ATG deficiency impairs stationary-phase microlipophagy through acetic acid-induced clustering of Niemann–Pick type C proteins

While the role of autophagy-related (ATG) proteins in microautophagy remains unclear, their absence in budding yeast has been reported to impair stationary-phase microlipophagy. Here, we show that this defect in ATG-deficient ( atg Δ) cells arises not from a direct requirement of ATG proteins for the execution of microlipophagy but from accumulation of acetic acid (AA) in the medium. High concentrations of AA in the medium of atg Δ cells trigger the clustering of Niemann–Pick type C (NPC) proteins, causing impairment of raft-like vacuolar microdomain formation and suppression of microlipophagy. Lowering extracellular AA rapidly dissolves NPC protein clusters, restores vacuolar microdomains, and rescues microlipophagy in atg Δ cells. Conversely, elevating AA concentrations in the medium of wild-type cells induces NPC protein clusters and microlipophagy defects. These findings demonstrate that stationary-phase microlipophagy can proceed independently of ATG proteins and that the defect in atg Δ cells can be rescued by normalizing extracellular AA levels.