WIPI2 Links LC3 Conjugation with PI3P, Autophagosome Formation, and Pathogen Clearance by Recruiting Atg12–5-16L1

TLDR

Autophagy initiation during starvation relies on ER‑localized PtdIns(3)P synthesis, and formation of double‑membrane autophagosomes requires the LC3‑conjugating Atg12–5‑16L1 complex, yet how PtdIns(3)P recruits this complex remains unclear. The study shows that WIPI2b, a WD‑repeat PtdIns(3)P effector, directly binds Atg16L1, positioning the Atg12–5‑16L1 complex at PtdIns(3)P‑rich sites. Loss of WIPI2b function blocks LC3 conjugation and starvation‑induced autophagy, and WIPI2b is essential for targeting the Atg12–5‑16L1 complex to Salmonella‑containing vacuoles, thereby driving autophagosome formation and bacterial clearance.

Abstract

Mammalian cell homeostasis during starvation depends on initiation of autophagy by endoplasmic reticulum-localized phosphatidylinositol 3-phosphate (PtdIns(3)P) synthesis. Formation of double-membrane autophagosomes that engulf cytosolic components requires the LC3-conjugating Atg12–5-16L1 complex. The molecular mechanisms of Atg12–5-16L1 recruitment and significance of PtdIns(3)P synthesis at autophagosome formation sites are unknown. By identifying interacting partners of WIPIs, WD-repeat PtdIns(3)P effector proteins, we found that Atg16L1 directly binds WIPI2b. Mutation experiments and ectopic localization of WIPI2b to plasma membrane show that WIPI2b is a PtdIns(3)P effector upstream of Atg16L1 and is required for LC3 conjugation and starvation-induced autophagy through recruitment of the Atg12–5-16L1 complex. Atg16L1 mutants, which do not bind WIPI2b but bind FIP200, cannot rescue starvation-induced autophagy in Atg16L1-deficient MEFs. WIPI2b is also required for autophagic clearance of pathogenic bacteria. WIPI2b binds the membrane surrounding Salmonella and recruits the Atg12–5-16L1 complex, initiating LC3 conjugation, autophagosomal membrane formation, and engulfment of Salmonella.