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Zsidó BZ, Bayarsaikhan B, Börzsei R, Szél V, Mohos V, Hetényi C. The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering. Int J Mol Sci 2023; 24:11784. [PMID: 37511543 PMCID: PMC10381018 DOI: 10.3390/ijms241411784] [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: 06/20/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Water is a key actor of various processes of nature and, therefore, molecular engineering has to take the structural and energetic consequences of hydration into account. While the present review focuses on the target-ligand interactions in drug design, with a focus on biomolecules, these methods and applications can be easily adapted to other fields of the molecular engineering of molecular complexes, including solid hydrates. The review starts with the problems and solutions of the determination of water structures. The experimental approaches and theoretical calculations are summarized, including conceptual classifications. The implementations and applications of water models are featured for the calculation of the binding thermodynamics and computational ligand docking. It is concluded that theoretical approaches not only reproduce or complete experimental water structures, but also provide key information on the contribution of individual water molecules and are indispensable tools in molecular engineering.
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Affiliation(s)
- Balázs Zoltán Zsidó
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Bayartsetseg Bayarsaikhan
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Rita Börzsei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Viktor Szél
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Violetta Mohos
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
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2
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Sutherland DM, Strebl M, Koehler M, Welsh OL, Yu X, Hu L, dos Santos Natividade R, Knowlton JJ, Taylor GM, Moreno RA, Wörz P, Lonergan ZR, Aravamudhan P, Guzman-Cardozo C, Kour S, Pandey UB, Alsteens D, Wang Z, Prasad BVV, Stehle T, Dermody TS. NgR1 binding to reovirus reveals an unusual bivalent interaction and a new viral attachment protein. Proc Natl Acad Sci U S A 2023; 120:e2219404120. [PMID: 37276413 PMCID: PMC10268256 DOI: 10.1073/pnas.2219404120] [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: 11/14/2022] [Accepted: 04/19/2023] [Indexed: 06/07/2023] Open
Abstract
Nogo-66 receptor 1 (NgR1) binds a variety of structurally dissimilar ligands in the adult central nervous system to inhibit axon extension. Disruption of ligand binding to NgR1 and subsequent signaling can improve neuron outgrowth, making NgR1 an important therapeutic target for diverse neurological conditions such as spinal crush injuries and Alzheimer's disease. Human NgR1 serves as a receptor for mammalian orthoreovirus (reovirus), but the mechanism of virus-receptor engagement is unknown. To elucidate how NgR1 mediates cell binding and entry of reovirus, we defined the affinity of interaction between virus and receptor, determined the structure of the virus-receptor complex, and identified residues in the receptor required for virus binding and infection. These studies revealed that central NgR1 surfaces form a bridge between two copies of viral capsid protein σ3, establishing that σ3 serves as a receptor ligand for reovirus. This unusual binding interface produces high-avidity interactions between virus and receptor to prime early entry steps. These studies refine models of reovirus cell-attachment and highlight the evolution of viruses to engage multiple receptors using distinct capsid components.
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Affiliation(s)
- Danica M. Sutherland
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
| | - Michael Strebl
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076Tübingen, Germany
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Olivia L. Welsh
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
| | - Xinzhe Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030
| | - Rita dos Santos Natividade
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Jonathan J. Knowlton
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Cryo-Electron Microscopy and Tomography Core, Baylor College of Medicine, Houston, TX77030
| | - Gwen M. Taylor
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
| | - Rodolfo A. Moreno
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030
| | - Patrick Wörz
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076Tübingen, Germany
| | - Zachery R. Lonergan
- Cryo-Electron Microscopy and Tomography Core, Baylor College of Medicine, Houston, TX77030
| | - Pavithra Aravamudhan
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
| | - Camila Guzman-Cardozo
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
| | - Sukhleen Kour
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
| | - Udai Bhan Pandey
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN37232
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA15261
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
- Children’s Neuroscience Institute, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030
- Walloon Excellence in Life Sciences and Biotechnology, 1300Wavre, Belgium
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - B. V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX77030
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076Tübingen, Germany
| | - Terence S. Dermody
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA15219
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3
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Siew ZY, Loh A, Segeran S, Leong PP, Voon K. Oncolytic Reoviruses: Can These Emerging Zoonotic Reoviruses Be Tamed and Utilized? DNA Cell Biol 2023. [PMID: 37015068 DOI: 10.1089/dna.2022.0561] [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: 04/06/2023] Open
Abstract
Orthoreovirus is a nonenveloped double-stranded RNA virus under the Reoviridae family. This group of viruses, especially mammalian orthoreovirus (MRV), are reported with great therapeutic values due to their oncolytic effects. In this review, the life cycle and oncolytic effect of MRV and a few emerging reoviruses were summarized. This article also highlights the challenges and strategies of utilizing MRV and the emerging reoviruses, avian orthoreovirus (ARV) and pteropine orthoreovirus (PRV), as oncolytic viruses (OVs). Besides, the emergence of potential ARV and PRV as OVs were discussed in comparison to MRV. Finally, the risk of reovirus as zoonosis or reverse zoonosis (zooanthroponosis) were debated, and concerns were raised in this article, which warrant continue surveillance of reovirus (MRV, ARV, and PRV) in animals, humans, and the environment.
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Affiliation(s)
- Zhen Yun Siew
- School of Pharmacy, University of Nottingham Malaysia, Semenyih, Malaysia
| | - Alson Loh
- School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia
| | - Sharrada Segeran
- School of Medicine, Australian National University, Canberra, Australia
| | - Pooi Pooi Leong
- Faculty of Medicine and Health Sciences, Universiti of Tunku Abdul Rahman, Kajang, Malaysia
| | - Kenny Voon
- School of Pharmacy, University of Nottingham Malaysia, Semenyih, Malaysia
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4
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In situ structures of polymerase complex of mammalian reovirus illuminate RdRp activation and transcription regulation. Proc Natl Acad Sci U S A 2022; 119:e2203054119. [PMID: 36469786 PMCID: PMC9897473 DOI: 10.1073/pnas.2203054119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
Mammalian reovirus (reovirus) is a multilayered, turreted member of Reoviridae characterized by transcription of dsRNA genome within the innermost capsid shell. Here, we present high-resolution in situ structures of reovirus transcriptase complex in an intact double-layered virion, and in the uncoated single-layered core particles in the unloaded, reloaded, pre-elongation, and elongation states, respectively, obtained by cryo-electron microscopy and sub-particle reconstructions. At the template entry of RNA-dependent RNA polymerase (RdRp), the RNA-loading region gets flexible after uncoating resulting in the unloading of terminal genomic RNA and inactivity of transcription. However, upon adding transcriptional substrates, the RNA-loading region is recovered leading the RNAs loaded again. The priming loop in RdRp was found to play a critical role in regulating transcription, which hinders the elongation of transcript in virion and triggers the rearrangement of RdRp C-terminal domain (CTD) during elongation, resulting in splitting of template-transcript hybrid and opening of transcript exit. With the integration of these structures, a transcriptional model of reovirus with five states is proposed. Our structures illuminate the RdRp activation and regulation of the multilayered turreted reovirus.
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5
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Hryc CF, Baker ML. AlphaFold2 and CryoEM: Revisiting CryoEM modeling in near-atomic resolution density maps. iScience 2022; 25:104496. [PMID: 35733789 PMCID: PMC9207676 DOI: 10.1016/j.isci.2022.104496] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/07/2022] [Accepted: 05/24/2022] [Indexed: 11/27/2022] Open
Abstract
With the advent of new artificial intelligence and machine learning algorithms, predictive modeling can, in some cases, produce structures on par with experimental methods. The combination of predictive modeling and experimental structure determination by electron cryomicroscopy (cryoEM) offers a tantalizing approach for producing robust atomic models of macromolecular assemblies. Here, we apply AlphaFold2 to a set of community standard data sets and compare the results with the corresponding reference maps and models. Moreover, we present three unique case studies from previously determined cryoEM density maps of viruses. Our results show that AlphaFold2 can not only produce reasonably accurate models for analysis and additional hypotheses testing, but can also potentially yield incorrect structures if not properly validated with experimental data. Whereas we outline numerous shortcomings and potential pitfalls of predictive modeling, the obvious synergy between predictive modeling and cryoEM will undoubtedly result in new computational modeling tools.
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Affiliation(s)
- Corey F. Hryc
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Matthew L. Baker
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
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6
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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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7
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Pan M, Alvarez-Cabrera AL, Kang JS, Wang L, Fan C, Zhou ZH. Asymmetric reconstruction of mammalian reovirus reveals interactions among RNA, transcriptional factor µ2 and capsid proteins. Nat Commun 2021; 12:4176. [PMID: 34234134 PMCID: PMC8263624 DOI: 10.1038/s41467-021-24455-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/17/2021] [Indexed: 12/02/2022] Open
Abstract
Mammalian reovirus (MRV) is the prototypical member of genus Orthoreovirus of family Reoviridae. However, lacking high-resolution structures of its RNA polymerase cofactor μ2 and infectious particle, limits understanding of molecular interactions among proteins and RNA, and their contributions to virion assembly and RNA transcription. Here, we report the 3.3 Å-resolution asymmetric reconstruction of transcribing MRV and in situ atomic models of its capsid proteins, the asymmetrically attached RNA-dependent RNA polymerase (RdRp) λ3, and RdRp-bound nucleoside triphosphatase μ2 with a unique RNA-binding domain. We reveal molecular interactions among virion proteins and genomic and messenger RNA. Polymerase complexes in three Spinoreovirinae subfamily members are organized with different pseudo-D3d symmetries to engage their highly diversified genomes. The above interactions and those between symmetry-mismatched receptor-binding σ1 trimers and RNA-capping λ2 pentamers balance competing needs of capsid assembly, external protein removal, and allosteric triggering of endogenous RNA transcription, before, during and after infection, respectively. Mammalian reovirus (MRV) is a double-stranded RNA (dsRNA) virus that affects the gastrointestinal and respiratory tracts. Here, the authors present the 3.3 Å cryo-EM asymmetric reconstruction of transcribing MRV that reveals the organization of the dsRNA genome, RNA interaction with the polymerase complex, and how the polymerase interacts extensively with its co-factor, µ2, to form a transcription enzyme complex, which engages and regulates RNA transcription.
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Affiliation(s)
- Muchen Pan
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.,California NanoSystems Institute, UCLA, Los Angeles, CA, USA.,University of Chinese Academy of Sciences, Beijing, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ana L Alvarez-Cabrera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.,California NanoSystems Institute, UCLA, Los Angeles, CA, USA
| | - Joon S Kang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.,California NanoSystems Institute, UCLA, Los Angeles, CA, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Lihua Wang
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA. .,California NanoSystems Institute, UCLA, Los Angeles, CA, USA. .,Molecular Biology Institute, UCLA, Los Angeles, CA, USA.
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8
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Thoner TW, Ye X, Karijolich J, Ogden KM. Reovirus Low-Density Particles Package Cellular RNA. Viruses 2021; 13:v13061096. [PMID: 34201386 PMCID: PMC8228547 DOI: 10.3390/v13061096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/03/2021] [Indexed: 12/02/2022] Open
Abstract
Packaging of segmented, double-stranded RNA viral genomes requires coordination of viral proteins and RNA segments. For mammalian orthoreovirus (reovirus), evidence suggests either all ten or zero viral RNA segments are simultaneously packaged in a highly coordinated process hypothesized to exclude host RNA. Accordingly, reovirus generates genome-containing virions and “genomeless” top component particles. Whether reovirus virions or top component particles package host RNA is unknown. To gain insight into reovirus packaging potential and mechanisms, we employed next-generation RNA-sequencing to define the RNA content of enriched reovirus particles. Reovirus virions exclusively packaged viral double-stranded RNA. In contrast, reovirus top component particles contained similar proportions but reduced amounts of viral double-stranded RNA and were selectively enriched for numerous host RNA species, especially short, non-polyadenylated transcripts. Host RNA selection was not dependent on RNA abundance in the cell, and specifically enriched host RNAs varied for two reovirus strains and were not selected solely by the viral RNA polymerase. Collectively, these findings indicate that genome packaging into reovirus virions is exquisitely selective, while incorporation of host RNAs into top component particles is differentially selective and may contribute to or result from inefficient viral RNA packaging.
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Affiliation(s)
- Timothy W. Thoner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (T.W.T.J.); (X.Y.); (J.K.)
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (T.W.T.J.); (X.Y.); (J.K.)
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (T.W.T.J.); (X.Y.); (J.K.)
| | - Kristen M. Ogden
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (T.W.T.J.); (X.Y.); (J.K.)
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Correspondence:
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9
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The reovirus μ2 C-terminal loop inversely regulates NTPase and transcription functions versus binding to factory-forming μNS and promotes replication in tumorigenic cells. J Virol 2021; 95:JVI.02006-20. [PMID: 33658345 PMCID: PMC8139653 DOI: 10.1128/jvi.02006-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Wild type reovirus serotype 3 'Dearing PL strain' (T3wt) is being heavily evaluated as an oncolytic and immunotherapeutic treatment for cancers. Mutations that promote reovirus entry into tumor cells were previously reported to enhance oncolysis; herein we aimed to discover mutations that enhance the post-entry steps of reovirus infection in tumor cells. Using directed evolution, we identified that reovirus variant T3v10M1 exhibited enhanced replication relative to T3wt on a panel of cancer cells. T3v10M1 contains an alanine-to-valine substitution (A612V) in the core-associated μ2, which was previously found to have NTPase activities in virions and to facilitate virus factory formation by association with μNS. Paradoxically, the A612V mutation in μ2 from T3v10M1 was discovered to impair NTPase activities and RNA synthesis, leading to five-fold higher probability of abortive infection for T3v10M1 relative to T3wt. The A612V mutation resides in a previously uncharacterized C-terminal region that juxtaposes the template entry site of the polymerase μ2; our findings thus support an important role for this domain during virus transcription. Despite crippled onset of infection, T3v10M1 exhibited greater accumulation of viral proteins and progeny during replication, leading to increased overall virus burst size. Both Far-Western and co-immunoprecipitation approaches corroborated that the A612V mutation in μ2 increased association with the non-structural virus protein μNS and enhances burst size. Altogether the data supports that mutations in the C-terminal loop domain of μ2 inversely regulate NTPase and RNA synthesis versus interactions with μNS, but with a net gain of replication in tumorigenic cells.SIGNIFICANCEReovirus is a model system for understanding virus replication but also a clinically relevant virus for cancer therapy. We identified the first mutation that increases reovirus infection in tumorigenic cells by enhancing post-entry stages of reovirus replication. The mutation is in a previously uncharacterized c-terminal region of the M1-derived μ2 protein, which we demonstrated affects multiple functions of μ2; NTPase, RNA synthesis, inhibition of antiviral immune response and association with the virus replication factory-forming μNS protein. These findings promote a mechanistic understanding of viral protein functions. In the future, the benefits of μ2 mutations may be useful for enhancing reovirus potency in tumors.
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10
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Arnold MM, Dijk A, López S. Double‐stranded RNA Viruses. Virology 2021. [DOI: 10.1002/9781119818526.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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11
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Smith SC, Gribble J, Diller JR, Wiebe MA, Thoner TW, Denison MR, Ogden KM. Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage. J Virol 2021; 95:JVI.02181-20. [PMID: 33472930 PMCID: PMC8103698 DOI: 10.1128/jvi.02181-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
For viruses with segmented genomes, genetic diversity is generated by genetic drift, reassortment, and recombination. Recombination produces RNA populations distinct from full-length gene segments and can influence viral population dynamics, persistence, and host immune responses. Viruses in the Reoviridae family, including rotavirus and mammalian orthoreovirus (reovirus), have been reported to package segments containing rearrangements or internal deletions. Rotaviruses with RNA segments containing rearrangements have been isolated from immunocompromised and immunocompetent children and in vitro following serial passage at relatively high multiplicity. Reoviruses that package small, defective RNA segments have established chronic infections in cells and in mice. However, the mechanism and extent of Reoviridae RNA recombination are undefined. Towards filling this gap in knowledge, we determined the titers and RNA segment profiles for reovirus and rotavirus following serial passage in cultured cells. The viruses exhibited occasional titer reductions characteristic of interference. Reovirus strains frequently accumulated segments that retained 5' and 3' terminal sequences and featured large internal deletions, while similarly fragmented segments were rarely detected in rotavirus populations. Using next-generation RNA-sequencing to analyze RNA molecules packaged in purified reovirus particles, we identified distinct recombination sites within individual viral genome segments. Recombination junctions were frequently but not always characterized by short direct sequence repeats upstream and downstream that spanned junction sites. Taken together, these findings suggest that reovirus accumulates defective gene segments featuring internal deletions during passage and undergoes sequence-directed recombination at distinct sites.IMPORTANCE Viruses in the Reoviridae family include important pathogens of humans and other animals and have segmented RNA genomes. Recombination in RNA virus populations can facilitate novel host exploration and increased disease severity. The extent, patterns, and mechanisms of Reoviridae recombination and the functions and effects of recombined RNA products are poorly understood. Here, we provide evidence that mammalian orthoreovirus regularly synthesizes RNA recombination products that retain terminal sequences but contain internal deletions, while rotavirus rarely synthesizes such products. Recombination occurs more frequently at specific sites in the mammalian orthoreovirus genome, and short regions of identical sequence are often detected at junction sites. These findings suggest that mammalian orthoreovirus recombination events are directed in part by RNA sequences. An improved understanding of recombined viral RNA synthesis may enhance our capacity to engineer improved vaccines and virotherapies in the future.
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Affiliation(s)
- Sydni Caet Smith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | - Jennifer Gribble
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | - Julia R Diller
- Department of Pediatrics, Vanderbilt University Medical Center
| | - Michelle A Wiebe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | - Timothy W Thoner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
| | - Mark R Denison
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
- Department of Pediatrics, Vanderbilt University Medical Center
| | - Kristen M Ogden
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center
- Department of Pediatrics, Vanderbilt University Medical Center
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12
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Mata CP, Rodríguez JM, Suzuki N, Castón JR. Structure and assembly of double-stranded RNA mycoviruses. Adv Virus Res 2020; 108:213-247. [PMID: 33837717 DOI: 10.1016/bs.aivir.2020.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycoviruses are a diverse group that includes ssRNA, dsRNA, and ssDNA viruses, with or without a protein capsid, as well as with a complex envelope. Most mycoviruses are transmitted by cytoplasmic interchange and are thought to lack an extracellular phase in their infection cycle. Structural analysis has focused on dsRNA mycoviruses, which usually package their genome in a 120-subunit T=1 icosahedral capsid, with a capsid protein (CP) dimer as the asymmetric unit. The atomic structure is available for four dsRNA mycovirus from different families: Saccharomyces cerevisiae virus L-A (ScV-L-A), Penicillium chrysogenum virus (PcV), Penicillium stoloniferum virus F (PsV-F), and Rosellinia necatrix quadrivirus 1 (RnQV1). Their capsids show structural variations of the same framework, with asymmetric or symmetric CP dimers respectively for ScV-L-A and PsV-F, dimers of similar domains of a single CP for PcV, or of two different proteins for RnQV1. The CP dimer is the building block, and assembly proceeds through dimers of dimers or pentamers of dimers, in which the genome is packed as ssRNA by interaction with CP and/or viral polymerase. These capsids remain structurally undisturbed throughout the viral cycle. The T=1 capsid participates in RNA synthesis, organizing the viral polymerase (1-2 copies) and a single loosely packaged genome segment. It also acts as a molecular sieve, to allow the passage of viral transcripts and nucleotides, but to prevent triggering of host defense mechanisms. Due to the close mycovirus-host relationship, CP evolved to allocate peptide insertions with enzyme activity, as reflected in a rough outer capsid surface.
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Affiliation(s)
- Carlos P Mata
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Javier M Rodríguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
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Sutton G, Sun D, Fu X, Kotecha A, Hecksel CW, Clare DK, Zhang P, Stuart DI, Boyce M. Assembly intermediates of orthoreovirus captured in the cell. Nat Commun 2020; 11:4445. [PMID: 32895380 PMCID: PMC7477198 DOI: 10.1038/s41467-020-18243-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 08/08/2020] [Indexed: 12/03/2022] Open
Abstract
Traditionally, molecular assembly pathways for viruses are inferred from high resolution structures of purified stable intermediates, low resolution images of cell sections and genetic approaches. Here, we directly visualise an unsuspected 'single shelled' intermediate for a mammalian orthoreovirus in cryo-preserved infected cells, by cryo-electron tomography of cellular lamellae. Particle classification and averaging yields structures to 5.6 Å resolution, sufficient to identify secondary structural elements and produce an atomic model of the intermediate, comprising 120 copies each of protein λ1 and σ2. This λ1 shell is 'collapsed' compared to the mature virions, with molecules pushed inwards at the icosahedral fivefolds by ~100 Å, reminiscent of the first assembly intermediate of certain prokaryotic dsRNA viruses. This supports the supposition that these viruses share a common ancestor, and suggests mechanisms for the assembly of viruses of the Reoviridae. Such methodology holds promise for dissecting the replication cycle of many viruses.
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Affiliation(s)
- Geoff Sutton
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Dapeng Sun
- Department of Structure Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Xiaofeng Fu
- Department of Structure Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Thermo Fisher Scientific, Achtseweg Noorg 5, 5651 GG, Eindhoven, The Netherlands
| | - Corey W Hecksel
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Daniel K Clare
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Department of Structure Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - David I Stuart
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Mark Boyce
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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Parvez MK. Geometric architecture of viruses. World J Virol 2020; 9:5-18. [PMID: 32923381 PMCID: PMC7459239 DOI: 10.5501/wjv.v9.i2.5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/02/2020] [Accepted: 07/19/2020] [Indexed: 02/06/2023] Open
Abstract
In the current SARS-CoV-2 disease (COVID-19) pandemic, the structural understanding of new emerging viruses in relation to developing effective treatment and interventions are very necessary. Viruses present remarkable differences in geometric shapes, sizes, molecular compositions and organizations. A detailed structural knowledge of a virion is essential for understanding the mechanisms of capsid assembly/disassembly, antigenicity, cell-receptor interaction, and designing therapeutic strategies. X-ray crystallography, cryo-electron microscopy and molecular simulations have elucidated atomic-level structure of several viruses. In view of this, a recently determined crystal structure of SARS-CoV-2 nucleocapsid has revealed its architecture and self-assembly very similar to that of the SARS-CoV-1 and the Middle-East respiratory syndrome virus (MERS-CoV). In structure determination, capsid symmetry is an important factor greatly contributing to its stability and balance between the packaged genome and envelope. Since the capsid protein subunits are asymmetrical, the maximum number of inter-subunit interactions can be established only when they are arranged symmetrically. Therefore, a stable capsid must be in a perfect symmetry and lowest possible free-energy. Isometric virions are spherical but geometrically icosahedrons as compared to complex virions that are both isometric and helical. Enveloped icosahedral or helical viruses are very common in animals but rare in plants and bacteria. Icosahedral capsids are defined by triangulation number (T = 1, 3, 4, 13, etc.), i.e., the identical equilateral-triangles formed of subunits. Biologically significant defective capsids with or without nucleic acids are common in enveloped alpha-, flavi- and hepadnaviruses. The self-assembling, stable and non-infectious virus-like particles have been widely exploited as vaccine candidates and therapeutic molecules delivery vehicles.
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Affiliation(s)
- Mohammad Khalid Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 22451, Saudi Arabia
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15
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Reovirus Core Proteins λ1 and σ2 Promote Stability of Disassembly Intermediates and Influence Early Replication Events. J Virol 2020; 94:JVI.00491-20. [PMID: 32581098 DOI: 10.1128/jvi.00491-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/15/2020] [Indexed: 12/11/2022] Open
Abstract
The capsids of mammalian reovirus contain two concentric protein shells, the core and the outer capsid. The outer capsid is composed of μ1-σ3 heterohexamers which surround the core. The core is composed of λ1 decamers held in place by σ2. After entry into the endosome, σ3 is proteolytically degraded and μ1 is cleaved and exposed to form infectious subvirion particles (ISVPs). ISVPs undergo further conformational changes to form ISVP*s, resulting in the release of μ1 peptides, which facilitate the penetration of the endosomal membrane to release transcriptionally active core particles into the cytoplasm. Previous work identified regions or specific residues within reovirus outer capsid proteins that impact the efficiency of cell entry. We examined the functions of the core proteins λ1 and σ2. We generated a reovirus T3D reassortant that carries strain T1L-derived σ2 and λ1 proteins (T3D/T1L L3S2). This virus displays lower ISVP stability and therefore converts to ISVP*s more readily. To identify the molecular basis for lability of T3D/T1L L3S2, we screened for hyperstable mutants of T3D/T1L L3S2 and identified three point mutations in μ1 that stabilize ISVPs. Two of these mutations are located in the C-terminal ϕ region of μ1, which has not previously been implicated in controlling ISVP stability. Independent of compromised ISVP stability, we also found that T3D/T1L L3S2 launches replication more efficiently and produces higher yields in infected cells than T3D. In addition to identifying a new role for the core proteins in disassembly events, these data highlight the possibility that core proteins may influence multiple stages of infection.IMPORTANCE Protein shells of viruses (capsids) have evolved to undergo specific changes to ensure the timely delivery of genetic material to host cells. The 2-layer capsid of reovirus provides a model system to study the interactions between capsid proteins and the changes they undergo during entry. We tested a virus in which the core proteins were derived from a different strain than the outer capsid. In comparison to the parental T3D strain, we found that this mismatched virus was less stable and completed conformational changes required for entry prematurely. Capsid stability was restored by introduction of specific changes to the outer capsid, indicating that an optimal fit between inner and outer shells maintains capsid function. Separate from this property, mismatch between these protein layers also impacted the capacity of the virus to initiate infection and produce progeny. This study reveals new insights into the roles of capsid proteins and their multiple functions during viral replication.
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Kaelber JT, Jiang W, Weaver SC, Auguste AJ, Chiu W. Arrangement of the Polymerase Complexes inside a Nine-Segmented dsRNA Virus. Structure 2020; 28:604-612.e3. [PMID: 32049031 PMCID: PMC7289189 DOI: 10.1016/j.str.2020.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/18/2019] [Accepted: 01/17/2020] [Indexed: 12/15/2022]
Abstract
Members of the family Reoviridae package several copies of the viral polymerase complex into their capsid to carry out replication and transcription within viral particles. Classical single-particle reconstruction encounters difficulties resolving structures such as the intraparticle polymerase complex because refinement can converge to an incorrect map and because the map could depict a nonrepresentative subset of particles or an average of heterogeneous particles. Using the nine-segmented Fako virus, we tested hypotheses for the arrangement and number of polymerase complexes within the virion by measuring how well each hypothesis describes the set of cryoelectron microscopy images of individual viral particles. We find that the polymerase complex in Fako virus binds at ten possible sites despite having only nine genome segments. A single asymmetric configuration describes the arrangement of these complexes in both virions and genome-free capsids. Similarities between the arrangements of Reoviridae with 9, 10, and 11 segments indicate the generalizability of this architecture.
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Affiliation(s)
- Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Scott C Weaver
- Institute for Human Infections and Immunity, World Reference Center for Emerging Viruses and Arboviruses, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Albert J Auguste
- Institute for Human Infections and Immunity, World Reference Center for Emerging Viruses and Arboviruses, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Wah Chiu
- Department of Bioengineering, Department of Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, CA, USA
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17
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Tenorio R, Fernández de Castro I, Knowlton JJ, Zamora PF, Sutherland DM, Risco C, Dermody TS. Function, Architecture, and Biogenesis of Reovirus Replication Neoorganelles. Viruses 2019; 11:v11030288. [PMID: 30901959 PMCID: PMC6466366 DOI: 10.3390/v11030288] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/17/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
Most viruses that replicate in the cytoplasm of host cells form neoorganelles that serve as sites of viral genome replication and particle assembly. These highly specialized structures concentrate viral proteins and nucleic acids, prevent the activation of cell-intrinsic defenses, and coordinate the release of progeny particles. Reoviruses are common pathogens of mammals that have been linked to celiac disease and show promise for oncolytic applications. These viruses form nonenveloped, double-shelled virions that contain ten segments of double-stranded RNA. Replication organelles in reovirus-infected cells are nucleated by viral nonstructural proteins µNS and σNS. Both proteins partition the endoplasmic reticulum to form the matrix of these structures. The resultant membranous webs likely serve to anchor viral RNA⁻protein complexes for the replication of the reovirus genome and the assembly of progeny virions. Ongoing studies of reovirus replication organelles will advance our knowledge about the strategies used by viruses to commandeer host biosynthetic pathways and may expose new targets for therapeutic intervention against diverse families of pathogenic viruses.
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Affiliation(s)
- Raquel Tenorio
- Cell Structure Laboratory, National Center for Biotechnology, CNB-CSIC, Cantoblanco Campus, 28049 Madrid, Spain.
| | - Isabel Fernández de Castro
- Cell Structure Laboratory, National Center for Biotechnology, CNB-CSIC, Cantoblanco Campus, 28049 Madrid, Spain.
| | - Jonathan J Knowlton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| | - Paula F Zamora
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Danica M Sutherland
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.
- Center for Microbial Pathogenesis, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.
| | - Cristina Risco
- Cell Structure Laboratory, National Center for Biotechnology, CNB-CSIC, Cantoblanco Campus, 28049 Madrid, Spain.
| | - Terence S Dermody
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.
- Center for Microbial Pathogenesis, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.
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18
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Mirzakhanyan Y, Gershon P. The Vaccinia virion: Filling the gap between atomic and ultrastructure. PLoS Pathog 2019; 15:e1007508. [PMID: 30615658 PMCID: PMC6336343 DOI: 10.1371/journal.ppat.1007508] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/17/2019] [Accepted: 12/06/2018] [Indexed: 01/19/2023] Open
Abstract
We have investigated the molecular-level structure of the Vaccinia virion in situ by protein-protein chemical crosslinking, identifying 4609 unique-mass crosslink ions at an effective FDR of 0.33%, covering 2534 unique pairs of crosslinked protein positions, 625 of which were inter-protein. The data were statistically non-random and rational in the context of known structures, and showed biological rationality. Crosslink density strongly tracked the individual proteolytic maturation products of p4a and p4b, the two major virion structural proteins, and supported the prediction of transmembrane domains within membrane proteins. A clear sub-network of four virion structural proteins provided structural insights into the virion core wall, and proteins VP8 and A12 formed a strongly-detected crosslinked pair with an apparent structural role. A strongly-detected sub-network of membrane proteins A17, H3, A27 and A26 represented an apparent interface of the early-forming virion envelope with structures added later during virion morphogenesis. Protein H3 seemed to be the central hub not only for this sub-network but also for an 'attachment protein' sub-network comprising membrane proteins H3, ATI, CAHH(D8), A26, A27 and G9. Crosslinking data lent support to a number of known interactions and interactions within known complexes. Evidence is provided for the membrane targeting of genome telomeres. In covering several orders of magnitude in protein abundance, this study may have come close to the bottom of the protein-protein crosslinkome of an intact organism, namely a complex animal virus.
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Affiliation(s)
- Yeva Mirzakhanyan
- Department of Molecular Biology & Biochemistry, UC-Irvine, Irvine, California, United States of America
| | - Paul Gershon
- Department of Molecular Biology & Biochemistry, UC-Irvine, Irvine, California, United States of America
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19
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Ramesh R, Lim XX, Raghuvamsi PV, Wu C, Wong SM, Anand GS. Uncovering metastability and disassembly hotspots in whole viral particles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:5-12. [PMID: 30553754 DOI: 10.1016/j.pbiomolbio.2018.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/26/2018] [Accepted: 12/12/2018] [Indexed: 01/18/2023]
Abstract
Viruses are metastable macromolecular assemblies that toggle between multiple conformational states through molecular rearrangements that are critical for mediating viral host entry. Viruses respond to different host specific environmental cues to form disassembly intermediates for the eventual release of genomic material required for replication. Although static snapshots of these intermediates have been captured through structural techniques such as X-ray crystallography and cryo-EM, the mechanistic details of these conformational rearrangements underpinning viral metastability have been poorly understood. Amide hydrogen deuterium exchange mass spectrometry (HDXMS) is a powerful tool that measures hydrogen bonding propensities to probe changes in the dynamics of different macromolecular interactions. Chaotropic agents such as urea can be used to disrupt hydrogen bonds between different subunits, thereby ranking regions of the virus that are critical in maintaining viral stability. By controlled urea denaturation with HDXMS, we have identified specific loci in a Turnip Crinkle Virus (TCV) model showing increased deuterium exchange with even minimally disruptive concentrations of urea. These loci represent dynamic disassembly hotspots. These hotspots are predominantly present at the quaternary contacts at the 3-fold and 5-fold axes. This approach can be applied to detect vulnerabilities in virus icosahedral structures to uncover the molecular mechanism of viral disassembly.
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Affiliation(s)
- Ranita Ramesh
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Xin Xiang Lim
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | | | - Chao Wu
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Sek Man Wong
- Department of Biological Sciences, National University of Singapore, 117543, Singapore; Temasek Life Sciences Laboratory, Singapore, 117604, Singapore
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20
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Fujimura T, Esteban R. The cap-snatching reaction of yeast L-A double-stranded RNA virus is reversible and the catalytic sites on both Gag and the Gag domain of Gag-Pol are active. Mol Microbiol 2018; 111:395-404. [PMID: 30427078 DOI: 10.1111/mmi.14161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2018] [Indexed: 02/01/2023]
Abstract
The yeast L-A double-stranded RNA virus synthesizes capped transcripts by a unique cap-snatching mechanism in which the m7 Gp moiety of host mRNA (donor) is transferred to the diphosphorylated 5' end of the viral transcript (acceptor). This reaction is activated by viral transcription. Here, we show that cap snatching can be reversible. Because only m7 Gp is transferred during the reaction, the resulting decapped donor, as expected, retained diphosphates at the 5' end. We also found that the 5' terminal nucleotide of the acceptor needs to be G but not A. Interestingly, the A-initiated molecule when equipped with a cap structure (m7 GpppA…) could work as cap donor. Because the majority of host mRNAs in yeast have A after the cap structures at the 5' ends, this finding implies that cap-snatching in vivo is virtually a one-way reaction, in favor of furnishing the viral transcript with a cap. The cap-snatching sites are located on the coat protein Gag and also the Gag domain of Gag-Pol. Here, we demonstrate that both sites are functional, indicating that activation of cap snatching by transcription is not transmitted through the peptide bonding between the Gag and Pol domains of Gag-Pol.
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Affiliation(s)
- Tsutomu Fujimura
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca, Spain
| | - Rosa Esteban
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca, Spain
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21
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Lemay G. Synthesis and Translation of Viral mRNA in Reovirus-Infected Cells: Progress and Remaining Questions. Viruses 2018; 10:E671. [PMID: 30486370 PMCID: PMC6315682 DOI: 10.3390/v10120671] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 11/23/2018] [Accepted: 11/25/2018] [Indexed: 12/11/2022] Open
Abstract
At the end of my doctoral studies, in 1988, I published a review article on the major steps of transcription and translation during the mammalian reovirus multiplication cycle, a topic that still fascinates me 30 years later. It is in the nature of scientific research to generate further questioning as new knowledge emerges. Our understanding of these fascinating viruses thus remains incomplete but it seemed appropriate at this moment to look back and reflect on our progress and most important questions that still puzzle us. It is also essential of being careful about concepts that seem so well established, but could still be better validated using new approaches. I hope that the few reflections presented here will stimulate discussions and maybe attract new investigators into the field of reovirus research. Many other aspects of the viral multiplication cycle would merit our attention. However, I will essentially limit my discussion to these central aspects of the viral cycle that are transcription of viral genes and their phenotypic expression through the host cell translational machinery. The objective here is not to review every aspect but to put more emphasis on important progress and challenges in the field.
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Affiliation(s)
- Guy Lemay
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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22
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Abstract
Double-stranded RNA viruses infect a wide spectrum of hosts, including animals, plants, fungi, and bacteria. Yet genome replication mechanisms of these viruses are conserved. During the infection cycle, a proteinaceous capsid, the polymerase complex, is formed. An essential component of this capsid is the viral RNA polymerase that replicates and transcribes the enclosed viral genome. The polymerase complex structure is well characterized for many double-stranded RNA viruses. However, much less is known about the hierarchical molecular interactions that take place in building up such complexes. Using the bacteriophage Φ6 self-assembly system, we obtained novel insights into the processes that mediate polymerase subunit incorporation into the polymerase complex for generation of functional structures. The results presented pave the way for the exploitation and engineering of viral self-assembly processes for biomedical and synthetic biology applications. An understanding of viral assembly processes at the molecular level may also facilitate the development of antivirals that target viral capsid assembly. Double-stranded RNA (dsRNA) viruses package several RNA-dependent RNA polymerases (RdRp) together with their dsRNA genome into an icosahedral protein capsid known as the polymerase complex. This structure is highly conserved among dsRNA viruses but is not found in any other virus group. RdRp subunits typically interact directly with the main capsid proteins, close to the 5-fold symmetric axes, and perform viral genome replication and transcription within the icosahedral protein shell. In this study, we utilized Pseudomonas phage Φ6, a well-established virus self-assembly model, to probe the potential roles of the RdRp in dsRNA virus assembly. We demonstrated that Φ6 RdRp accelerates the polymerase complex self-assembly process and contributes to its conformational stability and integrity. We highlight the role of specific amino acid residues on the surface of the RdRp in its incorporation during the self-assembly reaction. Substitutions of these residues reduce RdRp incorporation into the polymerase complex during the self-assembly reaction. Furthermore, we determined that the overall transcription efficiency of the Φ6 polymerase complex increased when the number of RdRp subunits exceeded the number of genome segments. These results suggest a mechanism for RdRp recruitment in the polymerase complex and highlight its novel role in virion assembly, in addition to the canonical RNA transcription and replication functions.
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23
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Capsid Structure of dsRNA Fungal Viruses. Viruses 2018; 10:v10090481. [PMID: 30205532 PMCID: PMC6164181 DOI: 10.3390/v10090481] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/05/2018] [Accepted: 09/05/2018] [Indexed: 01/27/2023] Open
Abstract
Most fungal, double-stranded (ds) RNA viruses lack an extracellular life cycle stage and are transmitted by cytoplasmic interchange. dsRNA mycovirus capsids are based on a 120-subunit T = 1 capsid, with a dimer as the asymmetric unit. These capsids, which remain structurally undisturbed throughout the viral cycle, nevertheless, are dynamic particles involved in the organization of the viral genome and the viral polymerase necessary for RNA synthesis. The atomic structure of the T = 1 capsids of four mycoviruses was resolved: the L-A virus of Saccharomyces cerevisiae (ScV-L-A), Penicillium chrysogenum virus (PcV), Penicillium stoloniferum virus F (PsV-F), and Rosellinia necatrix quadrivirus 1 (RnQV1). These capsids show structural variations of the same framework, with 60 asymmetric or symmetric homodimers for ScV-L-A and PsV-F, respectively, monomers with a duplicated similar domain for PcV, and heterodimers of two different proteins for RnQV1. Mycovirus capsid proteins (CP) share a conserved α-helical domain, although the latter may carry different peptides inserted at preferential hotspots. Insertions in the CP outer surface are likely associated with enzymatic activities. Within the capsid, fungal dsRNA viruses show a low degree of genome compaction compared to reoviruses, and contain one to two copies of the RNA-polymerase complex per virion.
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Fingas F, Volke D, Bielefeldt P, Hassert R, Hoffmann R. Detection of mammalian orthoreovirus type-3 (Reo-3) infections in mice based on serotype-specific hemagglutination protein sigma-1. Virol J 2018; 15:114. [PMID: 30049287 PMCID: PMC6062942 DOI: 10.1186/s12985-018-1021-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/11/2018] [Indexed: 12/05/2022] Open
Abstract
Background Reovirus type-3 infections cause severe pathologies in young mice and thus influence animal experiments in many ways. Therefore, the Federation of Laboratory Animal Science Associations (FELASA) recommends an annual screening in laboratory mice as part of a thorough health monitoring program. Based on the high protein sequence homology among the different reovirus serotypes, immunofluorescence antibody assay and other indirect methods relying on the whole virus are presumably cross-reactive to antibodies triggered by mammalian orthoreovirus infections independent of the serotype. Methods The serotype-specific protein σ-1 was expressed in Escherichia coli with an N-terminal Strep-tag and a C-terminal His-tag. The purified Strep-rσ-1-His-construct was used to develop an indirect ELISA by testing defined positive and negative sera obtained by experimental infection of mice as well as field sera. Results The Strep-rσ-1-His-ELISA provided high sensitivity and specificity during validation. Notably, a high selectivity was also observed for sera positively tested for other relevant FELASA-listed pathogens. Screening of field samples indicated that a commercial reovirus type-3-based ELISA might be cross-reactive to other murine reovirus serotypes and thus produces false-positive results. Conclusions The prevalence of reovirus type-3 might be overestimated in German animal facilities and most likely in other countries as well. The occurrence of other reovirus serotypes, however, raises the question if murine health monitoring programs should be extended to these pathogens. Electronic supplementary material The online version of this article (10.1186/s12985-018-1021-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Felix Fingas
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany.,GVG Diagnostics GmbH, Leipzig, Germany
| | - Daniela Volke
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Leipzig, Germany
| | | | - Rayk Hassert
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany. .,Center for Biotechnology and Biomedicine, Leipzig, Germany.
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25
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Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly. Proc Natl Acad Sci U S A 2018; 115:7344-7349. [PMID: 29941585 DOI: 10.1073/pnas.1803885115] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together with other capsid proteins and genomic RNA. Here we report the near-atomic resolution structure of the RdRp protein VP2 in complex with its cofactor protein VP4 and genomic RNA within an aquareovirus capsid using 200-kV cryoelectron microscopy and symmetry-mismatch reconstruction. The structure of these capsid proteins enabled us to observe the elaborate nonicosahedral structure within the double-layered icosahedral capsid. Our structure shows that the RdRp complex is anchored at the inner surface of the capsid shell and interacts with genomic dsRNA and four of the five asymmetrically arranged N termini of the capsid shell proteins under the fivefold axis, implying roles for these N termini in virus assembly. The binding site of the RNA end at VP2 is different from the RNA cap binding site identified in the crystal structure of orthoreovirus RdRp λ3, although the structures of VP2 and λ3 are almost identical. A loop, which was thought to separate the RNA template and transcript, interacts with an apical domain of the capsid shell protein, suggesting a mechanism for regulating RdRp replication and transcription. A conserved nucleoside triphosphate binding site was localized in our RdRp cofactor protein VP4 structure, and interactions between the VP4 and the genomic RNA were identified.
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26
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Wang JCY, Mukhopadhyay S, Zlotnick A. Geometric Defects and Icosahedral Viruses. Viruses 2018; 10:E25. [PMID: 29300359 PMCID: PMC5795438 DOI: 10.3390/v10010025] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 12/26/2017] [Accepted: 12/28/2017] [Indexed: 12/20/2022] Open
Abstract
We propose that viruses with geometric defects are not necessarily flawed viruses. A geometric defect may be a reactive site. Defects may facilitate assembly, dissociation, or accessibility of cellular proteins to virion components. In single molecule studies of hepadnavirus assembly, defects and overgrowth are common features. Icosahedral alphaviruses and flaviviruses, among others, have capsids with geometric defects. Similarly, immature retroviruses, which are non-icosahedral, have numerous "errors". In many viruses, asymmetric exposure of interior features allows for regulated genome release or supports intracellular trafficking. In these viruses, the defects likely serve a biological function. Commonly used approaches for spherical virus structure determination use symmetry averaging, which obscures defects. We suggest that there are three classes of asymmetry: regular asymmetry as might be found in a tailed phage, irregular asymmetry as found, for example, in defects randomly trapped during assembly, and dynamic asymmetry due to Brownian dynamics of virus capsids. Awareness of their presence and recent advances in electron microscopy will allow unprecedented investigation of capsid irregularities to investigate their biological relevance.
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Affiliation(s)
- Joseph Che-Yen Wang
- Indiana University Electron Microscopy Center, Indiana University, Bloomington, IN 47405, USA.
| | | | - Adam Zlotnick
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA.
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27
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Eichwald C, Kim J, Nibert ML. Dissection of mammalian orthoreovirus µ2 reveals a self-associative domain required for binding to microtubules but not to factory matrix protein µNS. PLoS One 2017; 12:e0184356. [PMID: 28880890 PMCID: PMC5589220 DOI: 10.1371/journal.pone.0184356] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/22/2017] [Indexed: 12/25/2022] Open
Abstract
Mammalian orthoreovirus protein μ2 is a component of the viral core particle. Its activities include RNA binding and hydrolysis of the γ-phosphate from NTPs and RNA 5´-termini, suggesting roles as a cofactor for the viral RNA-dependent RNA polymerase, λ3, first enzyme in 5´-capping of viral plus-strand RNAs, and/or prohibitory of RNA-5´-triphosphate-activated antiviral signaling. Within infected cells, μ2 also contributes to viral factories, cytoplasmic structures in which genome replication and particle assembly occur. By associating with both microtubules (MTs) and viral factory matrix protein μNS, μ2 can anchor the factories to MTs, the full effects of which remain unknown. In this study, a protease-hypersensitive region allowed μ2 to be dissected into two large fragments corresponding to residues 1-282 and 283-736. Fusions with enhanced green fluorescent protein revealed that these amino- and carboxyl-terminal regions of μ2 associate in cells with either MTs or μNS, respectively. More exhaustive deletion analysis defined μ2 residues 1-325 as the minimal contiguous region that associates with MTs in the absence of the self-associating tag. A region involved in μ2 self-association was mapped to residues 283-325, and self-association involving this region was essential for MT-association as well. Likewise, we mapped that μNS-binding site in μ2 relates to residues 290-453 which is independent of μ2 self-association. These findings suggest that μ2 monomers or oligomers can bind to MTs and μNS, but that self-association involving μ2 residues 283-325 is specifically relevant for MT-association during viral factories formation.
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Affiliation(s)
- Catherine Eichwald
- Department of Microbiology & Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Institute of Virology, University of Zurich, Zurich, Switzerland
- * E-mail:
| | - Jonghwa Kim
- Department of Microbiology & Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Laboratory of Gastroenterology, Samsung Medical Center, Seoul, Republic of Korea
| | - Max L. Nibert
- Department of Microbiology & Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
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28
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Ryabov EV. Invertebrate RNA virus diversity from a taxonomic point of view. J Invertebr Pathol 2017; 147:37-50. [PMID: 27793741 PMCID: PMC7094257 DOI: 10.1016/j.jip.2016.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 10/03/2016] [Accepted: 10/14/2016] [Indexed: 02/04/2023]
Abstract
Invertebrates are hosts to diverse RNA viruses that have all possible types of encapsidated genomes (positive, negative and ambisense single stranded RNA genomes, or a double stranded RNA genome). These viruses also differ markedly in virion morphology and genome structure. Invertebrate RNA viruses are present in three out of four currently recognized orders of RNA viruses: Mononegavirales, Nidovirales, and Picornavirales, and 10 out of 37 RNA virus families that have yet to be assigned to an order. This mini-review describes general properties of the taxonomic groups, which include invertebrate RNA viruses on the basis of their current classification by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Eugene V Ryabov
- ER Healthcare Consulting Ltd., Poundgate Lane, Coventry CV4 8HJ, United Kingdom.
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29
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Ertel KJ, Benefield D, Castaño-Diez D, Pennington JG, Horswill M, den Boon JA, Otegui MS, Ahlquist P. Cryo-electron tomography reveals novel features of a viral RNA replication compartment. eLife 2017; 6. [PMID: 28653620 PMCID: PMC5515581 DOI: 10.7554/elife.25940] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/20/2017] [Indexed: 12/18/2022] Open
Abstract
Positive-strand RNA viruses, the largest genetic class of viruses, include numerous important pathogens such as Zika virus. These viruses replicate their RNA genomes in novel, membrane-bounded mini-organelles, but the organization of viral proteins and RNAs in these compartments has been largely unknown. We used cryo-electron tomography to reveal many previously unrecognized features of Flock house nodavirus (FHV) RNA replication compartments. These spherular invaginations of outer mitochondrial membranes are packed with electron-dense RNA fibrils and their volumes are closely correlated with RNA replication template length. Each spherule’s necked aperture is crowned by a striking cupped ring structure containing multifunctional FHV RNA replication protein A. Subtomogram averaging of these crowns revealed twelve-fold symmetry, concentric flanking protrusions, and a central electron density. Many crowns were associated with long cytoplasmic fibrils, likely to be exported progeny RNA. These results provide new mechanistic insights into positive-strand RNA virus replication compartment structure, assembly, function and control. DOI:http://dx.doi.org/10.7554/eLife.25940.001
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Affiliation(s)
- Kenneth J Ertel
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, United States.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, United States
| | - Desirée Benefield
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, United States.,Morgridge Institute for Research, University of Wisconsin-Madison, Madison, United States
| | | | - Janice G Pennington
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, United States.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, United States
| | - Mark Horswill
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, United States.,Morgridge Institute for Research, University of Wisconsin-Madison, Madison, United States
| | - Johan A den Boon
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, United States.,Morgridge Institute for Research, University of Wisconsin-Madison, Madison, United States
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-Madison, Madison, United States.,Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, United States
| | - Paul Ahlquist
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, United States.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, United States.,Morgridge Institute for Research, University of Wisconsin-Madison, Madison, United States
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30
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African Swine Fever Virus NP868R Capping Enzyme Promotes Reovirus Rescue during Reverse Genetics by Promoting Reovirus Protein Expression, Virion Assembly, and RNA Incorporation into Infectious Virions. J Virol 2017; 91:JVI.02416-16. [PMID: 28298603 DOI: 10.1128/jvi.02416-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/07/2017] [Indexed: 12/25/2022] Open
Abstract
Reoviruses, like many eukaryotic viruses, contain an inverted 7-methylguanosine (m7G) cap linked to the 5' nucleotide of mRNA. The traditional functions of capping are to promote mRNA stability, protein translation, and concealment from cellular proteins that recognize foreign RNA. To address the role of mRNA capping during reovirus replication, we assessed the benefits of adding the African swine fever virus NP868R capping enzyme during reovirus rescue. C3P3, a fusion protein containing T7 RNA polymerase and NP868R, was found to increase protein expression 5- to 10-fold compared to T7 RNA polymerase alone while enhancing reovirus rescue from the current reverse genetics system by 100-fold. Surprisingly, RNA stability was not increased by C3P3, suggesting a direct effect on protein translation. A time course analysis revealed that C3P3 increased protein synthesis within the first 2 days of a reverse genetics transfection. This analysis also revealed that C3P3 enhanced processing of outer capsid μ1 protein to μ1C, a previously described hallmark of reovirus assembly. Finally, to determine the rate of infectious-RNA incorporation into new virions, we developed a new recombinant reovirus S1 gene that expressed the fluorescent protein UnaG. Following transfection of cells with UnaG and infection with wild-type virus, passage of UnaG through progeny was significantly enhanced by C3P3. These data suggest that capping provides nontraditional functions to reovirus, such as promoting assembly and infectious-RNA incorporation.IMPORTANCE Our findings expand our understanding of how viruses utilize capping, suggesting that capping provides nontraditional functions to reovirus, such as promoting assembly and infectious-RNA incorporation, in addition to enhancing protein translation. Beyond providing mechanistic insight into reovirus replication, our findings also show that reovirus reverse genetics rescue is enhanced 100-fold by the NP868R capping enzyme. Since reovirus shows promise as a cancer therapy, efficient reovirus reverse genetics rescue will accelerate production of recombinant reoviruses as candidates to enhance therapeutic potency. NP868R-assisted reovirus rescue will also expedite production of recombinant reovirus for mechanistic insights into reovirus protein function and structure.
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31
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32
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Wu W, Newcomb WW, Cheng N, Aksyuk A, Winkler DC, Steven AC. Internal Proteins of the Procapsid and Mature Capsids of Herpes Simplex Virus 1 Mapped by Bubblegram Imaging. J Virol 2016; 90:5176-86. [PMID: 26984725 PMCID: PMC4859710 DOI: 10.1128/jvi.03224-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/09/2016] [Indexed: 02/08/2023] Open
Abstract
UNLABELLED The herpes simplex virus 1 (HSV-1) capsid is a huge assembly, ∼1,250 Å in diameter, and is composed of thousands of protein subunits with a combined mass of ∼200 MDa, housing a 100-MDa genome. First, a procapsid is formed through coassembly of the surface shell with an inner scaffolding shell; then the procapsid matures via a major structural transformation, triggered by limited proteolysis of the scaffolding proteins. Three mature capsids are found in the nuclei of infected cells. A capsids are empty, B capsids retain a shrunken scaffolding shell, and C capsids-which develop into infectious virions-are filled with DNA and ostensibly have expelled the scaffolding shell. The possible presence of other internal proteins in C capsids has been moot as, in cryo-electron microscopy (cryo-EM), they would be camouflaged by the surrounding DNA. We have used bubblegram imaging to map internal proteins in all four capsids, aided by the discovery that the scaffolding protein is exceptionally prone to radiation-induced bubbling. We confirmed that this protein forms thick-walled inner shells in the procapsid and the B capsid. C capsids generate two classes of bubbles: one occupies positions beneath the vertices of the icosahedral surface shell, and the other is distributed throughout its interior. A likely candidate is the viral protease. A subpopulation of C capsids bubbles particularly profusely and may represent particles in which expulsion of scaffold and DNA packaging are incomplete. Based on the procapsid structure, we propose that the axial channels of hexameric capsomers afford the pathway via which the scaffolding protein is expelled. IMPORTANCE In addition to DNA, capsids of tailed bacteriophages and their distant relatives, herpesviruses, contain internal proteins. These proteins are often essential for infectivity but are difficult to locate within the virion. A novel adaptation of cryo-EM based on detecting gas bubbles generated by radiation damage was used to localize internal proteins of HSV-1, yielding insights into how capsid maturation is regulated. The scaffolding protein, which forms inner shells in the procapsid and B capsid, is exceptionally bubbling-prone. In the mature DNA-filled C capsid, a previously undetected protein was found to underlie the icosahedral vertices: this is tentatively assigned as a storage form of the viral protease. We also observed a capsid species that appears to contain substantial amounts of scaffolding protein as well as DNA, suggesting that DNA packaging and expulsion of the scaffolding protein are coupled processes.
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Affiliation(s)
- Weimin Wu
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - William W Newcomb
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Anastasia Aksyuk
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Dennis C Winkler
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
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33
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Collier AM, Lyytinen OL, Guo YR, Toh Y, Poranen MM, Tao YJ. Initiation of RNA Polymerization and Polymerase Encapsidation by a Small dsRNA Virus. PLoS Pathog 2016; 12:e1005523. [PMID: 27078841 PMCID: PMC4831847 DOI: 10.1371/journal.ppat.1005523] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/03/2016] [Indexed: 01/07/2023] Open
Abstract
During the replication cycle of double-stranded (ds) RNA viruses, the viral RNA-dependent RNA polymerase (RdRP) replicates and transcribes the viral genome from within the viral capsid. How the RdRP molecules are packaged within the virion and how they function within the confines of an intact capsid are intriguing questions with answers that most likely vary across the different dsRNA virus families. In this study, we have determined a 2.4 Å resolution structure of an RdRP from the human picobirnavirus (hPBV). In addition to the conserved polymerase fold, the hPBV RdRP possesses a highly flexible 24 amino acid loop structure located near the C-terminus of the protein that is inserted into its active site. In vitro RNA polymerization assays and site-directed mutagenesis showed that: (1) the hPBV RdRP is fully active using both ssRNA and dsRNA templates; (2) the insertion loop likely functions as an assembly platform for the priming nucleotide to allow de novo initiation; (3) RNA transcription by the hPBV RdRP proceeds in a semi-conservative manner; and (4) the preference of virus-specific RNA during transcription is dictated by the lower melting temperature associated with the terminal sequences. Co-expression of the hPBV RdRP and the capsid protein (CP) indicated that, under the conditions used, the RdRP could not be incorporated into the recombinant capsids in the absence of the viral genome. Additionally, the hPBV RdRP exhibited higher affinity towards the conserved 5'-terminal sequence of the viral RNA, suggesting that the RdRP molecules may be encapsidated through their specific binding to the viral RNAs during assembly.
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Affiliation(s)
- Aaron M. Collier
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Outi L. Lyytinen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Yusong R. Guo
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Yukimatsu Toh
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Minna M. Poranen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail: (YJT); (MMP)
| | - Yizhi J. Tao
- Department of BioSciences, Rice University, Houston, Texas, United States of America
- * E-mail: (YJT); (MMP)
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34
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Mohamed A, Johnston RN, Shmulevitz M. Potential for Improving Potency and Specificity of Reovirus Oncolysis with Next-Generation Reovirus Variants. Viruses 2015; 7:6251-78. [PMID: 26633466 PMCID: PMC4690860 DOI: 10.3390/v7122936] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 11/10/2015] [Accepted: 11/18/2015] [Indexed: 12/16/2022] Open
Abstract
Viruses that specifically replicate in tumor over normal cells offer promising cancer therapies. Oncolytic viruses (OV) not only kill the tumor cells directly; they also promote anti-tumor immunotherapeutic responses. Other major advantages of OVs are that they dose-escalate in tumors and can be genetically engineered to enhance potency and specificity. Unmodified wild type reovirus is a propitious OV currently in phase I–III clinical trials. This review summarizes modifications to reovirus that may improve potency and/or specificity during oncolysis. Classical genetics approaches have revealed reovirus variants with improved adaptation towards tumors or with enhanced ability to establish specific steps of virus replication and cell killing among transformed cells. The recent emergence of a reverse genetics system for reovirus has provided novel strategies to fine-tune reovirus proteins or introduce exogenous genes that could promote oncolytic activity. Over the next decade, these findings are likely to generate better-optimized second-generation reovirus vectors and improve the efficacy of oncolytic reotherapy.
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Affiliation(s)
- Adil Mohamed
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada.
| | - Randal N Johnston
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
| | - Maya Shmulevitz
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada.
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35
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Zhang X, Ding K, Yu X, Chang W, Sun J, Zhou ZH. In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus. Nature 2015; 527:531-534. [PMID: 26503045 PMCID: PMC5086257 DOI: 10.1038/nature15767] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 10/07/2015] [Indexed: 01/15/2023]
Abstract
Viruses in the Reoviridae, like the triple-shelled human rotavirus and the single-shelled insect cytoplasmic polyhedrosis virus (CPV), all package a genome of segmented double-stranded RNAs (dsRNAs) inside the viral capsid and carry out endogenous messenger RNA synthesis through a transcriptional enzyme complex (TEC). By direct electron-counting cryoelectron microscopy and asymmetric reconstruction, we have determined the organization of the dsRNA genome inside quiescent CPV (q-CPV) and the in situ atomic structures of TEC within CPV in both quiescent and transcribing (t-CPV) states. We show that the ten segmented dsRNAs in CPV are organized with ten TECs in a specific, non-symmetric manner, with each dsRNA segment attached directly to a TEC. The TEC consists of two extensively interacting subunits: an RNA-dependent RNA polymerase (RdRP) and an NTPase VP4. We find that the bracelet domain of RdRP undergoes marked conformational change when q-CPV is converted to t-CPV, leading to formation of the RNA template entry channel and access to the polymerase active site. An amino-terminal helix from each of two subunits of the capsid shell protein (CSP) interacts with VP4 and RdRP. These findings establish the link between sensing of environmental cues by the external proteins and activation of endogenous RNA transcription by the TEC inside the virus.
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MESH Headings
- Capsid Proteins/chemistry
- Capsid Proteins/metabolism
- Capsid Proteins/ultrastructure
- Catalytic Domain
- Cryoelectron Microscopy
- Genome, Viral/genetics
- Models, Molecular
- Multienzyme Complexes/chemistry
- Multienzyme Complexes/metabolism
- Multienzyme Complexes/ultrastructure
- Nucleoside-Triphosphatase/metabolism
- Nucleoside-Triphosphatase/ultrastructure
- Protein Subunits/chemistry
- Protein Subunits/metabolism
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/ultrastructure
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Messenger/ultrastructure
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- RNA, Viral/ultrastructure
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/metabolism
- RNA-Dependent RNA Polymerase/ultrastructure
- Reoviridae/enzymology
- Reoviridae/genetics
- Reoviridae/ultrastructure
- Templates, Genetic
- Transcription, Genetic
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Affiliation(s)
- Xing Zhang
- California Nanosystems Institute, Los Angeles, CA 90095, USA
| | - Ke Ding
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Xuekui Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Winston Chang
- California Nanosystems Institute, Los Angeles, CA 90095, USA
| | - Jingchen Sun
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Z. Hong Zhou
- California Nanosystems Institute, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Bioengineering, University of California, Los Angeles, CA 90095, USA
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36
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Liu H, Cheng L. Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus. Science 2015; 349:1347-50. [PMID: 26383954 DOI: 10.1126/science.aaa4938] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Double-stranded RNA (dsRNA) viruses possess a segmented dsRNA genome and a number of RNA-dependent RNA polymerases (RdRps) enclosed in a capsid. Until now, the precise structures of genomes and RdRps within the capsids have been unknown. Here we report the structures of RdRps and associated RNAs within nontranscribing and transcribing cypoviruses (NCPV and TCPV, respectively), using a combination of cryo-electron microscopy (cryo-EM) and a symmetry-mismatch reconstruction method. The RdRps and associated RNAs appear to exhibit a pseudo-D3 symmetric organization in both NCPV and TCPV. However, the molecular interactions between RdRps and the genomic RNA were found to differ in these states. Our work provides insight into the mechanisms of the replication and transcription in dsRNA viruses and paves a way for structural determination of lower-symmetry complexes enclosed in higher-symmetry structures.
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Affiliation(s)
- Hongrong Liu
- College of Physics and Information Science, Hunan Normal University, Changsha, Hunan 410081, China.
| | - Lingpeng Cheng
- School of Life Sciences, Tsinghua University, Beijing 100084, China.
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37
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Functional insights from molecular modeling, docking, and dynamics study of a cypoviral RNA dependent RNA polymerase. J Mol Graph Model 2015; 61:160-74. [PMID: 26264734 DOI: 10.1016/j.jmgm.2015.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/27/2015] [Accepted: 07/18/2015] [Indexed: 11/20/2022]
Abstract
Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV) contains 11 double stranded RNA genome segments and infects tasar silkworm A. mylitta. RNA-dependent RNA polymerase (RdRp) is reported as a key enzyme responsible for propagation of the virus in the host cell but its structure function relationship still remains elusive. Here a computational approach has been taken to compare sequence and secondary structure of AmCPV RdRp with other viral RdRps to identify consensus motifs. Then a reliable pairwise sequence alignment of AmCPV RdRp with its closest sequence structure homologue λ3 RdRp is done to predict three dimensional structure of AmCPV RdRp. After comparing with other structurally known viral RdRps, important sequence and/or structural features involved in substrate entry or binding, polymerase reaction and the product release events have been identified. A conserved RNA pentanucleotide (5'-AGAGC-3') at the 3'-end of virus genome is predicted as cis-acting signal for RNA synthesis and its docking and simulation study along with the model of AmCPV RdRp has allowed to predict mode of template binding by the viral polymerase. It is found that template RNA enters into the catalytic center through nine sequence-independent and two sequence-dependent interactions with the specific amino acid residues. However, number of sequence dependent interactions remains almost same during 10 nano-second simulation time while total number of interactions decreases. Further, docking of N(7)-methyl-GpppG (mRNA cap) on the model as well as prediction of RNA secondary structure has shown the template entry process in the active site. These findings have led to postulate the mechanism of RNA-dependent RNA polymerization process by AmCPV RdRp. To our knowledge, this is the first report to evaluate structure function relationship of a cypoviral RdRp.
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Reduction of virion-associated σ1 fibers on oncolytic reovirus variants promotes adaptation toward tumorigenic cells. J Virol 2015; 89:4319-34. [PMID: 25653434 DOI: 10.1128/jvi.03651-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED Wild-type mammalian orthoreovirus serotype 3 Dearing (T3wt) is nonpathogenic in humans but preferentially infects and kills cancer cells in culture and demonstrates promising antitumor activity in vivo. Using forward genetics, we previously isolated two variants of reovirus, T3v1 and T3v2, with increased infectivity toward a panel of cancer cell lines and improved in vivo oncolysis in a murine melanoma model relative to that of T3wt. Our current study explored how mutations in T3v1 and T3v2 promote infectivity. Reovirions contain trimers of σ1, the reovirus cell attachment protein, at icosahedral capsid vertices. Quantitative Western blot analysis showed that purified T3v1 and T3v2 virions had ∼ 2- and 4-fold-lower levels of σ1 fiber than did T3wt virions. Importantly, using RNA interference to reduce σ1 levels during T3wt production, we were able to generate wild-type reovirus with reduced levels of σ1 per virion. As σ1 levels were reduced, virion infectivity increased by 2- to 5-fold per cell-bound particle, demonstrating a causal relationship between virion σ1 levels and the infectivity of incoming virions. During infection of tumorigenic L929 cells, T3wt, T3v1, and T3v2 uncoated the outer capsid proteins σ3 and μ1C at similar rates. However, having started with fewer σ1 molecules, a complete loss of σ1 was achieved sooner for T3v1 and T3v2. Distinct from intracellular uncoating, chymotrypsin digestion, as a mimic of natural enteric infection, resulted in more rapid σ3 and μ1C removal, unique disassembly intermediates, and a rapid loss of infectivity for T3v1 and T3v2 compared to T3wt. Optimal infectivity toward natural versus therapeutic niches may therefore require distinct reovirus structures and σ1 levels. IMPORTANCE Wild-type reovirus is currently in clinical trials as a potential cancer therapy. Our molecular studies on variants of reovirus with enhanced oncolytic activity in vitro and in vivo now show that distinct reovirus structures promote adaptation toward cancer cells and away from conditions that mimic natural routes of infection. Specifically, we found that reovirus particles with fewer molecules of the cell attachment protein σ1 became more infectious toward transformed cells. Reduced σ1 levels conferred a benefit to incoming particles only, resulting in an earlier depletion of σ1 and a higher probability of establishing productive infection. Conversely, reovirus variants with fewer σ1 molecules showed reduced stability and infectivity and distinct disassembly when exposed to conditions that mimic natural intestinal proteolysis. These findings support a model where the mode of infection dictates the precise optimum of reovirus structure and provide a molecular rationale for considering alternative reovirus structures during oncolytic therapy.
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Adeno-associated virus serotype 1 (AAV1)- and AAV5-antibody complex structures reveal evolutionary commonalities in parvovirus antigenic reactivity. J Virol 2014; 89:1794-808. [PMID: 25410874 DOI: 10.1128/jvi.02710-14] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The clinical utility of the adeno-associated virus (AAV) gene delivery system has been validated by the regulatory approval of an AAV serotype 1 (AAV1) vector for the treatment of lipoprotein lipase deficiency. However, neutralization from preexisting antibodies is detrimental to AAV transduction efficiency. Hence, mapping of AAV antigenic sites and engineering of neutralization-escaping vectors are important for improving clinical efficacy. We report the structures of four AAV-monoclonal antibody fragment complexes, AAV1-ADK1a, AAV1-ADK1b, AAV5-ADK5a, and AAV5-ADK5b, determined by cryo-electron microscopy and image reconstruction to a resolution of ∼11 to 12 Å. Pseudoatomic modeling mapped the ADK1a epitope to the protrusions surrounding the icosahedral 3-fold axis and the ADK1b and ADK5a epitopes, which overlap, to the wall between depressions at the 2- and 5-fold axes (2/5-fold wall), and the ADK5b epitope spans both the 5-fold axis-facing wall of the 3-fold protrusion and portions of the 2/5-fold wall of the capsid. Combined with the six antigenic sites previously elucidated for different AAV serotypes through structural approaches, including AAV1 and AAV5, this study identified two common AAV epitopes: one on the 3-fold protrusions and one on the 2/5-fold wall. These epitopes coincide with regions with the highest sequence and structure diversity between AAV serotypes and correspond to regions determining receptor recognition and transduction phenotypes. Significantly, these locations overlap the two dominant epitopes reported for autonomous parvoviruses. Thus, rather than the amino acid sequence alone, the antigenic sites of parvoviruses appear to be dictated by structural features evolved to enable specific infectious functions. IMPORTANCE The adeno-associated viruses (AAVs) are promising vectors for in vivo therapeutic gene delivery, with more than 20 years of intense research now realized in a number of successful human clinical trials that report therapeutic efficacy. However, a large percentage of the population has preexisting AAV capsid antibodies and therefore must be excluded from clinical trials or vector readministration. This report represents our continuing efforts to understand the antigenic structure of the AAVs, specifically, to obtain a picture of "polyclonal" reactivity as is the situation in humans. It describes the structures of four AAV-antibody complexes determined by cryo-electron microscopy and image reconstruction, increasing the number of mapped epitopes to four and three, respectively, for AAV1 and AAV5, two vectors currently in clinical trials. The results presented provide information essential for generating antigenic escape vectors to overcome a critical challenge remaining in the optimization of this highly promising vector delivery system.
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Four levels of hierarchical organization, including noncovalent chainmail, brace the mature tumor herpesvirus capsid against pressurization. Structure 2014; 22:1385-98. [PMID: 25220471 DOI: 10.1016/j.str.2014.05.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 05/25/2014] [Accepted: 05/28/2014] [Indexed: 11/24/2022]
Abstract
Like many double-stranded DNA viruses, tumor gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus withstand high internal pressure. Bacteriophage HK97 uses covalent chainmail for this purpose, but how this is achieved noncovalently in the much larger gammaherpesvirus capsid is unknown. Our cryoelectron microscopy structure of a gammaherpesvirus capsid reveals a hierarchy of four levels of organization: (1) Within a hexon capsomer, each monomer of the major capsid protein (MCP), 1,378 amino acids and six domains, interacts with its neighboring MCPs at four sites. (2) Neighboring capsomers are linked in pairs by MCP dimerization domains and in groups of three by heterotrimeric triplex proteins. (3) Small (∼280 amino acids) HK97-like domains in MCP monomers alternate with triplex heterotrimers to form a belt that encircles each capsomer. (4) One hundred sixty-two belts concatenate to form noncovalent chainmail. The triplex heterotrimer orchestrates all four levels and likely drives maturation to an angular capsid that can withstand pressurization.
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Nibert ML, Ghabrial SA, Maiss E, Lesker T, Vainio EJ, Jiang D, Suzuki N. Taxonomic reorganization of family Partitiviridae and other recent progress in partitivirus research. Virus Res 2014; 188:128-41. [DOI: 10.1016/j.virusres.2014.04.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 10/25/2022]
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Encapsidated hepatitis B virus reverse transcriptase is poised on an ordered RNA lattice. Proc Natl Acad Sci U S A 2014; 111:11329-34. [PMID: 25034253 DOI: 10.1073/pnas.1321424111] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Assembly of a hepatitis B virus (HBV) virion begins with the formation of an RNA-filled core composed of a symmetrical capsid (built of core protein), viral pregenomic RNA, and viral reverse transcriptase. To generate the circular dsDNA genome of HBV, reverse transcription requires multiple template switches within the confines of the capsid. To date, most anti-HBV therapeutics target this reverse transcription process. The detailed molecular mechanisms of this crucial process are poorly understood because of the lack of structural information. We hypothesized that capsid, RNA, and viral reverse transcriptase would need a precise geometric organization to accomplish reverse transcription. Here we present the asymmetric structure of authentic RNA-filled cores, determined to 14.5-Å resolution from cryo-EM data. Capsid and RNA are concentric. On the interior of the RNA, we see a distinct donut-like density, assigned to viral reverse transcriptase, which pins the viral pregenomic RNA to the capsid inner surface. The observation of a unique ordered structure inside the core suggests that assembly and the first steps of reverse transcription follow a single, determinate pathway and strongly suggests that all subsequent steps in DNA synthesis do as well.
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Naim S, Brown JK, Nibert ML. Genetic diversification of penaeid shrimp infectious myonecrosis virus between Indonesia and Brazil. Virus Res 2014; 189:97-105. [PMID: 24874195 PMCID: PMC7114510 DOI: 10.1016/j.virusres.2014.05.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/15/2014] [Accepted: 05/16/2014] [Indexed: 11/26/2022]
Abstract
Infectious myonecrosis virus (IMNV) is a pathogen of penaeid shrimp, most notably the whiteleg shrimp Litopenaeus vannamei. First discovered in L. vannamei from Brazilian aquaculture farms in 2003, IMNV was additionally confirmed in L. vannamei from Indonesian farms in 2006 and has since been found in numerous provinces there. Only two complete sequences of IMNV strains have been reported to date, one strain from the Brazilian state of Piauí collected in 2003 and another from the Indonesian province of East Java collected in 2006. In this study, we determined the complete sequences of two additional Indonesian strains, one from Lampung province collected in 2011 and another from East Java province collected in 2012. We also determined partial sequences for six other strains to enhance phylogenetic comparisons, which have heretofore been limited by the small number of reported sequences, including only one for an Indonesian strain. The new results demonstrate clear genetic diversification of IMNV between Indonesia and Brazil, as well as within Indonesia. Analyses of conserved sequence motifs suggest a revised RNA pseudoknot prediction for ribosomal frameshifting.
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Affiliation(s)
- Sidrotun Naim
- Department of Microbiology & Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Center for Sustainable Aquaculture & Pathology Studies, Surya University, Banten 15810, Indonesia.
| | - Judith K Brown
- School of Plant Sciences, University of Arizona, 1140 E. South Campus Drive, Tucson, AZ 85721, USA.
| | - Max L Nibert
- Department of Microbiology & Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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Alphonse S, Arnold JJ, Bhattacharya S, Wang H, Kloss B, Cameron CE, Ghose R. Cystoviral polymerase complex protein P7 uses its acidic C-terminal tail to regulate the RNA-directed RNA polymerase P2. J Mol Biol 2014; 426:2580-93. [PMID: 24813120 DOI: 10.1016/j.jmb.2014.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/25/2014] [Accepted: 04/30/2014] [Indexed: 01/24/2023]
Abstract
In bacteriophages of the cystovirus family, the polymerase complex (PX) encodes a 75-kDa RNA-directed RNA polymerase (P2) that transcribes the double-stranded RNA genome. Also a constituent of the PX is the essential protein P7 that, in addition to accelerating PX assembly and facilitating genome packaging, plays a regulatory role in transcription. Deletion of P7 from the PX leads to aberrant plus-strand synthesis suggesting its influence on the transcriptase activity of P2. Here, using solution NMR techniques and the P2 and P7 proteins from cystovirus ϕ12, we demonstrate their largely electrostatic interaction in vitro. Chemical shift perturbations on P7 in the presence of P2 suggest that this interaction involves the dynamic C-terminal tail of P7, more specifically an acidic cluster therein. Patterns of chemical shift changes induced on P2 by the P7 C-terminus resemble those seen in the presence of single-stranded RNA suggesting similarities in binding. This association between P2 and P7 reduces the affinity of the former toward template RNA and results in its decreased activity both in de novo RNA synthesis and in extending a short primer. Given the presence of C-terminal acidic tracts on all cystoviral P7 proteins, the electrostatic nature of the P2/P7 interaction is likely conserved within the family and could constitute a mechanism through which P7 regulates transcription in cystoviruses.
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Affiliation(s)
- Sébastien Alphonse
- Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shibani Bhattacharya
- The New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - Hsin Wang
- Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Brian Kloss
- The New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ranajeet Ghose
- Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA; The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA.
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Zhu B, Yang C, Liu H, Cheng L, Song F, Zeng S, Huang X, Ji G, Zhu P. Identification of the active sites in the methyltransferases of a transcribing dsRNA virus. J Mol Biol 2014; 426:2167-74. [PMID: 24690366 PMCID: PMC7094362 DOI: 10.1016/j.jmb.2014.03.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/24/2014] [Accepted: 03/25/2014] [Indexed: 11/28/2022]
Abstract
Many double-stranded RNA (dsRNA) viruses are capable of transcribing and capping RNA within a stable icosahedral viral capsid. The turret of turreted dsRNA viruses belonging to the family Reoviridae is formed by five copies of the turret protein, which contains domains with both 7-N-methyltransferase and 2′-O-methyltransferase activities, and serves to catalyze the methylation reactions during RNA capping. Cypovirus of the family Reoviridae provides a good model system for studying the methylation reactions in dsRNA viruses. Here, we present the structure of a transcribing cypovirus to a resolution of ~ 3.8 Å by cryo-electron microscopy. The binding sites for both S-adenosyl-l-methionine and RNA in the two methyltransferases of the turret were identified. Structural analysis of the turret in complex with RNA revealed a pathway through which the RNA molecule reaches the active sites of the two methyltransferases before it is released into the cytoplasm. The pathway shows that RNA capping reactions occur in the active sites of different turret protein monomers, suggesting that RNA capping requires concerted efforts by at least three turret protein monomers. Thus, the turret structure provides novel insights into the precise mechanisms of RNA methylation. Structure of methyltransferases (MTases) and RNA in a transcribing dsRNA virus. S-Adenosyl-l-methionine/S-adenosyl-l-homocysteine was observed in the two MTases. A pathway was identified through which RNA reaches active sites of the two MTase. Methylation reactions require concerted efforts by turret protein monomers.
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Affiliation(s)
- Bin Zhu
- College of Physics and Information Science, Hunan Normal University, 36 Lushan Road, Changsha, Hunan 410081, China
| | - Chongwen Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hongrong Liu
- College of Physics and Information Science, Hunan Normal University, 36 Lushan Road, Changsha, Hunan 410081, China.
| | - Lingpeng Cheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.
| | - Feng Song
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Songjun Zeng
- College of Physics and Information Science, Hunan Normal University, 36 Lushan Road, Changsha, Hunan 410081, China
| | - Xiaojun Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Gang Ji
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Ping Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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Yan L, Liu H, Li X, Fang Q. The VP2 protein of grass carp reovirus (GCRV) expressed in a baculovirus exhibits RNA polymerase activity. Virol Sin 2014; 29:86-93. [PMID: 24643934 DOI: 10.1007/s12250-014-3366-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 01/03/2014] [Indexed: 10/25/2022] Open
Abstract
The double-shelled grass carp reovirus (GCRV) is capable of endogenous RNA transcription and processing. Genome sequence analysis has revealed that the protein VP2, encoded by gene segment 2 (S2), is the putative RNA-dependent RNA polymerase (RdRp). In previous work, we have ex-pressed the functional region of VP2 that is associated with RNA polymerase activity (denoted as rVP2(390-900)) in E. coli and have prepared a polyclonal antibody against VP2. To characterize the GCRV RNA polymerase, a recombinant full-length VP2 (rVP2) was first constructed and expressed in a baculovirus system, as a fusion protein with an attached His-tag. Immunofluorescence (IF) assays, together with immunoblot (IB) analyses from both expressed cell extracts and purified Histagged rVP2, showed that rVP2 was successfully expressed in Sf9 cells. Further characterization of the replicase activity showed that purified rVP2 and GCRV particles exhibited poly(C)-dependent poly(G) polymerase activity. The RNA enzymatic activity required the divalent cation Mg(2+), and was optimal at 28 °C. The results provide a foundation for further studies on the RNA polymerases of aquareoviruses during viral transcription and replication.
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Affiliation(s)
- Liming Yan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
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Abstract
This review is a partially personal account of the discovery of virus structure and its implication for virus function. Although I have endeavored to cover all aspects of structural virology and to acknowledge relevant individuals, I know that I have favored taking examples from my own experience in telling this story. I am anxious to apologize to all those who I might have unintentionally offended by omitting their work. The first knowledge of virus structure was a result of Stanley's studies of tobacco mosaic virus (TMV) and the subsequent X-ray fiber diffraction analysis by Bernal and Fankuchen in the 1930s. At about the same time it became apparent that crystals of small RNA plant and animal viruses could diffract X-rays, demonstrating that viruses must have distinct and unique structures. More advances were made in the 1950s with the realization by Watson and Crick that viruses might have icosahedral symmetry. With the improvement of experimental and computational techniques in the 1970s, it became possible to determine the three-dimensional, near-atomic resolution structures of some small icosahedral plant and animal RNA viruses. It was a great surprise that the protecting capsids of the first virus structures to be determined had the same architecture. The capsid proteins of these viruses all had a 'jelly-roll' fold and, furthermore, the organization of the capsid protein in the virus were similar, suggesting a common ancestral virus from which many of today's viruses have evolved. By this time a more detailed structure of TMV had also been established, but both the architecture and capsid protein fold were quite different to that of the icosahedral viruses. The small icosahedral RNA virus structures were also informative of how and where cellular receptors, anti-viral compounds, and neutralizing antibodies bound to these viruses. However, larger lipid membrane enveloped viruses did not form sufficiently ordered crystals to obtain good X-ray diffraction. Starting in the 1990s, these enveloped viruses were studied by combining cryo-electron microscopy of the whole virus with X-ray crystallography of their protein components. These structures gave information on virus assembly, virus neutralization by antibodies, and virus fusion with and entry into the host cell. The same techniques were also employed in the study of complex bacteriophages that were too large to crystallize. Nevertheless, there still remained many pleomorphic, highly pathogenic viruses that lacked the icosahedral symmetry and homogeneity that had made the earlier structural investigations possible. Currently some of these viruses are starting to be studied by combining X-ray crystallography with cryo-electron tomography.
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Abstract
Partitiviruses constitute one of the nine currently recognized families of viruses with encapsidated, double-stranded (ds)RNA genomes. The partitivirus genome is bisegmented, and each genome segment is packaged inside a separate viral capsid. Different partitiviruses infect plants, fungi, or protozoa. Recent studies have shed light on the three-dimensional structures of the virions of three representative fungal partitiviruses. These structures include a number of distinctive features, allowing informative comparisons with the structures of dsRNA viruses from other families. The results and comparisons suggest several new conclusions about the functions, assembly, and evolution of these viruses.
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49
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Capsid antibodies to different adeno-associated virus serotypes bind common regions. J Virol 2013; 87:9111-24. [PMID: 23760240 DOI: 10.1128/jvi.00622-13] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Interactions between viruses and the host antibody immune response are critical in the development and control of disease, and antibodies are also known to interfere with the efficacy of viral vector-based gene delivery. The adeno-associated viruses (AAVs) being developed as vectors for corrective human gene delivery have shown promise in clinical trials, but preexisting antibodies are detrimental to successful outcomes. However, the antigenic epitopes on AAV capsids remain poorly characterized. Cryo-electron microscopy and three-dimensional image reconstruction were used to define the locations of epitopes to which monoclonal fragment antibodies (Fabs) against AAV1, AAV2, AAV5, and AAV6 bind. Pseudoatomic modeling showed that, in each serotype, Fabs bound to a limited number of sites near the protrusions surrounding the 3-fold axes of the T=1 icosahedral capsids. For the closely related AAV1 and AAV6, a common Fab exhibited substoichiometric binding, with one Fab bound, on average, between two of the three protrusions as a consequence of steric crowding. The other AAV Fabs saturated the capsid and bound to the walls of all 60 protrusions, with the footprint for the AAV5 antibody extending toward the 5-fold axis. The angle of incidence for each bound Fab on the AAVs varied and resulted in significant differences in how much of each viral capsid surface was occluded beyond the Fab footprints. The AAV-antibody interactions showed a common set of footprints that overlapped some known receptor-binding sites and transduction determinants, thus suggesting potential mechanisms for virus neutralization by the antibodies.
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Abstract
The flagellated protozoan Trichomonas vaginalis is an obligate human genitourinary parasite and the most frequent cause of sexually transmitted disease worldwide. Most clinical isolates of T. vaginalis are persistently infected with one or more double-stranded RNA (dsRNA) viruses from the genus Trichomonasvirus, family Totiviridae, which appear to influence not only protozoan biology but also human disease. Here we describe the three-dimensional structure of Trichomonas vaginalis virus 1 (TVV1) virions, as determined by electron cryomicroscopy and icosahedral image reconstruction. The structure reveals a T = 1 capsid comprising 120 subunits, 60 in each of two nonequivalent positions, designated A and B, as previously observed for fungal Totiviridae family members. The putative protomer is identified as an asymmetric AB dimer consistent with either decamer or tetramer assembly intermediates. The capsid surface is notable for raised plateaus around the icosahedral 5-fold axes, with canyons connecting the 2- and 3-fold axes. Capsid-spanning channels at the 5-fold axes are unusually wide and may facilitate release of the viral genome, promoting dsRNA-dependent immunoinflammatory responses, as recently shown upon the exposure of human cervicovaginal epithelial cells to either TVV-infected T. vaginalis or purified TVV1 virions. Despite extensive sequence divergence, conservative features of the capsid reveal a helix-rich fold probably derived from an ancestor shared with fungal Totiviridae family members. Also notable are mass spectrometry results assessing the virion proteins as a complement to structure determination, which suggest that translation of the TVV1 RNA-dependent RNA polymerase in fusion with its capsid protein involves −2, and not +1, ribosomal frameshifting, an uncommonly found mechanism to date. Trichomonas vaginalis causes ~250 million new cases of sexually transmitted disease each year worldwide and is associated with serious complications, including premature birth and increased transmission of other pathogens, including HIV. It is an extracellular parasite that, in turn, commonly hosts infections with double-stranded RNA (dsRNA) viruses, trichomonasviruses, which appear to exacerbate disease through signaling of immunoinflammatory responses by human epithelial cells. Here we report the first three-dimensional structure of a trichomonasvirus, which is also the first such structure of any protozoan dsRNA virus; show that it has unusually wide channels at the capsid vertices, with potential for releasing the viral genome and promoting dsRNA-dependent responses by human cells; and provide evidence that it uses −2 ribosomal frameshifting, an uncommon mechanism, to translate its RNA polymerase in fusion with its capsid protein. These findings provide both mechanistic and translational insights concerning the role of trichomonasviruses in aggravating disease attributable to T. vaginalis.
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