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

Mol Cell Biol. 2015 Jul;35(14):2479-94. doi: 10.1128/MCB.00125-15. Epub 2015 May 11.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Transport Systems / genetics
  • Amino Acid Transport Systems / metabolism*
  • Amino Acids / metabolism*
  • Fluorescent Antibody Technique
  • GTP Phosphohydrolases / metabolism
  • HEK293 Cells
  • Humans
  • Immunoblotting
  • Lysosomes / metabolism*
  • Mechanistic Target of Rapamycin Complex 1
  • Monomeric GTP-Binding Proteins / metabolism
  • Multiprotein Complexes / metabolism*
  • Neuropeptides / metabolism
  • Protein Binding
  • Protein Interaction Maps
  • RNA Interference
  • Ras Homolog Enriched in Brain Protein
  • TOR Serine-Threonine Kinases / metabolism*


  • Amino Acid Transport Systems
  • Amino Acids
  • Multiprotein Complexes
  • Neuropeptides
  • RHEB protein, human
  • Ras Homolog Enriched in Brain Protein
  • SLC38A9 protein, human
  • TOR Serine-Threonine Kinases
  • Mechanistic Target of Rapamycin Complex 1
  • GTP Phosphohydrolases
  • Monomeric GTP-Binding Proteins