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 liked 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. Overall design: For the GPS peptidomic screen, amplicon sequencing was performed on GPS reporter library cells sorted into eight bins by fluorescence-activated cell sorting (FACS). Only reads that perfectly matched the designed sequences were retained. Two biological replicates were performed. For the CRISPR/Cas9 screen targeting proteostasis pathways, sgRNA sequences were amplified from reporter cells representing the top 5% of GFP/BFP ratios, while the total population was used as a control. The CRISPR screening results were analyzed using casTLE algorithm.