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 <i>Saccharomyces cerevisiae</i>, 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 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mrow></mml:mrow> <mml:mrow><mml:mo>+</mml:mo></mml:mrow> </mml:msup> </mml:math> -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 <i>SIR2</i> 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 <i>ATG8</i> transcription, thereby limiting autophagic activity. Deletion of <i>SIR2</i> 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.