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

Abstract

Coronaviruses (CoV) are positive-sense single-stranded RNA viruses, harboring the largest viral RNA genomes known to date. Apart from the primary sequence encoding for all the viral proteins needed for the generation of new viral particles, certain regions of CoV genomes are known to fold into stable structures, controlling several aspects of CoV life cycle, from the regulation of the discontinuous transcription of subgenomic mRNAs, to the packaging of the genome into new virions. Here we review the current knowledge on CoV RNA structures, discussing it in light of the most recent discoveries made possible by analyses of the SARS-CoV-2 genome.

Keywords: RNA structure; SARS-CoV-2; coronavirus.

Figure 1.. Structure of the SARS-CoV-2 5′ UTR.

Secondary structure of the SARS-CoV-2 5′ UTR, with superimposed in vivo SHAPE reactivities from Manfredonia et al. [39]. Highly (red) and moderately (yellow) reactive residues from in vitro SHAPE (circles; Manfredonia et al. [39]), in vitro DMS (triangles; Manfredonia et al. [39]), in vivo SHAPE (squares; Huston et al. [36]) and in vivo DMS (pentagons; Lan et al. 2020) experiments are also indicated [36,37,39]. A higher reactivity indicates a higher propensity of bases to be single-stranded (for DMS), or structurally flexible (for SHAPE). Base-paired regions are color-coded according to the number of supporting chimeric reads from Ziv et al. [38]. The number of reads supporting the existence of SL8 was calculated by reanalyzing data from Ziv et al. [38] (GEO dataset: GSE154662).

Figure 2.. Structure models of the SARS-CoV-2 FSE.

(A) Secondary structure of the SARS-CoV-2 FSE three-stem pseudoknotted conformation, with superimposed reactivities from Zhang et al. [59]. (B) Cryo-EM-derived structure of the SARS-CoV-2 FSE three-stem pseudoknotted conformation (PDB: 6XRZ). (C) On the left, the proposed secondary structure models of two coexisting mutually-exclusive alternative conformations of the SARS-CoV-2 FSE, as derived by in vivo DMS analysis, with superimposed reactivities from Lan et al. [37]. The alternative conformation of stem 1 is boxed. On the right, the same alternative conformation of stem 1 as confirmed by independent in vitro and in vivo DMS and SHAPE analyses, with reactivities superimposed from Manfredonia et al. [39]. The slippery site is boxed in blue. (D) Structure of the FSE-arch enclosing the FSE, as identified by direct RNA–RNA interaction mapping in the SARS-CoV-2 genome, with base-pairs colored according to their relative abundance from Ziv et al. [38].

Figure 3.. Landscape of SARS-CoV-2 RNA structures as revealed by high-throughput studies.

On the top, the structures of conserved secondary structure elements, supported by significant covariation, as determined by SHAPE analyses of the SARS-CoV-2 genome, with superimposed reactivities from Manfredonia et al. [39] (1, 2, 6, 7, 9, 10, 17) and Huston et al. [36] (3, 4, 5). In addition, the structures of seven stem–loops (8, 11, 12, 13, 14, 15, 16) proposed to enclose the TRS-Bs (boxed in green), with superimposed reactivities from Lan et al. [37], are shown. On the bottom, an arc plot shows the long-range interactions identified by direct RNA–RNA interaction mapping in the SARS-CoV-2 genome, colored according to their relative abundance from Ziv et al. [38]. The FSE-arch is also indicated.