RNA synthesis is modulated by G-quadruplex formation in Hepatitis C virus negative RNA strand

Abstract

DNA and RNA guanine-rich oligonucleotides can form non-canonical structures called G-quadruplexes or “G4” that are based on the stacking of G-quartets. The role of DNA and RNA G4 is documented in eukaryotic cells and in pathogens such as viruses. Yet, G4 have been identified only in a few RNA viruses, including the Flaviviridae family. In this study, we analysed the last 157 nucleotides at the 3′end of the HCV (−) strand. This sequence is known to be the minimal sequence required for an efficient RNA replication. Using bioinformatics and biophysics, we identified a highly conserved G4-prone sequence located in the stem-loop IIy’ of the negative strand. We also showed that the formation of this G-quadruplex inhibits the in vitro RNA synthesis by the RdRp. Furthermore, Phen-DC3, a specific G-quadruplex binder, is able to inhibit HCV viral replication in cells in conditions where no cytotoxicity was measured. Considering that this domain of the negative RNA strand is well conserved among HCV genotypes, G4 ligands could be of interest for new antiviral therapies.

In-Depth Bioinformatic Analyses of Nidovirales Including Human SARS-CoV-2, SARS-CoV, MERS-CoV Viruses Suggest Important Roles of Non-canonical Nucleic Acid Structures in Their Lifecycles

“…A similar strategy has been proposed against Hepatitis C virus belonging to the Flaviviridae family of positive ssRNA viruses. Stabilization of G4s by Phen-DC3 ligand has been shown to lead to inhibited replication of this virus (Jaubert et al, 2018). Viruses with singlestranded genomes are often non-symmetrically distributed with guanines and cytosines.…”

Colocalization of m6A and G-Quadruplex-Forming Sequences in Viral RNA (HIV, Zika, Hepatitis B, and SV40) Suggests Topological Control of Adenosine N6-Methylation

“…The flaviviruses include dengue, hepatitis C, West Nile, yellow fever, and Zika viruses that have significantly impacted human health. 37,49,50 The flaviviruses have positive-sense (+), single-stranded RNA (ssRNA) genomes devoid of a 3′-poly-A tail (Figure 2A). 51 Genome replication occurs in the cytosol through a double-stranded RNA (dsRNA) intermediate via a specialized RNA-dependent RNA polymerase (RdRp) encoded by the virus (Figure 2).…”

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

“…Moreover, in a luciferase system in which luciferase expression was directly related to viral replication, 60% reduction was observed upon treatment with the compound. 51 HCV was also used as the reference RNA virus to develop a fluorescence light-up probe, a thioflavine T derivative (ThT-NE), for the direct visualization of the native HCV RNA genome in living cells. ThT-NE showed remarkable specificity for HCV RNA G4s with respect to other G4s in different cell models, probably because during infections viral G4s outnumber cellular G4s in order to maximize viral replication.…”