PP2C phosphatases promote autophagy by dephosphorylation of the Atg1 complex

Autophagy is orchestrated by the Atg1-Atg13 complex in budding yeast. Under nutrient-rich conditions, Atg13 is maintained in a hyperphosphorylated state by TORC1 kinase. After nutrient starvation, Atg13 is dephosphorylated, triggering Atg1 kinase activity and autophagy induction. The phosphatases that dephosphorylate Atg13 remain uncharacterized. We show that two redundant PP2C phosphatases, Ptc2 and Ptc3, regulate autophagy via dephosphorylating both Atg13 and Atg1. In the absence of these phosphatases, starvation-induced macroautophagy is inhibited, as is the cytoplasm-to-vacuole targeting (Cvt) pathway, and the recruitment of the essential autophagy machinery to phagophore assembly sites (PAS) is impaired. Despite prolongation of the DNA damage-induced checkpoint in ptc2{Delta} ptc3{Delta} cells, genotoxin-induced autophagy is also blocked. Creating a genomic atg13-8SA allele under its endogenous promoter, lacking key TORC1 phosphorylation sites, bypasses the autophagy defect in ptc2{Delta} ptc3{Delta} strains. Taken together, these results imply that PP2C type phosphatases promote autophagy by regulating Atg1 complex.