microscopy, enabling understanding of complex biomolecules and their functions at atomic level.
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Affiliation(s)
- Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA.
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47
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Boudreaux CE, Kelly DF, McDonald SM. Electron microscopic analysis of rotavirus assembly-replication intermediates. Virology 2015; 477:32-41. [PMID: 25635339 PMCID: PMC4359669 DOI: 10.1016/j.virol.2015.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/14/2014] [Accepted: 01/05/2015] [Indexed: 11/24/2022]
Abstract
Rotaviruses (RVs) replicate their segmented, double-stranded RNA genomes in tandem with early virion assembly. In this study, we sought to gain insight into the ultrastructure of RV assembly-replication intermediates (RIs) using transmission electron microscopy (EM). Specifically, we examined a replicase-competent, subcellular fraction that contains all known RV RIs. Three never-before-seen complexes were visualized in this fraction. Using in vitro reconstitution, we showed that ~15-nm doughnut-shaped proteins in strings were nonstructural protein 2 (NSP2) bound to viral RNA transcripts. Moreover, using immunoaffinity-capture EM, we revealed that ~20-nm pebble-shaped complexes contain the viral RNA polymerase (VP1) and RNA capping enzyme (VP3). Finally, using a gel purification method, we demonstrated that ~30–70-nm electron-dense, particle-shaped complexes represent replicase-competent core RIs, containing VP1, VP3, and NSP2 as well as capsid proteins VP2 and VP6. The results of this study raise new questions about the interactions among viral proteins and RNA during the concerted assembly-replicase process.
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Affiliation(s)
- Crystal E Boudreaux
- Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA, USA
| | - Deborah F Kelly
- Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA, USA
| | - Sarah M McDonald
- Virginia Tech Carilion School of Medicine and Research Institute, Roanoke, VA, USA; Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, VA, USA.
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48
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Ma Y, Wen X, Hoshino Y, Yuan L. Cloning and nucleotide sequence analyses of 11 genome segments of two American and one British equine rotavirus strains. Vet Microbiol 2015; 176:172-8. [PMID: 25631250 DOI: 10.1016/j.vetmic.2015.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/27/2014] [Accepted: 01/08/2015] [Indexed: 01/17/2023]
Abstract
Group A equine rotavirus (ERV) is the main cause of diarrhea in foals and causes severe economic loss due to morbidity and mortality on stud farming worldwide. Molecular evolution of equine rotaviruses remains understudies. In this study, whole-genomic analysis of 2 group A ERV, FI-14 (G3P[12]), H-2 (G3P[12]) isolated from American, and FI23 (G14P[12]) from British was carried out and genotype constellations were determined as G3-P[12]-I6-R2-C2-M3-A10-N2-T3-E2-H7 for FI-14; G14-P[12]-I2-R2-C2-M3-A10-N2-T3-E2-H7 for FI23; and G3-P[12]-I6-R2-C2-M3-A10-N2-T3-E2-H7 for H-2, respectively. With the exception of the VP7 and VP6 gene, 2 G3P[12] strains (FI-14 and H-2) and one G14P[12] strain (FI23) were highly related genetically. Of note, the VP6 genotype of H-2 strain was previously reported to be I2, however, sequence and phylogenetic analyses demonstrated that it was I6. Therefore, it showed that G3P[12] ERV strains and G14P[12] ERV strains bore a distinct VP6 genotype: I6 for G3P[12] strains and I2 for G14P[12] strains. Moreover, it demonstrated that T-cell epitope 299P-300P/Q residues (PP/Q) of VP6 may be considered as I2 ERV typical molecular marker, which facilitates the analysis of the molecular evolution of equine rotaviruses.
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Affiliation(s)
- Yongping Ma
- Department of Biochemistry and Molecular Biology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, 400016 Chongqing, China; Epidemiology Section, Laboratory of Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Building 50, Room 6308, 50 South Drive, MSC 8026, Bethesda, MD 20892-8026, USA
| | - Xiaobo Wen
- Epidemiology Section, Laboratory of Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Building 50, Room 6308, 50 South Drive, MSC 8026, Bethesda, MD 20892-8026, USA; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang Province, China
| | - Yasutaka Hoshino
- Epidemiology Section, Laboratory of Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Building 50, Room 6308, 50 South Drive, MSC 8026, Bethesda, MD 20892-8026, USA
| | - L Yuan
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA.
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Abstract
When I entered graduate school in 1963, the golden age of molecular biology had just begun, and myoglobin was the only protein with a known high-resolution structure. The romance of working out the structure of a virus by X-ray crystallography nonetheless captured both my imagination and the ensuing 15 years of my scientific life, during which "protein crystallography" began to morph into "structural biology." The course of the research recounted here follows the broader, 50-year trajectory of structural biology, as I could rarely resist opportunities to capitalize on new technologies when they opened some interesting part of biology to three-dimensional rigor. That fascination shows no sign of subsiding.
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Affiliation(s)
- Stephen C Harrison
- Harvard Medical School, Boston Children's Hospital, and Howard Hughes Medical Institute, Boston, Massachusetts 02115;
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50
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Abdelhakim AH, Salgado EN, Fu X, Pasham M, Nicastro D, Kirchhausen T, Harrison SC. Structural correlates of rotavirus cell entry. PLoS Pathog 2014; 10:e1004355. [PMID: 25211455 PMCID: PMC4161437 DOI: 10.1371/journal.ppat.1004355] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 07/24/2014] [Indexed: 01/06/2023] Open
Abstract
Cell entry by non-enveloped viruses requires translocation into the cytosol of a macromolecular complex--for double-strand RNA viruses, a complete subviral particle. We have used live-cell fluorescence imaging to follow rotavirus entry and penetration into the cytosol of its ∼ 700 Å inner capsid particle ("double-layered particle", DLP). We label with distinct fluorescent tags the DLP and each of the two outer-layer proteins and track the fates of each species as the particles bind and enter BSC-1 cells. Virions attach to their glycolipid receptors in the host cell membrane and rapidly become inaccessible to externally added agents; most particles that release their DLP into the cytosol have done so by ∼ 10 minutes, as detected by rapid diffusional motion of the DLP away from residual outer-layer proteins. Electron microscopy shows images of particles at various stages of engulfment into tightly fitting membrane invaginations, consistent with the interpretation that rotavirus particles drive their own uptake. Electron cryotomography of membrane-bound virions also shows closely wrapped membrane. Combined with high resolution structural information about the viral components, these observations suggest a molecular model for membrane disruption and DLP penetration.
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Affiliation(s)
- Aliaa H. Abdelhakim
- Laboratory of Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Eric N. Salgado
- Laboratory of Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xiaofeng Fu
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Mithun Pasham
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniela Nicastro
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Tomas Kirchhausen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephen C. Harrison
- Laboratory of Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
- * E-mail:
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