Ribosome-dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE
Entidad
UAM. Departamento de Biología Molecular; Centro de Biología Molecular Severo Ochoa (CBM)Editor
Nature Publishing GroupFecha de edición
2018-12-01Cita
10.1038/s41598-018-23845-x
Scientific Reports 8.1 (2018): 5545
ISSN
2045-2322DOI
10.1038/s41598-018-23845-xFinanciado por
This work was supported by MINECO (BFU2014-54564-P, BIO2015-72716-EXP) and an Institutional grant from Fundación Ramón ArecesProyecto
Gobierno de España. BFU2014-54564-P; Gobierno de España. BIO2015-72716-EXPVersión del editor
https://doi.org/10.1038/s41598-018-23845-xMaterias
Ribosome; RNA; IRES; SHAPE; Biología y Biomedicina / BiologíaDerechos
© 2018 The Author(s)Resumen
Internal ribosome entry site (IRES) elements are RNA regions that recruit the translation machinery internally. Here we investigated the conformational changes and RNA dynamics of a picornavirus IRES upon incubation with distinct ribosomal fractions. Differential SHAPE analysis of the free RNA showed that nucleotides reaching the final conformation on long timescales were placed at domains 4 and 5, while candidates for long-range interactions were located in domain 3. Salt-washed ribosomes induced a fast RNA local flexibility modification of domains 2 and 3, while ribosome-associated factors changed domains 4 and 5. Consistent with this, modeling of the three-dimensional RNA structure indicated that incubation of the IRES with native ribosomes induced a local rearrangement of the apical region of domain 3, and a reorientation of domains 4 and 5. Furthermore, specific motifs within domains 2 and 3 showed a decreased flexibility upon incubation with ribosomal subunits in vitro, and presence of the IRES enhanced mRNA association to the ribosomal subunits in whole cell lysates. The finding that RNA modules can provide direct IRES-ribosome interaction suggests that linking these motifs to additional sequences able to recruit trans-acting factors could be useful to design synthetic IRESs with novel activities.
Lista de ficheros
Google Scholar:Lozano, Gloria
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Francisco-Velilla, Rosario
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Martínez-Salas, Encarnación
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