MTORC1 regulates autophagic membrane growth by targeting WIPI2.

WIPI2 contributes to autophagy by recruiting the ATG12-ATG5-ATG16L1 complex to PtdIns3P-rich membranes, which enables the growth and elongation of phagophores. So far, PtdIns3P and ATG16L1 are the best known WIPI2 interaction partners. In the screening of novel binding proteins for WIPI2, we recently identified interactions between WIPI2 and MTORC1 and the E3 ubiquitin ligase HUWE1. With this clue, we uncovered that WIPI2 is a phosphorylation substrate of MTORC1 and a ubiquitination target of HUWE1. Further, by determining the phosphorylation site on WIPI2 targeted by MTORC1, we show that MTORC1-dependent phosphorylation directs WIPI2 to interact with HUWE1, leading to WIPI2 ubiquitination and subsequent degradation by proteasomes. Finally, we provide evidence that this quantity control mechanism of WIPI2 is utilized by cells for not only the regulation of basal autophagy but also nutrient deprivation-stimulated autophagy. Together, these results indicate that WIPI2 protein level regulated by MTORC1 and HUWE1 is a pivotal determinant of cellular autophagy intensity. The findings firm up the role of MTORC1 as a master regulator of autophagy, suggesting that the quantity control of WIPI2 is a potential intervention point in autophagy-related physiopathological processes.