Blanc SVSE 8 - Blanc - SVSE 8 - Biochimie, biologie moléculaire et structurale

Fine-tuning of translational control through ribosomal RNA methylation: toward the specialized ribosome – RIBOMETH

Translational control by methylation of ribosomal RNA: toward the specialized ribosome.

Deciphering the variable components of the ribosomes contributing to translational regulation.

Deciphering the role of ribosomal RNA methylation in the mechanisms of translation.

Deciphering the mechanisms governing the regulation of protein synthesis is key to our understanding of gene expression, both in normal and pathological tissues. The post-genomic era brought a wealth of data on regulatory actors either trans-acting, or cis-acting.<br />Ribosomes have long been considered as mere effector of protein synthesis, being neutral in mRNA selection and translation efficiency. <br />However, this notion was recently challenged by several studies showing that ribosome composition is highly variable in cells and allowed a fine tuning of translational regulation.<br />The aim of RiboMeth project is to characterize the impact of ribosomal RNA variations, and notably methylation, in the control of protein synthesis.

The project relies on the complementarity of the technical know-how of the two partners, to analyze at the molecular level the role of methylation on the functioning of the ribosome, and to identify, through omics approaches, the cellular processes whose regulation relies on protein synthesis in a methylation-dependent manner.

The main parts of the project were initiated and are under way.

RiboMeth will help better understand how ribosomes contribute to protein synthesis control mechanisms. This project will provide a first detailed view of the relationship between methylation of ribosomal RNA, the ribosome composition and ribosome translational activity, and will open the way to detailed molecular exploration on how methylation impacts on the mains stages of translation, that are initiation, elongation and termination.

Publications des partenaires sur ce thème :

p53 acts as a safeguard of translational control by regulating fibrillarin and rRNA methylation in cancer.
Marcel V, Ghayad SE, Belin S, Therizols G, Morel AP, Solano-Gonzàlez E, Vendrell JA, Hacot S, Mertani HC, Albaret MA, Bourdon JC, Jordan L, Thompson A, Tafer Y, Cong R, Bouvet P, Saurin JC, Catez F, Prats AC, Puisieux A, Diaz JJ.
Cancer cell. 2013. 24:318-330.

p53, a translational regulator: contribution to its tumour-suppressor activity.
Marcel V, Catez F, Diaz JJ.
Oncogene. 2015 Mar 2. doi: 10.1038/onc.2015.25.


RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis.
Legendre R, Baudin-Baillieu A, Hatin I, Namy O.
Bioinformatics. 2015 Mar 25. pii: btv174.

New insights into stop codon recognition by eRF1.
Blanchet S, Rowe M, Von der Haar T, Fabret C, Demais S, Howard MJ, Namy O.
Nucleic Acids Res. 2015 Mar 31;43(6):3298-308. doi: 10.1093/nar/gkv154. Epub 2015 Mar 3.

In all living organisms, translation of mRNA into protein is carried out by the ribosomes, which ensure the decoding of the mRNA and peptide-bond formation. The ribosomes also support proofreading function that ensures translational fidelity, by watching frameshift, amino-acid misincorporation and stop codon read-through. Ribosomes are composed of proteins and RNAs and the description at the atomic level of the ribosome of archea, bacteria and more recently eukaryotes has confirmed rRNA as the molecular scaffold supporting the decoding, proofreading and peptide-bond formation activities of the ribosome. Ribosomal RNAs are chemically modified at more than 200 sites, carrying mainly ribose-methylation and pseudouridylation. rRNA chemical modifications have been shown in yeast to participate in ribosomal RNA structure, ribosomal translational activity, and to impact cell growth. However, the molecular function and biological role of the ribosomal RNA modifications remain to be defined.

Translational regulation plays an important role in several fundamental processes governing cell life such as proliferation, differentiation or stress response. It is now recognized that the ribosome is a regulatory platform participating in the selection of translated mRNA, translation efficiency and co-translational modification of nascent proteins. This notion is supported by the concept of "specialized ribosomes", which suggests that protein composition of ribosomes could differ within cells, and that different ribosomes could carry different translational activities.

While the "quality" of the ribosome emerges as a key element of its translational activity, data are still missing to firmly validate that human ribosomal function could be finely tuned through modifications of rRNAs. Furthermore, there is currently no information on the impact of variation of rRNA modifications on gene expression. The objective of the RIBOMETH project is to establish a detailed view of the relationships between rRNA methylation at specific sites and translational activity of human mature ribosomes. For this, we will modify the rRNA methylation pattern using different strategies, in several human cellular systems and analyze their impact on:
i) the ribosomal composition at the level of RNAs and proteins using dedicated innovative methods developed by Team 1
ii) the intrinsic translational activity and fidelity of ribosomes using dedicated reporter assays developed by Team 1 and 2, as well as on the selection of translated mRNAs, using the new ribosome profiling technology developed by Team 2.

The RIBOMETH project will provide the first integrated view of the role of rRNA modifications, from ribosome assembly, to ribosome activity, and up to physiological consequences. The main outcome of the RIBOMETH project will be the first map of rRNA methylation sites that are critical to the functioning of human ribosomes, and translation of specific mRNA. Such correlative map will allow to design and optimize new types of “antibiotic-like” molecules exhibiting the ability to modify the translational fidelity as it has been proposed for the treatment of stop codon diseases.

Project coordination

Jean-Jacques DIAZ (Centre de Recherche en Cancérologie de Lyon)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

GST, IGM Universite Paris XI (Paris-Sud)
CRCL - UMR Inserm 1052 CNRS 5286 Centre Léon Bérard Centre de Recherche en Cancérologie de Lyon

Help of the ANR 400,000 euros
Beginning and duration of the scientific project: December 2013 - 48 Months

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