Aging and diet alter the protein ubiquitylation landscape in the mouse brain

Post-translational modifications (PTMs) regulate protein homeostasis, but how aging impacts PTMs is unclear. Here, we used mass spectrometry to reveal changes in hundreds of protein ubiquitylation, acetylation, and phosphorylation sites in the mouse aging brain. We show that aging has a major impact on protein ubiquitylation. 29% of the ubiquitylation sites were affected independently of protein abundance, indicating altered PTM stoichiometry. Using iPSCs-derived neurons, we estimated that 35% of ubiquitylation changes observed in the aged brain can be recapitulated by reduced proteasome activity. Finally, we tested whether protein ubiquitylation in the brain can be influenced by dietary interventions. We found that one cycle of dietary restriction and re-feeding modifies the brain ubiquitylome, rescuing some but exacerbating other ubiquitylation changes observed in old brains. Our findings reveal an age-dependent ubiquitylation signature modifiable by dietary intervention providing insights into mechanisms of protein homeostasis impairment and highlighting new biomarkers of brain aging. Overall design: We investigated which proteome and posttranslational modifications (phosphorylation, acetylation, and ubiquitylation) changes the mouse brain undergoes during aging. Additionally, we measured changes at the transcriptome level to understand if mRNA levels were explaining the data coming from the proteomic datasets. We used brains coming from five young (3 months old) and five old (33 months old) wild-type mice and generated RNA-seq data to analyze gene expression profiles.