Distinct Evolutionary Trajectories of Major Intracellular Proteolytic Systems in Gilthead Seabream and European Seabass

Intracellular proteolysis is essential for protein turnover, cellular homeostasis, stress responses, immune function, development and tissue remodeling. In teleost fishes, ancient vertebrate and teleost-specific whole-genome duplication events (1R, 2R, Ts3R) increased gene copy number, followed by lineage-specific patterns of gene retention, loss and regulatory divergence. We investigated three major intracellular proteolytic systems, the ubiquitin–proteasome system (UPS), calpains and cathepsins, in gilthead seabream (Sparus aurata) and European seabass (Dicentrarchus labrax). Using comparative genomic, phylogenetic, syntenic and transcriptomic approaches, we identified and curated gene repertoires, inferred duplication histories and examined developmental and tissue-specific expression patterns. We identified 29 and 22 calpain genes, 23 and 17 cathepsin genes and 61 and 53 UPS genes in gilthead seabream and European seabass, respectively. Phylogenetic and synteny analyses indicated that retained paralogs were inferred to derive from a combination of ancient vertebrate duplications, teleost-specific whole-genome duplication and lineage- or species-specific events. Single copy genes predominated the UPS and only selected duplicated components showed patterns compatible with retention following the Ts3R. In contrast, calpains and cathepsins showed broader paralog retention, mixed duplication origins and greater diversity in developmental and tissue-specific expression patterns. Expression profiling indicated that most UPS genes were broadly expressed, whereas several calpain and cathepsin paralogs displayed stage- or tissue-dependent expression patterns. Overall, these results suggest that intracellular proteolytic systems in teleosts followed partly distinct evolutionary trajectories, with comparatively greater conservation of the multi-subunit UPS and expression patterns consistent with greater regulatory divergence among calpain and cathepsin paralogs. Retained proteolytic paralogs therefore displayed divergent expression patterns consistent with possible regulatory divergence which could reflect subfunctionalization following genome duplication.