Tracing dsDNA Virus-Host Coevolution through Correlation of Their G-Quadruplex-Forming Sequences.

Natália Bohálová,Petr Pečinka,Patrik Kaura,Václav Brázda,Jiří Šťastný,Alessio Cantara,Miroslav Fojta,Martin Bartas

doi:10.3390/ijms22073433

Abstract

The importance of gene expression regulation in viruses based upon G-quadruplex may point to its potential utilization in therapeutic targeting. Here, we present analyses as to the occurrence of putative G-quadruplex-forming sequences (PQS) in all reference viral dsDNA genomes and evaluate their dependence on PQS occurrence in host organisms using the G4Hunter tool. PQS frequencies differ across host taxa without regard to GC content. The overlay of PQS with annotated regions reveals the localization of PQS in specific regions. While abundance in some, such as repeat regions, is shared by all groups, others are unique. There is abundance within introns of Eukaryota-infecting viruses, but depletion of PQS in introns of bacteria-infecting viruses. We reveal a significant positive correlation between PQS frequencies in dsDNA viruses and corresponding hosts from archaea, bacteria, and eukaryotes. A strong relationship between PQS in a virus and its host indicates their close coevolution and evolutionarily reciprocal mimicking of genome organization.

Highlights

Viruses are intracellular parasites closely coevolving with their host organisms and shaping genotypic diversity [1,2]
Variation in Frequency for G4-Forming Sequences in dsDNA Viruses Grouped by Host
Using the National Center for Biotechnology Information (NCBI) taxonomy classification, the analyzed viruses were divided into three domains according to their host organisms: Archaea, Bacteria, and Eukaryota

Summary

Introduction

Viruses are intracellular parasites closely coevolving with their host organisms and shaping genotypic diversity [1,2]. It has been demonstrated that the G4 binding domain is conserved between SARS-CoV and SARS-CoV-2 genomes [16], and it was proven to be crucial for the SARS-CoV life cycle [17]. G4s can be found in all domains of life [18,19,20,21], and they have been described as constituting an important structural genomic feature with various functions in several viral classes [21,22]. Coevolution of viral and host loop sequences of the G-quadruplex-forming sequences in human Herpesviridae viruses was recently proposed [31]

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