Longitudinal in vivo metabolic labeling reveals tissue-specific mitochondrial proteome turnover rates and proteins selectively altered by parkin deficiency

Our study utilizes a longitudinal isotopic metabolic labeling approach in vivo in combination with organelle fraction proteomics to address the role of parkin in mitochondrial protein turnover in mice. The use of metabolic labeling provides a method to quantitatively determine the global changes in protein half-lives whilst simultaneously assessing protein expression. Studying two diverse mitochondrial populations, we demonstrated the median half-life of brain striatal synaptic mitochondrial proteins is significantly greater than that of hepatic mitochondrial proteins (25.7 vs. 3.5 days). Furthermore, loss of parkin resulted in an overall, albeit modest, increase in both mitochondrial protein abundance and half-life. Pathway and functional analysis of our proteomics data identified both known and novel pathways affected by loss of parkin that are consistent with its role in both mitochondrial quality control and neurodegeneration. Our study therefore adds to a growing body of evidence suggesting dependence on parkin is low for basal mitophagy in vivo and provides a foundation for the investigation of novel parkin targets.

Automated summary

Our study utilized a combination of longitudinal isotopic metabolic labeling and organelle fraction proteomics to investigate the role of parkin in mitochondrial protein turnover in mice. We found that the half-life of brain striatal synaptic mitochondrial proteins is significantly longer than that of hepatic mitochondrial proteins. Loss of parkin resulted in a modest increase in mitochondrial protein abundance and half-life, and affected both known and novel pathways related to mitochondrial quality control and neurodegeneration. This study adds to the evidence suggesting low dependence on parkin for basal mitophagy in vivo and provides insights for future research on parkin targets.