Mots-Clés
comparative genomics
microbial diversity
protein 3D structure
Description
Dinoflagellates are a diverse and ecologically important group of unicellular eukaryotes that play key roles in marine ecosystems. They are primary producers in phytoplankton and coral reef symbionts, and some of them are drivers of harmful algal blooms [1,2]. Alongside their remarkable biological innovations and trophic diversity [3], Dinoflagellate genomes remain among the most enigmatic in the eukaryotic domain, characterized by unusual features such as permanently condensed chromosomes, extensive gene duplication and atypical transcriptional regulation [4–6]. A significant proportion of dinoflagellate coding potential remains uncharacterized because of their very low similitude at the sequence level to reference protein databases[7]. These enigmatic proteins, which constitute their dark proteome, are key to understanding the molecular basis of their biological innovations and ecological success. To reduce this gap, in the framework of the ANR project “Exploring the functional diversity and genomic novelty of Dinoflagellates through the lens of their evolution and ecology”[8] we have compiled a dataset of diverse dinoflagellate proteomes and reconstructed gene families. Using sequence to sequence comparisons we have observed a number of protein coding gene families conserved and duplicated throughout the evolutionary history of dinoflagellate species potentially representing lineage innovations that have no sequence similarity to comprehensive annotation databases. Because the three-dimensional (3D) structure of a protein is more conserved than its sequence, comparing 3D structures offers a more sensitive way of identifying distant homologous proteins[9,10]. Therefore, we aim to better understand the origin and function of these conserved but enigmatic dinoflagellate proteins combining recently developed 3D protein structure prediction and structural homology search methods[11,12].
The particular objectives are :(1) Exploring gene families without annotations and originated and/or duplicated throughout the evolutionary history of dinoflagellates and investigate their features (disorder, transmembrane segments, cellular localization, etc), (2) Using 3D structure prediction methods on these prioritized lineage-specific proteins and (3) Looking for structural homologs of these proteins into 3D structure databases to find remote homologues that give us insights into their origin and functions and reveal potential novel protein folds originated in this eukaryotic lineage.
Références (iauthored by the supervising team)
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7. Meng A, Corre E, Probert I, Gutierrez-Rodriguez A, Siano R, Annamale A,Alberti A, Da Silva C, Wincker P, Le Crom S, Not . and Bittner L. Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network. Mol Ecol. 2018;27: 2365–2380.
8. Explorer la DIVErsité fonctionnelle et la nouveauté génomique des DINOflagellés à travers le prisme de leur évolution et de leur écologie. In: Agence nationale de la recherche granted to Lucie Bittner. [cited 1 Oct 2025]. Available: https://anr.fr/Projet-ANR-24-CE02-0557
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12. Barrio-Hernandez I, Yeo J, Jänes J, Wein T, Varadi M, Velankar S, et al. Clustering predicted structures at the scale of the known protein universe. bioRxiv. 2023. doi:10.1101/2023.03.09.531927