Cell growth and proliferation are tightly linked to nutrient availability. The mechanistic target of rapamycin complex 1 (mTORC1) integrates the presence of growth factors, energy levels, glucose and amino acids to modulate metabolic status and cellular responses1,2,3. mTORC1 is activated at the surface of lysosomes by the RAG GTPases and the Ragulator complex through a not fully understood mechanism monitoring amino acid availability in the lysosomal lumen and involving the vacuolar H+-ATPase4,5,6,7,8. Here we describe the uncharacterized human member 9 of the solute carrier family 38 (SLC38A9) as a lysosomal membrane-resident protein competent in amino acid transport. Extensive functional proteomic analysis established SLC38A9 as an integral part of the Ragulator–RAG GTPases machinery. Gain of SLC38A9 function rendered cells resistant to amino acid withdrawal, whereas loss of SLC38A9 expression impaired amino-acid-induced mTORC1 activation. Thus SLC38A9 is a physical and functional component of the amino acid sensing machinery that controls the activation of mTOR.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


Primary accessions


Data deposits

The protein-protein interactions have been submitted to the IMEx ( consortium through IntAct ( and assigned the identifier IM-23283. The SLC network has the IntAct accession number EBI-9975668 and the RAGA-RAGC-LAMTOR network is EBI-9975664. RNA-Seq data is available in ArrayExpress ( under the accession number E-MTAB-3102.


  1. 1.

    & Signal integration by mTORC1 coordinates nutrient input with biosynthetic output. Nature Cell Biol. 15, 555–564 (2013)

  2. 2.

    & mTOR signaling in growth control and disease. Cell 149, 274–293 (2012)

  3. 3.

    , & mTOR in aging, metabolism, and cancer. Curr. Opin. Genet. Dev. 23, 53–62 (2013)

  4. 4.

    , , , & Regulation of TORC1 by Rag GTPases in nutrient response. Nature Cell Biol. 10, 935–945 (2008)

  5. 5.

    et al. The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1. Science 320, 1496–1501 (2008)

  6. 6.

    et al. Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids. Cell 141, 290–303 (2010)

  7. 7.

    et al. mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H+-ATPase. Science 334, 678–683 (2011)

  8. 8.

    , , & Ragulator is a GEF for the rag GTPases that signal amino acid levels to mTORC1. Cell 150, 1196–1208 (2012)

  9. 9.

    , & Amino acid signalling upstream of mTOR. Nature Rev. Mol. Cell Biol. 14, 133–139 (2013)

  10. 10.

    et al. A tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1. Science 340, 1100–1106 (2013)

  11. 11.

    et al. The folliculin tumor suppressor is a GAP for the RagC/D GTPases that signal amino acid levels to mTORC1. Mol. Cell 52, 495–505 (2013)

  12. 12.

    et al. Leucyl-tRNA synthetase is an intracellular leucine sensor for the mTORC1-signaling pathway. Cell 149, 410–424 (2012)

  13. 13.

    , & Amino acid deprivation inhibits TORC1 through a GTPase-activating protein complex for the Rag family GTPase Gtr1. Sci. Signal. 6, ra42 (2013)

  14. 14.

    et al. Bidirectional transport of amino acids regulates mTOR and autophagy. Cell 136, 521–534 (2009)

  15. 15.

    , , & The ABCs of membrane transporters in health and disease (SLC series): introduction. Mol. Aspects Med. 34, 95–107 (2013)

  16. 16.

    et al. Towards a knowledge-based Human Protein Atlas. Nature Biotechnol. 28, 1248–1250 (2010)

  17. 17.

    et al. An extended proteome map of the lysosomal membrane reveals novel potential transporters. Mol. Cell. Proteomics 12, 1572–1588 (2013)

  18. 18.

    , , & Evolutionary origin of amino acid transporter families SLC32, SLC36 and SLC38 and physiological, pathological and therapeutic aspects. Mol. Aspects Med. 34, 571–585 (2013)

  19. 19.

    et al. Proton-assisted amino acid transporter PAT1 complexes with Rag GTPases and activates TORC1 on late endosomal and lysosomal membranes. PLoS ONE 7, e36616 (2012)

  20. 20.

    et al. Identification of SLC38A7 (SNAT7) protein as a glutamine transporter expressed in neurons. J. Biol. Chem. 286, 20500–20511 (2011)

  21. 21.

    et al. Glutaminolysis activates Rag-mTORC1 signaling. Mol. Cell 47, 349–358 (2012)

  22. 22.

    , & Highly conserved asparagine 82 controls the interaction of Na+ with the sodium-coupled neutral amino acid transporter SNAT2. J. Biol. Chem. 283, 12284–12292 (2008)

  23. 23.

    , , & The B degrees AT1 amino acid transporter from rat kidney reconstituted in liposomes: kinetics and inactivation by methylmercury. Biochim. Biophys. Acta 1808, 2551–2558 (2011)

  24. 24.

    Amino-acid-induced signalling via the SPS-sensing pathway in yeast. Biochem. Soc. Trans. 37, 242–247 (2009)

  25. 25.

    , , & PAT-related amino acid transporters regulate growth via a novel mechanism that does not require bulk transport of amino acids. Development 132, 2365–2375 (2005)

  26. 26.

    et al. A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB. EMBO J. 31, 1095–1108 (2012)

  27. 27.

    et al. Membrane transporters in drug development. Nature Rev. Drug Discov. 9, 215–236 (2010)

  28. 28.

    et al. Competitive intra- and extracellular nutrient sensing by the transporter homologue Ssy1p. J. Cell Biol. 173, 327–331 (2006)

  29. 29.

    , , , & From transporter to transceptor: signaling from transporters provokes re-evaluation of complex trafficking and regulatory controls. BioEssays 33, 870–879 (2011)

  30. 30.

    Amino acid transporters: eminences grises of nutrient signalling mechanisms? Biochem. Soc. Trans. 37, 237–241 (2009)

  31. 31.

    et al. Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. Nature Methods 10, 307–314 (2013)

  32. 32.

    et al. Affinity purification strategies for proteomic analysis of transcription factor complexes. J. Proteome Res. 12, 4018–4027 (2013)

  33. 33.

    et al. Viral immune modulators perturb the human molecular network by common and unique strategies. Nature 487, 486–490 (2012)

  34. 34.

    , , , & OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 3, 1454–1463 (2003)

  35. 35.

    et al. Proteomic analysis of human cataract aqueous humour: Comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ(R)-labelled specimens. J. Proteomics 74, 151–166 (2011)

  36. 36.

    et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nature Methods 8, 70–73 (2011)

  37. 37.

    et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nature Methods 10, 730–736 (2013)

  38. 38.

    et al. Population context determines cell-to-cell variability in endocytosis and virus infection. Nature 461, 520–523 (2009)

  39. 39.

    et al. Over-expression in E. coli and purification of the human OCTN1 transport protein. Protein Expr. Purif. 68, 215–220 (2009)

  40. 40.

    , , , & Reconstitution in liposomes of the functionally active human OCTN1 (SLC22A4) transporter overexpressed in Escherichia coli. Biochem. J. 439, 227–233 (2011)

Download references


We thank D. M. Sabatini, S. Wang and Z. Tsun for discussing results before publication and generously providing Flag–SLC38A9 and Flag–METAP2 stably expressing cells, all members of the Superti-Furga laboratory for discussions, the Bennett laboratory for the proteomic analyses, F. Pauler and the Barlow laboratory for the RNA-seq analysis and M. Gstaiger for providing expression vectors. This work was supported by the Austrian Academy of Sciences, ERC grant to G.S.-F. (i-FIVE 250179), EMBO long-term and Marie Curie fellowships to M.R. (ALTF 1346-2011, IEF 301663), EMBO long-term fellowship to R.K.K. (ALTF 314-2012), Swiss NSF fellowship (P300P3_147897) to B.S., Vienna Science and Technology Fund (WWTF VRG10-001) and the Austrian Science Fund (FWF P 25522-B20) to C.K., the Italian Ministry of Instruction University and Research, PON-ricerca e competitività 2007-2013 (no. PON01_00937) to C.I., the Austrian Federal Ministry for Science and Research (GenAu projects, APP-III and BIN-III) to L.A.H., K.L.B. and G.S.-F., the Austrian Science Fund MCBO/SFB021 to L.A.H.

Author information

Author notes

    • Elena L. Rudashevskaya

    Present address: Institute of Medical Chemistry, Medical University of Vienna, 1090 Vienna, Austria.


  1. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria

    • Manuele Rebsamen
    • , Richard K. Kandasamy
    • , Berend Snijder
    • , Astrid Fauster
    • , Elena L. Rudashevskaya
    • , Manuela Bruckner
    • , Stefania Scorzoni
    • , Kilian V. M. Huber
    • , Johannes W. Bigenzahn
    • , Leonhard X. Heinz
    • , Keiryn L. Bennett
    •  & Giulio Superti-Furga
  2. Department DiBEST (Biology, Ecology and Earth Sciences), University of Calabria, 87036 Arcavacata di Rende, Italy

    • Lorena Pochini
    • , Michele Galluccio
    •  & Cesare Indiveri
  3. Biocenter, Division of Cell Biology, Innsbruck Medical University, 6020 Innsbruck, Austria

    • Taras Stasyk
    • , Mariana E. G. de Araújo
    • , Przemyslaw A. Filipek
    •  & Lukas A. Huber
  4. Max F. Perutz Laboratories, University of Vienna, 1030 Vienna, Austria

    • Claudine Kraft


  1. Search for Manuele Rebsamen in:

  2. Search for Lorena Pochini in:

  3. Search for Taras Stasyk in:

  4. Search for Mariana E. G. de Araújo in:

  5. Search for Michele Galluccio in:

  6. Search for Richard K. Kandasamy in:

  7. Search for Berend Snijder in:

  8. Search for Astrid Fauster in:

  9. Search for Elena L. Rudashevskaya in:

  10. Search for Manuela Bruckner in:

  11. Search for Stefania Scorzoni in:

  12. Search for Przemyslaw A. Filipek in:

  13. Search for Kilian V. M. Huber in:

  14. Search for Johannes W. Bigenzahn in:

  15. Search for Leonhard X. Heinz in:

  16. Search for Claudine Kraft in:

  17. Search for Keiryn L. Bennett in:

  18. Search for Cesare Indiveri in:

  19. Search for Lukas A. Huber in:

  20. Search for Giulio Superti-Furga in:


M.R. and G.S.-F. conceived the study. L.P., M.G. and C.I. designed and performed transport assays. M.R., T.S., M.E.G.d.A., E.L.R., M.B., K.L.B., L.A.H. and G.S.-F. designed and performed TAP-mass spectrometry experiments. M.R., M.E.G.d.A., B.S., A.F., M.B., S.S. and P.A.F. performed the other experiments. M.R., L.A.H. and G.S.-F. designed the other experiments. R.K.K. and B.S. performed bioinformatic data and image analysis. K.V.M.H., J.W.B., L.X.H., C.K. generated reagents and provided scientific insight. M.R. and G.S.-F. wrote the manuscript. All authors contributed to the discussion of results and participated in manuscript preparation.

Competing interests

A patent has been filed with data generated in this manuscript where M.R. and G.S.-F. are listed as inventors.

Corresponding author

Correspondence to Giulio Superti-Furga.

Extended data

About this article

Publication history





Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.