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

Abstract

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.

Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses

“…As part of the sample characterization prior to the diffraction experiment, the expected particle size of $40 nm (Okamoto et al, 2016) was confirmed by EM imaging of negatively stained particles (Fig. 6a) and by sizing of aerosolized particles by SMPS spectrometry (Fig.…”

“…In this experiment, we explored the capabilities of the CXI instrument for imaging small biological samples in the submicrometre focus using a well characterized sample, the $40 nm Omono River virus (Okamoto et al, 2016). From a collection of 4555 diffraction patterns, we individually estimated the corresponding particle sizes and found that most injected particles were of spherical shape and followed a wide size distribution.…”

An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome

“…These represented RdRps ( n = 4) and capsid (Cp) proteins ( n = 2), with one contig ( S. horrens contig 5835) bearing an overlapping Cp-RdRp region, with a possible frameshift at position 882, characteristic of totivirus ORFs [ 70 ]. Predicted secondary structure (PSIPRED V4.0 [ 71 ]) of the S. horrens contig 5835 major capsid protein region revealed a 5′ α- and β-strand rich region, followed by a β-helix rich region at the 3′ end, which is most similar to fungal totiviruses and less similar to metazoan totiviruses, which have an α-helix rich 3′ region [ 72 ]. The Cp on S. horrens contig 17482, on the other hand, bears an α- and β-rich region at the 5′ end, followed by a β-rich region and terminating in an α-rich region, which suggests it may be more closely related to arthropod totiviruses [ 72 ].…”

“…Predicted secondary structure (PSIPRED V4.0 [71]) of the S. horrens contig 5835 major capsid protein region revealed a 5' α-and β-strand rich region, followed by a β-helix rich region at the 3' end, which is most similar to fungal totiviruses and less similar to metazoan totiviruses, which have an α-helix rich 3' region [72]. The Cp on S. horrens contig 17482, on the other hand, bears an α-and β-rich region at the 5' end, followed by a β-rich region and terminating in an α-rich region, which suggests it may be more closely related to arthropod totiviruses [72]. Phylogenetically, the Cp regions on both S. horrens 5835 and 17,482 match more closely fungal totivirus Cp regions, as do all RdRp fragments recovered in this study ( Figure 6).…”

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

“…The asymmetric unit of the first capsid layer in the T = 1 lattice consists of a homo-dimer, in which two monomers are in different conformations. This first capsid layer is highly conserved in almost all dsRNA viruses and particularly in the reoviruses and responsible for enclosing the viral genome along with enzymes required for facilitating their transcription, suggesting that these dsRNA viruses have evolved from a common ancestor with a simple single-layered capsid (Hill et al, 1999;Miyazaki et al, 2008;Okamoto et al, 2016). Fungal dsRNA viruses in the family Totiviridae (the most primitive dsRNA viruses) only possess this conserved first capsid layer, and the situation may explain their lack of an extracellular phase to their life cycle (Ghabrial, 1998;Goodman et al, 2011).…”