The Eukaryotic Proteome Is Shaped by E3 Ubiquitin Ligases Targeting C-Terminal Degrons

• Published in: Cell 2018-06, Vol.173 (7), p.1622-1635.e14
• Main Authors: Koren, Itay, Timms, Richard T., Kula, Tomasz, Xu, Qikai, Li, Mamie Z., Elledge, Stephen J.
• Format: Article
• Language: English
• Subjects: Amino Acid Motifs; Animals; Antigens, Neoplasm - metabolism; C terminus; Computational Biology - methods; CRISPR-Cas Systems - genetics; CRL; Cullin; degron; DesCEND; E3 ubiquitin ligase; Genetic Vectors - genetics; Genetic Vectors - metabolism; global protein stability; GPS; HEK293 Cells; Humans; Lentivirus - genetics; Leupeptins - pharmacology; Open Reading Frames - genetics; Peptides - metabolism; Proteasome Endopeptidase Complex - chemistry; Proteasome Endopeptidase Complex - metabolism; protein degradation; Protein Stability - drug effects; Protein Subunits - metabolism; Proteolysis; Proteome - genetics; Proteome - metabolism; Receptors, Cytokine - genetics; Receptors, Cytokine - metabolism; Ubiquitin-Protein Ligases - metabolism; ubiquitination
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2018.04.028

Degrons are minimal elements that mediate the interaction of proteins with degradation machineries to promote proteolysis. Despite their central role in proteostasis, the number of known degrons remains small, and a facile technology to characterize them is lacking. Using a strategy combining global protein stability (GPS) profiling with a synthetic human peptidome, we identify thousands of peptides containing degron activity. Employing CRISPR screening, we establish that the stability of many proteins is regulated through degrons located at their C terminus. We characterize eight Cullin-RING E3 ubiquitin ligase (CRL) complex adaptors that regulate C-terminal degrons, including six CRL2 and two CRL4 complexes, and computationally implicate multiple non-CRLs in end recognition. Proteome analysis revealed that the C termini of eukaryotic proteins are depleted for C-terminal degrons, suggesting an E3-ligase-dependent modulation of proteome composition. Thus, we propose that a series of “C-end rules” operate to govern protein stability and shape the eukaryotic proteome. [Display omitted] •GPS-peptidome is a high-throughput technology for identifying degrons in mammalian cells•C-terminal degrons regulate the stability of many proteins•Distinct classes of C-terminal degrons are degraded by Cullin-RING E3 ubiquitin ligase complexes•DesCEND (destruction via C-end degrons) has shaped the eukaryotic proteome C-terminal degron motifs regulate mammalian protein stability via interactions with Cullin-RING E3 ubiquitin ligase complexes.