Coronavirus cis-Acting RNA Elements

Abstract

Coronaviruses have exceptionally large RNA genomes of approximately 30 kilobases. Genome replication and transcription is mediated by a multisubunit protein complex comprised of more than a dozen virus-encoded proteins. The protein complex is thought to bind specific cis-acting RNA elements primarily located in the 5'- and 3'-terminal genome regions and upstream of the open reading frames located in the 3'-proximal one-third of the genome. Here, we review our current understanding of coronavirus cis-acting RNA elements, focusing on elements required for genome replication and packaging. Recent bioinformatic, biochemical, and genetic studies suggest a previously unknown level of conservation of cis-acting RNA structures among different coronavirus genera and, in some cases, even beyond genus boundaries. Also, there is increasing evidence to suggest that individual cis-acting elements may be part of higher-order RNA structures involving long-range and dynamic RNA-RNA interactions between RNA structural elements separated by thousands of nucleotides in the viral genome. We discuss the structural and functional features of these cis-acting RNA elements and their specific functions in coronavirus RNA synthesis.

Keywords: Coronavirus; Genome packaging; RNA structure; RNA virus; Replication; cis-Acting element.

Fig. 1

Conserved cis-acting RNA elements in the 5′- and 3′-proximal genome regions of coronaviruses. Shown is the coronavirus genome organization with the two large 5′ ORFs, 1a and 1b, that together constitute the replicase gene, while details of structural and accessory protein ORFs are not shown. Black circles at the RNA 5′ ends indicate the 5′ cap structure, while (A)_n indicates the 3′ poly(A) tail. The − 1 ribosomal frameshift signal (RFS) at the ORF1a/1b junction site is indicated by an asterisk. S, S gene; N, N gene. Approximate positions of the packaging signals (PS) determined for MHV and TGEV are indicated by arrows. (A) Schematic representation of RNA structural elements in the 5′-terminal genome regions of MHV, BCoV, and HCoV-229E. Filled boxes indicate the leader-TRS (TRS-L). Boxes in light gray indicate the start codons of the uORF(s) located upstream of ORF1a. Boxes in dark gray indicate the position of the ORF1a start codon. (B) Schematic representation of RNA structural elements in the 3′-terminal genome regions of MHV, BCoV, and HCoV-229E. Major conserved RNA structural elements are shown, together with base-pairing interactions required to form a pseudoknot (PK) structure. Also shown is the position of a highly conserved octanucleotide sequence that is located in a single-stranded region. BSL, bulged stem-loop; L, loop; S, stem; SL, stem-loop structure; HVR, hypervariable region; PK, pseudoknot.