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Study of the translation initiation mechanism of histone H4

Research unit

UPR 9002 - Architecture et réactivité de l'ARN (IBMC)
15, rue Rene Descartes 67084 - Strasbourg Cedex

Group

Name: Evolution des systèmes d'initiation de la traduction chez les eucaryotes

Group leader: ERIANI Gilbert - g.eriani@ibmc-cnrs.unistra.fr

Group leader's phone: 0388417042

Group organization:
- Chercheurs: 4
- ITA: 1
- Doctorants: 1
- Post-Docs: 1
- Autres: 0

Publications of the team linked to the topic (3 last years):
1) Martin, F., Barends, S., Jaeger, S., Schaeffer, L., Prongidi-Fix, L. et Eriani, G. (2011)
Cap-assisted internal initiation of translation of histone H4.
Molecular Cell 41, 197-209.

2) Prongidi-Fix L., Schaeffer L., Simonetti A., Barends S., Ménétret J.F., Klaholz B., Eriani G., Martin F. (2013). Rapid purification of ribosomal particles assembled on histone H4 mRNA: a new method based on mRNA-DNA chimaeras. Biochem J. 449, 719-728.
3) Martin, F. (2012). 15 years of the Yeast Three-hybrid System: RNA-protein interactions Under investigation. Methods. 58, 367-375.

About PhD

PhD Director: MARTIN Franck - f.martin@ibmc-cnrs.unistra.fr

Phone: 0388417042

Junior advisor: non

Co-tutely: non

Co-Director: non

About PhD topic :

Title: Study of the translation initiation mechanism of histone H4

Project: In eukaryotes, canonical translation initiation is cap-dependent and requires a scanning step of the 5' untranslated region by the ribosomes in order to find the initiation codon. Our lab has recently shown that some cellular mRNAs such as histone H4 mRNA escape to this standard model. Histone H4 translation is initiated through an original mechanism that combines cellular (cap-dependence) and viral properties (no scanning and internal entry of ribosomes). Such mechanism of tethering of ribosomes to initiation factors bound to mRNA sequences may explain the absence of scanning and very efficient translation of histone H4 protein during the S-phase of the cell-cycle (Martin and coll. (2011) Molecular Cell 41, 197-209).
In a preliminary study, histone H4 mRNA has been probed by enzymatic and chemical probes and the secondary structure of H4 mRNA has been solved. Some remarkable secondary structure elements have been identified in the ORF, elements that will be studied by the PhD candidate. A first structural element consists in a 80-nt structure composed of 3 helices connected by a 3 way junction. This domain is located 20-nt downstream the AUG initiation codon and it is supposed to interact with the ribosome during the initiation step and the cap structure located on the 5' end. The second essential structure is located in the middle of the mRNA. It is folded as a double stem-loop structure and binds eIF4E (the cap-binding initiation factor) trough a binding site that is distinct from the cap-binding site. A third essential domain is made by the interaction of distal RNA sequences, forming a complex architecture that is highly dynamic and might adopt an alternative conformation. The thesis project will consist in deciphering the molecular mechanisms that lead to ribosome recruitment and very efficient translation. More specifically, the function of the 3 RNA elements will be investigated using RNA-protein interactions tools: RNA probing, mutagenesis, RNA cross-linking, interactions with ribosomes and initiation factors. The project will rely on structural studies performed in collaboration with two external groups: cryo-Electro-Microscopy will be used to reconstruct a 3D model of H4 mRNA bound to the ribosome, X-ray analysis will be used to solve the 3D structure of the whole H4 mRNA or of some parts.

Wished skills: Good knowledge of molecular biology basics (gene cloning, gene expression, mutagenesis), of biochemistry and bio-informatics. Competences in cell-culture will be appreciated.

Expertises which will be acquired during the training: At the end of the thesis, students will be familiar with techniques related to RNA, DNA and protein experimentation. They will be able to identify proteic or nucleic partners involved in supramolecular complex formation. Skills in bioinformatics, and MS analysis.