Expansion of viral genomes with viral protein genome linked copies.

Autor: Warsaba R; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada., Salcedo-Porras N; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada., Flibotte S; Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; UBC/LSI Bioinformatics Facility, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada., Jan E; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada; Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada. Electronic address: ej@mail.ubc.ca.
Jazyk: angličtina
Zdroj: Virology [Virology] 2022 Dec; Vol. 577, pp. 174-184. Date of Electronic Publication: 2022 Nov 11.
DOI: 10.1016/j.virol.2022.10.012
Abstrakt: Virus protein-linked genome (VPg) proteins are required for replication. VPgs are duplicated in a subset of RNA viruses however their roles are not fully understood and the extent of viral genomes containing VPg copies has not been investigated in detail. Here, we generated a novel bioinformatics approach to identify VPg sequences in viral genomes using hidden Markov models (HMM) based on alignments of dicistrovirus VPg sequences. From metagenomic datasets of dicistrovirus genomes, we identified 717 dicistrovirus genomes containing VPgs ranging from a single copy to 8 tandem copies. The VPgs are classified into nine distinct types based on their sequence and length. The VPg types but not VPg numbers per viral genome followed specific virus clades, thus suggesting VPgs co-evolved with viral genomes. We also identified VPg duplications in aquamavirus and mosavirus genomes. This study greatly expands the number of viral genomes that contain VPg copies and indicates that duplicated viral sequences are more widespread than anticipated.
Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
Externí odkaz: