Missions

Eukaryotic photosynthesis is ensured by plastids, organelles originally acquired from a primary endosymbiosis with a cyanobacterial ancestor that gave rise to the extant green algae and land plants (together Viridiplantae), red algae and glaucophyte algae(Archibald 2015). nucleus. Re-importing back the products of those genes, now translated in the cytosol but functioning in the organelle, was one of the major issues faced by the endosymbiont. Such import relies on organelle targeting peptides (oTPs) at the N-terminus of most organelle targeted proteins. These oTPs enable passage across the organelle envelope, before being cleaved from the mature protein after import by processing peptidases and subsequently degraded by oligopeptidases. How the protein products of the nucleus-relocated genes acquired a targeting sequence allowing their import back to the organelle and how the organelle progenitors acquired the corresponding import machinery is a fascinating question. We recently challenged the hypothesis that organelle protein import machinery originated through co-opting an ancient bacterial resistance mechanism against antimicrobial peptides (AMPs) (Wollman 2016; Caspari and Lafontaine 2021). To that end we characterized the sequence and physico-chemical similarities of oTPs helical-amphiphilic ribosomally synthesised AMPs (HA-RAMPs) and experimentally assessed the ability of HA-RAMPs to target proteins into organelles as well as the antimicrobial potential of oTPs (Garrido et al. 2020), with a determination of the key residues involved in the evolutionary switch from one function to the other (Caspari et al. 2023). We have also retraced the evolutionary history of 4 peptidases involved in the cleavage and degradation of targeting peptides (Garrido et al. 2022).
The objective of the present project is to gain a better understanding of the molecular determinants governing protein targeting to the chloroplast and antimicrobial activity of with the aim to develop predictive models that can correctly identify such activities and to develop generative models able to output custom peptides. This work will be performed in close collaboration with the experimental team at the University of Bonn. We also want to retrace the comparative evolutionary analysis of canonical translocation pathways for mitochondria (TOM/TIM for translocase of the outer/inner membrane) and chloroplast (TOC/TIC for translocon on the outer/inner chloroplast membrane) through which proteins are imported into the organelles.


Within this evolutionary perspective, she/he will also revisit the evolution of the Calvin-Benson Cycle (CBC) towards an increase in its CO2-fixing activity. To this end, the candidate will infer ancestral sequences of the CBC enzymes, in order for experimentalists to design strains of two model organisms carrying these ancestral sequences, that will undergo directed evolution and be selected for their increased fitness. She/he will also analyze the mutational trajectories of the evolved strains.

The candidate will benefit from the presence in the host laboratory of senior experts in sequence analysis and genome evolution, chloroplast biology and photosynthesis. This unique environment should allow him/her to imagine and design new experiments as she/he progresses in this research project.

Activités

- Compile a comprehensive bibliography of TIC/TOC, TOM/TIM complexes and bacterial translocons involved in antimicrobial resistance.
- Retrace the evolutionary and comparative history of these three protein systems
- Perform phylogenetic analyses on CBC enzymes
- Analyze the evolution of genome structure in a microalgae population during an experimental evolution experiment
- Possible supervision of M2 interns

Compétences

- Produce an exhaustive bibliography of TIC/TOC, TOM/TIM complexes and bacterial translocons involved in antimicrobial peptide resistance.
– Trace the evolutionary and comparative history of these three protein systems
- Perform phylogenetic analyses on CBC enzymes
- Analyze the evolution of the genome structure of a microalgal population during an experimental evolution experiment
- Supervision of M2 trainees possible.

Skills/Knowledge:
- General knowledge of bioinformatics
- In-depth knowledge and strong experience in comparative genomics and genome evolution
- In-depth knowledge of NGS data analysis
- Knowledge of evolutionary biology
- Fluency in scientific English (reading and writing)
- Basic knowledge of genetics

Know-how:
- Design and implement experimental protocols
- Ability to analyze and report information (keep laboratory notebooks, prepare tables summarizing results, prepare oral presentations).
- Prepare articles for publication in international peer-reviewed journals
- Innovation, rigor and reliability in the execution of work.
- Organizational skills.
- Ability to work as part of a team

Contexte de travail

The work will be carried out in the UMR7141 host laboratory “Photobiology and Physiology of Plastids and Microalgae (P3M)”, headed by Dr. Angela Falciatore at the Institut de Biologie-Physico-chimique in Paris (http://www.ibpc.fr/UMR7141/en/home/). This laboratory, located in the heart of the Latin Quarter, employs just over 30 people, including 19 statutory members. It addresses key questions on the biology, evolution and ecology of microalgae, focusing on various model species (e.g. Chlamydomonas reinhardtii and Phaeodactylum tricornutum) and ecologically important phytoplankton species, studied using ecophysiological, biophysical, biochemical, genomic and genetic approaches.
The project will be performed under the supervision of Ingrid Lafontaine.