PAQR3 controls autophagy by integrating AMPK signaling to enhance ATG14L-associated PI3K activity

The Beclin1-VPS34 complex is recognized as a central node in regulating autophagy via interacting with diverse molecules such as ATG14L for autophagy initiation and UVRAG for autophagosome maturation. However, the underlying molecular mechanism that coordinates the timely activation of VPS34 complex is poorly understood. Here, we identify that PAQR3 governs the preferential formation and activation of ATG14L-linked VPS34 complex for autophagy initiation via two levels of regulation. Firstly, PAQR3 functions as a scaffold protein that facilitates the formation of ATG14L- but not UVRAG-linked VPS34 complex, leading to elevated capacity of PI(3)P generation ahead of starvation signals. Secondly, AMPK phosphorylates PAQR3 at threonine 32 and switches on PI(3)P production to initiate autophagosome formation swiftly after glucose starvation. Deletion of PAQR3 leads to reduction of exercise-induced autophagy in mice, accompanied by a certain degree of disaggregation of ATG14L-associated VPS34 complex. Together, this study uncovers that PAQR3 can not only enhance the capacity of pro-autophagy class III PI3K due to its scaffold function, but also integrate AMPK signal to activation of ATG14L-linked VPS34 complex upon glucose starvation. Synopsis Golgi-resident protein PAQR3 facilitates formation of the autophagy-initiating ATG14L-VPS34 complex. Upon glucose starvation, AMPK phosphorylates PAQR3 to enhance this function, thus integrating nutrient sensing with VPS34 activity. PAQR3 enhances autophagosome formation and ATG14L-linked class III PI3K activity without altering AMPK or mTOR activity. PAQR3 facilitates the formation of the ATG14L-linked VPS34 complex, but not the UVRAG-associated VPS34 complex. PAQR3 T32 is phosphorylated by AMPK upon glucose starvation in an ATG14L-dependent manner. PAQR3 T32 phosphorylation is required for ATG14L-linked class III PI3K activation and autophagy initiation upon glucose starvation. PAQR3-deleted mice display deficiencies in exercise-induced autophagy as well as behavioral disorders. Golgi-resident protein PAQR3 facilitates formation of the autophagy-initiating ATG14L-VPS34 complex. Upon glucose starvation, AMPK phosphorylates PAQR3 to enhance this function, thus integrating nutrient sensing with VPS34 activity.