Efficient protein turnover is essential for cell homeostasis and organ function. Loss of proteostasis is a hallmark of aging, which culminates as a severe reduction in protein turnover rates. To investigate protein turnover dynamics during aging, we performed continuous in vivo metabolic stable isotope labeling using 15N amino acid precursors and TMT-based multiplexed proteomic analysis. First, we discovered that the brain proteome uniquely experiences dynamic global turnover fluctuations during aging compared to heart and liver tissue. Second, in the brain proteome, global protein turnover trends across aging displayed sex-specific differences that were tightly linked to their cellular compartments. Next, parallel analyses of the insoluble proteome revealed that distinct cellular compartments experience hampered turnover, at least partially due to misfolding. Finally, we discovered that age-associated fluctuations in the activity of the ubiquitin proteasome system were linked to the turnover of the catalytic core subunits. Taken together, our study provides a proteome-wide atlas of protein turnover across the aging continuum and highlights a new link between the turnover of individual proteasome subunits and the age-associated decline in proteosome activity.

Learning Objectives

• Recognize the importance of using metabolic stable isotope labeling with multiplexed TMT-based quantification to probe age associated change in brain protein turnover.
• Describe the importance of protein degradation in hampering protein degradation.
• Understand sex specific change in brain protein turnover.
• Interpret change in protein levels and relative changes in protein turnover.