Conservation and Diversity Among the Three-dimensional Folds of the Dicistroviridae Intergenic Region IRESes

Abstract

Internal ribosome entry site (IRES) RNAs are necessary for successful infection of many pathogenic viruses, but the details of the RNA structure-based mechanism used to bind and manipulate the ribosome remain poorly understood. The IRES RNAs from the Dicistroviridae intergenic region (IGR) are an excellent model system to understand the fundamental tenets of IRES function, requiring no protein factors to manipulate the ribosome and initiate translation. Here, we explore the architecture of four members of the IGR IRESes, representative of the two divergent classes of these IRES RNAs. Using biochemical and structural probing methods, we show that despite sequence variability they contain a common three-dimensional fold. The three-dimensional architecture of the ribosome binding domain from these IRESes is organized around a core helical scaffold, around which the rest of the RNA molecule folds. However, subtle variation in the folds of these IRESes and the presence of an additional secondary structure element suggest differences in the details of their manipulation of the large ribosomal subunit. Overall, the results demonstrate how a conserved three-dimensional RNA fold governs ribosome binding and manipulation.

Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA–like structural element in the ribosomal decoding center

“…It is likely that the contact between SLIII and ASF also contributes to the mechanism of translocation of the PKI-SLIII domain from the A site to the P site of the ribosome. In fact, deletion of SLIII of the TSV IRES did not significantly hamper the formation of the 40S • IRES and 80S • IRES complexes (13,30), whereas the efficiency of in vitro translation was inhibited (30), consistent with the proposed role of SLIII in the initial positioning and/or translocation of the TSV IRES.…”

“…PKI, located immediately upstream of the start codon, forms a separate domain at the 3′ region of the IRES. This domain is essential for the function of IGR IRESs (13). The crystal structure of an isolated PKI of the CrPV IGR IRES shows that the pseudoknot resembles the anticodon stem loop of tRNA bound to a cognate mRNA codon (14,15).…”

Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection

“…Disruption of SLIII base pairing inhibits TSV IRES translation, which can be effectively restored by compensatory mutations (29). Similarly, deletion of SLIII abrogates IRES activity and proper ribosome positioning on the IRES, but does not affect ribosome binding (27,31). Although such findings indicate that SLIII is indispensable, its exact role in IRESmediated translation has not been unambiguously defined.…”

“…Because type I and II IGR IRESs adopt overall comparable secondary structures, they generally have been considered functionally and mechanistically similar (27)(28)(29). Indeed, with chimeric IRESs, the ribosome-binding and PKI domains of type I and II IRESs are functionally interchangeable (30,31).…”

Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome

“…1B) (14). Despite some sequence differences and secondary structure variations, the members of the IGR IRES family fold into similar three-dimensional architectures (19). The crystal structures of the unbound domains 1 and 2 of the Plautia stali intestine virus (PSIV) IRES (20) and domain 3 of the cricket paralysis virus (CrPV) IRES (21) have been solved by X-ray crystallography (Fig.…”