Mechanistic insights into the distinct functions of ATG16L1 in canonical autophagy and selective autophagy

Abstract

Macroautophagy plays crucial roles in the regulation of cellular physiology, and requires de novo synthesis of double-membrane autophagosomes. The formation of autophagosomes entails the lipidation of ATG8 family proteins catalyzed by the ATG12 ~ ATG5-ATG16L1 complex, which is recruited to the pre-autophagosomal membrane through a direct interaction between ATG16L1 and WIPI2b. In addition, ATG16L1 can function as an adaptor to specifically recognize invading pathogens to mediate antibacterial selective autophagy, and the T300A polymorphism of ATG16L1 has been associated with the Crohn's disease, an inflammatory bowel disease mainly caused by the defect in antibacterial autophagy. However, the molecular mechanism governing the interaction of ATG16L1 with WIPI2b and the precise role of ATG16L1 in selective autophagy remain elusive. Here, we reported the atomic structure of the WIPI2b/ATG16L1 complex, and elucidated the mechanistic basis underpinning the recruitment of ATG16L1 by WIPI2b. Moreover, we discovered that the FIR motif of ATG16L1 not only can directly interact with RB1CC1 Claw domain, but also can selectively recognize mammalian ATG8 family proteins. We determined the high-resolution crystal structures of ATG16L1 FIR in complex with RB1CC1 Claw and GABARAPL1 respectively, and uncovered the molecular mechanism underlying the interactions of ATG16L1 with RB1CC1 and ATG8 family proteins. On this basis, we proposed the concept that ATG16L1 can be categorized as a potential autophagy receptor. In all, our findings provide novel mechanistic insights into the interactions of ATG16L1 with WIPI2b, RB1CC1 and ATG8 family proteins, and are valuable for further understanding the distinct functions of ATG16L1 in autophagy.