Wide Diversity and Complex Evolution of M42 Aminopeptidases With Contrasted Functional Properties in Archaea

M42 peptidases (TET) are ubiquitous, giant self-compartmentalized aminopeptidases forming unique tetrahedral structures. TETs may participate in protein homeostasis and amino acid recycling by processing peptides downstream of the proteasome and other related proteolytic complexes. Currently, only five TETs have been extensively studied in Archaea from 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 is lacking. In this study, we establish robust criteria for high-throughput identification of TET peptidases from sequence data and reveal their wide taxonomic distribution in Archaea. We functionally characterize six additional TETs, including four from Asgardarcheota. Our results identify two main functional classes, with generalist TETs displaying broad-spectrum activities and specialized TETs with more selective activities. We also report the first description of methionyl- and isoleucyl-aminopeptidases in the TET family. In addition to their diverse substrate specificities, the characterized TETs exhibit distinct activation profiles, varying in optimal temperature, pH, and metal cofactor requirements. Combining functional and phylogenetic analyses, 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 TETs arose following gene duplication or horizontal transfer. Finally, we highlight the presence of multiple TETs 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 that shaped their functional diversification.