101
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Abstract
Bluetongue is a vector-borne viral disease of ruminants that is endemic in tropical and subtropical countries. Since 1998 the virus has also appeared in Europe. Partly due to the seriousness of the disease, bluetongue virus (BTV), a member of genus Orbivirus within the family Reoviridae, has been a subject of intense molecular study for the last three decades and is now one of the best understood viruses at the molecular and structural levels. BTV is a complex non-enveloped virus with seven structural proteins arranged in two capsids and a genome of ten double-stranded (ds) RNA segments. Shortly after cell entry, the outer capsid is lost to release an inner capsid (the core) which synthesizes capped mRNAs from each genomic segment, extruding them into the cytoplasm. This requires the efficient co-ordination of a number of enzymes, including helicase, polymerase and RNA capping activities. This review will focus on our current understanding of these catalytic proteins as derived from the use of recombinant proteins, combined with functional assays and the in vitro reconstitution of the transcription/replication complex. In some cases, 3D structures have complemented this analysis to reveal the fine structural detail of these proteins. The combined activities of the core enzymes produce infectious transcripts necessary and sufficient to initiate BTV infection. Such infectious transcripts can now be synthesized wholly in vitro and, when introduced into cells by transfection, lead to the recovery of infectious virus. Future studies thus hold the possibility of analysing the consequence of mutation in a replicating virus system.
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Affiliation(s)
- Polly Roy
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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102
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Ochoa WF, Havens WM, Sinkovits RS, Nibert ML, Ghabrial SA, Baker TS. Partitivirus structure reveals a 120-subunit, helix-rich capsid with distinctive surface arches formed by quasisymmetric coat-protein dimers. Structure 2008; 16:776-86. [PMID: 18462682 DOI: 10.1016/j.str.2008.02.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 02/07/2008] [Accepted: 02/09/2008] [Indexed: 11/30/2022]
Abstract
Two distinct partitiviruses, Penicillium stoloniferum viruses S and F, can be isolated from the fungus Penicillium stoloniferum. The bisegmented dsRNA genomes of these viruses are separately packaged in icosahedral capsids containing 120 coat-protein subunits. We used transmission electron cryomicroscopy and three-dimensional image reconstruction to determine the structure of Penicillium stoloniferum virus S at 7.3 A resolution. The capsid, approximately 350 A in outer diameter, contains 12 pentons, each of which is topped by five arched protrusions. Each of these protrusions is, in turn, formed by a quasisymmetric dimer of coat protein, for a total of 60 such dimers per particle. The density map shows numerous tubular features, characteristic of alpha helices and consistent with secondary structure predictions for the coat protein. This three-dimensional structure of a virus from the family Partitiviridae exhibits both similarities to and differences from the so-called "T = 2" capsids of other dsRNA viruses.
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Affiliation(s)
- Wendy F Ochoa
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, USA
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103
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Cheng L, Fang Q, Shah S, Atanasov IC, Zhou ZH. Subnanometer-resolution structures of the grass carp reovirus core and virion. J Mol Biol 2008; 382:213-22. [PMID: 18625243 DOI: 10.1016/j.jmb.2008.06.075] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 06/22/2008] [Accepted: 06/25/2008] [Indexed: 01/10/2023]
Abstract
Grass carp reovirus (GCRV) is a member of the Aquareovirus genus of the family Reoviridae, a large family of double-stranded RNA (dsRNA) viruses infecting plants, insects, fishes and mammals. We report the first subnanometer-resolution three-dimensional structures of both GCRV core and virion by cryoelectron microscopy. These structures have allowed the delineation of interactions among the over 1000 molecules in this enormous macromolecular machine and a detailed comparison with other dsRNA viruses at the secondary-structure level. The GCRV core structure shows that the inner proteins have strong structural similarities with those of orthoreoviruses even at the level of secondary-structure elements, indicating that the structures involved in viral dsRNA interaction and transcription are highly conserved. In contrast, the level of similarity in structures decreases in the proteins situated in the outer layers of the virion. The proteins involved in host recognition and attachment exhibit the least similarities to other members of Reoviridae. Furthermore, in GCRV, the RNA-translocating turrets are in an open state and lack a counterpart for the sigma1 protein situated on top of the close turrets observed in mammalian orthoreovirus. Interestingly, the distribution and the organization of GCRV core proteins resemble those of the cytoplasmic polyhedrosis virus, a cypovirus and the structurally simplest member of the Reoviridae family. Our results suggest that GCRV occupies a unique structure niche between the simpler cypoviruses and the considerably more complex mammalian orthoreovirus, thus providing an important model for understanding the structural and functional conservation and diversity of this enormous family of dsRNA viruses.
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Affiliation(s)
- Lingpeng Cheng
- Department of Microbiology, Immunology and Molecular Genetics, The University of California at Los Angeles, CA 90095-7364, USA
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104
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Zhou ZH. Towards atomic resolution structural determination by single-particle cryo-electron microscopy. Curr Opin Struct Biol 2008; 18:218-28. [PMID: 18403197 PMCID: PMC2714865 DOI: 10.1016/j.sbi.2008.03.004] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 03/01/2008] [Accepted: 03/04/2008] [Indexed: 11/19/2022]
Abstract
Recent advances in cryo-electron microscopy and single-particle reconstruction (collectively referred to as 'cryoEM') have made it possible to determine the three-dimensional (3D) structures of several macromolecular complexes at near-atomic resolution ( approximately 3.8-4.5A). These achievements were accomplished by overcoming the challenges in sample handling, instrumentation, image processing, and model building. At near-atomic resolution, many detailed structural features can be resolved, such as the turns and deep grooves of helices, strand separation in beta sheets, and densities for loops and bulky amino acid side chains. Such structural data of the cytoplasmic polyhedrosis virus (CPV), the Epsilon 15 bacteriophage and the GroEL complex have provided valuable constraints for atomic model building using integrative tools, thus significantly enhancing the value of the cryoEM structures. The CPV structure revealed a drastic conformational change from a helix to a beta hairpin associated with RNA packaging and replication, coupling of RNA processing and release, and the long sought-after polyhedrin-binding domain. These latest advances in single-particle cryoEM provide exciting opportunities for the 3D structural determination of viruses and macromolecular complexes that are either too large or too heterogeneous to be investigated by conventional X-ray crystallography or nuclear magnetic resonance (NMR) methods.
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Affiliation(s)
- Z Hong Zhou
- Department of Microbiology, Immunology & Molecular Genetics and the California NanoSystems Institute, University of California at Los Angeles, 237 BSRB, 615 Charles E. Young Dr. S., Los Angeles, CA 90095-7364, USA.
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105
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Functional mapping of bluetongue virus proteins and their interactions with host proteins during virus replication. Cell Biochem Biophys 2008; 50:143-57. [PMID: 18299997 DOI: 10.1007/s12013-008-9009-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2008] [Indexed: 10/22/2022]
Abstract
Bluetongue virus (BTV) is a double-stranded RNA (dsRNA) virus which is transmitted by blood-feeding gnats to wild and domestic ruminants, causing high morbidity and often high mortality. Partly due to this BTV has been in the forefront of molecular studies for last three decades and now represents one of the best understood viruses at the molecular and structural levels. BTV, like the other members of the Reoviridae family is a complex non-enveloped virus with seven structural proteins and a RNA genome consisting of 10 dsRNA segments of different sizes. In virus infected cells, three other virus encoded nonstructural proteins are synthesized. Significant recent advances have been made in understanding the structure-function relationships of BTV proteins and their interactions during virus assembly. By combining structural and molecular data it has been possible to make progress on the fundamental mechanisms used by the virus to invade, replicate in, and escape from, susceptible host cells. Data obtained from studies over a number of years have defined the key players in BTV entry, replication, assembly and egress. Specifically, it has been possible to determine the complex nature of the virion through three dimensional structure reconstructions; atomic structure of proteins and the internal capsid; the definition of the virus encoded enzymes required for RNA replication; the ordered assembly of the capsid shell and the protein sequestration required for it; and the role of three NS proteins in virus replication, assembly and release. Overall, this review demonstrates that the integration of structural, biochemical and molecular data is necessary to fully understand the assembly and replication of this complex RNA virus.
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106
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Sen A, Heymann JB, Cheng N, Qiao J, Mindich L, Steven AC. Initial location of the RNA-dependent RNA polymerase in the bacteriophage Phi6 procapsid determined by cryo-electron microscopy. J Biol Chem 2008; 283:12227-31. [PMID: 18287088 DOI: 10.1074/jbc.m710508200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA-dependent RNA polymerases (RdRPs) of Cystoviridae bacteriophages, like those of eukaryotic viruses of the Reoviridae, function inside the inner capsid shell in both replication and transcription. In bacteriophage Phi6, this inner shell is first assembled as an icosahedral procapsid with recessed 5-fold vertices that subsequently undergoes major structural changes during maturation. The tripartite genome is packaged as single-stranded RNA molecules via channels on the 5-fold vertices, and transcripts probably exit the mature capsid by the same route. The RdRP (protein P2) is assembled within the procapsid, and it was thought that it should be located on the 5-fold axes near the RNA entry and exit channels. To determine the initial location of the RdRP inside the procapsid of bacteriophage Phi6, we performed cryo-electron microscopy of wild type and mutant procapsids and complemented these data with biochemical determinations of copy numbers. We observe ring-like densities on the 3-fold axes that are strong in a mutant that has approximately 10 copies of P2 per particle; faint in wild type, reflecting the lower copy number of approximately 3; and completely absent in a P2-null mutant. The dimensions and shapes of these densities match those of the known crystal structure of the P2 monomer. We propose that, during maturation, the P2 molecules rotate to occupy positions closer to adjacent 5-fold vertices where they conduct replication and transcription.
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Affiliation(s)
- Anindito Sen
- Laboratory of Structural Biology Research, NIAMS, National Institutes of Health, Bethesda, Maryland 20892, USA
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107
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Conformational changes accompany activation of reovirus RNA-dependent RNA transcription. J Struct Biol 2008; 162:277-89. [PMID: 18321727 DOI: 10.1016/j.jsb.2008.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Revised: 12/07/2007] [Accepted: 01/17/2008] [Indexed: 12/28/2022]
Abstract
Many critical biologic processes involve dynamic interactions between proteins and nucleic acids. Such dynamic processes are often difficult to delineate by conventional static methods. For example, while a variety of nucleic acid polymerase structures have been determined at atomic resolution, the details of how some multi-protein transcriptase complexes actively produce mRNA, as well as conformational changes associated with activation of such complexes, remain poorly understood. The mammalian reovirus innermost capsid (core) manifests all enzymatic activities necessary to produce mRNA from each of the 10 encased double-stranded RNA genes. We used rapid freezing and electron cryo-microscopy to trap and visualize transcriptionally active reovirus core particles and compared them to inactive core images. Rod-like density centered within actively transcribing core spike channels was attributed to exiting nascent mRNA. Comparative radial density plots of active and inactive core particles identified several structural changes in both internal and external regions of the icosahedral core capsid. Inactive and transcriptionally active cores were partially digested with trypsin and identities of initial tryptic peptides determined by mass spectrometry. Differentially-digested peptides, which also suggest transcription-associated conformational changes, were placed within the known three-dimensional structures of major core proteins.
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108
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Fang Q, Seng EK, Dai W, Zhang LL. Construction and co-expression of grass carp reovirus VP6 protein and enhanced green fluorescence protein in the insect cells. Virol Sin 2008. [DOI: 10.1007/s12250-007-0038-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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109
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Abstract
Protein misfolding and the subsequent assembly of protein molecules into aggregates of various morphologies represent common mechanisms that link a number of important human diseases, known as protein-misfolding diseases. The current list of these disorders includes (but is not limited to) numerous neurodegenerative diseases, cataracts, arthritis, medullary carcinoma of the thyroid, late-onset diabetes mellitus, symptomatic (hemodialysis-related) beta(2)-microglobulin amyloidosis, arthritis and many other systemic, localized and familial amyloidoses. Progress in understanding protein-misfolding pathologies and in potential rational drug design aimed at the inhibition or reversal of protein aggregation depends on our ability to study the details of the misfolding process, to follow the aggregation process and to see and analyze the structure and mechanical properties of the aggregated particles. Nanoimaging provides a method to monitor the aggregation process, visualize protein aggregates and analyze their properties and provides fundamental knowledge of key factors that lead to protein misfolding and self-assembly in various protein-misfolding pathologies, therefore advancing medicine dramatically.
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Affiliation(s)
- Vladimir N Uversky
- Indiana University School of Medicine, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, IN, USA.
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110
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Murray KE, Nibert ML. Guanidine hydrochloride inhibits mammalian orthoreovirus growth by reversibly blocking the synthesis of double-stranded RNA. J Virol 2007; 81:4572-84. [PMID: 17301147 PMCID: PMC1900160 DOI: 10.1128/jvi.02106-06] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Millimolar concentrations of guanidine hydrochloride (GuHCl) are known to inhibit the replication of many plant and animal viruses having positive-sense RNA genomes. For example, GuHCl reversibly interacts with the nucleotide-binding region of poliovirus protein 2C(ATPase), resulting in a specific inhibition of viral negative-sense RNA synthesis. The use of GuHCl thereby allows for the spatiotemporal separation of poliovirus gene expression and RNA replication and provides a powerful tool to synchronize the initiation of negative-sense RNA synthesis during in vitro replication reactions. In the present study, we examined the effect of GuHCl on mammalian orthoreovirus (MRV), a double-stranded RNA (dsRNA) virus from the family Reoviridae. MRV growth in murine L929 cells was reversibly inhibited by 15 mM GuHCl. Furthermore, 15 mM GuHCl provided specific inhibition of viral dsRNA synthesis while sparing both positive-sense RNA synthesis and viral mRNA translation. By using GuHCl to provide temporal separation of MRV gene expression and genome replication, we obtained evidence that MRV primary transcripts support sufficient protein synthesis to assemble morphologically normal viral factories containing functional replicase complexes. In addition, the coordinated use of GuHCl and cycloheximide allowed us to demonstrate that MRV dsRNA synthesis can occur in the absence of ongoing protein synthesis, although to only a limited extent. Future studies utilizing the reversible inhibition of MRV dsRNA synthesis will focus on elucidating the target of GuHCl, as well as the components of the MRV replicase complexes.
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Affiliation(s)
- Kenneth E Murray
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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111
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Benavente J, Martínez-Costas J. Avian reovirus: Structure and biology. Virus Res 2007; 123:105-19. [PMID: 17018239 DOI: 10.1016/j.virusres.2006.09.005] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 09/06/2006] [Accepted: 09/07/2006] [Indexed: 11/28/2022]
Abstract
Avian reoviruses are important pathogens that cause considerable losses to the poultry industry, but they have been poorly characterized at the molecular level in the past, mostly because they have been considered to be very similar to the well-studied mammalian reoviruses. Studies performed over the last 20 years have revealed that avian reoviruses have unique properties and activities, different to those displayed by their mammalian counterparts, and of considerable interest to molecular virologists. Notably, the avian reovirus S1 gene is unique, in that it is a functional tricistronic gene that possesses three out-of-phase and partially overlapping open reading frames; the identification of the mechanisms that govern the initiation of translation of the three S1 cistrons, and the study of the properties and activities displayed by their encoded proteins, are particularly interesting areas of research. For instance, avian reoviruses are one of the few nonenveloped viruses that cause cell-cell fusion, and their fusogenic phenotype has been associated with a nonstructural 10 kDa transmembrane protein, which is expressed by the second cistron of the S1 gene; the small size of this atypical fusion protein offers an interesting model for studying the mechanisms of cell-cell fusion and for identifying fusogenic domains. Finally, avian reoviruses are highly resistant to interferon, and therefore they may be useful for investigating the mechanisms and strategies that viruses utilize to counteract the antiviral actions of interferons.
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Affiliation(s)
- Javier Benavente
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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112
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Xuong NH, Jin L, Kleinfelder S, Li S, Leblanc P, Duttweiler F, Bouwer JC, Peltier ST, Milazzo AC, Ellisman M. Future directions for camera systems in electron microscopy. Methods Cell Biol 2007; 79:721-39. [PMID: 17327181 DOI: 10.1016/s0091-679x(06)79028-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Nguyen-Huu Xuong
- University of California, San Diego, La Jolla, California 92093, USA
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113
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Pesavento JB, Crawford SE, Estes MK, Prasad BVV. Rotavirus proteins: structure and assembly. Curr Top Microbiol Immunol 2006; 309:189-219. [PMID: 16913048 DOI: 10.1007/3-540-30773-7_7] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Rotavirus is a major pathogen of infantile gastroenteritis. It is a large and complex virus with a multilayered capsid organization that integrates the determinants of host specificity, cell entry, and the enzymatic functions necessary for endogenous transcription of the genome that consists of 11 dsRNA segments. These segments encode six structural and six nonstructural proteins. In the last few years, there has been substantial progress in our understanding of both the structural and functional aspects of a variety of molecular processes involved in the replication of this virus. Studies leading to this progress using of a variety of structural and biochemical techniques including the recent application of RNA interference technology have uncovered several unique and intriguing features related to viral morphogenesis. This review focuses on our current understanding of the structural basis of the molecular processes that govern the replication of rotavirus.
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Affiliation(s)
- J B Pesavento
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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114
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Agosto MA, Ivanovic T, Nibert ML. Mammalian reovirus, a nonfusogenic nonenveloped virus, forms size-selective pores in a model membrane. Proc Natl Acad Sci U S A 2006; 103:16496-501. [PMID: 17053074 PMCID: PMC1637610 DOI: 10.1073/pnas.0605835103] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Indexed: 01/24/2023] Open
Abstract
During cell entry, reovirus particles with a diameter of 70-80 nm must penetrate the cellular membrane to access the cytoplasm. The mechanism of penetration, without benefit of membrane fusion, is not well characterized for any such nonenveloped animal virus. Lysis of RBCs is an in vitro assay for the membrane perforation activity of reovirus; however, the mechanism of lysis has been unknown. In this report, osmotic-protection experiments using PEGs of different sizes revealed that reovirus-induced lysis of RBCs occurs osmotically, after formation of small size-selective lesions or "pores." Consistent results were obtained by monitoring leakage of fluorophore-tagged dextrans from the interior of resealed RBC ghosts. Gradient fractionations showed that whole virus particles, as well as the myristoylated fragment mu1N that is released from particles, are recruited to RBC membranes in association with pore formation. We propose that formation of small pores is a discrete, intermediate step in the reovirus membrane-penetration pathway, which may be shared by other nonenveloped animal viruses.
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Affiliation(s)
- Melina A. Agosto
- Department of Microbiology and Molecular Genetics
- Biological and Biomedical Sciences Training Program, and
| | - Tijana Ivanovic
- Department of Microbiology and Molecular Genetics
- Training Program in Virology, Harvard Medical School, Boston, MA 02115
| | - Max L. Nibert
- Department of Microbiology and Molecular Genetics
- Biological and Biomedical Sciences Training Program, and
- Training Program in Virology, Harvard Medical School, Boston, MA 02115
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115
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Sherman MB, Guenther RH, Tama F, Sit TL, Brooks CL, Mikhailov AM, Orlova EV, Baker TS, Lommel SA. Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release. J Virol 2006; 80:10395-406. [PMID: 16920821 PMCID: PMC1641784 DOI: 10.1128/jvi.01137-06] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structure of Red clover necrotic mosaic virus (RCNMV), an icosahedral plant virus, was resolved to 8.5 A by cryoelectron microscopy. The virion capsid has prominent surface protrusions and subunits with a clearly defined shell and protruding domains. The structures of both the individual capsid protein (CP) subunits and the entire virion capsid are consistent with other species in the Tombusviridae family. Within the RCNMV capsid, there is a clearly defined inner cage formed by complexes of genomic RNA and the amino termini of CP subunits. An RCNMV virion has approximately 390 +/- 30 Ca2+ ions bound to the capsid and 420 +/- 25 Mg2+ ions thought to be in the interior of the capsid. Depletion of both Ca2+ and Mg2+ ions from RCNMV leads to significant structural changes, including (i) formation of 11- to 13-A-diameter channels that extend through the capsid and (ii) significant reorganization within the interior of the capsid. Genomic RNA within native capsids containing both Ca2+ and Mg2+ ions is extremely resistant to nucleases, but depletion of both of these cations results in nuclease sensitivity, as measured by a significant reduction in RCNMV infectivity. These results indicate that divalent cations play a central role in capsid dynamics and suggest a mechanism for the release of viral RNA in low-divalent-cation environments such as those found within the cytoplasm of a cell.
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Affiliation(s)
- Michael B Sherman
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.
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116
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Sousa D, Grigorieff N. Ab initio resolution measurement for single particle structures. J Struct Biol 2006; 157:201-10. [PMID: 17029845 DOI: 10.1016/j.jsb.2006.08.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 08/03/2006] [Accepted: 08/04/2006] [Indexed: 10/24/2022]
Abstract
A computational method is described that allows the measurement of the signal-to-noise ratio and resolution of a three-dimensional structure obtained by single particle electron microscopy and reconstruction. The method does not rely on the availability of the original image data or the calculation of several structures from different parts of the data that are needed for the commonly used Fourier Shell Correlation criterion. Instead, the correlation between neighboring Fourier pixels is calculated and used to distinguish signal from noise. The new method has been conveniently implemented in a computer program called RMEASURE and is available to the microscopy community.
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Affiliation(s)
- Duncan Sousa
- Howard Hughes Medical Institute and Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
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117
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Huiskonen JT, de Haas F, Bubeck D, Bamford DH, Fuller SD, Butcher SJ. Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging. Structure 2006; 14:1039-48. [PMID: 16765897 DOI: 10.1016/j.str.2006.03.018] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 03/29/2006] [Accepted: 03/29/2006] [Indexed: 12/01/2022]
Abstract
Bacteriophage phi6 is an enveloped dsRNA virus with a segmented genome. Phi6 specifically packages one copy of each of its three genome segments into a preassembled polymerase complex. This leads to expansion of the polymerase complex, minus and plus strand RNA synthesis, and assembly of the nucleocapsid. The phi6 in vitro assembly and packaging system is a valuable model for dsRNA virus replication. The structure of the nucleocapsid at 7.5 A resolution presented here reveals the secondary structure of the two major capsid proteins. Asymmetric P1 dimers organize as an inner T = 1 shell, and P8 trimers organize as an outer T = 13 laevo shell. The organization of the P1 molecules in the unexpanded and expanded polymerase complex suggests that the expansion is accomplished by rigid body movements of the P1 monomers. This leads to exposure of new potential RNA binding surfaces to control the sequential packaging of the genome segments.
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Affiliation(s)
- Juha T Huiskonen
- Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65 (Viikinkaari 1), FIN-00014 Helsinki, Finland
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118
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Yan X, Dryden KA, Tang J, Baker TS. Ab initio random model method facilitates 3D reconstruction of icosahedral particles. J Struct Biol 2006; 157:211-25. [PMID: 16979906 PMCID: PMC1919437 DOI: 10.1016/j.jsb.2006.07.013] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 07/20/2006] [Accepted: 07/29/2006] [Indexed: 01/01/2023]
Abstract
Model-based, three-dimensional (3D) image reconstruction procedures require a starting model to initiate data analysis. We have designed an ab initio method, which we call the random model (RM) method, that automatically generates models to initiate structural analysis of icosahedral viruses imaged by cryo-electron microscopy. The robustness of the RM procedure was demonstrated on experimental sets of images for five representative viruses. The RM method also provides a straightforward way to generate unbiased starting models to derive independent 3D reconstructions and obtain a more reliable assessment of resolution. The fundamental scheme embodied in the RM method should be relatively easy to integrate into other icosahedral software packages.
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Affiliation(s)
- Xiaodong Yan
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, USA.
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119
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Ahlquist P. Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses. Nat Rev Microbiol 2006; 4:371-82. [PMID: 16582931 PMCID: PMC7097367 DOI: 10.1038/nrmicro1389] [Citation(s) in RCA: 212] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Viruses are exceptionally diverse and are grouped by genome replication and encapsidation strategies into seven distinct classes: two classes of DNA viruses (encapsidating single-stranded (ss)DNA or double-stranded (ds)DNA), three classes of RNA viruses (encapsidating mRNA-sense ssRNA, antisense ssRNA or dsRNA) and two classes of reverse-transcribing viruses (encapsidating RNA or DNA). Despite substantial life-cycle differences, positive-strand RNA ((+)RNA) viruses, dsRNA viruses and reverse-transcribing viruses share multiple similarities in genome replication. All replicate their genomes through RNA intermediates that also serve as mRNAs. Moreover, the intracellular RNA-replication complexes of (+)RNA viruses share similarities in structure, assembly and function with the polymerase-containing virion cores of dsRNA and reverse transcribing viruses. Brome mosaic virus (BMV) RNA-replication factors 1a and 2apol and cis-acting template-recruitment signals parallel retrovirus Gag, Pol and RNA-packaging signals in virion assembly: 1a localizes to specific membranes, self-interacts and induces ∼60-nm membrane invaginations to which it recruits 2apol and viral RNAs for replication. Therefore, like retroviruses and dsRNA viruses, BMV sequesters its genomic RNA and polymerase in a virus-induced compartment for replication. BMV and some other alphavirus-like (+)RNA viruses also parallel retroviruses in using tRNA-related sequences to initiate genome replication, and share with dsRNA reoviruses aspects of the function and interaction of their RNA polymerase and RNA-capping enzymes. Emerging results indicate that the genome-replication machineries of these viruses might share other mechanistic features. Whereas (+)RNA alphavirus-like viruses, dsRNA reoviruses and retroviruses are linked by the above similarities, (+)RNA picornaviruses, dsRNA birnaviruses and reverse-transcribing hepadnaviruses share some distinct features, including protein-primed nucleic-acid synthesis. Such parallels suggest that at least some (+)RNA viruses, dsRNA viruses and reverse-transcribing viruses might have evolved from common ancestors. The transitions required for such evolution can be readily envisioned and some have precedents. These underlying parallels in genome replication by four of the seven main virus classes might provide a basis for more generalizable or broader-spectrum approaches for virus control.
Despite major differences in the life cycles of the seven different classes of known viruses, the genome-replication processes of certain positive-strand RNA viruses, double-stranded RNA viruses and reverse-transcribing viruses show striking parallels. Paul Ahlquist highlights these similarities and discusses their intriguing evolutionary implications. Viruses are divided into seven classes on the basis of differing strategies for storing and replicating their genomes through RNA and/or DNA intermediates. Despite major differences among these classes, recent results reveal that the non-virion, intracellular RNA-replication complexes of some positive-strand RNA viruses share parallels with the structure, assembly and function of the replicative cores of extracellular virions of reverse-transcribing viruses and double-stranded RNA viruses. Therefore, at least four of seven principal virus classes share several underlying features in genome replication and might have emerged from common ancestors. This has implications for virus function, evolution and control.
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Affiliation(s)
- Paul Ahlquist
- Institute for Molecular Virology and Howard Hughes Medical Institute, University of Wisconsin--Madison, Madison, Wisconsin 53706, USA.
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Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ. EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol 2006; 157:38-46. [PMID: 16859925 DOI: 10.1016/j.jsb.2006.05.009] [Citation(s) in RCA: 2318] [Impact Index Per Article: 128.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 05/29/2006] [Accepted: 05/31/2006] [Indexed: 10/24/2022]
Abstract
EMAN is a scientific image processing package with a particular focus on single particle reconstruction from transmission electron microscopy (TEM) images. It was first released in 1999, and new versions have been released typically 2-3 times each year since that time. EMAN2 has been under development for the last two years, with a completely refactored image processing library, and a wide range of features to make it much more flexible and extensible than EMAN1. The user-level programs are better documented, more straightforward to use, and written in the Python scripting language, so advanced users can modify the programs' behavior without any recompilation. A completely rewritten 3D transformation class simplifies translation between Euler angle standards and symmetry conventions. The core C++ library has over 500 functions for image processing and associated tasks, and it is modular with introspection capabilities, so programmers can add new algorithms with minimal effort and programs can incorporate new capabilities automatically. Finally, a flexible new parallelism system has been designed to address the shortcomings in the rigid system in EMAN1.
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Affiliation(s)
- Guang Tang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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Mukhopadhyay S, Zhang W, Gabler S, Chipman PR, Strauss EG, Strauss JH, Baker TS, Kuhn RJ, Rossmann MG. Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses. Structure 2006; 14:63-73. [PMID: 16407066 PMCID: PMC2757649 DOI: 10.1016/j.str.2005.07.025] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2005] [Revised: 07/11/2005] [Accepted: 07/16/2005] [Indexed: 11/25/2022]
Abstract
The 9 A resolution cryo-electron microscopy map of Sindbis virus presented here provides structural information on the polypeptide topology of the E2 protein, on the interactions between the E1 and E2 glycoproteins in the formation of a heterodimer, on the difference in conformation of the two types of trimeric spikes, on the interaction between the transmembrane helices of the E1 and E2 proteins, and on the conformational changes that occur when fusing with a host cell. The positions of various markers on the E2 protein established the approximate topology of the E2 structure. The largest conformational differences between the icosahedral surface spikes at icosahedral 3-fold and quasi-3-fold positions are associated with the monomers closest to the 5-fold axes. The long E2 monomers, containing the cell receptor recognition motif at their extremities, are shown to rotate by about 180 degrees and to move away from the center of the spikes during fusion.
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Affiliation(s)
- Suchetana Mukhopadhyay
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.
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122
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Noad L, Shou J, Coombs KM, Duncan R. Sequences of avian reovirus M1, M2 and M3 genes and predicted structure/function of the encoded mu proteins. Virus Res 2006; 116:45-57. [PMID: 16297481 PMCID: PMC5123877 DOI: 10.1016/j.virusres.2005.08.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 08/23/2005] [Accepted: 08/24/2005] [Indexed: 12/29/2022]
Abstract
We report the first sequence analysis of the entire complement of M-class genome segments of an avian reovirus (ARV). We analyzed the M1, M2 and M3 genome segment sequences, and sequences of the corresponding muA, muB and muNS proteins, of two virus strains, ARV138 and ARV176. The ARV M1 genes were 2,283 nucleotides in length and predicted to encode muA proteins of 732 residues. Alignment of the homologous mammalian reovirus (MRV) mu2 and ARV muA proteins revealed a relatively low overall amino acid identity ( approximately 30%), although several highly conserved regions were identified that may contribute to conserved structural and/or functional properties of this minor core protein (i.e. the MRV mu2 protein is an NTPase and a putative RNA-dependent RNA polymerase cofactor). The ARV M2 genes were 2158 nucleotides in length, encoding predicted muB major outer capsid proteins of 676 amino acids, more than 30 amino acids shorter than the homologous MRV mu1 proteins. In spite of the difference in size, the ARV/MRV muB/mu1 proteins were more conserved than any of the homologous proteins encoded by other M- or S-class genome segments, exhibiting percent amino acid identities of approximately 45%. The conserved regions included the residues involved in the maturation- and entry- specific proteolytic cleavages that occur in the MRV mu1 protein. Notably missing was a region recently implicated in MRV mu1 stabilization and in forming "hub and spokes" complexes in the MRV outer capsid. The ARV M3 genes were 1996 nucleotides in length and predicted to encode a muNS non-structural protein of 635 amino acids, significantly shorter than the homologous MRV muNS protein, which is attributed to several substantial deletions in the aligned ARV muNS proteins. Alignments of the ARV and MRV muNS proteins revealed a low overall amino acid identity ( approximately 25%), although several regions were relatively conserved.
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Affiliation(s)
- Lindsay Noad
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Man., Canada R3E 0W3
| | - Jingyun Shou
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada B3H 4H7
| | - Kevin M. Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Man., Canada R3E 0W3
| | - Roy Duncan
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada B3H 4H7
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Zhang X, Tang J, Walker SB, O’Hara D, Nibert ML, Duncan R, Baker TS. Structure of avian orthoreovirus virion by electron cryomicroscopy and image reconstruction. Virology 2005; 343:25-35. [PMID: 16153672 PMCID: PMC4152769 DOI: 10.1016/j.virol.2005.08.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Revised: 06/06/2005] [Accepted: 08/04/2005] [Indexed: 12/30/2022]
Abstract
Among members of the genus Orthoreovirus, family Reoviridae, a group of non-enveloped viruses with genomes comprising ten segments of double-stranded RNA, only the "non-fusogenic" mammalian orthoreoviruses (MRVs) have been studied to date by electron cryomicroscopy and three-dimensional image reconstruction. In addition to MRVs, this genus comprises other species that induce syncytium formation in cultured cells, a property shared with members of the related genus Aquareovirus. To augment studies of these "fusogenic" orthoreoviruses, we used electron cryomicroscopy and image reconstruction to analyze the virions of a fusogenic avian orthoreovirus (ARV). The structure of the ARV virion, determined from data at an effective resolution of 14.6 A, showed strong similarities to that of MRVs. Of particular note, the ARV virion has its pentameric lambda-class core turret protein in a closed conformation as in MRVs, not in a more open conformation as reported for aquareovirus. Similarly, the ARV virion contains 150 copies of its monomeric sigma-class core-nodule protein as in MRVs, not 120 copies as reported for aquareovirus. On the other hand, unlike that of MRVs, the ARV virion lacks "hub-and-spokes" complexes within the solvent channels at sites of local sixfold symmetry in the incomplete T=13l outer capsid. In MRVs, these complexes are formed by C-terminal sequences in the trimeric mu-class outer-capsid protein, sequences that are genetically missing from the homologous protein of ARVs. The channel structures and C-terminal sequences of the homologous outer-capsid protein are also genetically missing from aquareoviruses. Overall, the results place ARVs between MRVs and aquareoviruses with respect to the highlighted features.
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Affiliation(s)
- Xing Zhang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Jinghua Tang
- Department of Chemistry and Biochemistry and Department of Molecular Biology, University of California-San Diego, La Jolla, CA 92093, USA
| | - Stephen B. Walker
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - David O’Hara
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada B3H4H7
| | - Max L. Nibert
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Roy Duncan
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada B3H4H7
| | - Timothy S. Baker
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- Department of Chemistry and Biochemistry and Department of Molecular Biology, University of California-San Diego, La Jolla, CA 92093, USA
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124
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Ji Y, Marinescu DC, Zhang W, Zhang X, Yan X, Baker TS. A model-based parallel origin and orientation refinement algorithm for cryoTEM and its application to the study of virus structures. J Struct Biol 2005; 154:1-19. [PMID: 16459100 PMCID: PMC4147871 DOI: 10.1016/j.jsb.2005.06.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2005] [Accepted: 06/01/2005] [Indexed: 11/22/2022]
Abstract
We present a model-based parallel algorithm for origin and orientation refinement for 3D reconstruction in cryoTEM. The algorithm is based upon the Projection Theorem of the Fourier Transform. Rather than projecting the current 3D model and searching for the best match between an experimental view and the calculated projections, the algorithm computes the Discrete Fourier Transform (DFT) of each projection and searches for the central section ("cut") of the 3D DFT that best matches the DFT of the projection. Factors that affect the efficiency of a parallel program are first reviewed and then the performance and limitations of the proposed algorithm are discussed. The parallel program that implements this algorithm, called PO(2)R, has been used for the refinement of several virus structures, including those of the 500 Angstroms diameter dengue virus (to 9.5 Angstroms resolution), the 850 Angstroms mammalian reovirus (to better than 7A), and the 1800 Angstroms paramecium bursaria chlorella virus (to 15 Angstroms).
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Affiliation(s)
- Yongchang Ji
- School of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Dan C. Marinescu
- School of Computer Science, University of Central Florida, Orlando, FL 32816, USA
- Corresponding authors. Fax: +1 407 823 5419 (D.C. Marinescu); fax: +1 858 534 5846 (T.S. Baker)
| | - Wei Zhang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Xing Zhang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Xiaodong Yan
- Department of Chemistry and Biochemistry and Division of Biological Sciences, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0378, USA
| | - Timothy S. Baker
- Department of Chemistry and Biochemistry and Division of Biological Sciences, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0378, USA
- Corresponding authors. Fax: +1 407 823 5419 (D.C. Marinescu); fax: +1 858 534 5846 (T.S. Baker)
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125
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Roy P. Bluetongue virus proteins and particles and their role in virus entry, assembly, and release. Adv Virus Res 2005; 64:69-123. [PMID: 16139593 DOI: 10.1016/s0065-3527(05)64004-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Polly Roy
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
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126
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Jiang W, Ludtke SJ. Electron cryomicroscopy of single particles at subnanometer resolution. Curr Opin Struct Biol 2005; 15:571-7. [PMID: 16140524 DOI: 10.1016/j.sbi.2005.08.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 07/09/2005] [Accepted: 08/24/2005] [Indexed: 11/24/2022]
Abstract
Electron cryomicroscopy and single-particle reconstruction have advanced substantially over the past two decades. There are now numerous examples of structures that have been solved using this technique to better than 10 A resolution. At such resolutions, direct identification of alpha helices is possible and, often, beta-sheet-containing regions can be identified. The most numerous subnanometer resolution structures are the icosahedral viruses, as higher resolution is easier to achieve with higher symmetry. Important non-icosahedral structures solved to subnanometer resolution include several ribosome structures, clathrin assemblies and, most recently, the Ca2+ release channel. There is now hope that, in the next few years, this technique will achieve resolutions approaching 4 A, permitting a complete trace of the protein backbone without reference to a crystal structure.
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Affiliation(s)
- Wen Jiang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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127
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Zhang X, Ji Y, Zhang L, Harrison SC, Marinescu DC, Nibert ML, Baker TS. Features of reovirus outer capsid protein mu1 revealed by electron cryomicroscopy and image reconstruction of the virion at 7.0 Angstrom resolution. Structure 2005; 13:1545-57. [PMID: 16216585 PMCID: PMC4126556 DOI: 10.1016/j.str.2005.07.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Revised: 07/14/2005] [Accepted: 07/16/2005] [Indexed: 12/23/2022]
Abstract
Reovirus is a useful model for addressing the molecular basis of membrane penetration by one of the larger nonenveloped animal viruses. We now report the structure of the reovirus virion at approximately 7.0 A resolution as obtained by electron cryomicroscopy and three-dimensional image reconstruction. Several features of the myristoylated outer capsid protein mu1, not seen in a previous X-ray crystal structure of the mu1-sigma3 heterohexamer, are evident in the virion. These features appear to be important for stabilizing the outer capsid, regulating the conformational changes in mu1 that accompany perforation of target membranes, and contributing directly to membrane penetration during cell entry.
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Affiliation(s)
- Xing Zhang
- Department of Biological Sciences Purdue University West Lafayette, Indiana 47907
| | - Yongchang Ji
- Computer Sciences Department University of Central Florida Orlando, Florida 32816
| | - Lan Zhang
- Laboratory of Molecular Medicine, Children’s Hospital Boston, Massachusetts 02115
| | - Stephen C. Harrison
- Laboratory of Molecular Medicine, Children’s Hospital Boston, Massachusetts 02115
- Howard Hughes Medical Institute Children’s Hospital Boston, Massachusetts 02115
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston, Massachusetts 02115
| | - Dan C. Marinescu
- Computer Sciences Department University of Central Florida Orlando, Florida 32816
| | - Max L. Nibert
- Department of Microbiology and Molecular Genetics Harvard Medical School Boston, Massachusetts 02115
| | - Timothy S. Baker
- Department of Biological Sciences Purdue University West Lafayette, Indiana 47907
- Department of Chemistry and Biochemistry and Department of Molecular Biology University of California, San Diego La Jolla, California 92093
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128
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Yan X, Chipman PR, Castberg T, Bratbak G, Baker TS. The marine algal virus PpV01 has an icosahedral capsid with T=219 quasisymmetry. J Virol 2005; 79:9236-43. [PMID: 15994818 PMCID: PMC1168743 DOI: 10.1128/jvi.79.14.9236-9243.2005] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phaeocystis pouchetii virus (PpV01) infects and lyses the haptophyte Phaeocystis pouchetii (Hariot) Lagerheim and was first isolated from Norwegian coastal waters. We have used electron cryomicroscopy and three-dimensional image reconstruction methods to examine the native morphology of PpV01 at a resolution of 3 nm. The icosahedral capsid of PpV01 has a maximum diameter of 220 nm and is composed of 2,192 capsomers arranged with T=219 quasisymmetry. One specific capsomer in each asymmetric unit contains a fiber-like protrusion. Density attributed to the presence of a lipid membrane appears just below (inside) the capsid. PpV01 is the largest icosahedral virus whose capsid structure has been determined in three dimensions from images of vitrified samples. Striking similarities in the structures of PpV01 and a number of other large double-stranded DNA viruses are consistent with a growing body of evidence that they share a common evolutionary origin.
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Affiliation(s)
- Xiaodong Yan
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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129
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Wu Y, Chen M, Lu M, Wang Q, Ma J. Determining Protein Topology from Skeletons of Secondary Structures. J Mol Biol 2005; 350:571-86. [PMID: 15961102 DOI: 10.1016/j.jmb.2005.04.064] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2004] [Revised: 04/24/2005] [Accepted: 04/27/2005] [Indexed: 11/16/2022]
Abstract
We report a novel computational procedure for determining protein native topology, or fold, by defining loop connectivity based on skeletons of secondary structures that can usually be obtained from low to intermediate-resolution density maps. The procedure primarily involves a knowledge-based geometry filter followed by an energetics-based evaluation. It was tested on a large set of skeletons covering a wide range of protein architecture, including one modeled from an experimentally determined 7.6A cryo-electron microscopy (cryo-EM) density map. The results showed that the new procedure could effectively deduce protein folds without high-resolution structural data, a feature that could also be used to recognize native fold in structure prediction and to interpret data in fields like structure genomics. Most importantly, in the energetics-based evaluation, it was revealed that, despite the inevitable errors in the artificially constructed structures and limited accuracy of knowledge-based potential functions, the average energy of an ensemble of structures with slightly different configurations around the native skeleton is a much more robust parameter for marking native topology than the energy of individual structures in the ensemble. This result implies that, among all the possible topology candidates for a given skeleton, evolution has selected the native topology as the one that can accommodate the largest structural variations, not the one rigidly trapped in a deep, but narrow, conformational energy well.
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Affiliation(s)
- Yinghao Wu
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
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130
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Zhang W, Heil M, Kuhn RJ, Baker TS. Heparin binding sites on Ross River virus revealed by electron cryo-microscopy. Virology 2005; 332:511-8. [PMID: 15680416 PMCID: PMC4152768 DOI: 10.1016/j.virol.2004.11.043] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Revised: 09/20/2004] [Accepted: 11/29/2004] [Indexed: 10/25/2022]
Abstract
Cell surface glycosaminoglycans play important roles in cell adhesion and viral entry. Laboratory strains of two alphaviruses, Sindbis and Semliki Forest virus, have been shown to utilize heparan sulfate as an attachment receptor, whereas Ross River virus (RRV) does not significantly interact with it. However, a single amino acid substitution at residue 218 in the RRV E2 glycoprotein adapts the virus to heparan sulfate binding and expands the host range of the virus into chicken embryo fibroblasts. Structures of the RRV mutant, E2 N218R, and its complex with heparin were determined through the use of electron cryo-microscopy and image reconstruction methods. Heparin was found to bind at the distal end of the RRV spikes, in a region of the E2 glycoprotein that has been previously implicated in cell-receptor recognition and antibody binding.
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131
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Jaafar FM, Attoui H, Mertens PPC, de Micco P, de Lamballerie X. Structural organization of an encephalitic human isolate of Banna virus (genus Seadornavirus, family Reoviridae). J Gen Virol 2005; 86:1147-1157. [PMID: 15784909 DOI: 10.1099/vir.0.80578-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Banna virus (BAV) is the type species of the genus Seadornavirus within the family Reoviridae. The Chinese BAV isolate (BAV-Ch), which causes encephalitis in humans, was shown to have a structural organization and particle morphology reminiscent of that of rotaviruses, with fibre proteins projecting from the surface of the particle. Intact BAV-Ch virus particles contain seven structural proteins, two of which (VP4 and VP9) form the outer coat. The inner (core) particles contain five additional proteins (VP1, VP2, VP3, VP8 and VP10) and are ‘non-turreted’, with a relatively smooth surface appearance. VP2 is the ‘T=2’ protein that forms the innermost ‘subcore’ layer, whilst VP8 is the ‘T=13’ protein forming the core-surface layer. Sequence comparisons indicate that BAV VP9 and VP10 are equivalent to the VP8* and VP5* domains, respectively, of rotavirus outer-coat protein VP4 (GenBank accession no. P12976). VP9 has also been shown to be responsible for virus attachment to the host-cell surface and may be involved in internalization. These similarities reveal a previously unreported genetic link between the genera Rotavirus and Seadornavirus, although the expression of BAV VP9 and VP10 from two separate genome segments, rather than by the proteolytic cleavage of a single gene product (as seen in rotavirus VP4), suggests a significant evolutionary jump between the members of these two genera.
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Affiliation(s)
- Fauziah Mohd Jaafar
- Unité des Virus Emergents: EFS Alpes-Méditerranée and Faculté de Médecine de Marseille, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13005 Marseille cedex 5, France
| | - Houssam Attoui
- Unité des Virus Emergents: EFS Alpes-Méditerranée and Faculté de Médecine de Marseille, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13005 Marseille cedex 5, France
| | - Peter P C Mertens
- Institute for Animal Health, Pirbright Laboratory, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Philippe de Micco
- Unité des Virus Emergents: EFS Alpes-Méditerranée and Faculté de Médecine de Marseille, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13005 Marseille cedex 5, France
| | - Xavier de Lamballerie
- Maladies Virales Émergentes et Systèmes d'Information UR034, Institut de Recherche pour le Développement, Marseille, France
- Unité des Virus Emergents: EFS Alpes-Méditerranée and Faculté de Médecine de Marseille, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13005 Marseille cedex 5, France
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132
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Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Curr Opin Struct Biol 2004; 14:313-24. [PMID: 15193311 DOI: 10.1016/j.sbi.2004.04.006] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Structures of macromolecular complexes are necessary for a mechanistic description of biochemical and cellular processes. They can be solved by experimental methods, such as X-ray crystallography, NMR spectroscopy and electron microscopy, as well as by computational protein structure prediction, docking and bioinformatics. Recent advances and applications of these methods emphasize the need for hybrid approaches that combine a variety of data to achieve better efficiency, accuracy, resolution and completeness.
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133
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Orlova EV, Saibil HR. Structure determination of macromolecular assemblies by single-particle analysis of cryo-electron micrographs. Curr Opin Struct Biol 2004; 14:584-90. [PMID: 15465319 DOI: 10.1016/j.sbi.2004.08.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A new generation of electron microscopes equipped with field emission gun electron sources and the ability to image molecules in their native environment at liquid nitrogen or helium temperatures has enabled the analysis of macromolecular structures at medium resolution (approximately 10 angstroms) and in different conformational states. The amalgamation of electron microscopy and X-ray crystallographic approaches makes it possible to solve structures in the 100-1000 angstroms size range, advancing our understanding of the function of complex assemblies. Many new structures have been solved during the past two years, including one of the smallest complexes to be determined by single-particle cryo-electron microscopy, the transferrin receptor-transferrin complex. Other notable results include the near atomic level resolution structure of the nicotinic acetylcholine receptor in helical arrays and an icosahedral virus structure with an asymmetric polymerase resolved.
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Affiliation(s)
- Elena V Orlova
- School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
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134
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Yin P, Keirstead ND, Broering TJ, Arnold MM, Parker JSL, Nibert ML, Coombs KM. Comparisons of the M1 genome segments and encoded mu2 proteins of different reovirus isolates. Virol J 2004; 1:6. [PMID: 15507160 PMCID: PMC524354 DOI: 10.1186/1743-422x-1-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Accepted: 09/23/2004] [Indexed: 12/03/2022] Open
Abstract
Background The reovirus M1 genome segment encodes the μ2 protein, a structurally minor component of the viral core, which has been identified as a transcriptase cofactor, nucleoside and RNA triphosphatase, and microtubule-binding protein. The μ2 protein is the most poorly understood of the reovirus structural proteins. Genome segment sequences have been reported for 9 of the 10 genome segments for the 3 prototypic reoviruses type 1 Lang (T1L), type 2 Jones (T2J), and type 3 Dearing (T3D), but the M1 genome segment sequences for only T1L and T3D have been previously reported. For this study, we determined the M1 nucleotide and deduced μ2 amino acid sequences for T2J, nine other reovirus field isolates, and various T3D plaque-isolated clones from different laboratories. Results Determination of the T2J M1 sequence completes the analysis of all ten genome segments of that prototype. The T2J M1 sequence contained a 1 base pair deletion in the 3' non-translated region, compared to the T1L and T3D M1 sequences. The T2J M1 gene showed ~80% nucleotide homology, and the encoded μ2 protein showed ~71% amino acid identity, with the T1L and T3D M1 and μ2 sequences, respectively, making the T2J M1 gene and μ2 proteins amongst the most divergent of all reovirus genes and proteins. Comparisons of these newly determined M1 and μ2 sequences with newly determined M1 and μ2 sequences from nine additional field isolates and a variety of laboratory T3D clones identified conserved features and/or regions that provide clues about μ2 structure and function. Conclusions The findings suggest a model for the domain organization of μ2 and provide further evidence for a role of μ2 in viral RNA synthesis. The new sequences were also used to explore the basis for M1/μ2-determined differences in the morphology of viral factories in infected cells. The findings confirm the key role of Ser/Pro208 as a prevalent determinant of differences in factory morphology among reovirus isolates and trace the divergence of this residue and its associated phenotype among the different laboratory-specific clones of type 3 Dearing.
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Affiliation(s)
- Peng Yin
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3E 0W3 Canada
- Thrasos Therapeutics, Hopkinton, MA 01748 USA
| | - Natalie D Keirstead
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3E 0W3 Canada
- Department of Pathobiology, Ontario Veterinary College, Guelph, ON, N1G 2W1 Canada
| | - Teresa J Broering
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA, 02115 USA
- Massachusetts Biologic Laboratories, Jamaica Plain, MA 02130-3597 USA
| | - Michelle M Arnold
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA, 02115 USA
- Virology Training Program, Division of Medical Sciences, Harvard University, Cambridge, MA 02138 USA
| | - John SL Parker
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA, 02115 USA
- James A. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 USA
| | - Max L Nibert
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA, 02115 USA
- Virology Training Program, Division of Medical Sciences, Harvard University, Cambridge, MA 02138 USA
| | - Kevin M Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3E 0W3 Canada
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135
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Nason EL, Rothagel R, Mukherjee SK, Kar AK, Forzan M, Prasad BVV, Roy P. Interactions between the inner and outer capsids of bluetongue virus. J Virol 2004; 78:8059-67. [PMID: 15254177 PMCID: PMC446137 DOI: 10.1128/jvi.78.15.8059-8067.2004] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bluetongue virus is a large and structurally complex virus composed of three concentric capsid layers that surround 10 segments of a double-stranded RNA genome. X-ray crystallographic analysis of the particles without the outer capsid layer has provided atomic structural details of VP3 and VP7, which form the inner two layers. However, limited structural information is available on the other five proteins in the virion-two of which are important for receptor recognition, hemagglutination, and membrane interaction-are in the outer layer, and the others, important for endogenous transcriptase activity are internal. Here we report the electron cryomicroscopy (cryo-EM) reconstruction of the mature particle, which shows that the outer layer has a unique non-T = 13 icosahedral organization consisting of two distinct triskelion and globular motifs interacting extensively with the underlying T = 13 layer. Comparative cryo-EM analysis of the recombinant corelike particles has shown that VP1 (viral polymerase) and VP4 (capping enzyme) together form a flower-shaped structure attached to the underside of VP3, directly beneath the fivefold axis. The structural data have been substantiated by biochemical studies demonstrating the interactions between the individual outer and inner capsid proteins.
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Affiliation(s)
- Emma L Nason
- Verna and Marrs McLean Department of Biochemistry and Molecular Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA
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136
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Kong Y, Zhang X, Baker TS, Ma J. A Structural-informatics approach for tracing beta-sheets: building pseudo-C(alpha) traces for beta-strands in intermediate-resolution density maps. J Mol Biol 2004; 339:117-30. [PMID: 15123425 PMCID: PMC4148645 DOI: 10.1016/j.jmb.2004.03.038] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Revised: 02/03/2004] [Accepted: 03/09/2004] [Indexed: 10/26/2022]
Abstract
We report the development of two computational methods to assist density map interpretation at intermediate resolutions: sheettracer for building pseudo-C(alpha) models of beta-sheets, and a deconvolution method for enhancing features attributed to major secondary structural elements. Sheettracer is tightly coupled with sheetminer, which was developed to locate sheet densities in intermediate-resolution density maps. The results from sheetminer are used as inputs to sheettracer, which employs a multi-step ad hoc morphological analysis of sheet densities to trace individual strands of beta-sheets. The methods were tested on simulated density maps from 12 protein crystal structures that represent a reasonably complete sampling of sheet morphology. The sheet-tracing results were quantitatively assessed in terms of sensitivity, specificity and rms deviations. Furthermore, sheettracer and the deconvolution method were rigorously tested on experimental maps of the lambda2 protein of reovirus at resolutions of 7.6A and 11.8A. Our results clearly demonstrate the capability of sheettracer in building pseudo-C(alpha) models of beta-sheets in intermediate-resolution density maps and the power of the deconvolution method in enhancing the performance of sheettracer. These computational methods, along with other related ones, should facilitate recognition and analysis of folding motifs from experimental data at intermediate resolutions.
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Affiliation(s)
- Yifei Kong
- Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza Houston, TX 77030, USA
| | - Xing Zhang
- Department of Biological Sciences, Purdue University West Lafayette, IN 47907, USA
| | - Timothy S. Baker
- Department of Biological Sciences, Purdue University West Lafayette, IN 47907, USA
| | - Jianpeng Ma
- Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza Houston, TX 77030, USA
- Department of Bioengineering Rice University, Houston, TX 77005, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Corresponding author:
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137
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Kim J, Tao Y, Reinisch KM, Harrison SC, Nibert ML. Orthoreovirus and Aquareovirus core proteins: conserved enzymatic surfaces, but not protein-protein interfaces. Virus Res 2004; 101:15-28. [PMID: 15010214 DOI: 10.1016/j.virusres.2003.12.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Orthoreoviruses and Aquareoviruses constitute two respective genera in the family Reoviridae of double-stranded RNA viruses. Orthoreoviruses infect mammals, birds, and reptiles and have a genome comprising 10 RNA segments. Aquareoviruses infect fish and have a genome comprising 11 RNA segments. Despite these differences, recent structural and nucleotide sequence evidence indicate that the proteins of Orthoreoviruses and Aquareoviruses share many similarities. The focus of this review is on the structure and function of the Orthoreovirus core proteins lambda1, lambda2, lambda3, and sigma2, for which X-ray crystal structures have been recently reported. The homologous core proteins in Aquareoviruses are VP3, VP1, VP2, and VP6, respectively. By mapping the locations of conserved residues onto the Orthoreovirus crystal structures, we have found that enzymatic surfaces involved in mRNA synthesis are well conserved between these two groups of viruses, whereas several surfaces involved in protein-protein interactions are not well conserved. Other evidence indicates that the Orthoreovirus mu2 and Aquareovirus VP5 proteins are homologous, suggesting that VP5 is a core protein as mu2 is known to be. These findings provide further evidence that Orthoreoviruses and Aquareoviruses have diverged from a common ancestor and contribute to a growing understanding of the functions of the core proteins in viral mRNA synthesis.
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Affiliation(s)
- Jonghwa Kim
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02115, USA
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138
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Nibert ML, Kim J. Conserved sequence motifs for nucleoside triphosphate binding unique to turreted reoviridae members and coltiviruses. J Virol 2004; 78:5528-30. [PMID: 15113934 PMCID: PMC400372 DOI: 10.1128/jvi.78.10.5528-5530.2004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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139
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Saunders J. Locating reovirus polymerase. Nat Rev Microbiol 2004. [DOI: 10.1038/nrmicro806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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140
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Kim J, Parker JSL, Murray KE, Nibert ML. Nucleoside and RNA triphosphatase activities of orthoreovirus transcriptase cofactor mu2. J Biol Chem 2003; 279:4394-403. [PMID: 14613938 DOI: 10.1074/jbc.m308637200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mammalian Orthoreovirus (mORV) core particle is an icosahedral multienzyme complex for viral mRNA synthesis and provides a delimited system for mechanistic studies of that process. Previous genetic results have identified the mORV mu2 protein as a determinant of viral strain differences in the transcriptase and nucleoside triphosphatase activities of cores. New results in this report provided biochemical and genetic evidence that purified mu2 is itself a divalent cation-dependent nucleoside triphosphatase that can remove the 5' gamma-phosphate from RNA as well. Alanine substitutions in a putative nucleotide binding region of mu2 abrogated both functions but did not affect the purification profile of the protein or its known associations with microtubules and mORV microNS protein in vivo. In vitro microtubule binding by purified mu2 was also demonstrated and not affected by the mutations. Purified mu2 was further demonstrated to interact in vitro with the mORV RNA-dependent RNA polymerase, lambda3, and the presence of lambda3 mildly stimulated the triphosphatase activities of mu2. These findings confirm that mu2 is an enzymatic component of the mORV core and may contribute several possible functions to viral mRNA synthesis.
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Affiliation(s)
- Jonghwa Kim
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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