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. 2015 Aug 3;206:120-33.
doi: 10.1016/j.virusres.2015.02.025. Epub 2015 Feb 28.

The Structure and Functions of Coronavirus Genomic 3' and 5' Ends

Free PMC article

The Structure and Functions of Coronavirus Genomic 3' and 5' Ends

Dong Yang et al. Virus Res. .
Free PMC article


Coronaviruses (CoVs) are an important cause of illness in humans and animals. Most human coronaviruses commonly cause relatively mild respiratory illnesses; however two zoonotic coronaviruses, SARS-CoV and MERS-CoV, can cause severe illness and death. Investigations over the past 35 years have illuminated many aspects of coronavirus replication. The focus of this review is the functional analysis of conserved RNA secondary structures in the 5' and 3' of the betacoronavirus genomes. The 5' 350 nucleotides folds into a set of RNA secondary structures which are well conserved, and reverse genetic studies indicate that these structures play an important role in the discontinuous synthesis of subgenomic RNAs in the betacoronaviruses. These cis-acting elements extend 3' of the 5'UTR into ORF1a. The 3'UTR is similarly conserved and contains all of the cis-acting sequences necessary for viral replication. Two competing conformations near the 5' end of the 3'UTR have been shown to make up a potential molecular switch. There is some evidence that an association between the 3' and 5'UTRs is necessary for subgenomic RNA synthesis, but the basis for this association is not yet clear. A number of host RNA proteins have been shown to bind to the 5' and 3' cis-acting regions, but the significance of these in viral replication is not clear. Two viral proteins have been identified as binding to the 5' cis-acting region, nsp1 and N protein. A genetic interaction between nsp8 and nsp9 and the region of the 3'UTR that contains the putative molecular switch suggests that these two proteins bind to this region.

Keywords: Coronaviruses; RNA binding proteins; RNA secondary structure; Virus replication; cis-Acting sequences.


Fig. 1
Fig. 1
Comparison of secondary structure models of the 5′ regions of MHV-A59, BCoV, MERS-CoV and SARS-CoV. (A) The MHV-A59 model was generated by SHAPE analysis. (B) The thermodynamically most stable models of the corresponding regions of BCoV-Mebus, (C) MERS-CoV (Al-Hasan 3), and SARS-CoV (D) were generated by RNAstructure. The gray and italicized text denotes the core leader TRS regions. The gray AUGs represent the start codons of the short open reading frames (heavy black lines) that are upstream from the nsp1 initiating AUG codons (pink shading) in all four viruses. The nsp1 open reading frames are indicated by the red lines. Note that the nomenclature for BCoV is not equivalent to that of previous studies by the Brian Laboratory (see text); SL1 and SL2 corresponds to SLI, SL3 to SLII, SL4 to SLIII, SL5A to SLIV, SL5B to SLV, SL5C to SLVI, S5 to a long-range RNA–RNA interaction, and SL6 to SLVIII.
Fig. 2
Fig. 2
A schematic drawing of the secondary structures of the 3′ untranslated regions of MHV and MERS-CoV. For the MERS-CoV the dotted line in the pseudoknot (PK) represent a potential non-canonical UC base pair.

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