Credit: Nature Publishing Group

The mitochondria-associated kinase PINK1 and the cytoplasmic E3 ubiquitin ligase parkin mediate the recognition and disposal of damaged mitochondria by mitophagy; failure of this pathway has been associated with early-onset familial Parkinson's disease. PINK1, degraded upon entry into healthy mitochondria, accumulates on the surface of damaged mitochondria, where it recruits parkin to ubiquitinate substrate proteins. Sensing of the ubiquitinated proteins activates the ubiquitin-proteasome system and triggers an autophagic pathway leading to mitochondrial degradation. However, ubiquitination of mitochondrial surface proteins is kept in check by the surface-bound deubiquitinase USP30. Kirkpatrick, Bingol, Corn and colleagues now explore the mechanistic interplay between USP30 and parkin in the coordination of mitophagy. Induction of mitochondrial damage with the membrane-depolarizing agent CCCP in parkin-overexpressing cells had previously identified mitochondrial parkin substrates. Here the authors analyzed parkin-dependent ubiquitin linkages associated with mitochondrial fractions and found enrichment of Lys63- and atypical Lys6- and Lys11-linked ubiquitin chains. Interestingly, USP30 showed preferential activity toward Lys6-linked ubiquitin in vitro. In addition, purified USP30 removed Lys6- and Lys11-linked chains from anchored substrates on intact mitochondria isolated from CCCP-treated cells. Proteome-wide changes in ubiquitination upon USP30 overexpression identified a set of USP30 substrates, several of which overlap with known parkin substrates, suggesting that this subset of proteins may undergo coordinated regulation by the two enzymes. That USP30 activity has a major role in inhibiting ubiquitin-directed organelle degradation was further exemplified by its ability to block pexophagy upon ectopic expression on the surfaces of peroxisomes. These findings provide mechanistic insight into a pathway, governed by the intricate balance between ubiquitination and deubiquitination, that regulates homeostasis of mitochondria and possibly other organelles. (Nat. Cell. Biol. 17, 160–169, 2015)