title: The DegraBase: a database of proteolysis in healthy and apoptotic human cells.
abstract: Proteolysis is a critical post-translational modification for regulation of cellular processes. Our lab has previously developed a technique for specifically labeling unmodified protein N termini, the α-aminome, using the engineered enzyme, subtiligase. Here we present a database, called the DegraBase (http://wellslab.ucsf.edu/degrabase/), which compiles 8090 unique N termini from 3206 proteins directly identified in subtiligase-based positive enrichment mass spectrometry experiments in healthy and apoptotic human cell lines. We include both previously published and unpublished data in our analysis, resulting in a total of 2144 unique α-amines identified in healthy cells, and 6990 in cells undergoing apoptosis. The N termini derive from three general categories of proteolysis with respect to cleavage location and functional role: translational N-terminal methionine processing (∼10% of total proteolysis), sites close to the translational N terminus that likely represent removal of transit or signal peptides (∼25% of total), and finally, other endoproteolytic cuts (∼65% of total). Induction of apoptosis causes relatively little change in the first two proteolytic categories, but dramatic changes are seen in endoproteolysis. For example, we observed 1706 putative apoptotic caspase cuts, more than double the total annotated sites in the CASBAH and MEROPS databases. In the endoproteolysis category, there are a total of nearly 3000 noncaspase nontryptic cleavages that are not currently reported in the MEROPS database. These studies significantly increase the annotation for all categories of proteolysis in human cells and allow public access for investigators to explore interesting proteolytic events in healthy and apoptotic human cells.
authors.affiliation: Department of Pharmaceutical Chemistry, University of California-San Francisco, CA 94158, USA.
authors.forename: Emily D
authors.initials: ED
authors.lastname: Crawford
authors.forename: Julia E
authors.initials: JE
authors.lastname: Seaman
authors.forename: Nick
authors.initials: N
authors.lastname: Agard
authors.forename: Gerald W
authors.initials: GW
authors.lastname: Hsu
authors.forename: Olivier
authors.initials: O
authors.lastname: Julien
authors.forename: Sami
authors.initials: S
authors.lastname: Mahrus
authors.forename: Huy
authors.initials: H
authors.lastname: Nguyen
authors.forename: Kazutaka
authors.initials: K
authors.lastname: Shimbo
authors.forename: Hikari A I
authors.initials: HA
authors.lastname: Yoshihara
authors.forename: Min
authors.initials: M
authors.lastname: Zhuang
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Chalkley
authors.forename: James A
authors.initials: JA
authors.lastname: Wells
mesh_terms: D017209:Apoptosis; D020169:Caspases / Q000378:metabolism; D045744:Cell Line, Tumor; D002853:Chromatography, Liquid / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D019169:Jurkat Cells; D010453:Peptide Synthases / Q000378:metabolism; D010455:Peptides / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D059748:Proteolysis; D020543:Proteome / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D013381:Subtilisins / Q000378:metabolism; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides; D020543:Proteome; D013381:Subtilisins; D020169:Caspases; D010453:Peptide Synthases; C117282:subtiligase