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Internal ribosome entry site ( IRES ) elements are high‐order  RNA  structures that promote internal initiation of translation to allow protein synthesis under situations that compromise the general cap‐dependent translation mechanism. Picornavirus  IRES  elements are highly efficient elements with a modular  RNA  structure organization. Here we investigated the effect of Mg 2+  concentration on the local flexibility and solvent accessibility of the foot‐and‐mouth disease virus ( FMDV )  IRES  element measured on the basis of selective 2′‐hydroxyl acylation analyzed by primer extension ( SHAPE ) reactivity and hydroxyl radical cleavage. We have found that Mg 2+  concentration affects the organization of discrete  IRES  regions, mainly the apical region of domain 3, the 10 nt loop of domain 4, and the pyrimidine tract of domain 5. In support of the effect of  RNA  structure on  IRES  activity, substitution or deletion mutants of the 10 nt loop of domain 4 impair internal initiation. In addition, divalent cations affect the binding of eIF4G, a eukaryotic initiation factor that is essential for  IRES ‐dependent translation that interacts with domain 4. Binding of eIF4G is favored by the local  RNA  flexibility adopted at low Mg 2+  concentration, while eIF4B interacts with the  IRES  independently of the compactness of the RNA structure. Our study shows that the  IRES  element adopts a near‐native structure in the absence of proteins, shedding light on the influence of Mg 2+  ions on the local flexibility and binding of eIF4G in a model  IRES  element.

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