Protein C-terminal variations impact proteostasis

Protein C-termini can vary due to errors or programmed regulation, contributing to proteome diversity, yet their impact on the proteome remains poorly understood. Although aberrant C-termini are often linked to protein degradation, it is unclear if this holds true universally. In this study, we examine how C-terminal variations—arising from disease-associated nonstop mutations, alternative splicing, and translational readthrough—affect protein half-lives. Our findings indicate that, contrary to previous studies, erroneous C-termini can either stabilize or destabilize proteins. We have identified multiple oncoproteins and tumor suppressors whose protein stability is altered by disease-relevant nonstop mutations. Notably, we have found that C-terminal variations commonly influence the stability of canonical proteins, extending beyond their role in protein quality control. Furthermore, we have uncovered C-terminal features that distinguish erroneous from wild-type proteins and reveal that hydrophobic C-termini are targeted by a complex ubiquitin ligase network. Overall, our work broadens the understanding of C-terminal-dependent protein degradation and supports that C-terminal variation is a widespread strategy for generating protein forms with distinct half-lives to exert diverse biological functions. Protein C-terminal diversity is widespread, yet its proteome-wide impact remains unclear. Here, the authors show that C-terminal variations influence the stability of canonical and disease associated mutant proteins and define the sequence features and degradative mechanisms underlying this regulation.