Turnover and replication analysis by isotope labeling (TRAIL) reveals the influence of tissue context on protein and organelle lifetimes

Abstract

The lifespans of proteins range from minutes to years within mammalian tissues. Protein lifespan is relevant to organismal aging, as long‐lived proteins accrue damage over time. It is unclear how protein lifetime is shaped by tissue context, where both cell turnover and proteolytic degradation contribute to protein turnover. We develop t urnover and r eplication a nalysis by 15 N i sotope l abeling (TRAIL) to quantify protein and cell lifetimes with high precision and demonstrate that cell turnover, sequence‐encoded features, and environmental factors modulate protein lifespan across tissues . Cell and protein turnover flux are comparable in proliferative tissues, while protein turnover outpaces cell turnover in slowly proliferative tissues. Physicochemical features such as hydrophobicity, charge, and disorder influence protein turnover in slowly proliferative tissues, but protein turnover is much less sequence‐selective in highly proliferative tissues. Protein lifetimes vary nonrandomly across tissues after correcting for cell turnover. Multiprotein complexes such as the ribosome have consistent lifetimes across tissues, while mitochondria, peroxisomes, and lipid droplets have variable lifetimes. TRAIL can be used to explore how environment, aging, and disease affect tissue homeostasis. image A new 15 N metabolic labeling method for parallel quantification of cell and protein turnover rates in mouse tissues illustrates the variable influence of “nature” versus “nurture” on protein turnover rates in vivo . The median proteome turnover rate and the identity of the longest‐ and shortest‐lived proteins vary across tissues. Protein turnover and cell turnover occur at similar rates in proliferative tissues, but protein turnover outpaces cell turnover in less proliferative tissues. Sequence features such as hydrophobicity, disorder, and isoelectric point contribute to protein turnover rate only in less proliferative tissues. Protein and organelle turnover rates remain very different from tissue to tissue even after correcting for cell turnover rates.