The N-degron pathway modulates autophagosome biogenesis in selective autophagy via the p62-TRAF6-VPS34 circuit

Abstract Selective macroautophagy degrades specific pathological bio-materials by encapsulating them with the double-layered phagophore as a defense mechanism in response to cellular stress such as proteotoxicity, necessitating a dynamic and cargo-specific means of membrane initiation and elongation. Here, we show that the Arg/N-degron pathway facilitates autophagosome biogenesis during selective autophagy via the p62-VPS34-TRAF6 circuit. Proteomic analyses identified a subset of regulators specific to chemical toxicity-induced selective autophagy, among which is the archetypal autophagy cargo receptor p62/SQSTM1/Sequestosome-1. Physiological and chemical N-degrons are agonists for p62 as an Arg/N-recognin via its ZZ domain, inducing its liquid-liquid phase separation into oligomers for the recruitment and stabilization of VPS34/PI3KCIII via TRAF6-mediated K63-ubiquitination. This complex promoted phagophore biogenesis independently of the mTORC1-ULK1-BECN1 circuit used in bulk autophagy. Chemical N-degrons restored p62 oligomerization and targeting of ubiquitinated proteins in cell models of Down syndrome, characterized by mTOR hyperactivation and autophagy deficiency. Our results highlight p62 as a central hub for autophagosome biogenesis during selective autophagy.