Evolutionary conserved motifs constrain the RNA structure organization of picornavirus IRES

Abstract

a b s t r a c tPicornavirus RNAs initiate translation using a 5 0 end-independent mechanism based on internal ribosome entry site (IRES) elements. Despite performing similar functions, IRES elements present in genetically distant RNAs differ in primary sequence, RNA secondary structure and trans-acting factors requirement. The lack of conserved features amongst IRESs represents obstacles for the understanding of the internal initiation process. RNA structure is tightly linked to picornavirus IRES activity, consistent with the conservation of RNA motifs. This study extends the functional relevance of evolutionary conserved motifs of foot-and-mouth disease virus (FMDV) IRES. SHAPE structural analysis of mutant IRESs revealed local changes in RNA flexibility indicating the existence of an interactive structure constrained by lateral bulges that maintain the RNA conformation necessary for IRES-mediated translation.

Magnesium‐dependent folding of a picornavirus IRES element modulates RNA conformation and eIF4G interaction

“…With regard to the changes induced by different Mg 2+ concentrations on the local RNA flexibility of the apical region of domain 3, it is worth noting that this region harbors three conserved motifs (GNRA, RAAA and the C‐rich loop). Disruption of these motifs or destabilization of the corresponding stems led to a defective IRES and induced changes in the RNA structure of this region . The SHAPE reactivity changes observed upon Mg 2+ increase in the folding buffer are consistent with a strong influence of the divalent cation on the structural organization of this RNA domain.…”

Local RNA flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation

“…In support of this hypothesis, a mutational analysis carried out on SL1 residues showed that disruption of the stem reduced IRES activity whereas compensatory mutations restoring the secondary structure recovered translation. 59 Although the nucleotides involved in tertiary interactions remain elusive, our results support the existence of a complex network of long-distant interactions within this IRES region. This hypothesis is in agreement with earlier proposals in which nucleotides belonging to the GNRA motif, the RAAA stem-loop and G 240 within the C-rich bulge are linked in the three-dimensional RNA structure.…”

Picornavirus IRES elements: RNA structure and host protein interactions

“…The relationship between RNA structure and biological function of types I and II has been analyzed by mutational analysis and RNA probing (Bailey and Tapprich, 2007;Fernandez et al, 2013;Haller and Semler, 1992;Haller et al, 1996;Malnou et al, 2002;Serrano et al, 2009). Additionally, RNA modeling agrees with the experimental observation that mutations disrupting certain stems impaired IRES activity, and conversely, compensatory mutations restored IRES function (Hoffman and Palmenberg, 1996;Martinez-Salas et al, 1996).…”