Cleaving Expectations: A Review of Proteasome Functional and Catalytic Diversity

The proteasome is a central proteolytic complex that maintains protein homeostasis by eliminating damaged, misfolded, and regulatory proteins. Beyond this quality control role, it generates bioactive peptides that contribute to immune surveillance, intracellular signaling, neuronal communication, and antimicrobial defense. Proteolysis is mediated by the catalytic β1, β2, and β5 subunits, traditionally defined by caspase-like, trypsin-like, and chymotrypsin-like activities. However, these sites display overlapping and flexible specificities, enabling cleavage after nearly all amino acids. This review focuses on proteasome catalytic activity, with particular emphasis on the biochemical and structural features of the catalytic subunits that define cleavage selectivity. We first provide a historical overview of the discovery of proteolytic activities and trace the evolutionary diversification of subunits that gave rise to specialized variants such as the immunoproteasome, thymoproteasome, intermediate proteasomes, and the spermatoproteasome. We then highlight how advances in computational modeling and structural biology have refined our understanding of cleavage preferences. In addition, we examine how regulatory particles, post-translational modifications, and physiological conditions, including inflammation, oxidative stress, and aging, modulate proteolytic activity. Finally, we discuss the development of selective inhibitors targeting individual catalytic sites, emphasizing their therapeutic potential in cancer, autoimmunity, and infectious disease, and outline future directions for the field.