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.

Martin Bartas,Tereza Stachurová,Natália Bohálová,Kateřina Malachová,Adriana Volná,Václav Brázda,Eva B Jagelská,Jiří Červeň,Alessio Cantara,Otília Porubiaková,Petr Pečinka

doi:10.3389/fmicb.2020.01583

Abstract

Non-canonical nucleic acid structures play important roles in the regulation of molecular processes. Considering the importance of the ongoing coronavirus crisis, we decided to evaluate genomes of all coronaviruses sequenced to date (stated more broadly, the order Nidovirales) to determine if they contain non-canonical nucleic acid structures. We discovered much evidence of putative G-quadruplex sites and even much more of inverted repeats (IRs) loci, which in fact are ubiquitous along the whole genomic sequence and indicate a possible mechanism for genomic RNA packaging. The most notable enrichment of IRs was found inside 5′UTR for IRs of size 12+ nucleotides, and the most notable enrichment of putative quadruplex sites (PQSs) was located before 3′UTR, inside 5′UTR, and before mRNA. This indicates crucial regulatory roles for both IRs and PQSs. Moreover, we found multiple G-quadruplex binding motifs in human proteins having potential for binding of SARS-CoV-2 RNA. Non-canonical nucleic acids structures in Nidovirales and in novel SARS-CoV-2 are therefore promising druggable structures that can be targeted and utilized in the future.

Highlights

The order Nidovirales is a monophyletic group of animal RNA viruses
The conserved putative quadruplex sites (PQSs) sequence present in the L gene of Zaire ebolavirus and related to its replication is inhibited by interaction with G-quadruplex ligand TMPyP4, and this finding has led to suggestions that Gquadruplex RNA stabilization could constitute a new strategy against Ebola virus disease (Wang et al, 2016)
We analyzed all accessible genomes of Nidovirales, including the contemporary pandemic SARS-CoV-2 genome

Summary

Introduction

The order Nidovirales is a monophyletic group of animal RNA viruses. This group can be divided into the six distinct families of Arteriviridae, Coronaviridae, Mesnidovirineae, Mononiviridae, Ronidovirineae, and Tobaniviridae. This combination of features means that RNA viruses are able to adapt to new environmental conditions, but they are limited in expanding their genomes because they must keep their mutation load low so that their survival is possible (Eigen and Schuster, 1977; Lauring et al, 2013; Carrasco-Hernandez et al, 2017) Nidovirales bind to their host cell receptors on the cell surface, after which fusion of the viral and cellular membranes is mediated by one of the surface glycoproteins. After genome “transportation,” translation of two replicase open reading frames (ORFs) is initiated by host ribosomes This results in large polyprotein precursors that undergo autoproteolysis to eventually produce a membrane-bound replicase/transcriptase complex. The newly formed virions leave the cell by following the exocytic pathway toward the plasma membrane (Lai and Cavanagh, 1997; Gorbalenya, 2001; Snijder et al, 2003; Ziebuhr, 2004; Gorbalenya et al, 2006)

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