title: Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation.
abstract: RNA structure plays a fundamental role in internal initiation of translation. Picornavirus internal ribosome entry site (IRES) are long, efficient cis-acting elements that recruit the ribosome to internal mRNA sites. However, little is known about long-range constraints determining the IRES RNA structure. Here, we sought to investigate the functional and structural relevance of the invariant apical stem of a picornavirus IRES. Mutation of this apical stem revealed better performance of G:C compared with C:G base pairs, demonstrating that the secondary structure solely is not sufficient for IRES function. In turn, mutations designed to disrupt the stem abolished IRES activity. Lack of tolerance to accept genetic variability in the apical stem was supported by the presence of coupled covariations within the adjacent stem-loops. SHAPE structural analysis, gel mobility-shift and microarrays-based RNA accessibility revealed that the apical stem contributes to maintain IRES RNA structure through the generation of distant interactions between two adjacent stem-loops. Our results demonstrate that a highly interactive structure constrained by distant interactions involving invariant G:C base pairs plays a key role in maintaining the RNA conformation necessary for IRES-mediated translation.
authors: Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
authors: Noemí
authors: N
authors: Fernández
authors: Olga
authors: O
authors: Fernandez-Miragall
authors: Jorge
authors: J
authors: Ramajo
authors: Ana
authors: A
authors: García-Sacristán
authors: Nicolás
authors: N
authors: Bellora
authors: Eduardo
authors: E
authors: Eyras
authors: Carlos
authors: C
authors: Briones
authors: Encarnación
authors: E
authors: Martínez-Salas
mesh_terms: D020121:5' Untranslated Regions; D020029:Base Pairing; D001483:Base Sequence; D029544:Foot-and-Mouth Disease Virus / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010442:Peptide Chain Initiation, Translational; D012367:RNA, Viral / Q000737:chemistry*
chemical_list: D020121:5' Untranslated Regions; D012367:RNA, Viral