Wide diversity and complex evolution of M42 aminopeptidases with contrasted functional activities in Archaea
Description
M42 peptidases (TET) are ubiquitous and unique types of giant self-compartmentalized aminopeptidases forming distinctive tetrahedral structures. TET may participate in protein homeostasis and amino acid recycling by processing peptides downstream of the proteasome and other related proteolytic complexes. Currently, only five TET have been studied in archaea of the Thermococcales order, with a predominant focus on structural characterization. Therefore, a clear view of the diversity and biological activities of this large enzymatic family has been lacking. In this study, we establish robust criteria for high-throughput identification of TET peptidases from sequence data. We reveal a wide taxonomic distribution of these enzymes across the whole archaea. We functionally characterize six additional TET including four from Asgardarcheota. Our results highlight the existence of two main functional classes, with generalist TET displaying broad-spectrum activities preferentially cleaving hydrophobic residues, and specialized TET with more selective activities targeting acidic amino acids. We also report the first description of methionyl and isoleucyl aminopeptidases in the TET family. In addition to their diverse substrate specificities, the characterized TET exhibit distinct activation profiles, with variations in optimal temperature, pH, and metal cofactor requirements. Combining our functional and phylogenetic results, we propose a classification of TET peptidases into 11 groups. Notably, we identify generalist group 11 as the ancestral TET in Archaea, from which specialized TET arose following gene duplication or horizontal transfers. Finally, we highlight the abundance of TET with selective activities in heterotrophic and mixotrophic organisms, suggesting a metabolic role for these enzymes in the degradation of environmental peptides. Overall, our work illuminates an underexplored diversity of TET enzymes, uncovering a complex evolutionary history which shaped their functional diversification. Owing to their functional versatility, TET peptidases hold significant potential for biotechnologial applications in nutrition, health, and cosmetics.