Biology subjects

Lafontaine, I.

Publications and source records attributed to Lafontaine, I..

4 recordsLinked to original sources

bioRxiv2025

Searching α-solenoid proteins involved in organellar gene expression

In photosynthetic eukaryotes of the green lineage, the expression of the chloroplast genome is mainly regulated post-transcriptionally, by RNA-binding proteins encoded in the nuclear genome (OTAF for Organelle Trans-Acting Factor). Most of those identified to date belong to two families of -solenoid proteins - the pentatrico-peptide repeat (PPR) and octatrico-peptide repeat (OPR) families - and interact with specific sequences on their target mRNAs through a domain composed of repeated motifs, allowing their maturation, splicing, editing, stabilization and translation activation. To identify new OTAFs, we developed three approaches for annotating - solenoid proteins targeted to the chloroplast or the mitochondria. One to identify distant homologs of existing OTAF families, and two others (decision tree and random forest classifiers) to identify new OTAF families. The combined approaches efficiently retrieve previously annotated OTAFs in 2 model organisms. It identified 1067 OPR proteins and 4983 PPR proteins in 43 proteomes of Archaeplastida. Our analysis also identified putative proteins composed of both OPR and PPR domains. Finally, our results identified 3300 other -solenoid candidates which are likely to participate as new regulators of organelle gene expression. In particular, we identified new candidates in species in which the regulatory mechanisms of plastid gene expression are still understudied, such as in the glaucophyte Cyanophora paradoxa and the red alga Porphyridium purpureum. We thus provide valuable new tools to decipher the repertoire of OTAF, as well as new candidates for experimental characterization in the entire eukaryotic tree of life.

evolutionary biology↗

bioRxiv2021

Retracing the evolution from antimicrobial to targeting peptides

We asked what peptide features govern targeting to the mitochondria versus the chloroplast using antimicrobial peptides as a starting point. This approach was inspired by the endosymbiotic hypothesis that organelle-targeting peptides derive from antimicrobial amphipathic peptides delivered by the host cell, to which organelle progenitors became resistant. To explore the molecular changes required to convert antimicrobial into targeting peptides, we expressed a set of 13 antimicrobial peptides in Chlamydomonas reinhardtii. Peptides were systematically modified to test distinctive features of mitochondrial and chloroplast targeting peptides, and we assessed their targeting potential by following the intracellular localization and maturation of a Venus fluorescent reporter used as cargo protein. Mitochondrial targeting can be achieved by some unmodified antimicrobial peptide sequences. Targeting to both organelles is improved by replacing Lysines with Arginines. Chloroplast targeting is enabled by the presence of flanking unstructured sequences, additional constraints consistent with chloroplast endosymbiosis having occurred in a cell that already contained mitochondria. If indeed targeting peptides evolved from antimicrobial peptides, required modifications imply a temporal evolutionary scenario with an early exchange of cationic residues, and a late acquisition of chloroplast specific motifs.

evolutionary biology↗

bioRxiv2020

An antimicrobial origin of targeting peptides to endosymbiotic organelles

Mitochondria and chloroplasts emerged from primary endosymbiosis. Most proteins of the endosymbiont were subsequently expressed in the nucleo-cytosol of the host and organelle-targeted via the acquisition of N-terminal presequences, whose evolutionary origin remains enigmatic. Using a quantitative assessment of their physico-chemical properties, we show that organelle targeting peptides, which are distinct from signal peptides targeting other subcellular compartments, group with a subset of antimicrobial peptides. We demonstrate that extant antimicrobial peptides target a fluorescent reporter to either the mitochondria or the chloroplast in the green alga Chlamydomonas reinhardtii and, conversely, that extant targeting peptides still display antimicrobial activity. Thus, we provide strong computational and functional evidence for an evolutionary link between organelle-targeting and antimicrobial peptides. Our results support the view that resistance of bacterial progenitors of organelles to the attack of host antimicrobial peptides has been instrumental in eukaryogenesis and in emergence of photosynthetic eukaryotes.

evolutionary biology↗

bioRxiv2017

A Molecular Portrait Of De Novo Genes

New genes, with novel protein functions, can evolve \"from scratch\" out of intergenic sequences. These de novo genes can integrate the cells genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes. To overcome these limitations, we developed a procedure that handles the usual pitfalls in de novo gene identification and predicted the emergence of 703 de novo genes in 15 yeast species from two genera whose phylogeny spans at least 100 million years of evolution. We established that de novo gene origination is a widespread phenomenon in yeasts, only a few being ultimately maintained by selection. We validated 82 candidates, by providing new translation evidence for 25 of them through mass spectrometry experiments. We also unambiguously identified the mutations that enabled the transition from non-coding to coding for 30 Saccharomyces de novo genes. We found that de novo genes preferentially emerge next to divergent promoters in GC-rich intergenic regions where the probability of finding a fortuitous and transcribed ORF is the highest. We found a more than 3-fold enrichment of de novo genes at recombination hot spots, which are GC-rich and nucleosome-free regions, suggesting that meiotic recombination would be a major driving force of de novo gene emergence in yeasts.

evolutionary biology↗