Sir2 regulates selective autophagy in stationary-phase yeast cells

Autophagy contributes to cellular homeostasis by degrading and recycling intracellular components, especially under nutrient-limited conditions. While autophagy is well characterized under acute starvation in synthetic media in Saccharomyces cerevisiae, its regulation during the stationary phase of prolonged growth in nutrient-rich complex media, when cells experience gradual metabolic shifts and sustained stress, remains poorly understood. In this study, we identified Sir2, an NAD ${}^{+}$ -dependent histone deacetylase, as a key suppressor of autophagy during the stationary phase in YPD complex medium. Using GFP-Atg8 processing as a readout of autophagic flux, we demonstrated that SIR2 deletion led to sustained autophagy activation. Notably, Sir2 selectively inhibited mitophagy, pexophagy, and the Cvt pathway, while non-selective autophagy remained largely unaffected. Transcriptomic analysis revealed that Sir2 facilitates a coordinated entry into quiescence, in part by regulating ribosome biogenesis and nutrient-responsive pathways during the stationary phase. Mechanistically, Sir2 stabilized Ume6, a repressor of ATG8 transcription, thereby limiting autophagic activity. Deletion of SIR2 drastically increased the phosphorylation and stabilization of the mitochondrial receptor Atg32 during the stationary phase, leading to enhanced mitophagy. Additionally, we found that ROS generated by mitophagy enhanced autophagy through a positive feedback loop. Collectively, our findings establish Sir2 as a previously unrecognized regulator of selective autophagy during the stationary phase in complex medium and highlight how cells dynamically control organelle degradation to maintain viability under extended metabolic stress.