Regulation of the mTORC1 growth pathway by amino acids

Abstract

The mTORC1 kinase is a master growth regulator that responds to numerous environmental cues, including amino acids, to regulate many processes, such as protein, lipid, and nucleotide synthesis, as well as autophagy. Given that mTORC1 regulates a multitude of processes, it is not surprising that the pathway it anchors is deregulated in various common diseases, including cancer. The Rag GTPases interact with mTORC1 and signal amino acid sufficiency by promoting the translocation of mTORC1 to the lysosomal surface, its site of activation. The Rags are unusual GTPases in that they function as obligate heterodimers, which consist of RagA or B bound to RagC or D. We show that RagC/D is a key regulator of the interaction of mTORC1 with the Rag heterodimer and that, unexpectedly, RagC/D must be GDP-bound for the interaction to occur. We identify FLCN and its binding partners, FNIP1/2, as Rag-interacting proteins with GTPase activating activity for RagC/D, but not RagA/B. Given that many proteins known to signal amino acid sufficiency to mTORC1, including the Rag GTPases, localize to the lysosome and that intralysosomal amino acid accumulation is necessary for mTORC1 activation, we began our search for potential direct amino acid sensors at the lysosomal membrane. We identify SLC38A9, an uncharacterized protein with homology to amino acid transporters, as a lysosomal transmembrane protein. SLC38A9 forms a supercomplex with Ragulator, the Rag GTPases and the v-ATPase and is necessary for mTORC1 activation by amino acids, particularly arginine. Overexpression of the full-length protein or just its Ragulator-binding domain makes mTORC1 signaling insensitive to amino acid starvation but does not affect its dependence on Rag activity. SLC38A9 reconstituted in proteoliposomes transports arginine, an abundant amino acid in the lysosome and necessary for mTORC1 pathway activity. These results place SLC38A9 between amino acids and the Rag GTPases and are consistent with the notion that amino acids are sensed at the lysosome. Thus, SLC38A9 is an excellent candidate for being an amino acid sensor upstream of mTORC1.