Cabecera CBMSO CSIC UAM

Monday, 9th December 2019

Internal initiation of translation in eukaryotic mRNAs

 

Grupo400

 


Encarnación Martínez-Salas

ESciStaff

EPublications

 

 

Research summary:

Our main interests are focused to understand the principles guiding alternative mechanisms of translation initiation in eukaryotes. This includes structural and functional analysis of non-coding regions, and identification and characterization of RNA-binding proteins (RBPs) interacting with internal ribosome entry sites (IRES). Genomic and proteomic approaches lead us to identify the network of interactions of RBPs that perform key roles on gene expression. A representative example is Gemin5, the RNA-binding protein of the SMN complex. Defects on the SMN complex cause SMA (Spinal muscular atrophy), an autosomal rare disease. This multifunctional protein performs a critical role in translation control (Fig. 1). Gemin5 harbors a bipartite non-conventional RNA-binding site (RBS1-RBS2) on its C-terminal region, while the N-terminal domain contains 14 WD repeats that mediate the interaction with the ribosome. Using a CLIP-based procedure to search for the cellular targets of the RBS1 domain we identified an internal region of Gemin5 mRNA as a hit of RBS1. Functional analysis of this hit unveiled a feedback loop with its own mRNA, counteracting the negative effect of Gemin5 on translation.

We continue our efforts to understand RNA regulatory elements with the aim to explain the coding potential of eukaryotic genomes, expanding the number of RNAs that can be translated using cap-independent mechanisms under normal conditions or cellular stress. IRESs 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, distinct IRESs assemble ribonucleoprotein complexes, which include a subset of eIFs and diverse RBPs. In all cases, RNA structure and IRES function is tightly coupled. Our specific aims were the identification of of factors modulating IRES activity, the evaluation of synergism and/or interference with other factors involved in translation control, and the understanding of RNA structural constraints which are essential for its activity. Fig. 2 shows the conformational changes observed by SHAPE upon incubation of the IRES with native ribosomes. Our findings could allow the prediction of IRES-like motifs in the cellular transcriptome, as well as to infer the role of novel RBPs harboring non-conventional RBDs in translation control.

 

figure 1

Fig. 1

 

figure 1

Fig. 2

 


 

Relevant publications:

  • Francisco-Velilla R, Embarc-Buh A, Martinez-Salas E (2019) RNA-binding modes impacting on translation control: the versatile multidomain protein Gemin5. BioEssays 41(4):e1800241.
  • Fernandez-Chamorro J, Francisco Velilla R, Ramajo J, Martinez-Salas E (2019) IRES-driven RNA localization at ER-Golgi compartment is mediated by RAB1b and ARF5. Life Sci Alliance 2(1). pii: e201800131.
  • Lozano G, Francisco-Velilla R, Martinez-Salas E (2018) Deconstructing IRES elements: an update of structural motifs and functional divergences. Open Biology 8 (11).  pii: 180155.
  • Rodriguez-Pulido M, Sanchez-Aparicio MT, Martinez-Salas E, Garcia-Sastre A, Sobrino F, Saiz M (2018) Innate immune sensor LGP2 is cleaved by the leader protease of foot-and-mouth disease virus. Plos Pathog 14(6): e1007135.
  • Francisco-Velilla R, Fernandez-Chamorro J, Dotu I, Martinez-Salas E (2018) The RNA landscape of the non-canonical RNA-binding domain of Gemin5 unveils a feedback loop with its own mRNA counteracting the negative effect on translation. Nucleic Acids Res 46, 7339-7353.
  • Lozano G, Francisco-Velilla R, Martinez-Salas E (2018) Ribosome-dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE. Sci Rep 8(1): 5545.
  • Martínez-Salas E, Francisco-Velilla R, Fernandez-Chamorro J, Embarek MA (2018) Insights into structural and mechanistic features of viral IRES elements. Front Microbiol 8:2629.
  • Galan A, Lozano G, Piñeiro D, Martinez-Salas E (2017) G3BP1 interacts directly with the FMDV IRES and negatively regulates translation. FEBS J 284, 3202-3217.
  • Diaz-Toledano R, Lozano G, 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, 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, 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 JA, Ramajo J, Dotu I, Clote P, Martínez-Salas E (2016) Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements. Sci Rep 6, 24243.
  • Garcia-Martin JA, Dotu I, Fernandez-Chamorro J, Lozano G, Ramajo J, Martínez-Salas E, Clote P (2016) RNAiFold2T: constraint programming design of thermo-IRES switches. Bioinformatics 32, i360-i368.
  • Lozano G, Trapote A, Ramajo J, Elduque X, Grandas A, Robles J, Pedroso E, 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, 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, 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, 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, Martínez-Salas E (2015) RNA-protein interaction methods to study viral IRES elements. Methods 91, 3-12.

https://www.ncbi.nlm.nih.gov/pubmed/?term=Martinez-Salas+E

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