Journal of
Bioinformatics and Sequence Analysis

  • Abbreviation: J. Bioinform. Seq. Anal.
  • Language: English
  • ISSN: 2141-2464
  • DOI: 10.5897/JBSA
  • Start Year: 2009
  • Published Articles: 45

Full Length Research Paper

Computational characterization of providence virus non-structural proteins: Evolutionary and functional implications

Nakayinga Ritah
  • Nakayinga Ritah
  • Department of Biological Sciences, Faculty of Science, Kyambogo University, Kampala, Uganda.
  • Google Scholar


  •  Received: 09 January 2019
  •  Accepted: 27 March 2019
  •  Published: 31 March 2019

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.