The serine/threonine kinase mTORC1 regulates cellular homeostasis in response to many cues, such as nutrient status and energy level. Amino acids induce mTORC1 activation on lysosomes via the small Rag GTPases and the Ragulator complex, thereby controlling protein translation and cell growth. Here, we identify the human 11-pass transmembrane protein SLC38A9 as a novel component of the Rag-Ragulator complex. SLC38A9 localizes with Rag-Ragulator complex components on lysosomes and associates with Rag GTPases in an amino acid-sensitive and nucleotide binding state-dependent manner. Depletion of SLC38A9 inhibits mTORC1 activity in the presence of amino acids and in response to amino acid replenishment following starvation. Conversely, SLC38A9 overexpression causes RHEB (Ras homolog enriched in brain) GTPase-dependent hyperactivation of mTORC1 and partly sustains mTORC1 activity upon amino acid deprivation. Intriguingly, during amino acid starvation mTOR is retained at the lysosome upon SLC38A9 depletion but fails to be activated. Together, the findings of our study reveal SLC38A9 as a Rag-Ragulator complex member transducing amino acid availability to mTORC1 activity.
The mechanistic target of rapamycin complex 1 (mTORC1) regulates cell growth and metabolism; therefore, its activity often is altered in cancer (1). mTORC1 comprises several subunits, including the serine/threonine kinase mTOR, regulatoryassociated protein of mTOR (RPTOR), mammalian lethal with SEC13 protein 8 (MLST8), AKT1 substrate 1 (AKT1S1), and DEP domain containing mTOR-interacting protein (DEPTOR) (2, 3). The mTORC1 complex serves as a platform to integrate upstream signals, such as the nutritional state, growth factors, and energy level. Some of these signals, for example, insulin stimulation or low energy levels, are converged by phosphorylation of the tuberous sclerosis complex (TSC), as reviewed in reference 4. The TSC is composed of the proteins TSC1, TSC2, and TBC1D7 and acts as a GTPase-activating protein (GAP) for the small GTPase RHEB (Ras homolog enriched in brain), stimulating the transition from its active GTP-bound to its inactive GDP-bound state (5-7). RHEB is anchored to endomembranes, especially to lysosomes, via its prenylated C-terminal CAAX box motif and promotes mTORC1 kinase activity in its GTP-bound state (8)(9)(10)(11)(12)(13)(14).Nutrient sensing is a key upstream signal for mTORC1 regulation, as growth factors or hormones are not sufficient to fully activate mTORC1 (9, 15). Whereas mTOR is dispersed within the cell upon amino acid starvation, amino acid replenishment redistributes mTOR to active, GTP-bound RHEB at the lysosomal surface (9). mTOR translocation is differentially regulated by the family of heterodimeric small Rag (Ras-related GTP binding) GTPases, which consists of four highly similar mammalian homologues (RagA, RagB, RagC, and RagD) (9,(16)(17)(18)(19). Recruitment of mTOR to the lysosome is promoted by GTP-bound RagA/B and GDP-bound RagC/D, whereas it is inhibited by GDP-bound RagA/B and GTP-bound RagC/D ...