Amino Acid-Dependent mTORC1 Regulation by the Lysosomal Membrane Protein SLC38A9

Abstract

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.

Supplemental material for this article may be found at http://dx.doi.org/10.1128/MCB.00125-15.

ACKNOWLEDGMENTS

We are grateful to J. W. Harper for critical access to CompPASS. We thank S. Müller, I. Dikic, and S. Oess for readily sharing protocols and reagents and D. McEwan for helpful discussions. Anti-Deptor antibody and RHEB GTPase cDNA were kind gifts from I. Dikic. We received RHEB shRNAs from S. Fulda. We are thankful to members of the Behrends laboratory for resources and discussions. We thank I. Dikic for generous support.

This work was supported by grants from the German Research Foundation (BE 4685/1-1) and the European Research Council (282333).

J.J. and H.M.G. performed all experiments. C.B. and J.J. conceived the study. J.J., H.M.G., and C.B. wrote the manuscript.