The impact and function of C-terminal degrons and protein misfolding in the degradation of truncated proteins

Abstract

Premature Termination Codons (PTCs) are mainly generated after nonsense and frameshift alterations. The Nonsense Mediated Decay (NMD) system detects and degrades mRNAs containing PTCs. However, the efficiency of this surveillance mechanism is limited and some PTC-containing mRNAs can escape from degradation, thus potentially generating truncated protein forms. The Ubiquitin Proteasome System (UPS) is involved in the degradation of proteins either by detecting specific amino acid sequence motifs (degrons) or by detecting misfolding features of the protein. Degrons located at the c-terminal region of proteins (c-degrons) potentiate a rapid degradation of proteins, however, their impact on the degradation of proteins with truncated c-terminus remains unknown. In this study, we employed two cancer datasets as natural experiments to study the degradation of truncated proteins: a dataset of more than 600 primary tumor biopsies from the Clinical Proteomics Tumor Analysis Consortium (CPTAC), and a dataset with more than 300 cancer-derived cell lines from CCLE with integrated genome, transcriptome and proteome information. In order to select those mutations producing truncated proteins, we annotated the NMD efficiency probability of all the PTCs in both datasets and classified them between NMD-skipping or NMD-triggering. To our surprise, not only NMD-skipping but also NMD-triggering showed decreased protein stability. We annotated all c-degrons instances in the predicted truncated proteins and analysed the changes in protein stability, but no significant differences nor tendencies were observed. We further explored whether the length of the truncated protein could impact protein stability and yet that was the case for NMD-skipping protein products but not for NMD-triggering, where protein stability decrease was independent of the mutation localization in the protein. In conclusion, c-degrons failed to explain the overall protein stability decrease of truncated proteins. However, major protein sequence loss increases destabilisation but only for proteins from NMD-skipping PTCs. Results presented in this study suggest that truncated proteins could follow different degradation pathways depending on NMD efficiency.