Viral Release Threshold in the Salivary Gland of Leafhopper Vector Mediates the Intermittent Transmission of Rice Dwarf Virus

Numerous piercing-sucking insects can persistently transmit viral pathogens in combination with saliva to plant phloem in an intermittent pattern. Insect vectors maintain viruliferous for life. However, the reason why insect vectors discontinuously transmit the virus remains unclear. Rice dwarf virus (RDV), a plant reovirus, was found to replicate and assemble the progeny virions in salivary gland cells of the leafhopper vector. We observed that the RDV virions moved into saliva-stored cavities in the salivary glands of leafhopper vectors via an exocytosis-like mechanism, facilitating the viral horizontal transmission to plant hosts during the feeding of leafhoppers. Interestingly, the levels of viral accumulation in the salivary glands of leafhoppers during the transmitting period were significantly lower than those of viruliferous individuals during the intermittent period. A putative viral release threshold, which was close to 1.79 × 104 copies/μg RNA was proposed from the viral titers in the salivary glands of 52 leafhoppers during the intermittent period. Thus, the viral release threshold was hypothesized to mediate the intermittent release of RDV from the salivary gland cells of leafhoppers. We anticipate that viral release threshold-mediated intermittent transmission by insect vectors is the conserved strategy for the epidemic and persistence of vector-borne viruses in nature.

Flash X-ray diffraction imaging in 3D: a proposed analysis pipeline

Modern Flash X-ray diffraction Imaging (FXI) acquires diffraction signals from single biomolecules at a high repetition rate from X-ray Free Electron Lasers (XFELs), easily obtaining millions of 2D diffraction patterns from a single experiment. Due to the stochastic nature of FXI experiments and the massive volumes of data, retrieving 3D electron densities from raw 2D diffraction patterns is a challenging and time-consuming task. We propose a semi-automatic data analysis pipeline for FXI experiments, which includes four steps: hit-finding and preliminary filtering, pattern classification, 3D Fourier reconstruction, and post-analysis. We also include a recently developed bootstrap methodology in the post-analysis step for uncertainty analysis and quality control. To achieve the best possible resolution, we further suggest using background subtraction, signal windowing, and convex optimization techniques when retrieving the Fourier phases in the post-analysis step. As an application example, we quantified the 3D electron structure of the PR772 virus using the proposed data analysis pipeline. The retrieved structure was above the detector edge resolution and clearly showed the pseudo-icosahedral capsid of the PR772.

An Assembly Intermediate Structure of Rice Dwarf Virus Reveals a Hierarchical Outer Capsid Shell Assembly Mechanism

Nearly all viruses of the Reoviridae family possess a multi-layered capsid consisting of an inner layer with icosahedral T = 1 symmetry and a second-outer layer (composed of 260 copies of a trimeric protein) exhibiting icosahedral T = 13 symmetry. Here we describe the construction and structural evaluation of an assembly intermediate of the Rice dwarf virus of the family Reoviridae stalled at the second capsid layer via targeted disruption of the trimer-trimer interaction interface in the second-layer capsid protein. Structural determination was performed by conventional and Zernike/Volta phase-contrast cryoelectron microscopy. The assembly defect second-layer capsid trimers bound exclusively to the outer surface of the innermost capsid layer at the icosahedral 3-fold axis. Furthermore, the second-layer assembly could not proceed without specific inter-trimer interactions. Our results suggest that the correct assembly pathway for second-layer capsid formation is highly controlled at the inter-layer and inter-trimer interactions.

Single-particle imaging without symmetry constraints at an X-ray free-electron laser

The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints. The analysis developed here revealed and quantified nanoscale features of the PR772 virus measured in this experiment, with the obtained resolution better than 10 nm, with a clear indication that the structure was compressed in one direction and, as such, deviates from ideal icosahedral symmetry.

Hierarchical structure assembly model of rice dwarf virus particle formation

Rice dwarf virus (RDV) of the family Reoviridae and genus Phytoreovirus, is the cause of rice dwarf disease, a major negative effector of rice production throughout East Asia, including Japan. RDV has an icosahedral double-layered shell of approximately 70 nm diameter. The structural proteins constituting the capsid can self-assemble into a correct particle without requiring the help of any external factors in vitro. A total of more than 900 components assemble to make the full particle. A series of structural and functional studies of RDV, including X-ray crystallography and cryo-electron microscopy, suggest a hierarchical self-assembly mechanism involving both homologous and heterologous interactions. As such, systems for the recognition of each component should be essential for particle formation.

The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes

Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper describes electron cryo-microscopy (cryoEM) structures for the intact OmRV virion to 8.9 Å resolution and the structure of the empty virus-like-particle, that lacks RNA, to 8.3 Å resolution. The icosahedral capsid contains 120-subunits and resembles another closely related arthropod-borne totivirus-like virus, the infectious myonecrosis virus (IMNV) from shrimps. Both viruses have an elevated plateau around their icosahedral 5-fold axes, surrounded by a deep canyon. Sequence and structural analysis suggests that this plateau region is mainly composed of the extended C-terminal region of the capsid proteins. In contrast to IMNV, the infectious form of OmRV lacks extensive fibre complexes at its 5-fold axes as directly confirmed by a contrast-enhancement technique, using Zernike phase-contrast cryo-EM. Instead, these fibre complexes are replaced by a short “plug” structure at the five-fold axes of OmRV. OmRV and IMNV have acquired an extracellular phase, and the structures at the five-fold axes may be significant in adaptation to cell-to-cell transmission in metazoan hosts.

Electron microscopic imaging revealed the flexible filamentous structure of the cell attachment protein P2 of Rice dwarf virus located around the icosahedral 5-fold axes

The minor outer capsid protein P2 of Rice dwarf virus (RDV), a member of the genus Phytoreovirus in the family Reoviridae, is essential for viral cell entry. Here, we clarified the structure of P2 and the interactions to host insect cells. Negative stain electron microscopy (EM) showed that P2 proteins are monomeric and flexible L-shaped filamentous structures of ∼20 nm in length. Cryo-EM structure revealed the spatial arrangement of P2 in the capsid, which was prescribed by the characteristic virion structure. The P2 proteins were visualized as partial rod-shaped structures of ∼10 nm in length in the cryo-EM map and accommodated in crevasses on the viral surface around icosahedral 5-fold axes with hydrophobic interactions. The remaining disordered region of P2 assumed to be extended to the radial direction towards exterior. Electron tomography clearly showed that RDV particles were away from the cellular membrane at a uniform distance and several spike-like densities, probably corresponding to P2, connecting a viral particle to the host cellular membrane during cell entry. By combining the in vitro and in vivo structural information, we could gain new insights into the detailed mechanism of the cell entry of RDV.

Nonstructural protein Pns12 of rice dwarf virus is a principal regulator for viral replication and infection in its insect vector

Plant reoviruses are thought to replicate and assemble within cytoplasmic structures called viroplasms. The molecular mechanisms underling the formation of the viroplasm during infection of rice dwarf virus (RDV), a plant reovirus, in its leafhopper vector cells remain poorly understood. Viral nonstructural protein Pns12 forms viroplasm-like inclusions in the absence of viral infection, suggesting that the viroplasm matrix is basically composed of Pns12. Here, we demonstrated that core capsid protein P3 and nonstructural protein Pns11 were recruited in the viroplasm by direct interaction with Pns12, whereas nonstructural protein Pns6 was recruited through interaction with Pns11. The introduction of dsRNA from Pns12 gene into cultured insect vector cells or intact insect strongly inhibited such viroplasm formation, preventing efficient viral spread in the leafhopper in vitro and in vivo. Thus, nonstructural protein Pns12 of RDV is a principal regulator for viral replication and infection in its insect vector.

Cryo-electron tomography: moving towards revealing the viral life cycle of Rice dwarf virus

It is well known that viruses utilize the host cellular systems for their infection and replication processes. However, the molecular mechanisms underlying these processes are poorly understood for most viruses. To understand these molecular mechanisms, it is essential to observe the viral and virus-related structures and analyse their molecular interactions within a cellular context. Cryo-electron microscopy and tomography offer the potential to observe macromolecular structures and to analyse their molecular interactions within the cell. Here, using cryo-electron microscopy and tomography, the structures of Rice dwarf virus are reported within fully hydrated insect vector cells grown on electron microscopy grids towards revealing the viral infection and replication mechanisms.

Life cycle of phytoreoviruses visualized by electron microscopy and tomography

Rice dwarf virus and Rice gall dwarf virus, members of the genus Phytoreovirus in the family Reoviridae,are known as agents of rice disease, because their spread results in substantial economic damage in many Asian countries. These viruses are transmitted via insect vectors, and they multiply both in the plants and in the insect vectors. Structural information about the viruses and their interactions with cellular components in the life cycle are essential for understanding viral infection and replication mechanisms. The life cycle of the viruses involves various cellular events such as cell entry, synthesis of viral genome and proteins, assembly of viral components, viral egress from infected cells, and intra- and intercellular transports. This review focuses on the major events underlying the life cycle of phytoreoviruses, which has been visualized by various electron microscopy (EM) imaging techniques, including cryo-electron microscopy and tomography, and demonstrates the advantage of the advanced EM imaging techniques to investigate the viral infection and replication mechanisms.

Probing, by self-assembly, the number of potential binding sites for minor protein subunits in the procapsid of double-stranded RNA bacteriophage Φ6

The double-stranded RNA bacteriophage Φ6 is an extensively studied prokaryotic model system for virus assembly. There are established in vitro assembly protocols available for the Φ6 system for obtaining infectious particles from purified protein and RNA constituents. The polymerase complex is a multifunctional nanomachine that replicates, transcribes, and translocates viral RNA molecules in a highly specific manner. The complex is composed of (i) the major structural protein (P1), forming a T=1 icosahedral lattice with two protein subunits in the icosahedral asymmetric unit; (ii) the RNA-dependent RNA polymerase (P2); (iii) the hexameric packaging nucleoside triphosphatase (NTPase) (P4); and (iv) the assembly cofactor (P7). In this study, we analyzed several Φ6 virions and recombinant polymerase complexes to investigate the relative copy numbers of P2, P4, and P7, and we applied saturated concentrations of these proteins in the self-assembly system to probe their maximal numbers of binding sites in the P1 shell. Biochemical quantitation confirmed that the composition of the recombinant particles was similar to that of the virion cores. By including a high concentration of P2 or P7 in the self-assembly reaction mix, we observed that the numbers of these proteins in the resulting particles could be increased beyond those observed in the virion. Our results also suggest a previously unidentified P2-P7 dependency in the assembly reaction. Furthermore, it appeared that P4 must initially be incorporated at each, or a majority, of the 5-fold symmetry positions of the P1 shell for particle assembly. Although required for nucleation, excess P4 resulted in slower assembly kinetics.

Outer-capsid P8 proteins of phytoreoviruses mediate secretion of assembled virus-like particles from insect cells

Phytoreoviruses are composed of two concentric capsid layers that surround a viral genome. The capsids are formed mainly by the inner-capsid P3 protein and the outer-capsid P8 protein. During the infection of insect-vector cells, these play important roles in packaging the viral genome and the enzymes required for its transcription. P3 and P8 proteins, when co-expressed in Spodoptera frugiperda cells, co-localized in cells and were released as spherical clusters. In contrast P3 proteins expressed in the absence of P8 protein were associated with the cells when they were examined by confocal microscopy. Cryo-electron microscopy revealed that the secreted clusters, composed of P3 and P8 proteins, were double-layered virus-like particles that were indistinguishable from intact viral particles. Our results indicate that P8 proteins mediate the secretion of assembled virus-like particles from S. frugiperda insect cells and, therefore, most probably from insect-vector cells also.