Three-dimensional Structure of Victorivirus HvV190S Suggests Coat Proteins in Most Totiviruses Share a Conserved Core

Abstract

Double-stranded (ds)RNA fungal viruses are currently assigned to six different families. Those from the family Totiviridae are characterized by nonsegmented genomes and single-layer capsids, 300–450 Å in diameter. Helminthosporium victoriae virus 190S (HvV190S), prototype of recently recognized genus Victorivirus, infects the filamentous fungus Helminthosporium victoriae (telomorph: Cochliobolus victoriae), which is the causal agent of Victoria blight of oats. The HvV190S genome is 5179 bp long and encompasses two large, slightly overlapping open reading frames that encode the coat protein (CP, 772 aa) and the RNA-dependent RNA polymerase (RdRp, 835 aa). To our present knowledge, victoriviruses uniquely express their RdRps via a coupled termination–reinitiation mechanism that differs from the well-characterized Saccharomyces cerevisiae virus L-A (ScV-L-A, prototype of genus Totivirus), in which the RdRp is expressed as a CP/RdRp fusion protein due to ribosomal frameshifting. Here, we used transmission electron cryomicroscopy and three-dimensional image reconstruction to determine the structures of HvV190S virions and two types of virus-like particles (capsids lacking dsRNA and capsids lacking both dsRNA and RdRp) at estimated resolutions of 7.1, 7.5, and 7.6 Å, respectively. The HvV190S capsid is thin and smooth, and contains 120 copies of CP arranged in a “T = 2” icosahedral lattice characteristic of ScV-L-A and other dsRNA viruses. For aid in our interpretations, we developed and used an iterative segmentation procedure to define the boundaries of the two, chemically identical CP subunits in each asymmetric unit. Both subunits have a similar fold, but one that differs from ScV-L-A in many details except for a core α-helical region that is further predicted to be conserved among many other totiviruses. In particular, we predict the structures of other victoriviruses to be highly similar to HvV190S and the structures of most if not all totiviruses including, Leishmania RNA virus 1, to be similar as well.

Three-Dimensional Structure of a Protozoal Double-Stranded RNA Virus That Infects the Enteric Pathogen Giardia lamblia

“…As expected for totiviruses (32,(35)(36)(37)(38)(39), a surface view of the 3D reconstruction revealed that GLV appears to possess a so-called "Tϭ2" capsid (34) comprising 120 CP subunits in a Tϭ1 lattice ( Fig. 4A and C).…”

“…The Segger v1.7 tool in the Chimera visualization package (48) was used to segment out individual CP-A and CP-B subunits in the final map and to examine interactions between them as described previously (38). Briefly, segmentation is obtained with this tool by means of an iterative procedure, starting from an initial arbitrary assignment of density regions to the two subunits and then refining those assignments in a semiautomatic manner by imposing additional restrictions.…”

“…Location and length of density features that could be assigned to putative ␣-helical segments in the segmented A subunits of the different totiviruses were predicted automatically using the VolTrac algorithm (49) implemented in the Sculptor graphics software (50). The procedure was performed as described by Dunn et al (38).…”

“…The virions of one of these viruses, penaeid shrimp infectious myonecrosis virus (IMNV), have been analyzed by transmission electron cryomicroscopy (cryo-TEM) and icosahedral three-dimensional (3D) image reconstruction, which revealed an unusual proteinfiber complex that projects above the so-called "Tϭ2" capsid at the icosahedral 5-fold axes and is likely to play one or more key roles in cell entry (32,33). Such "Tϭ2" capsid organization (34) reflects a Tϭ1 structure in which a CP dimer occupies each of the icosahedral asymmetric units (120 CP subunits per capsid) and is common to many dsRNA viruses, including other members of family Totiviridae (35)(36)(37)(38)(39).…”

Characterization of virus-like particles and identification of capsid proteins in Xanthophyllomyces dendrorhous

“…Recently, it was described that the core region in the crystal structure of ScV-L-A CP composed by helix 3-5 (aa 85-139) and helix 12-13 (aa 345-383) correspond closely in size and location to helices 2-3 (aa 84-122) and H10-12 (aa 350-397) of Helminthosporium victoriae virus 190S (HvV190S) CP, both members of different genera totiviruses. This centrally located stretch of residues with predominantly helical content was observed too in predicted secondary structures of CPs of representative members of Victorivirus, Giardiavirus, Leishmaniavirus, and Trichomonasvirus genera, suggesting a conservation of this helical core in Totiviridae family [28]. We compared the predicted secondary structure of CP of several totiviruses (Fig.…”