The AAA-ATPase Yta4 inhibits the interaction between Ppa2 and Atg43 to promote Atg43 phosphorylation and mitophagy.

AAA-ATPase Yta4/Msp1/ATAD1 is a well-known quality control factor that clears mistargeted tail-anchored proteins and precursor proteins on mitochondria. However, whether Yta4 preserves mitochondrial homeostasis through alternate pathways remains unclear. Traditionally, mitophagy has been recognized as a crucial pathway for eliminating dysfunctional mitochondria, thereby ensuring the maintenance of mitochondrial homeostasis. In this study, we unveil a novel role for Yta4 in sustaining mitochondrial homeostasis by facilitating mitophagy in fission yeast. The absence of Yta4 delays the phosphorylation of the mitophagy receptor Atg43 and specifically inhibits mitophagy. Additionally, Atg43 phosphorylation sites Ser32, Ser35, and Ser36, which are crucial for mitophagy, were identified. We further found that the phosphatase Ppa2 plays a major role in Atg43 dephosphorylation and inhibits excessive mitophagy. Yta4 physically interacts with both Atg43 and Ppa2, and coordinates with Ppa2 to modulate Atg43 phosphorylation and mitophagy. Moreover, Yta4 and Ppa2 bind to the same cytosolic region of Atg43, and Yta4 inhibits the interaction between Atg43 and Ppa2. Collectively, our findings suggest that Yta4 promotes mitophagy by ensuring the effectiveness of Atg43 phosphorylation. Thus, our findings reveal the novel function of Yta4 in regulating mitophagy and expand the understanding of the molecular mechanisms underlying mitophagy in fission yeast.