1
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Knobler CM, Gelbart WM. How and why RNA genomes are (partially) ordered in viral capsids. Curr Opin Virol 2021; 52:203-210. [PMID: 34959081 DOI: 10.1016/j.coviro.2021.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/25/2021] [Indexed: 11/26/2022]
Abstract
There is a long and productive progression of X-ray crystallographic and electron microscopy studies establishing the structures of the spherical/icosahedral and cylindrical/helical capsids of a wide range of virus particles. This is because of the high degree of order - down to the Angstrom scale - in the secondary/tertiary/quaternary structure of the proteins making up the capsids. In stark contradistinction, very little is known about the structure of DNA or RNA genomes inside these capsids. This is because of the relatively large extent of disorder in the confined DNA or RNA, due to several fundamental reasons: topological defects in the DNA case, and secondary/tertiary structural disorder in the RNA case. In this article we discuss the range of partial order associated with the encapsidated genomes of single-stranded RNA viruses, focusing on the contrast between mono-partite and multi-partite viruses and on the effects of sequence-specific and non-specific interactions between RNA and capsid proteins.
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Affiliation(s)
- Charles M Knobler
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, United States
| | - William M Gelbart
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, United States; Molecular Biology Institute, UCLA, United States; California NanoSystems Institute, UCLA, United States.
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2
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RNA Structures and Their Role in Selective Genome Packaging. Viruses 2021; 13:v13091788. [PMID: 34578369 PMCID: PMC8472981 DOI: 10.3390/v13091788] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution.
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3
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Naitow H, Hamaguchi T, Maki-Yonekura S, Isogai M, Yoshikawa N, Yonekura K. Apple latent spherical virus structure with stable capsid frame supports quasi-stable protrusions expediting genome release. Commun Biol 2020; 3:488. [PMID: 32887929 PMCID: PMC7474077 DOI: 10.1038/s42003-020-01217-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 08/11/2020] [Indexed: 01/30/2023] Open
Abstract
Picorna-like plant viruses are non-enveloped RNA spherical viruses of ~30 nm. Part of the survival of these viruses depends on their capsid being stable enough to harbour the viral genome and yet malleable enough to allow its release. However, molecular mechanisms remain obscure. Here, we report a structure of a picorna-like plant virus, apple latent spherical virus, at 2.87 Å resolution by single-particle cryo-electron microscopy (cryo-EM) with a cold-field emission beam. The cryo-EM map reveals a unique structure composed of three capsid proteins Vp25, Vp20, and Vp24. Strikingly Vp25 has a long N-terminal extension, which substantially stabilises the capsid frame of Vp25 and Vp20 subunits. Cryo-EM images also resolve RNA genome leaking from a pentameric protrusion of Vp24 subunits. The structures and observations suggest that genome release occurs through occasional opening of the Vp24 subunits, possibly suppressed to a low frequency by the rigid frame of the other subunits.
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Affiliation(s)
- Hisashi Naitow
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Saori Maki-Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Masamichi Isogai
- Plant Pathology Laboratory, Faculty of Agriculture, Iwate University, Ueda 3-chome 18-8, Morioka, Iwate, 020-8550, Japan
| | - Nobuyuki Yoshikawa
- Agri-Innovation Center, Iwate University, Ueda 3-chome 18-8, Morioka, Iwate, 020-8550, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan. .,Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
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4
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Hesketh EL, Meshcheriakova Y, Thompson RF, Lomonossoff GP, Ranson NA. The structures of a naturally empty cowpea mosaic virus particle and its genome-containing counterpart by cryo-electron microscopy. Sci Rep 2017; 7:539. [PMID: 28373698 PMCID: PMC5428714 DOI: 10.1038/s41598-017-00533-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/28/2017] [Indexed: 11/09/2022] Open
Abstract
Cowpea mosaic virus (CPMV) is a picorna-like plant virus. As well as an intrinsic interest in CPMV as a plant pathogen, CPMV is of major interest in biotechnology applications such as nanotechnology. Here, we report high resolution cryo electron microscopy (cryo-EM) maps of wild type CPMV containing RNA-2, and of naturally-formed empty CPMV capsids. The resolution of these structures is sufficient to visualise large amino acids. We have refined an atomic model for each map and identified an essential amino acid involved in genome encapsidation. This work has furthered our knowledge of Picornavirales genome encapsidation and will assist further work in the development of CPMV as a biotechnological tool.
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Affiliation(s)
- Emma L Hesketh
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Yulia Meshcheriakova
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - George P Lomonossoff
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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5
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Rolfsson Ó, Middleton S, Manfield IW, White SJ, Fan B, Vaughan R, Ranson NA, Dykeman E, Twarock R, Ford J, Kao CC, Stockley PG. Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2. J Mol Biol 2016; 428:431-48. [PMID: 26608810 PMCID: PMC4751978 DOI: 10.1016/j.jmb.2015.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/06/2015] [Accepted: 11/08/2015] [Indexed: 01/20/2023]
Abstract
Using cross-linking coupled to matrix-assisted laser desorption/ionization mass spectrometry and CLIP-Seq sequencing, we determined the peptide and oligonucleotide sequences at the interfaces between the capsid proteins and the genomic RNA of bacteriophage MS2. The results suggest that the same coat protein (CP)-RNA and maturation protein (MP)-RNA interfaces are used in every viral particle. The portions of the viral RNA in contact with CP subunits span the genome, consistent with a large number of discrete and similar contacts within each particle. Many of these sites match previous predictions of the locations of multiple, dispersed and degenerate RNA sites with cognate CP affinity termed packaging signals (PSs). Chemical RNA footprinting was used to compare the secondary structures of protein-free genomic fragments and the RNA in the virion. Some PSs are partially present in protein-free RNA but others would need to refold from their dominant solution conformations to form the contacts identified in the virion. The RNA-binding peptides within the MP map to two sections of the N-terminal half of the protein. Comparison of MP sequences from related phages suggests a similar arrangement of RNA-binding sites, although these N-terminal regions have only limited sequence conservation. In contrast, the sequences of the C-termini are highly conserved, consistent with them encompassing pilin-binding domains required for initial contact with host cells. These results provide independent and unambiguous support for the assembly of MS2 virions via a PS-mediated mechanism involving a series of induced-fit viral protein interactions with RNA.
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Affiliation(s)
- Óttar Rolfsson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Stefani Middleton
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA; The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Baochang Fan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Robert Vaughan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Eric Dykeman
- Department of Biology and Mathematics and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Biology and Mathematics and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - James Ford
- The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - C Cheng Kao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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6
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Mechanisms of assembly and genome packaging in an RNA virus revealed by high-resolution cryo-EM. Nat Commun 2015; 6:10113. [PMID: 26657148 PMCID: PMC4682053 DOI: 10.1038/ncomms10113] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/03/2015] [Indexed: 12/14/2022] Open
Abstract
Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of Picornavirales capsids, relatively little is known about the mechanisms of capsid assembly and genome encapsidation. Here we have determined cryo-electron microscopy reconstructions for the wild-type virus and an empty virus-like particle, to 3.4 Å and 3.0 Å resolution, respectively, and built de novo atomic models of their capsids. These new structures reveal the C-terminal region of the small coat protein subunit, which is essential for virus assembly and which was missing from previously determined crystal structures, as well as residues that bind to the viral genome. These observations allow us to develop a new model for genome encapsidation and capsid assembly. Little is known about how the plant-infecting cowpea mosaic virus (CPMV)—an invaluable tool in several biotechnology applications—packages its single-strand RNA genome into the capsid. Here the authors present two high-resolution cryo-EM structures of CPMV and a new model for RNA recognition and capsid assembly.
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7
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Geraets JA, Dykeman EC, Stockley PG, Ranson NA, Twarock R. Asymmetric genome organization in an RNA virus revealed via graph-theoretical analysis of tomographic data. PLoS Comput Biol 2015; 11:e1004146. [PMID: 25793998 PMCID: PMC4368512 DOI: 10.1371/journal.pcbi.1004146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/22/2015] [Indexed: 11/18/2022] Open
Abstract
Cryo-electron microscopy permits 3-D structures of viral pathogens to be determined in remarkable detail. In particular, the protein containers encapsulating viral genomes have been determined to high resolution using symmetry averaging techniques that exploit the icosahedral architecture seen in many viruses. By contrast, structure determination of asymmetric components remains a challenge, and novel analysis methods are required to reveal such features and characterize their functional roles during infection. Motivated by the important, cooperative roles of viral genomes in the assembly of single-stranded RNA viruses, we have developed a new analysis method that reveals the asymmetric structural organization of viral genomes in proximity to the capsid in such viruses. The method uses geometric constraints on genome organization, formulated based on knowledge of icosahedrally-averaged reconstructions and the roles of the RNA-capsid protein contacts, to analyse cryo-electron tomographic data. We apply this method to the low-resolution tomographic data of a model virus and infer the unique asymmetric organization of its genome in contact with the protein shell of the capsid. This opens unprecedented opportunities to analyse viral genomes, revealing conserved structural features and mechanisms that can be targeted in antiviral drug design.
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Affiliation(s)
- James A Geraets
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
| | - Eric C Dykeman
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Reidun Twarock
- York Centre for Complex Systems Analysis, University of York, York, United Kingdom
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8
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Ravantti J, Bamford D, Stuart DI. Automatic comparison and classification of protein structures. J Struct Biol 2013; 183:47-56. [DOI: 10.1016/j.jsb.2013.05.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 05/02/2013] [Accepted: 05/08/2013] [Indexed: 12/18/2022]
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9
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Dykeman EC, Stockley PG, Twarock R. Packaging signals in two single-stranded RNA viruses imply a conserved assembly mechanism and geometry of the packaged genome. J Mol Biol 2013; 425:3235-49. [PMID: 23763992 DOI: 10.1016/j.jmb.2013.06.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/22/2013] [Accepted: 06/03/2013] [Indexed: 11/29/2022]
Abstract
The current paradigm for assembly of single-stranded RNA viruses is based on a mechanism involving non-sequence-specific packaging of genomic RNA driven by electrostatic interactions. Recent experiments, however, provide compelling evidence for sequence specificity in this process both in vitro and in vivo. The existence of multiple RNA packaging signals (PSs) within viral genomes has been proposed, which facilitates assembly by binding coat proteins in such a way that they promote the protein-protein contacts needed to build the capsid. The binding energy from these interactions enables the confinement or compaction of the genomic RNAs. Identifying the nature of such PSs is crucial for a full understanding of assembly, which is an as yet untapped potential drug target for this important class of pathogens. Here, for two related bacterial viruses, we determine the sequences and locations of their PSs using Hamiltonian paths, a concept from graph theory, in combination with bioinformatics and structural studies. Their PSs have a common secondary structure motif but distinct consensus sequences and positions within the respective genomes. Despite these differences, the distributions of PSs in both viruses imply defined conformations for the packaged RNA genomes in contact with the protein shell in the capsid, consistent with a recent asymmetric structure determination of the MS2 virion. The PS distributions identified moreover imply a preferred, evolutionarily conserved assembly pathway with respect to the RNA sequence with potentially profound implications for other single-stranded RNA viruses known to have RNA PSs, including many animal and human pathogens.
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Affiliation(s)
- Eric C Dykeman
- Departments of Mathematics and Biology and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, UK
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10
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Ren J, Wang X, Hu Z, Gao Q, Sun Y, Li X, Porta C, Walter TS, Gilbert RJ, Zhao Y, Axford D, Williams M, McAuley K, Rowlands DJ, Yin W, Wang J, Stuart DI, Rao Z, Fry EE. Picornavirus uncoating intermediate captured in atomic detail. Nat Commun 2013; 4:1929. [PMID: 23728514 PMCID: PMC3709478 DOI: 10.1038/ncomms2889] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Accepted: 04/13/2013] [Indexed: 01/07/2023] Open
Abstract
It remains largely mysterious how the genomes of non-enveloped eukaryotic viruses are transferred across a membrane into the host cell. Picornaviruses are simple models for such viruses, and initiate this uncoating process through particle expansion, which reveals channels through which internal capsid proteins and the viral genome presumably exit the particle, although this has not been clearly seen until now. Here we present the atomic structure of an uncoating intermediate for the major human picornavirus pathogen CAV16, which reveals VP1 partly extruded from the capsid, poised to embed in the host membrane. Together with previous low-resolution results, we are able to propose a detailed hypothesis for the ordered egress of the internal proteins, using two distinct sets of channels through the capsid, and suggest a structural link to the condensed RNA within the particle, which may be involved in triggering RNA release.
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Affiliation(s)
- Jingshan Ren
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK,These authors contributed equally to this work
| | - Xiangxi Wang
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China,These authors contributed equally to this work
| | - Zhongyu Hu
- National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Beijing 100050, China
| | - Qiang Gao
- Sinovac Biotech Co., Ltd, Beijing 100085, China
| | - Yao Sun
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Xuemei Li
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Claudine Porta
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Thomas S. Walter
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Robert J. Gilbert
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Yuguang Zhao
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
| | - Danny Axford
- Diamond Light Sources, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Mark Williams
- Diamond Light Sources, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Katherine McAuley
- Diamond Light Sources, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - David J. Rowlands
- Faculty of Biological Sciences, Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Weidong Yin
- Sinovac Biotech Co., Ltd, Beijing 100085, China
| | - Junzhi Wang
- National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Beijing 100050, China,
| | - David I. Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK,Diamond Light Sources, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK,
| | - Zihe Rao
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China,Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, 100084, China,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Elizabeth E. Fry
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK
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11
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Agirre J, Goret G, LeGoff M, Sánchez-Eugenia R, Marti GA, Navaza J, Guérin DMA, Neumann E. Cryo-electron microscopy reconstructions of triatoma virus particles: a clue to unravel genome delivery and capsid disassembly. J Gen Virol 2013; 94:1058-1068. [PMID: 23288423 DOI: 10.1099/vir.0.048553-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Triatoma virus (TrV) is a member of the insect virus family Dicistroviridae and consists of a small, non-enveloped capsid that encloses its positive-sense ssRNA genome. Using cryo-transmission electron microscopy and three-dimensional reconstruction techniques combined with fitting of the available crystallographic models, this study analysed the capsids corresponding to mature and several RNA-empty TrV particles. After genome release, the resulting reconstruction of the empty capsids displayed no prominent conformational changes with respect to the full virion capsid. The results showed that RNA delivery led to empty capsids with an apparent overall intact protein shell and suggested that, in a subsequent step, empty capsids disassemble into small symmetrical particles. Contrary to what is observed upon genome release in mammalian picornaviruses, the empty TrV capsid maintained a protein shell thickness and size identical to that in full virions.
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Affiliation(s)
- J Agirre
- Fundación Biofísica Bizkaia, B° Sarriena S/N, 48940 Leioa, Bizkaia, Spain.,Unidad de Biofisica (CSIC, UPV/EHU), PO Box 644, E-48080 Bilbao, Spain
| | - G Goret
- IBS, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-UJF, 41 rue Jules Horowitz, F-38027 Grenoble, France
| | - M LeGoff
- IBS, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-UJF, 41 rue Jules Horowitz, F-38027 Grenoble, France
| | - R Sánchez-Eugenia
- Unidad de Biofisica (CSIC, UPV/EHU), PO Box 644, E-48080 Bilbao, Spain
| | - G A Marti
- Centro de Estudios Parasitológicos y de Vectores (CEPAVE-CCT-La Plata-CONICET-UNLP), 2#584 (1900) La Plata, Argentina
| | - J Navaza
- IBS, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-UJF, 41 rue Jules Horowitz, F-38027 Grenoble, France
| | - D M A Guérin
- Fundación Biofísica Bizkaia, B° Sarriena S/N, 48940 Leioa, Bizkaia, Spain.,Unidad de Biofisica (CSIC, UPV/EHU), PO Box 644, E-48080 Bilbao, Spain
| | - E Neumann
- IBS, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 CNRS-CEA-UJF, 41 rue Jules Horowitz, F-38027 Grenoble, France
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12
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Larsson DSD, van der Spoel D. Screening for the Location of RNA using the Chloride Ion Distribution in Simulations of Virus Capsids. J Chem Theory Comput 2012; 8:2474-83. [PMID: 26588976 DOI: 10.1021/ct3002128] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The complete structure of the genomic material inside a virus capsid remains elusive, although a limited amount of symmetric nucleic acid can be resolved in the crystal structure of 17 icosahedral viruses. The negatively charged sugar-phosphate backbone of RNA and DNA as well as the large positive charge of the interior surface of the virus capsids suggest that electrostatic complementarity is an important factor in the packaging of the genomes in these viruses. To test how much packing information is encoded by the electrostatic and steric envelope of the capsid interior, we performed extensive all-atom molecular dynamics (MD) simulations of virus capsids with explicit water molecules and solvent ions. The model systems were two small plant viruses in which significant amounts of RNA has been observed by X-ray crystallography: satellite tobacco mosaic virus (STMV, 62% RNA visible) and satellite tobacco necrosis virus (STNV, 34% RNA visible). Simulations of half-capsids of these viruses with no RNA present revealed that the binding sites of RNA correlated well with regions populated by chloride ions, suggesting that it is possible to screen for the binding sites of nucleic acids by determining the equilibrium distribution of negative ions. By including the crystallographically resolved RNA in addition to ions, we predicted the localization of the unresolved RNA in the viruses. Both viruses showed a hot-spot for RNA binding at the 5-fold symmetry axis. The MD simulations were compared to predictions of the chloride density based on nonlinear Poisson-Boltzmann equation (PBE) calculations with mobile ions. Although the predictions are superficially similar, the PBE calculations overestimate the ion concentration close to the capsid surface and underestimate it far away, mainly because protein dynamics is not taken into account. Density maps from chloride screening can be used to aid in building atomic models of packaged virus genomes. Knowledge of the principles of genome packaging might be exploited for both antiviral therapy and technological applications.
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Affiliation(s)
- Daniel S D Larsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , Box 596, SE-751 24 Uppsala, Sweden
| | - David van der Spoel
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , Box 596, SE-751 24 Uppsala, Sweden
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13
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Armored long RNA controls or standards for branched DNA assay for detection of human immunodeficiency virus type 1. J Clin Microbiol 2009; 47:2571-6. [PMID: 19494069 DOI: 10.1128/jcm.00232-09] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The branched DNA (bDNA) assay is a reliable method for quantifying the RNA of human immunodeficiency virus type 1 (HIV-1). The positive controls and standards for this assay for the detection of HIV-1 consist of naked RNA, which is susceptible to degradation by RNase. Armored RNA is a good candidate for an RNase-resistant positive control or standard. However, its use has been limited by the maximal length of the exogenous RNA packaged into virus-like particles by routine armored RNA technology. In the present study, we produced armored long RNA (armored L-RNA) controls or standards (AR-HIV-pol-3034b) for a bDNA assay of HIV-1 by increasing the amount and affinity of the pac sites (the pac site is a specific 19-nucleotide stem-loop region located at the 5' terminus of the MS2 bacteriophage replicase gene) by a one-plasmid double-expression system. AR-HIV-pol-3034b was completely resistant to DNase and RNase, was stable in normal human EDTA-preserved plasma at 4 degrees C for at least 6 months, and produced reproducible, linear results in the Versant HIV-1 RNA 3.0 assay. In conclusion, AR-HIV-pol-3034b could act as a positive control or standard in a bDNA assay for the detection of HIV-1. In addition, the one-plasmid double-expression system can be used as a better platform than the one-plasmid expression system and the two-plasmid coexpression system for expressing armored L-RNA.
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14
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Toropova K, Basnak G, Twarock R, Stockley PG, Ranson NA. The three-dimensional structure of genomic RNA in bacteriophage MS2: implications for assembly. J Mol Biol 2007; 375:824-36. [PMID: 18048058 DOI: 10.1016/j.jmb.2007.08.067] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 08/23/2007] [Indexed: 10/22/2022]
Abstract
Using cryo-electron microscopy, single particle image processing and three-dimensional reconstruction with icosahedral averaging, we have determined the three-dimensional solution structure of bacteriophage MS2 capsids reassembled from recombinant protein in the presence of short oligonucleotides. We have also significantly extended the resolution of the previously reported structure of the wild-type MS2 virion. The structures of recombinant MS2 capsids reveal clear density for bound RNA beneath the coat protein binding sites on the inner surface of the T=3 MS2 capsid, and show that a short extension of the minimal assembly initiation sequence that promotes an increase in the efficiency of assembly, interacts with the protein capsid forming a network of bound RNA. The structure of the wild-type MS2 virion at approximately 9 A resolution reveals icosahedrally ordered density encompassing approximately 90% of the single-stranded RNA genome. The genome in the wild-type virion is arranged as two concentric shells of density, connected along the 5-fold symmetry axes of the particle. This novel RNA fold provides new constraints for models of viral assembly.
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Affiliation(s)
- Katerina Toropova
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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Bahadur RP, Rodier F, Janin J. A Dissection of the Protein–Protein Interfaces in Icosahedral Virus Capsids. J Mol Biol 2007; 367:574-90. [PMID: 17270209 DOI: 10.1016/j.jmb.2006.12.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2006] [Revised: 12/11/2006] [Accepted: 12/14/2006] [Indexed: 10/23/2022]
Abstract
We selected 49 icosahedral virus capsids whose crystal structures are reported in the Protein Data Bank. They belong to the T=1, T=3, pseudo T=3 and other lattice types. We identified in them 779 unique interfaces between pairs of subunits, all repeated by icosahedral symmetry. We analyzed the geometric and physical chemical properties of these interfaces and compared with interfaces in protein-protein complexes and homodimeric proteins, and with crystal packing contacts. The capsids contain one to 16 subunits implicated in three to 66 unique interfaces. Each subunit loses 40-60% of its accessible surface in contacts with an average of 8.5 neighbors. Many of the interfaces are very large with a buried surface area (BSA) that can exceed 10,000 A(2), yet 39% are small with a BSA<800 A(2) comparable to crystal packing contacts. Pairwise capsid interfaces overlap, so that one-third of the residues are part of more than one interface. Those with a BSA>800 A(2) resemble homodimer interfaces in their chemical composition. Relative to the protein surface, they are non-polar, enriched in aliphatic residues and depleted of charged residues, but not of neutral polar residues. They contain one H-bond per about 200 A(2) BSA. Small capsid interfaces (BSA<800 A(2)) are only slightly more polar. They have a similar amino acid composition, but they bury fewer atoms and contain fewer H-bonds for their size. Geometric parameters that estimate the quality of the atomic packing suggest that the small capsid interfaces are loosely packed like crystal packing contacts, whereas the larger interfaces are close-packed as in protein-protein complexes and homodimers. We discuss implications of these findings on the mechanism of capsid assembly, assuming that the larger interfaces form first to yield stable oligomeric species (capsomeres), and that medium-size interfaces allow the stepwise addition of capsomeres to build larger intermediates.
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Affiliation(s)
- Ranjit Prasad Bahadur
- Yeast Structural Genomics, IBBMC Université Paris-Sud, CNRS UMR 8619, 91405-Orsay, France
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Abstract
Despite tremendous advances in high-resolution structure determination of virus particles, the organization of encapsidated genomes and their role during assembly are poorly understood. This article summarizes recent insights from structural, biochemical, and genetic analyses of icosahedral viruses that contain single-stranded, positive-sense RNA genomes. X-ray crystallography of several viruses in this category has provided tantalizing glimpses of portions of the packaged nucleic acid, contributing crucial information on how the genome might be folded within the virion. This information combined with theoretical considerations and data from molecular approaches suggests mechanisms by which coat proteins interact with genomic RNA to shape it into a conformation that is compatible with the geometry of the virion. It appears that RNA, in addition to its function as a repository for genetic information, plays an important structural role during assembly and can on occasion override the ability of the coat protein to form a particle with defined icosahedral symmetry.
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Affiliation(s)
- Anette Schneemann
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
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Freddolino PL, Arkhipov AS, Larson SB, McPherson A, Schulten K. Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus. Structure 2006; 14:437-49. [PMID: 16531228 DOI: 10.1016/j.str.2005.11.014] [Citation(s) in RCA: 263] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Revised: 11/22/2005] [Accepted: 11/22/2005] [Indexed: 11/16/2022]
Abstract
This work presents an all-atom molecular dynamics simulation of a complete virus, the satellite tobacco mosaic virus. Simulations with up to 1 million atoms for over 50 ns demonstrate the stability of the entire virion and of the RNA core alone, while the capsid without RNA exhibits a pronounced instability. Physical properties of the simulated virus particle including electrostatic potential, radial distribution of viral components, and patterns of correlated motion are analyzed, and the implications for the assembly and infection mechanism of the virus are discussed.
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Affiliation(s)
- Peter L Freddolino
- Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
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Hartley CJ, Greenwood DR, Gilbert RJC, Masoumi A, Gordon KHJ, Hanzlik TN, Fry EE, Stuart DI, Scotti PD. Kelp fly virus: a novel group of insect picorna-like viruses as defined by genome sequence analysis and a distinctive virion structure. J Virol 2005; 79:13385-98. [PMID: 16227260 PMCID: PMC1262566 DOI: 10.1128/jvi.79.21.13385-13398.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Accepted: 08/05/2005] [Indexed: 11/20/2022] Open
Abstract
The complete genomic sequence of kelp fly virus (KFV), originally isolated from the kelp fly, Chaetocoelopa sydneyensis, has been determined. Analyses of its genomic and structural organization and phylogeny show that it belongs to a hitherto undescribed group within the picorna-like virus superfamily. The single-stranded genomic RNA of KFV is 11,035 nucleotides in length and contains a single large open reading frame encoding a polypeptide of 3,436 amino acids with 5' and 3' untranslated regions of 384 and 343 nucleotides, respectively. The predicted amino acid sequence of the polypeptide shows that it has three regions. The N-terminal region contains sequences homologous to the baculoviral inhibitor of apoptosis repeat domain, an inhibitor of apoptosis commonly found in animals and in viruses with double-stranded DNA genomes. The second region contains at least two capsid proteins. The third region has three sequence motifs characteristic of replicase proteins of many plant and animal viruses, including a helicase, a 3C chymotrypsin-like protease, and an RNA-dependent RNA polymerase. Phylogenetic analysis of the replicase motifs shows that KFV forms a distinct and distant taxon within the picorna-like virus superfamily. Cryoelectron microscopy and image reconstruction of KFV to a resolution of 15 A reveals an icosahedral structure, with each of its 12 fivefold vertices forming a turret from the otherwise smooth surface of the 20-A-thick capsid. The architecture of the KFV capsid is unique among the members of the picornavirus superfamily for which structures have previously been determined.
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Affiliation(s)
- C J Hartley
- CSIRO Entomology, GPO Box 1700, Acton, ACT 2601, Australia.
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Affiliation(s)
- Tianwei Lin
- Department of Molecular Biology, Center for Integrative Molecular Biosciences, Scripps Research Institute, La Jolla, California 92037, USA
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