Mots-Clés

Chloroplast biology genetic innovations comparative genomics phylogenomics experimental evolution

Description

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). Later, some of microalgae these were in turn incorporated into a variety of heterotrophic protists through secondary and tertiary endosymbiotic events, creating the astounding diversity of eukaryotic algae. These various endosymbiotic events were followed by massive gene transfers from the plastid progenitors to the host nucleus.  Re-importing back the products of these 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) located 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 the 4 major 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 an experimental team at the University of Bonn. In addition, we will 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 the oTPs drive protein import 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.

Required skills: applicants should be skilled in programming and statistics and have a genuine interest for evolutionary biology. Some experience in comparative genomics or machine learning approaches would be appreciated.

References:

Archibald JM. 2015. Endosymbiosis and Eukaryotic Cell Evolution. Current Biology 25: R911–R921.

Caspari OD, Garrido C, Law CO, Choquet Y, Wollman F-A, Lafontaine I. 2023. Converting antimicrobial into targeting peptides reveals key features governing protein import into mitochondria and chloroplasts. Plant Communications 100555.

Caspari OD, Lafontaine I. 2021. The role of antimicrobial peptides in the evolution of endosymbiotic protein import. PLOS Pathogens 17: e1009466.

Garrido C, Caspari OD, Choquet Y, Wollman F-A, Lafontaine I. 2020. Evidence Supporting an Antimicrobial Origin of Targeting Peptides to Endosymbiotic Organelles. Cells 9: 1795.

Garrido C, Wollman F-A, Lafontaine I. 2022. The Evolutionary History of Peptidases Involved in the Processing of Organelle-Targeting Peptides. Genome Biology and Evolution 14: evac101.

Wollman F-A. 2016. An antimicrobial origin of transit peptides accounts for early endosymbiotic events. Traffic 17: 1322–1328.