Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family - Inria - Institut national de recherche en sciences et technologies du numérique Accéder directement au contenu
Article Dans Une Revue PLoS Computational Biology Année : 2023

Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family

Résumé

Numerous computational methods based on sequences or structures have been developed for the characterization of protein function, but they are still unsatisfactory to deal with the multiple functions of multi-domain protein families. Here we propose an original approach based on 1) the detection of conserved sequence modules using partial local multiple alignment, 2) the phylogenetic inference of species/genes/modules/functions evolutionary histories, and 3) the identification of co-appearances of modules and functions. Applying our framework to the multidomain ADAMTS-TSL family including ADAMTS (A Disintegrin-like and Metalloproteinase with ThromboSpondin motif) and ADAMTS-like proteins over nine species including human, we identify 45 sequence module signatures that are associated with the occurrence of 278 Protein-Protein Interactions in ancestral genes. Some of these signatures are supported by published experimental data and the others provide new insights (e.g. ADAMTS-5). The module signatures of ADAMTS ancestors notably highlight the dual variability of the propeptide and ancillary regions suggesting the importance of these two regions in the specialization of ADAMTS during evolution. Our analyses further indicate convergent interactions of ADAMTS with COMP and CCN2 proteins. Overall, our study provides 186 sequence module signatures that discriminate distinct subgroups of ADAMTS and ADAMTSL and that may result from selective pressures on novel functions and phenotypes.
Fichier principal
Vignette du fichier
journal.pcbi.1011404.pdf (5.93 Mo) Télécharger le fichier
Origine : Publication financée par une institution
Licence : CC BY - Paternité

Dates et versions

hal-04248728 , version 1 (18-10-2023)

Licence

Paternité

Identifiants

Citer

Olivier Dennler, François Coste, Samuel Blanquart, Catherine Belleannée, Nathalie Théret. Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family. PLoS Computational Biology, 2023, 19 (8), pp.e1011404. ⟨10.1371/journal.pcbi.1011404⟩. ⟨hal-04248728⟩
23 Consultations
14 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More