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FEBS J. 2014 Aug;281(16):3685-700. doi: 10.1111/febs.12890. Epub 2014 Jul 14.

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

Author information

1
Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Cantoblanco, Spain.

Abstract

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.

KEYWORDS:

IRES-dependent translation initiation; RNA structure; SHAPE footprint; eIF4G-binding; magnesium ions

PMID:
24961997
PMCID:
PMC4163634
DOI:
10.1111/febs.12890
[Indexed for MEDLINE]
Free PMC Article

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