Thursday, 21st June 2018

Genome Dynamics and Function

    Internal initiation of translation in eurkaryotic mRNAs



2014 06 30 Grupo Encarna Sanchez 400px


Encarnación Martínez-Salas





Research summary:

Regulation of protein synthesis is a key step of many biological processes; its dysfunction leads to severe diseases. In adddition, the coding capacity of the genome is much larger that ever anticipated. Our main goal is to understand alternative mechanism of translation initiation in eukaryotes. Internal Ribosome Entry Site (IRES) elements are mRNA regions that govern internal initiation of translation. IRES elements substitute the function of the 5’ terminal cap present in conventional mRNAs, which is the anchoring point of the translation machinery. To achieve their function, IRES elements assemble ribonucleoprotein complexes in which RNA structure and IRES function is tightly coupled. However, a universal IRES motif remains to be elucidated, hampering the prediction of these regulatory elements genome-wide. During this period, we have important contributions to the functional and structural characterization of a model IRES element, and the characterization of proteins involved in internal initiation of translation. Our specific aims were the identification of protein and RNA partners of factors modulating IRES activity, the evaluation of synergism and/or interference with other factors involved in translation control, and the understanding of structural constraints in IRES elements which are essential for its activity (Figure 1). Using a multidisciplinary approach based on proteomic and genomic data, combined with functional and structural assays, we have shown that IRES-dependent translation is downregulated by Gemin5. This multifunctional protein harbors a bipartite non-conventional RNA-binding site on its C-terminal region. In turn, the N-terminal domain of this protein contains 14 WD repeats. This region mediates the interaction with the ribosome via the 60S subunit (Figure 2). Achievement of these goals has shed light on the molecular mechanism governing internal initiation driven by a model IRES element, allowing the prediction of hidden IRES-like motifs in the cellular transcriptome


 E martinezSalas Fig 1


E martinezSalas Fig 2
Fig 1   Fig 2

Relevant publications:

Diaz-Toledano, R., Lozano, G., and Martínez-Salas, E (2017) In-cell SHAPE uncovers dynamic interactions between the untranslated regions of the foot-and-mouth disease virus RNA Nucleic Acids Res, 45, 1416-1432.

Francisco-Velilla, R., Fernandez-Chamorro, J., Ramajo, J., and Martínez-Salas, E. (2016) The RNA-binding protein Gemin5 binds directly to the ribosome and regulates global translation. Nucleic Acids Res. 44, 8335-8351.

Lozano, G., Jimenez-Aparicio, R, Herrero, S., and Martínez-Salas, E. (2016) Fingerprinting the junctions of RNA secondary structure by an open-paddle wheel diruthenium compound. RNA 22, 330-338

Lozano, G., Fernandez, N., and Martínez-Salas, E. (2016) Modeling three-dimensional structural motifs of viral IRES. J. Mol. Biol. 2016, 428, 767-776

Fernandez-Chamorro, J., Lozano, G., Garcia-Martin, J.A., Ramajo, J, Dotu, I., Clote, P., and Martínez-Salas, E. (2016) Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements.. Sci. Rep. 6, 24243.

Garcia-Martin, J.A., Dotu, I., Fernandez-Chamorro, J., Lozano, G., Ramajo, J., Martínez-Salas, E., and Clote, P. (2016) RNAiFold2T: constraint programming design of thermo-IRES switches. Bioinformatics 32, i360-i368.

Francisco-Velilla, R., Lozano, G., Diaz-Toledano, R., Fernandez-Chamorro, J., Embarek, M. A., and Martínez-Salas, E. (2016) IRES elements: issues, controversies and evolutionary perspectives.In: R. Jagus, G. Hernandez (Eds) Evolution of the protein synthesis machinery and its regulation. Springer, Springer International Publishing AG Switzerland. pp. 547-564

Lozano, G., Trapote, A., Ramajo, J., Elduque, X., Grandas, A., Robles, J., Pedroso, E., and Martínez-Salas, E. (2015) RNA local flexibility perturbation of the IRES element induced by a novel ligand inhibits viral RNA translation. RNA Biol. 12, 555-568

Lozano, G., and Martínez-Salas, E. (2015) Structural insights into viral IRES-dependent translation mechanisms. Curr. Opin. Virol.12, 113-120

Piñeiro, D., Fernandez-Chamorro, J., Francisco-Velilla, R., and Martínez-Salas, E. (2015) Gemin5: a multitasking RNA-binding protein involved in translation control. Biomolecules 5, 528-544

Martínez-Salas, E., Francisco-Velilla, R., Fernandez-Chamorro, J., Lozano, G., and Diaz-Toledano, R. (2015) Picornavirus IRES elements: RNA structure and host protein interactions.. Virus Res. 206, 62-73

Francisco-Velilla, R., Fernandez-Chamorro, J., Lozano, G., Diaz-toledano, R., and Martínez-Salas, E. (2015) RNA-protein interaction methods to study viral IRES elements. Methods 91, 3-12