N. Terrapon team’s guest: Sophie Abby, TIMC, University of Grenoble -“From genome annotation to the origins of new functions: the case of quinone biosynthetic pathways”

Abstract

In this seminar, I will present a multi-scale view of the evolution and diversification of enzymes and biosynthetic pathways. To this end, I will use the perspective of the isoprenoid quinones production in Bacteria. Isoprenoid quinones are lipids that shuttle electrons in electron transfer chains: they are therefore at the heart of cellular energy production via respiration and photosynthesis. Despite their essentiality and overall conservation, quinone biosynthetic pathways endured a variety of evolutionary events that led to their diversification that we aim to unravel. Our first endeavor is thus to produce highly reliable genomic annotations of the enzymes and proteins involved, and sometimes to propose novel proteins for missing steps in the pathways. To this end, we integrate the information of genome context conservation, taxonomic distribution, phylogenetic grouping, and experimental validation. The study of quinone pathways illustrates how enzymes from a same protein family can evolve distinct yet close functions through gene duplication, but also how biosynthetic pathways can evolve variants while conserving the same precursor and end-product. The study of the quinone repertoire across the bacterial phylum Pseudomonadota enabled us to infer how its dynamics involved genetic transfers and losses of entire quinone pathways, and how this dynamics likely accompanied the metabolic transition between oxic and anoxic environments. Finally, I’ll show how the discovery of novel respiratory quinones can help understand the early diversification of bacterial metabolisms.

Biography:

Sophie Abby is a CNRS researcher and professor at Université Grenoble Alpes, specializing in evolutionary biology with a focus on the mechanisms of diversification in prokaryotes, including bacteria and archaea. She is affiliated with the TIMC-IMAG laboratory, specifically the TrEE (Translational microbiology – Evolution – Engineering) team, where she studies microbial evolution at multiple scales, from enzymes to macromolecular complexes and genome dynamics in relation to environmental adaptation.
 Her research integrates computational and biological approaches, combining genomics, phylogenetics, and bioinformatics to understand molecular evolution and functional diversification.
Abby’s work has been recognized with the CNRS Bronze Medal in 2023, awarded for her early-career contributions and fruitful research in microbial evolution and bioinformatics.