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Significance Macroautophagy/autophagy removes surplus and/or dysfunctional cellular components for recycling in the lysosome/vacuole. During times of stress, autophagy is upregulated to ensure survival. A set of autophagy-related (Atg) proteins act in concert in a highly regulated manner to ensure proper levels of autophagy; aberrant induction of this process is correlated with numerous diseases. In this work, we show a nuanced mechanism by which autophagy is kept at a basal level via the ubiquitin−proteasome system-dependent reduction of Atg9, a transmembrane protein essential to autophagy. Macroautophagy/autophagy is a highly conserved eukaryotic molecular process that facilitates the recycling of superfluous cytoplasmic materials, damaged organelles, and invading pathogens, resulting in proper cellular homeostasis and survival during stress conditions. Autophagy is stringently regulated at multiple stages, including control at transcriptional, translational, and posttranslational levels. In this work, we identified a mechanism by which regulation of autophagy is achieved through the posttranslational modification of Atg9. Here, we show that, in order to limit autophagy to a low, basal level during normal conditions, Atg9 is ubiquitinated and subsequently targeted for degradation in a proteasome-dependent manner through the action of the E3 ligase Met30. When cells require increased autophagy flux to respond to nutrient deprivation, the proteolysis of Atg9 is significantly reduced. Overall, this work reveals an additional layer of mechanistic regulation that allows cells to further maintain appropriate levels of autophagy and to rapidly induce this process in response to stress.

Downregulation of autophagy by Met30-mediated Atg9 ubiquitination