Apoptosis, or programmed cell death, represents an ultimate fate decision in cell biology. This process is critical for cellular differentiation and remodeling of tissues, and for anti-viral and anti-tumor defense. The study of apoptotic pathways has important ramifications for determining what is critical for cellular homeostasis, and for the development of potential anti-cancer therapeutics. A distinct molecular feature of apoptosis is the widespread but controlled cellular proteolysis, that is predominantly mediated by eight members of the caspase family of cysteine proteases. These enzymes are like demolition experts that cleave protein targets critical for cellular life. We have designed new enzymes and antibodies to study and activate individual caspases and the proteins they cleave. A robust proteomic method for global profiling of proteolysis (“degradomics”) in cells has been developed. Key to this is an engineered enzyme, subtiligase, that permits selective labeling and enrichment for the protein N-termini created as a result of proteolysis. Using this approach we have already identified >300 caspase substrates from Jurkat cells that were induced to undergo apoptosis by treatment with the chemotherapeutic agent etoposide. The proteins fall into a wide range of functional classes, and reveal much about the molecular components, logic, and timed sequence of events that drive a cell from life to death. We believe these engineered enzymes and proteomic appproaches will be useful for characterizing the proteolysis of apoptosis induced by various agents or in different cell types, and will be generally useful for dissecting protease signaling pathways.

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