PROTEOMICS 2015* Tales from protein TAILS: the protease web deciphers the N terminome (#42)
Biological systems are complex and so model systems leading to models to predict human biological processes are required for mechanistic understanding of physiological pathways in all biological events and responses, signaling pathways and their perturbations in disease, and drug target validation. For example, interactions of proteases and inhibitors through protein cleavage and inhibition play crucial roles in the regulation of biological systems. Well studied as classically described protein cascades e.g. the complement system and coagulation, or newer recognized cascades of kallikreins in skin and caspases in apoptosis, these interactions have been proposed 10 years ago to expand pervasively in a network termed the protease web.
We compiled large-scale data of protease web interaction and expression to investigate the regulatory potential of the protease web. Using graph theory to represent the protease web of annotated cleavage and inhibition information, we investigated connectivity in the protease web. We identified a pervasive human protease web, where interactions between protease classes and cascades are common with protease inhibitors, in particular serpins, often forming network hubs. The model describes how proteases can influence the cleavage of many more proteins than their direct substrates through protease activation pathways or inactivation of protease inhibitors. Our model successfully predicted a perplexing proteolytic pathway in vivo, where activities of MMP8 and neutrophil elastase are linked by an inactivating cleavage of serpin A1 by MMP8 that we experimentally validated. We also found that protein interaction databases frequently contain protease interactions, in particular inhibitions, and improved our model of the protease web. Degradomics analysis using TAILS N-terminomics allowed us to dissect proteolysis in skin inflammation and demonstrated the interconnectivity of the protease web and new roles for proteases in vivo. By removing serpin blocks, MMPs flip the “Metallic Serpin Switch” and so dynamically regulate serine protease cascades by altering the balance between intact inhibitory serpins and inactivated cleaved serpins.
Our findings supply systematically derived and validated evidence for the existence of the protease web, where interactions are potentially broad but are fine tuned by expression and localization of interactors leading to specific interactions in- and outside cells and in specific tissues.
