Ribosome-dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE
Entity
UAM. Departamento de Biología Molecular; Centro de Biología Molecular Severo Ochoa (CBM)Publisher
Nature Publishing GroupDate
2018-12-01Citation
10.1038/s41598-018-23845-x
Scientific Reports 8.1 (2018): 5545
ISSN
2045-2322DOI
10.1038/s41598-018-23845-xFunded by
This work was supported by MINECO (BFU2014-54564-P, BIO2015-72716-EXP) and an Institutional grant from Fundación Ramón ArecesProject
Gobierno de España. BFU2014-54564-P; Gobierno de España. BIO2015-72716-EXPEditor's Version
https://doi.org/10.1038/s41598-018-23845-xSubjects
Ribosome; RNA; IRES; SHAPE; Biología y Biomedicina / BiologíaRights
© 2018 The Author(s)Abstract
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.
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Google Scholar:Lozano, Gloria
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Francisco-Velilla, Rosario
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Martínez-Salas, Encarnación
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