Functional Interplay between Caspase Cleavage and Phosphorylation Sculpts the Apoptotic Proteome

Melissa M. Dix*, Gabriel M. Simon*, Chu Wang, Eric Okerberg1, Matthew P. Patricelli1, Benjamin F. Cravatt†

The Skaggs Institute for Chemical Biology and Department of Chemical Physiology
The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA 92037
1ActivX Biosciences, La Jolla, CA 92307, USA
*These authors contributed equally to the work
†To whom correspondence should be addressed: cravatt@scripps.edu

SUMMARY: Caspase proteases are principal mediators of apoptosis, where they cleave hundreds of proteins. Phosphorylation also plays an important role in apoptosis, although the extent to which proteolytic and phosphorylation pathways crosstalk during programmed cell death remains poorly understood. Using a quantitative proteomic platform that integrates phosphorylation sites into the topographical maps of proteins, we identify a cohort of over 500 apoptosis-specific phosphorylation events and show that they are enriched on cleaved proteins and clustered around sites of caspase proteolysis. We find that caspase cleavage can expose new sites for phosphorylation, and, conversely, that phosphorylation at the +3 position of cleavage sites can directly promote substrate proteolysis by caspase-8. This study provides a global portrait of the apoptotic phosphoproteome, revealing heretofore unrecognized forms of functional crosstalk between phosphorylation and caspase proteolytic pathways that lead to enhanced rates of protein cleavage and the unveiling of new sites for phosphorylation.


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This paper was published in Cell in the 20 July 2012 edition.


Global Mapping of the Topography and Magnitude of Proteolytic Events in Apoptosis

Melissa M. Dix*, Gabriel M. Simon*, Benjamin F. Cravatt†

The Skaggs Institute for Chemical Biology and Department of Chemical Physiology
The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA 92037
*These authors contributed equally to the work
†To whom correspondence should be addressed: cravatt@scripps.edu

SUMMARY: Proteolysis is a key regulatory process that promotes the (in)activation, translocation, and/or degradation of proteins. As such, there is considerable interest in methods to comprehensively characterize proteolytic pathways in biological systems. Here, we describe a robust and versatile proteomic platform that enables direct visualization of the topography and magnitude of proteolytic events on a global scale. We use this method to generate a proteome-wide map of proteolytic events induced by the intrinsic apoptotic pathway. This profile contained 91 characterized caspase substrates as well as 170 additional proteins not previously known to be cleaved during apoptosis. Surprisingly, the vast majority of proteolyzed proteins, regardless of the extent of cleavage, yielded persistent fragments that correspond to discrete protein domains, suggesting that the generation of active effector proteins may be a principal function of apoptotic proteolytic cascades.

Read the full-manuscript here:

This paper was published in Cell in the 22 August 2008 edition.