Structural analysis provides insights into the modular organization of picornavirus IRES |
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Authors: | Fernández Noemí García-Sacristán Ana Ramajo Jorge Briones Carlos Martínez-Salas Encarnación |
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Affiliation: | a Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spainb Laboratorio de Evolución Molecular, Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir Km. 4, 28850 Madrid, Spainc Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain |
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Abstract: | Picornavirus RNA translation is driven by the internal ribosome entry site (IRES) element. The impact of RNA structure on the foot-and-mouth disease virus (FMDV) IRES activity has been analyzed using Selective 2'Hydroxyl Acylation analyzed by Primer Extension (SHAPE) and high throughput analysis of RNA conformation by antisense oligonucleotides printed on microarrays. SHAPE reactivity revealed the self-folding capacity of domain 3 and evidenced a change of RNA structure in a defective GNRA mutant. A modified RNA conformation of this mutant was also evidenced by RNA accessibility to oligonucleotides. Interestingly, comparison of nucleotide reactivity with RNA accessibility revealed that SHAPE reactive nucleotides corresponding to the GNRA motif were not accessible to their respective target oligonucleotides. The differential response was observed both in domain 3 and the entire IRES. Our results demonstrate distant effects of the GNRA motif in the domain 3 RNA conformation, and highlight the modular organization of a picornavirus IRES. |
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Keywords: | Translation initiation Picornavirus IRES GNRA motif SHAPE probing RNA accessibility DNA microarrays |
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