Phosphorylation of mitochondrial matrix proteins regulates their selective mitophagic degradation

Mitophagy, the autophagic degradation, is an important quality control mechanism in eukaryotic cells. In mammals, inability to identify defective mitochondria is associated with aging phenomena and neurodegenerative disorders. Previous studies from our lab showed that different mitochondrial matrix proteins undergo mitophagy with very different rates, but the underlying mechanism behind this surprising selectivity has remained obscure. We also demonstrated that AUP1, a mitochondrial protein phosphatase, is required for efficient mitophagy. In the current study, we wanted to test whether mitochondrial protein phosphorylation plays a role in regulating the selectivity of mitophagic processes. Our results show that mutant cells lacking Aup1 are affected in the mitophagy of some mitochondrial matrix proteins but not others, implying a role for matrix protein phosphorylation in the selectivity of mitophagy. We also find that deletion of additional mitochondrial kinases and phosphatases has different effects on mitophagy of different matrix proteins, consistent with a general role of phosphorylation in determining mitophagic selectivity. To better understand the relationship between mitochondrial protein phosphorylation and mitophagy rates, we mutagenized known phosphorylation sites in specific matrix phospho-protein to alanine and aspartate. Our results indicate that structural determinants on a mitochondrial matrix protein can govern its mitophagic fate, and that protein phosphorylation in the mitochondrial matrix can regulate these determinants and segregate proteins into sub-compartments destined for mitophagic degradation.