Proteome-wide C-degron activity profiling connects conditional regulation of the CTLH E3 ligase complex to ribosome biogenesis.

Many E3 ubiquitin ligases recognize degrons located at protein termini, but the paucity of bona fide substrates of N-degron and C-degron pathways hampers our understanding of their physiological significance. Devising an expression screening strategy to assess the effect of C-terminal "capping" on the stability of thousands of human proteins, we systematically identify substrates harboring C-degrons. Interrogating one leading candidate, ZMYND19, we characterize a C-degron pathway governed via the C-terminal to LisH (CTLH) E3 ligase complex subunit Muskelin. Cell-to-cell variability in ZMYND19 stability uncovered conditional regulation, with CTLH-mediated degradation impaired by TNF-α stimulation but enhanced by mTOR inhibition. Parallel genetic and proteomic screens identified angio-associated migratory protein (AAMP) and apoptosis-enhancing nuclease (AEN) as additional substrates of the CTLHMuskelin C-degron pathway, leading us to define an essential role for AAMP in ribosome maturation through chaperone activity toward uL16. Altogether, these data define a C-degron pathway connecting conditional regulation of the CTLH E3 ligase complex to ribosome biogenesis.