The Atomic Structure of Rice dwarf Virus Reveals the Self-Assembly Mechanism of Component Proteins

Nakagawa, Atsushi; Miyazaki, Naoyuki; Taka, Junichiro; Naitow, Hisashi; Ogawa, Akira; Fujimoto, Zui; Mizuno, Hiroshi; Higashi, Tsuneyuki; Watanabe, Yasuo; Omura, Toshihiro; Cheng, R. Holland; Tsukihara, Tomitake

doi:10.1016/j.str.2003.08.012

Cited by 141 publications

(172 citation statements)

References 31 publications

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“…2A). The organization of VP1A and VP1B in the capsid shell is identical to that of other reoviruses analyzed by X-ray crystallography or cryo-EM (2,8,9,(18)(19)(20)(21). A previous structural study by Yu et al has shown that the capsid shell protein VP1 has an overall thin-plate-like shape similar to that of orthoreovirus λ1 with the exception of a small protrusion domain (6).…”

supporting

confidence: 53%

Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping

Cheng

Sun

Zhang

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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The cytoplasmic polyhedrosis virus (CPV) from the family Reoviridae belongs to a subgroup of "turreted" reoviruses, in which the mRNA capping activity occurs in a pentameric turret. We report a full atomic model of CPV built from a 3D density map obtained using cryoelectron microscopy. The image data for the 3D reconstruction were acquired exclusively from a CCD camera. Our structure shows that the enzymatic domains of the pentameric turret of CPV are topologically conserved and that there are five unique channels connecting the guanylyltransferase and methyltransferase regions. This structural organization reveals how the channels guide nascent mRNA sequentially to guanylyltransferase, 7-Nmethyltransferase, and 2′-O-methyltransferase in the turret, undergoing the highly coordinated mRNA capping activity. Furthermore, by fitting the deduced amino acid sequence of the protein VP5 to 120 large protrusion proteins on the CPV capsid shell, we confirmed that this protrusion protein is encoded by CPV RNA segment 7.V iruses of the family Reoviridae have a segmented dsRNA genome enclosed by single, double, or triple capsid shells. They share a similar transcription mechanism in which the inner capsids (core) remain intact and serve as shelters protecting the transcriptional process from antiviral defense mechanisms inside the cytoplasm of the host cell during replication of their dsRNA genomes. Despite the absence of significant sequence homology among different genera of the Reoviridae, the innermost capsid shells, which are formed by two conformers of the one protein, of all members of the Reoviridae and the majority of dsRNA viruses share common functions (1).The "turreted" reoviruses have been defined as a subgroup of the Reoviridae due to their similar protein composition and capsid architecture. For this subgroup of reoviruses, a pentameric turret formed by five copies of turret proteins on fivefold vertex of the innermost shell functions in the catalysis of mRNA 5′ cap synthesis (2-5). Cryo-EM or crystal structures are available for four turreted virus genera of the family Reoviridae: the Cypovirus (6), Orthoreovirus (2), Oryzavirus (7), and Aquareovirus (8, 9) genera. These viruses have a segmented genome consisting of 10-12 linear segments of dsRNA and their hosts include vertebrates (orthoreoviruses and aquareovriuses), invertebrates (cypoviruses), and plants (oryzaviruses).The cytoplasmic polyhedrosis virus (CPV) belongs to the genus Cypovirus and has a dsRNA genome of 10 segments. It is unique among dsRNA viruses in having a single capsid layer (10), which corresponds to the core of orthoreoviruses and functions as a stable mRNA synthesis machine in the cytoplasm of host cells that transcribes mRNAs from the segmented double-stranded RNA templates (11). CPV virions are embedded in polyhedra capable of surviving dehydration, freezing, and chemical treatments that would denature most proteins (12). The polyhedra dissolve in the alkaline midgut of their hosts and release infectious virions during the infection ...

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supporting

confidence: 53%

Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping

Cheng

Sun

Zhang

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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“…The genome is composed of 12 double-stranded RNA segments. The structure of RDV has been solved by cryo-EM (Zhou et al, 2001) and X-ray crystallography (Nakagawa et al, 2003). In this study, RDV was used as the test case to validate the algorithm development.…”

Section: Resultsmentioning

confidence: 99%

“…The resolutions of the 3-D reconstructed maps were measured against the known X-ray structure (PDB ID: 1UF2) (Nakagawa et al, 2003) using the 0.5 criterion in the Fourier Shell Correlation (FSC) (Harauz and van Heel 1986) curves. The secondary structure elements were identified computationally by SSEHunter and visualized with Chimera (Pettersen et al, 2004).…”

Section: Cryo-em Images Of Rdvmentioning

confidence: 99%

Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-path Simulated Annealing optimization algorithm

Liu

Jiang

Jakana

et al. 2007

Journal of Structural Biology

108

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Accurately determining a cryoEM particle's alignment parameters is crucial to high resolution single particle 3-D reconstruction. We developed Multi-Path Simulated Annealing, a Monte Carlo type of optimization algorithm, for globally aligning the center and orientation of a particle simultaneously. A consistency criterion was developed to ensure the alignment parameters are correct and to remove some bad particles from a large pool of images of icosahedral particles. Without using any a priori model, this procedure is able to reconstruct a structure from a random initial model. Combining the procedure above with a new empirical double threshold particle selection method, we are able to pick tens of best quality particles to reconstruct a subnanometer resolution map from scratch. Using the best 62 particles of rice dwarf virus, the reconstruction reached 9.6Å resolution at which 4 helices of the P3A subunit of RDV are resolved. Furthermore, with the 284 best particles, the reconstruction is improved to 7.9Å resolution, and 21 of 22 helices and 6 of 7 beta sheets are resolved.

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“…For the more highly segmented Reoviridae, a model similarly based on specific RNA-protein interactions may be considered unlikely as it would require up to 11 distinct intermediate binding specificities to be generated in the capsid. There is no evidence that such structurally distinct capsid variants exist amongst the known capsid structures of this family (Grimes et al, 1998;Lawton et al, 1997;Mindich, 1999;Nakagawa et al, 2003;Pesavento et al, 2006;Reinisch et al, 2000). Additionally, the highly reiterative nature of the structural proteins which define the architecture of the virus particle argues that they would be poor candidates for providing a unique copy of a binding site for each segment during genome packaging.…”

Section: Introductionmentioning

confidence: 99%

Inter-segment complementarity in orbiviruses: a driver for co-ordinated genome packaging in the Reoviridae?

Boyce

McCrae

Boyce

et al. 2016

Journal of General Virology

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The process by which eukaryotic viruses with segmented genomes select a complete set of genome segments for packaging into progeny virus particles is not understood. In this study a model based on the association of genome segments through specific RNA-RNA interactions driven by base pairing was formalized and tested in the Orbivirus genus of the Reoviridae family. A strategy combining screening of the genomic sequences for inter-segment complementarity with direct functional testing of inter-segment RNA-RNA interactions using reverse genetics is described in the type species of the Orbivirus genus, Bluetongue virus (BTV). Two examples, involving four of the ten BTV genomic segments, of specific intersegment interaction motifs whose maintenance is essential for the generation of infectious virus, were identified. Equivalent inter-segment complementarities were found between the identified regions of the orthologous genome segments of all orbiviruses, including phylogenetically distant species. Specific interaction of the participating RNA segments was confirmed in vitro using electrophoretic mobility shift assays, with the interactions inhibited using oligonucleotides complementary to the interaction motif of one of the interacting partners, and also through mutagenesis of the motifs. In each example, the base pairing rather than the absolute sequence was critical to the formation of a functional inter-segment interaction, with mutations only being tolerated in rescued virus if compensating changes were made in the interacting partner to restore uninterrupted base pairing. The absolute sequence of the complementarity motifs varied between species, indicating that this newly identified phenomenon may contribute to the observed lack of reassortment between Orbivirus species.

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The Atomic Structure of Rice dwarf Virus Reveals the Self-Assembly Mechanism of Component Proteins

Cited by 141 publications

References 31 publications

Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping

Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping

Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-path Simulated Annealing optimization algorithm

Inter-segment complementarity in orbiviruses: a driver for co-ordinated genome packaging in the Reoviridae?

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