Fig. 7. Model.

GABARAP-dependent membrane sequestration of the FLCN-FNIP complex represents a TFEB activation paradigm distinct from nutrient starvation. The FLCN-FNIP GAP complex critically regulates the mTOR-dependent phosphorylation and cytosolic retention of the TFEB/TFE3 transcription factors by promoting the GDP-bound state of RagC/D. GDP-bound RagC/D directly binds to and presents TFEB/TFE3 as a substrate to mTOR (center inset), as described previously. During nutrient starvation (A), recruitment of FLCN-FNIP to the lysosomal membrane helps form the LFC, which has reduced GAP activity toward RagC/D. This is coincident with mTORC1 inhibition. Independently of LFC formation, GABARAP proteins bind directly to the FLCN-FNIP complex and sequester it at diverse intracellular membranes (B). This membrane recruitment is required for TFEB activation in response to endolysosomal ion disruption (CASM) and forms of selective autophagy (xenophagy and mitophagy). This suggests that FLCN-FNIP regulates cytosolic RagC-GTP (guanosine triphosphate) and its sequestration on intracellular membranes reduces access to this substrate, allowing nuclear retention of TFEB/TFE3 due to impaired Rag binding. Unlike (A), this novel TFEB activation pathway is permissive with mTORC1 activity. Subcellular redistribution of the FLCN-FNIP complex to both single and double membranes serves to broadly coordinate lysosomal capacity with homeostasis and perturbations within the endolysosomal network.