Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses

Abstract

G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter. Folding of HIV-1 LTR G4s inhibits viral transcription; stabilization by G4 ligands intensifies this effect. Cellular proteins modulate viral transcription by inducing/unfolding LTR G4s. We here expanded our investigation on the presence of LTR G4s to all lentiviruses. G4s in the 5′-LTR U3 region were completely conserved in primate lentiviruses. A G4 was also present in a cattle-infecting lentivirus. All other non-primate lentiviruses displayed hints of less stable G4s. In primate lentiviruses, the possibility to fold into G4s was highly conserved among strains. LTR G4 sequences were very similar among phylogenetically related primate viruses, while they increasingly differed in viruses that diverged early from a common ancestor. A strong correlation between primate lentivirus LTR G4s and Sp1/NFκB binding sites was found. All LTR G4s folded: their complexity was assessed by polymerase stop assay. Our data support a role of the lentiviruses 5′-LTR G4 region as control centre of viral transcription, where folding/unfolding of G4s and multiple recruitment of factors based on both sequence and structure may take place.

G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide

“…One genome per each group of aligned sequences was chosen to serve as reference sequence, possibly belonging to the manually curated RefSeq database [https://www.ncbi.nlm.nih.gov/ refseq/]. The complete list of selected reference sequences is reported in S1 Table. PQSs were searched in all multiple-aligned nucleotide sequences with an in-house developed tool, as previously described [36,52]. Briefly, a PQS was reported when at least four consecutive guanine islands (G-islands) were detected.…”

“…A G4 was also detected in hepatitis B virus (HBV) genome, the only member of dsDNA viruses with RT activity [27]. Finally, functionally significant G4s were identified both in the RNA and DNA proviral genome of the human immunodeficiency virus (HIV), a retrovirus belonging to group 6 ( Table 1) [28][29][30][31][32][33][34][35], and [33,34]in the LTR region of lentiviruses in general (ssRNA RT) [36]. Given this amount of scattered data, we here aimed at analyzing the presence of PQSs in the genome of all known viruses that can cause infections in humans.…”

G-Quadruplexes: More Than Just a Kink in Microbial Genomes

“…In addition to HIV-1 evolution, other functional aspects of G4s discussed in this review, and the selective retention or exclusion of G4s from specific genomic loci in bacteria and yeast, indicate that G4s play a role in the evolution of microbes ( Figure 3) [30,[37][38][39][40][41][42].…”

“…G4s negatively regulate the activity of the LTR promoter and hence the replication of HIV-1. Interestingly, the presence of the quadruplex in the LTR promoter is not restricted to HIV-1 but is evolutionarily conserved among the primate lentiviruses [41].…”

G-quadruplex forming sequences in the genome of all known human viruses: a comprehensive guide

“…The cellular proteins nucleolin and hnRNP A2/B1 regulate the G4/ds equilibrium in the LTR promoter (Tosoni et al 2015;Lago et al 2017;Scalabrin et al 2017) and G4 ligands induced significant antiviral effects in a G4-mediated mechanism of action (Perrone et al 2013a;Perrone et al 2014;Perrone et al 2015). The LTR region of lentiviruses in general (ssRNA RT) present stable and conserved G4s (Perrone et al 2017a).…”