Abstract
Providence virus is the only member of the family Carmotetraviridae and carries a positive single stranded RNA genome that encodes three open reading frames. The smallest open reading frame encodes the structural proteins. The largest open reading frame encodes a large putative protein, p130. The second overlapping open reading frame encodes two non-structural proteins; p40, a proposed accessory protein and p104, the replicase, containing the RdRp domain. Till date, p130 and p40 are not associated with any related open reading frames in the databases. The purpose of this study is to identify sequences within these non-structural proteins with potential roles in replication and evolution using computational tools. Our results revealed that p130 has a putative arginine-rich sequence which lies in the disordered region also found in the Umbravirus, Groundnut rosette virus p27. Analysis of the p40 revealed a sequence with a coiled-coil conformation and surface-exposed characteristics comparable to the interaction domain of Tombusvirus, Tomato bushy stunt virus p33 accessory protein. The hypothetical two transmembrane helix topology of PrV p104 oriented the putative localization signal at the N-terminus, the same way the localization signal of Tomato bushy stunt virus p92 is oriented. This study concluded that Providence virus non-structural proteins are structurally related to Tombusvirus and Umbravirus accessory proteins and contain sequences with predicted functions in replication. Findings from this study have led us to propose a co-evolutionary event between an insect and plant virus resulting in a hybrid virus with the potential to infect and replicate in both host plant and animal systems. Key words: Providence virus, non-structural proteins, p40, p130, sequence comparison, replication, evolution.
Highlights
The evolutionary relatedness between Providence virus (PrV), tombusviruses and umbraviruses (Walter et al, 2010) led to the search for amino acid sequences shared between PrV p130 and the non-structural proteins of tombusviruses and umbraviruses
An arginine-rich sequence, RRRRRPRDNLR, was found at amino acids 1047 to 1057 of PrV p130 (Figure 1). This sequence shares arginine residues with the arginine-rich sequence, RPRRRAGRSGGMDPR, at amino acid positions 108 – 122, of Umbravirus Groundnut rosette virus (GRV) ORF3 that encodes p27 (GRV p27)
We revisit computational analysis of PrV non-structural proteins and we showed that the C-terminal sequence of p130 has an arginine-rich sequence that lie within the disordered region and covers 703 amino acid residues, most of which are mainly loop structures
Summary
The monopartite genome of PrV differs from other tetraviruses in that it encodes three open reading frames (ORF) instead of the typical two ORFs (Walter et al, 2010). The putative viral replicase ORF (p104) and viral capsid precursor ORF (p81) are conserved among all tetraviruses (Walter et al, 2010). The presence of a read through stop type 1 signal, UAGCAACUA, within the replicase results in the production of the accessory protein, p40 and full-length protein, p104 characterized with RdRp motifs, required for the establishment of infection (Walter et al, 2010). The protein consists of a putative 2A-like processing site (PrV-2A1) whose activity is predicted to produce two translation products of 17 kDa and 113 kDa and is functional in in vitro studies (Walter et al, 2010; Luke et al, 2008)
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