Exploring the Staphylococcus aureus host-pathogen interface using degradomic technologies

Staphylococcus aureus deploys an arsenal of secreted proteases to remodel the host environment during infection. While traditional substrate-by-substrate characterization has revealed critical host proteins under protease modulation, these conventional strategies cannot reveal the full scope of proteolytic activity occurring at the host-pathogen interface. Degradomic and N-terminomic technologies have begun to bridge this gap by enabling an unbiased, global mapping of protease-generated neo-N-termini across complex host tissues and cell proteomes. Recent work applying these tools to define discrete S. aureus protease pathodegradomes has propelled the field toward a system-level understanding of proteolytic activity. In this minireview, we highlight how terminal amine isotopic labeling of substrates and a newer methodology, terminal amine guanidination of substrates-charge reversal, have captured a deeper understanding of the V8 protease and how this enzyme can dismantle host immune defenses and engender disease. These techniques offer a powerful framework for the future in characterizing the substrate repertoires of other S. aureus secreted proteases, such as aureolysin, staphopain A and B, and the Spls. Furthermore, these advances demonstrate the applicability of degradomic profiling to diverse infection niches, revealing previously unrecognized roles for proteolytic activity in varying host contexts. Finally, we consider how this comprehensive understanding of S. aureus protease activity can inform clinical applications such as protease inhibitor design, host-directed therapies, and pathodegradome-based diagnostics.