Harmonizing labeling and analytical strategies to obtain protein turnover rates in intact adult animals

Changes in the abundance of individual proteins in the proteome can be elicited by modulation of protein synthesis (the rate of input of newly synthesised proteins into the protein pool) or degradation (the rate of removal of protein molecules from the pool). A full understanding of proteome changes therefore requires a definition of the roles of these two processes in proteostasis, collectively known as protein turnover. Because protein turnover occurs even in the absence of overt changes in pool abundance, turnover measurements necessitate monitoring the flux of stable isotope labeled precursors through the protein pool such as labeled amino acids or metabolic precursors such as ammonium chloride or heavy water. In cells in culture, the ability to manipulate precursor pools by rapid medium changes is simple, but for more complex systems such as intact animals, the approach becomes more convoluted. Individual methods bring specific complications, and the suitability of different methods has not been comprehensively explored. In this study we compare the turnover rates of proteins across four mouse tissues, obtained from the same inbred mouse strain maintained under identical husbandry conditions, measured using either [13C6]lysine or [2H2]O as the labeling precursor. We show that for long lived proteins, the two approaches yield essentially identical measures of the first order rate constant for degradation, but that for short lived proteins, there is a need to compensate for the slower equilibration of lysine through the precursor pools. The two approaches yield comparable turnover rates when certain amino acid labeling precursor enrichment rate constants are used in a two-compartment kinetics model; however, the measurement of precursor enrichment rate remains a challenge.