Genome organization and translation products of Providence virus: insight into a unique tetravirus

Abstract

Providence virus (PrV) is a member of the family Tetraviridae, a family of small, positive-sense, ssRNA viruses that exclusively infect lepidopteran insects. PrV is the only known tetravirus that replicates in tissue culture. We have analysed the genome and characterized the viral translation products, showing that PrV has a monopartite genome encoding three ORFs: (i) p130, unique to PrV and of unknown function; (ii) p104, which contains a read-through stop signal, producing an N-terminal product of 40 kDa (p40) and (iii) the capsid protein precursor (p81). There are three 2A-like processing sequences: one at the N terminus of p130 (PrV-2A 1 ) and two more (PrV-2A 2 and PrV-2A 3 ) at the N terminus of p81. Metabolic radiolabelling identified viral translation products corresponding to all three ORFs in persistently infected cells and showed that the readthrough stop in p104 and PrV-2A 3 in p81 are functional in vivo and these results were confirmed by in vitro translation experiments. The RNA-dependent RNA polymerase domain of the PrV replicase is phylogenetically most closely related to members of the families Tombusviridae and Umbraviridae rather than to members of the family Tetraviridae. The unique genome organization, translational control systems and phylogenetic relationship with the replicases of (+ve) plant viruses lead us to propose that PrV represents a novel family of small insect RNA viruses, distinct from current members of the family Tetraviridae.

Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the “Gene Nursery” of Deltaretroviruses

“…We established that horizontal transfer took place towards alphacarmotetravirus and machlomovirus from the other families by analysing the phylogenetic distribution of homologs of the ancestral proteins (not shown). Our results agree with previously reported findings that Providence virus has originated through recombination between a Tombusviridae -like and a Tetraviridae -like virus [31], and that the machlomovirus capsid protein is taxonomically incongruent [32]. We excluded these two cases from our analyses, and the final benchmark dataset is thus composed of 25 overlaps (Table 1).…”

Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element

“…The RT site in gammaretroviruses has been studied in depth and our computational analysis supported the known stimulatory spacer sequence and pseudoknot structure but did not reveal further conservation in the vicinity (39)(40)(41)(42). RT sites in enamoviruses, carrot red leaf luteovirus-associated RNA, Middelburg and Barmah Forest alphaviruses, Providence tetravirus and others, were not analyzed in detail due to lack of sequence data for useful comparative computational analysis (70)(71)(72).…”

Identification and characterization of RNA duplex unwinding and ATPase activities of an alphatetravirus superfamily 1 helicase

“…Recently, this group of viruses has been re-classified into three families, i.e., Alphatetraviridae, Carmotetraviridae and Permutotetraviridae (http://www.ictvonline. org/virusTaxonomy.asp?version=2011), based on their genome organizations and translation products (Adams and Carstens, 2012;Dorrington, 2011;Walter et al, 2010;Zeddam et al, 2010). For the Alphatetraviridae family, two genera are classified, including betatetravirus and omegatetravirus.…”