G-quadruplexes may determine the landscape of recombination in HSV-1

Abstract

Background Several lines of evidence suggest that recombination plays a central role in replication and evolution of herpes simplex virus-1 (HSV-1). G-quadruplex (G4)-motifs have been linked to recombination events in human and microbial genomes, but their role in recombination has not been studied in DNA viruses. Results The availability of near full-length sequences from 40 HSV-1 recombinant strains with exact position of the recombination breakpoints provided us with a unique opportunity to investigate the role of G4-motifs in recombination among herpes viruses. We mapped the G4-motifs in the parental and all the 40 recombinant strains. Interestingly, the genome-wide distribution of breakpoints closely mirrors the G4 densities in the HSV-1 genome; regions of the genome with higher G4 densities had higher number of recombination breakpoints. Biophysical characterization of oligonucleotides from a subset of predicted G4-motifs confirmed the formation of G-quadruplex structures. Our analysis also reveals that G4-motifs are enriched in regions flanking the recombination breakpoints. Interestingly, about 11% of breakpoints lie within a G4-motif, making these DNA secondary structures hotspots for recombination in the HSV-1 genome. Breakpoints within G4-motifs predominantly lie within G4-clusters rather than individual G4-motifs. Of note, we identified the terminal guanosine of G4-clusters at the boundaries of the U L (unique long) region on either side of the OriL (origin of replication within U L ) represented the commonest breakpoint among the HSV-1 recombinants. Conclusion Our findings suggest a correlation between the HSV-1 recombination landscape and the distribution of G4-motifs and G4-clusters, with possible implications for the evolution of DNA viruses. Electronic supplementary material The online version of this article (10.1186/s12864-019-5731-0) contains supplementary material, which is available to authorized users.

Viral G-quadruplexes: New frontiers in virus pathogenesis and antiviral therapy

“…16 Bioinformatics and the following experimental analysis traced conserved PQSs in: (i) the promoter region of immediate-early genes of all alpha-HHVs, genes that are expressed at the very early stage of viral infection and encode for regulatory proteins involved in all subsequent viral steps 17 (ii) the terminal and internal repeated regions, which include packaging signals involved in concatemer cleavage during replication 13 (iii) the proximity of recombination breakpoints. 18 Most of the identified G4s proved to be exceptionally stable when tested in vitro through biochemical and biophysical assays.…”

G-Quadruplexes in Neurobiology and Virology: Functional Roles and Potential Therapeutic Approaches

“…The terminal guanosine of G4 clusters at the boundaries of unique long (U L ) region represent the most common breakpoint among the HSV-1 recombinants. 133 On the basis of the accumulating evidence, G4s in these regions might play a role in the evolution of viruses, suggesting that RNA G4s are fundamental for the evolution of viruses.…”

“…The investigation of the G4-motifs in recombination among HSV-1 found that the PQS of the genome are enriched in recombination breakpoints and in regions flanking the recombination breakpoints. The terminal guanosine of G4 clusters at the boundaries of unique long (U L ) region represent the most common breakpoint among the HSV-1 recombinants . On the basis of the accumulating evidence, G4s in these regions might play a role in the evolution of viruses, suggesting that RNA G4s are fundamental for the evolution of viruses.…”

Rapid adaptation to human protein kinase R by a unique genomic rearrangement in rhesus cytomegalovirus

“…With the homology between the pac1 and pac1-like sequences, it seems likely that pac1-like could also form G-quadruplexes. A recent report highlighted the enrichment of G-quadruplexes in the regions flanking DNA breakpoints in HSV-1 and demonstrated that they are sites of recombination [51]. Additionally, reports that HSV-1 recombination factors such as ICP8 have been shown to co-localize with G-quadruplexes, and that UL12, an alkaline nuclease that binds the cellular double strand break-sensing MRN complex, co-localizes with ICP8 [52] suggest that G-quadruplexes may play a role in recruiting recombination machinery during herpesvirus DNA replication.…”