The deubiquitinase USP11 is a versatile and conserved regulator of autophagy.

Autophagy is a major cellular quality control system responsible for degradation of proteins and organelles in response to stress and damage in order to maintain homeostasis. Ubiquitination of autophagy-related proteins or regulatory components is important for the precise control of autophagy pathways. Here, we show that the deubiquitinase USP11 restricts autophagy and that knockout (KO) of USP11 in mammalian cells results in elevated autophagic flux. We also demonstrate that depletion of the USP11 homolog H34C03.2 in Caenorhabditis elegans triggers hyperactivation of autophagy and protects the animals against human β-amyloid peptide 42 aggregation-induced paralysis. USP11 co-precipitated with the autophagy-specific class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) and limited its interaction with nuclear receptor-binding factor 2 (NRBF2), thus decreasing lipid kinase activity of the PI3KC3-C1 and subsequent recruitment of effectors like WIPI proteins to the autophagosomal membrane. Accordingly, more WIPI2-puncta accumulated in USP11 KO cells. In addition, USP11 interacts with and stabilizes the serine/threonine kinase mTOR, thereby further contributing to the regulation of autophagy induction. Taken together, our data suggested that USP11 impinges on the autophagy pathway at multiple sites and that inhibiting USP11 alleviates symptoms of proteotoxicity, which is a major hallmark of neurodegenerative diseases.