Kinetic Analysis of Protein Stability Reveals Age-Dependent Degradation

• Published in: Cell 2016-10, Vol.167 (3), p.803-815.e21
• Main Authors: McShane, Erik, Sin, Celine, Zauber, Henrik, Wells, Jonathan N., Donnelly, Neysan, Wang, Xi, Hou, Jingyi, Chen, Wei, Storchova, Zuzana, Marsh, Joseph A., Valleriani, Angelo, Selbach, Matthias
• Format: Article
• Language: English
• Subjects: Alanine - analogs & derivatives; Alanine - chemistry; Aneuploidy; bioorthogonal amino acid tagging; Cell Line; Click Chemistry; Gene Amplification; gene copy-number alterations; Humans; Kinetics; Markov Chains; metabolic labeling; posttranslational control; Proteasome Endopeptidase Complex - chemistry; Protein Biosynthesis; protein complex assembly; protein degradation; Protein Stability; Proteins - chemistry; Proteins - genetics; Proteins - metabolism; Proteolysis; Proteome; proteomics; pulse chase experiment; trisomy; Ubiquitin - chemistry
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2016.09.015

Do young and old protein molecules have the same probability to be degraded? We addressed this question using metabolic pulse-chase labeling and quantitative mass spectrometry to obtain degradation profiles for thousands of proteins. We find that >10% of proteins are degraded non-exponentially. Specifically, proteins are less stable in the first few hours of their life and stabilize with age. Degradation profiles are conserved and similar in two cell types. Many non-exponentially degraded (NED) proteins are subunits of complexes that are produced in super-stoichiometric amounts relative to their exponentially degraded (ED) counterparts. Within complexes, NED proteins have larger interaction interfaces and assemble earlier than ED subunits. Amplifying genes encoding NED proteins increases their initial degradation. Consistently, decay profiles can predict protein level attenuation in aneuploid cells. Together, our data show that non-exponential degradation is common, conserved, and has important consequences for complex formation and regulation of protein abundance. [Display omitted] •Global pulse-chase experiments identify non-exponentially degraded (NED) proteins•NED proteins become more stable with age•Many NED proteins are over-synthesized subunits of multiprotein complexes•Decay profiles can predict steady-state protein levels in aneuploid cells The ability to track protein degradation kinetics across the mammalian proteome reveals that a subset of proteins is less likely to be degraded the more time has passed since synthesis. Effects of genetic copy-number variation can be predicted by the properties of these proteins.