Missions

This position is part of a project funded by the French National Research Agency (ANR) aimed at studying the role of ABC-F proteins in the translation process in the bacterium E. coli. The recruited postdoctoral researcher will be part of the “Physiology and regulation of protein synthesis” team led by Grégory Boël at the Institute of Physical and Chemical Biology (IBPC) and will work in close collaboration with Axel Innis's team (University of Bordeaux, ARNA INSERM U1212). This project aims to understand the physiological functions and the mechanisms of action on the ribosome of the four ABC-F family proteins in E. coli (EttA, YbiT, YheS and Uup).

Activités

-A few years ago, we identified that members of the ABC-F protein family act as translation factors and that they are ubiquitous across prokaryotes and eukaryotes (Boël et al., NSMB 2014; Chen, Boël et al., NSMB 2014). Multiple occurrences of ABC-F proteins are often found within a genome, suggesting different functions for each paralog (Fostier et al., FEMS Letters 2021). Recently, we showed that the ABC-F protein EttA targeted the translation of specific mRNAs. Some of these mRNAs encode enzymes of the glyoxylate shunt of the Krebs cycle. Moreover, identifying specific EttA targets revealed a peptide signature: the presence of negatively charged residues in the initial coding region (Ousalem et al., Nat. Comm. 2024). Based on this discovery, we have developed the RiboStallRescue project in collaboration with Axel Innis's team (University of Bordeaux). This project aims to identify context-dependent ribosomal stalls (Context-Dependent Ribosomal Stalling, CDRS) that are resolved by each of E. coli's ABC-F proteins, and to elucidate the specificity of each ABC-F. To obtain a comprehensive understanding and to limit risks, we propose a two-pronged approach combining global in vivo and in vitro methods. The in vivo methods are intended to establish the physiological functions of each ABC-F protein, while the in vitro experiments, carried out in Dr. Innis's team, will not only confirm these results but also reveal additional CDRS that may be undetectable in vivo. Sequences identified in vivo will then be tested in vitro to clarify the direct role of each ABC-F in translation and to elucidate their mechanisms of action. Conversely, CDRS sequences identified in vitro will be validated in vivo. Finally, the ribosomal complexes stalled on these identified CDRS, in the presence or absence of ABC-F proteins, will either be reconstituted in vitro or purified from cells, and their structures will be determined by cryo-electron microscopy (cryo-EM) in Dr. Innis's team.

Compétences

We are looking for a curious and highly motivated person holding a PhD in microbiology with demonstrated expertise in bacterial culture and genetics and solid experience working with RNA. The candidate must be comfortable with molecular biology techniques (cloning, mutagenesis, etc.) and familiar with the preparation and analysis of RNA samples by high-throughput sequencing (mRNA-seq and/or ribo-seq). Experience in protein purification and analyses such as Northern blot and Western blot would be a plus. Strong knowledge of protein synthesis and RNA biochemistry is required. The recruited person must demonstrate autonomy, rigor and good organizational skills in conducting experiments. Teamwork and the ability to present work orally and in writing are also essential criteria. Finally, a good command of spoken and written English is necessary. Applicants are invited to submit their CV with a complete list of publications, a cover letter and three references who may be contacted, via the CNRS Jobs website.

Contexte de travail

The candidate will conduct research within G. Boël's team in the unit “Microbial Gene Expression” (UMR8261) at the IBPC. The IBPC is a multidisciplinary institute of the National Centre for Scientific Research (CNRS) located in central Paris on the Pierre and Marie Curie campus (Paris 5th). The institute notably has a proteomics platform and a bioinformatics platform that will be used for this project. The EGM unit employs 35 people grouped into 5 teams focused on the study of RNA and the control of gene expression. G. Boël's team is interested in translation in bacteria through two aspects: (1) the characterization of ABC-F family translation factors and (2) the identification of determinants (motifs/structures) on mRNA that affect its stability and translatability. The team comprises three permanent staff: a CNRS research director, a CNRS engineer and a lecturer from Université Paris Cité, as well as a postdoctoral researcher. In addition, Master's students (M1 and M2) are regularly recruited for various projects within the team.

Contraintes et risques

This research project may involve the use of radioisotopes.

Informations complémentaires

EGM unit website: http://www.ibpc.fr/UMR8261/AccueilUMR8261.html For further information, candidates may contact Grégory Boël (boel@ibpc.fr).