Elsevier

Biochimie

Volume 186, July 2021, Pages 13-27
Biochimie

Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection

https://doi.org/10.1016/j.biochi.2021.03.017Get rights and content
Under a Creative Commons license
open access

Highlights

  • G4Hunter analyses show unique and non-random localization of G-quadruplex forming sequences in viral genomes.

  • Putative G-quadruplex forming sequences (PQS) density is only moderately correlated with GC content.

  • Viruses causing persistent infections in Metazoa hosts are significantly enriched for PQS.

  • Viruses causing acute infections are significantly depleted in PQS.

  • The Grapevine fleck virus is the most G4 rich organism found to date: PQS cover 66% of its genome.

  • PQS are associated with specific regions such as repeats, replication origins, 5’UTRs and 3’UTRs.

Abstract

G-quadruplexes contribute to the regulation of key molecular processes. Their utilization for antiviral therapy is an emerging field of contemporary research. Here we present comprehensive analyses of the presence and localization of putative G-quadruplex forming sequences (PQS) in all viral genomes currently available in the NCBI database (including subviral agents). The G4Hunter algorithm was applied to a pool of 11,000 accessible viral genomes representing 350 Mbp in total. PQS frequencies differ across evolutionary groups of viruses, and are enriched in repeats, replication origins, 5′UTRs and 3′UTRs. Importantly, PQS presence and localization is connected to viral lifecycles and corresponds to the type of viral infection rather than to nucleic acid type; while viruses routinely causing persistent infections in Metazoa hosts are enriched for PQS, viruses causing acute infections are significantly depleted for PQS. The unique localization of PQS identifies the importance of G-quadruplex-based regulation of viral replication and life cycle, providing a tool for potential therapeutic targeting.

Keywords

G-quadruplex
Viral genome
Bioinformatics
Persistent infection
Acute infection
G4Hunter

Cited by (0)

1

These authors contributed equally.