G-Quadruplexes Are Present in Human Coronaviruses Including SARS-CoV-2

Abstract

The global coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is one of seven human coronaviruses. G-quadruplexes are intrinsic obstacles to genome replication. Whether G-quadruplexes are present in human coronaviruses is unknown. In the current study, we have predicted that all seven human coronaviruses harbor G-quadruplex sequences. Conserved G-quadruplex sequences in SARS-CoV and SARS-CoV-2 were analyzed and verified by circular dichroism (CD) spectroscopy and Thioflavin T fluorescence assay. Similar to SARS-CoV, SARS-CoV-2 encodes an nsP3 protein, which is predicted to associate with G-quadruplexes. Targeting G-quadruplex sequences in the SARS-CoV-2 genome by G-quadruplex ligands could be a new way to conquer COVID-19.

CNBP Binds and Unfolds In Vitro G-Quadruplexes Formed in the SARS-CoV-2 Positive and Negative Genome Strands

“…During the COVID-19 pandemic, mainly along the last half of 2020, several works analyzed the SARS-CoV-2 RNA genome to seek PQSs. All of them analyzed the +gRNA [ 30 , 31 , 32 , 33 , 34 , 35 , 36 ], while a few made a superficial overview of PQSs on the −gRNA [ 32 , 33 , 36 ]. Although −gRNA and −sgRNAs are minority in respect of their positive-sense RNA counterparts and represent only about 1% of viral RNA [ 9 , 10 ], negative-sense RNAs are key intermediates functioning as templates for +gRNA replication and +sgRNAs transcription.…”

“…Consequently, −gRNA and −sgRNAs may contain G4s with putative regulative functions on these processes. In addition, most of the previous PQSs analyses on SARS-CoV-2 genome have used different bioinformatics prediction tools, some of them designed for DNA-G4, and a variety of criteria for selecting the best PQS candidates, mainly including higher prediction scores [ 30 , 31 , 32 , 33 , 34 , 35 , 36 ] combined with lower potential thermodynamic stability of secondary structures competitive with G4s [ 32 ], uniqueness in SARS-CoV-2 and conservation among variants of SARS-CoV-2 [ 34 ], and conservation among human coronaviruses [ 36 ]. Although there is divergence in G4 prediction tools and selection criteria, none of the predictions have found PQSs with four tracts of three consecutive guanines (with the potential of forming three-tetrads G4s), and have only found PQSs with four tracts of two consecutive guanines (with the potential of forming two-tetrads G4s).…”

“…Critical roles for viral G4s have been described in human viruses, including immunodeficiency virus (HIV), herpes simplex virus (HSV), Epstein-Barr virus (EBV), human papillomavirus (HPV), hepatitis B virus (HBV), Nipah virus, hepatitis C virus (HCV), Zika virus, and Ebola virus [ 27 , 28 , 29 ], and some G4-specific compounds have shown powerful antiviral activity by targeting G4 structures [ 28 , 29 ]. Very recent reports have initiated the search for G4s in the genomes of human coronaviruses, including SARS-CoV-2 [ 30 , 31 , 32 , 33 , 34 , 35 , 36 ]. Beyond the prediction of PQSs, some works have demonstrated the formation of a few G4s in vitro by PQSs found in the +gRNA [ 30 , 34 , 35 , 36 ] and one of them was demonstrated to be formed within cultured human cells and controls the translation efficiency of the nucleocapsid N protein [ 35 , 36 ].…”

“…Very recent reports have initiated the search for G4s in the genomes of human coronaviruses, including SARS-CoV-2 [ 30 , 31 , 32 , 33 , 34 , 35 , 36 ]. Beyond the prediction of PQSs, some works have demonstrated the formation of a few G4s in vitro by PQSs found in the +gRNA [ 30 , 34 , 35 , 36 ] and one of them was demonstrated to be formed within cultured human cells and controls the translation efficiency of the nucleocapsid N protein [ 35 , 36 ].…”

Structure and regulation of coronavirus genomes: state-of-the-art and novel insights from SARS-CoV-2 studies

“…Several studies have further started investigating the presence of RNA G-quadruplexes (G4s) in the SARS-CoV-2 genome [73][74][75][76]. Of the many predicted G4s, one G4 located within ORF1a ( position 13385) was shown to bind and to be stabilized by BRACO-19 and TMPyP4, two known G4 binders, suggesting that these compounds might represent good scaffolds for the development of RNA-targeted small-molecule drugs [74]. Nevertheless, currently available studies only analyzed the candidate G4s under in vitro conditions.…”