mTOR (mammalian target of rapamycin) signalling and macroautophagy (henceforth autophagy) regulate numerous pathological and physiological processes, including cellular responses to altered nutrient levels. However, the mechanisms regulating mTOR and autophagy remain incompletely understood. Lysosomes are dynamic intracellular organelles1,2 intimately involved both in the activation of mTOR complex 1 (mTORC1) signalling and in degrading autophagic substrates3,4,5,6,7,8. Here we report that lysosomal positioning coordinates anabolic and catabolic responses with changes in nutrient availability by orchestrating early plasma-membrane signalling events, mTORC1 signalling and autophagy. Activation of mTORC1 by nutrients correlates with its presence on peripheral lysosomes that are physically close to the upstream signalling modules, whereas starvation causes perinuclear clustering of lysosomes, driven by changes in intracellular pH. Lysosomal positioning regulates mTORC1 signalling, which in turn influences autophagosome formation. Lysosome positioning also influences autophagosome–lysosome fusion rates, and thus controls autophagic flux by acting at both the initiation and termination stages of the process. Our findings provide a physiological role for the dynamic state of lysosomal positioning in cells as a coordinator of mTORC1 signalling with autophagic flux.
This is a preview of subscription content, access via your institution
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Rent or buy this article
Prices vary by article type
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Heuser, J. Changes in lysosome shape and distribution correlated with changes in cytoplasmic pH. J. Cell Biol. 108, 855–864 (1989).
Luzio, J. P., Pryor, P. R. & Bright, N. A. Lysosomes: fusion and function. Nat. Rev. Mol. Cell Biol. 8, 622–632 (2007).
Sancak, Y. 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).
Sancak, Y. et al. The Rag GTPases bind raptor and mediate amino acid signalling to mTORC1. Science 320, 1496–1501 (2008).
Jahreiss, L., Menzies, F. M. & Rubinsztein, D. C. The itinerary of autophagosomes: from peripheral formation to kiss-and-run fusion with lysosomes. Traffic 9, 574–587 (2008).
Kimura, S., Noda, T. & Yoshimori, T. Dynein-dependent movement of autophagosomes mediates efficient encounters with lysosomes. Cell Struct. Funct. 33, 109–122 (2008).
Klionsky, D. J. Autophagy: from phenomenology to molecular understanding in less than a decade. Nat. Rev. Mol. Cell Biol. 8, 931–937 (2007).
Ravikumar, B. et al. Mammalian macroautophagy at a glance. J. Cell Sci. 122, 1707–1711 (2009).
Sengupta, S., Peterson, T. R. & Sabatini, D. M. Regulation of the mTOR complex 1 pathway by nutrients, growth factors, and stress. Mol. Cell 40, 310–322 (2010).
Tee, A. R., Anjum, R. & Blenis, J. Inactivation of the tuberous sclerosis complex-1 and -2 gene products occurs by phosphoinositide 3-kinase/Akt-dependent and-independent phosphorylation of tuberin. J. Biol. Chem. 278, 37288–37296 (2003).
Tee, A. R., Manning, B. D., Roux, P. P., Cantley, L. C. & Blenis, J. Tuberous sclerosis complex gene products, Tuberin and Hamartin, control mTOR signaling by acting as a GTPase-activating protein complex toward Rheb. Curr. Biol. 13, 1259–1268 (2003).
Soulard, A. & Hall, M. N. SnapShot: mTOR signaling. Cell 129, 434 (2007).
Kim, E., Goraksha-Hicks, P., Li, L., Neufeld, T. P. & Guan, K. L. Regulation of TORC1 by Rag GTPases in nutrient response. Nat. Cell Biol. 10, 935–945 (2008).
Cai, S. L. et al. Activity of TSC2 is inhibited by AKT-mediated phosphorylation and membrane partitioning. J. Cell Biol. 173, 279–289 (2006).
Jiang, H. & Vogt, P. K. Constitutively active Rheb induces oncogenic transformation. Oncogene 27, 5729–5740 (2008).
Santama, N. et al. KIF2β, a new kinesin superfamily protein in non-neuronal cells, is associated with lysosomes and may be implicated in their centrifugal translocation. EMBO J. 17, 5855–5867 (1998).
Matsushita, M., Tanaka, S., Nakamura, N., Inoue, H. & Kanazawa, H. A novel kinesin-like protein, KIF1Bβ3 is involved in the movement of lysosomes to the cell periphery in non-neuronal cells. Traffic 5, 140–151 (2004).
Bagshaw, R. D., Callahan, J. W. & Mahuran, D. J. The Arf-family protein, Arl8b, is involved in the spatial distribution of lysosomes. Biochem. Biophys. Res. Commun. 344, 1186–1191 (2006).
Hofmann, I. & Munro, S. An N-terminally acetylated Arf-like GTPase is localised to lysosomes and affects their motility. J. Cell Sci. 119, 1494–1503 (2006).
Okai, T. et al. Novel small GTPase subfamily capable of associating with tubulin is required for chromosome segregation. J. Cell Sci. 117, 4705–4715 (2004).
Kimura, S., Noda, T. & Yoshimori, T. Dissection of the autophagosome maturation process by a novel reporter protein, tandem fluorescent-tagged LC3. Autophagy 3, 452–460 (2007).
Tanida, I., Minematsu-Ikeguchi, N., Ueno, T. & Kominami, E. Lysosomal turnover, but not a cellular level, of endogenous LC3 is a marker for autophagy. Autophagy 1, 84–91 (2005).
Ravikumar, B., Duden, R. & Rubinsztein, D. C. Aggregate-prone proteins with polyglutamine and polyalanine expansions are degraded by autophagy. Hum. Mol. Genet. 11, 1107–1117 (2002).
Webb, J. L., Ravikumar, B., Atkins, J., Skepper, J. N. & Rubinsztein, D. C. α-Synuclein is degraded by both autophagy and the proteasome. J. Biol. Chem. 278, 25009–25013 (2003).
Gutierrez, M. G. et al. Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages. Cell 119, 753–766 (2004).
Singh, S. B., Davis, A. S., Taylor, G. A. & Deretic, V. Human IRGM induces autophagy to eliminate intracellular mycobacteria. Science 313, 1438–1441 (2006).
Merlot, S. & Firtel, R. A. Leading the way: directional sensing through phosphatidylinositol 3-kinase and other signaling pathways. J. Cell Sci. 116, 3471–3478 (2003).
Mohamed, M. M. & Sloane, B. F. Cysteine cathepsins: multifunctional enzymes in cancer. Nat. Rev. Cancer 6, 764–775 (2006).
Kuma, A. et al. The role of autophagy during the early neonatal starvation period. Nature 432, 1032–1036 (2004).
Noda, Y., Sato-Yoshitake, R., Kondo, S., Nangaku, M. & Hirokawa, N. KIF2 is a new microtubule-based anterograde motor that transports membranous organelles distinct from those carried by kinesin heavy chain or KIF3A/B. J. Cell Biol. 129, 157–167 (1995).
Berger, Z. et al. Rapamycin alleviates toxicity of different aggregate-prone proteins. Hum. Mol. Genet. 15, 433–442 (2006).
Narain, Y., Wyttenbach, A., Rankin, J., Furlong, R. A. & Rubinsztein, D. C. A molecular investigation of true dominance in Huntington’s disease. J. Med. Genet. 36, 739–746 (1999).
Sarkar, S. et al. A rational mechanism for combination treatment of Huntington’s disease using lithium and rapamycin. Hum. Mol. Genet. 17, 170–178 (2008).
Schlisio, S. et al. The kinesin KIF1Bβ acts downstream from EglN3 to induce apoptosis and is a potential 1p36 tumor suppressor. Genes Dev. 22, 884–893 (2008).
Sarbassov, D. D. et al. Rictor, a novel binding partner of mTOR, defines a rapamycin-insensitive and raptor-independent pathway that regulates the cytoskeleton. Curr. Biol. 14, 1296–1302 (2004).
Pryor, P. R., Reimann, F., Gribble, F. M. & Luzio, J. P. Mucolipin-1 is a lysosomal membrane protein required for intracellular lactosylceramide traffic. Traffic 7, 1388–1398 (2006).
Zhou, X. et al. Rheb controls misfolded protein metabolism by inhibiting aggresome formation and autophagy. Proc. Natl Acad. Sci. USA 106, 8923–8928 (2009).
Korolchuk, V. I., Mansilla, A., Menzies, F. M. & Rubinsztein, D. C. Autophagy inhibition compromises degradation of ubiquitin-proteasome pathway substrates. Mol. Cell 33, 517–527 (2009).
Tafani, M. et al. Regulation of intracellular pH mediates Bax activation in HeLa cells treated with staurosporine or tumor necrosis factor-α. J. Biol. Chem. 277, 49569–49576 (2002).
Ong, V. et al. A role for altered microtubule polymer levels in vincristine resistance of childhood acute lymphoblastic leukemia xenografts. J. Pharmacol. Exp. Ther. 324, 434–442 (2008).
Sarkar, S., Korolchuk, V., Renna, M., Winslow, A. & Rubinsztein, D. C. Methodological considerations for assessing autophagy modulators: a study with calcium phosphate precipitates. Autophagy 5, 307–313 (2009).
Ryder, E. et al. The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster. Genetics 167, 797–813 (2004).
Thibault, S. T. et al. A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac. Nat. Genet. 36, 283–287 (2004).
We thank S. Munro (Medical Research Council, Laboratory of Molecular Biology, Cambridge; ARL8 constructs and antibody), T. Katada (University of Tokyo; anti-ARL8 antibody), W. G. Kaelin (Harvard Medical School; KIF1Bβ), N. Hirokawa (University of Tokyo; KIF2), D. M. Sabatini (Massachusetts Institute of Technology; mTOR, raptor, rictor), T. Yoshimori (Osaka University; eGFP–LC3, mRFP–GFP–LC3), N. Mizushima (Tokyo Medical and Dental University; Atg5-deficient and wild-type Atg5 mouse embryonic fibroblast cell lines), W. J. Strittmatter (Duke University; Q81–eGFP), J. P. Luzio (University of Cambridge; lgp120–eGFP), A. Tolkovsky (University of Cambridge; GFP–LC3 cells), R. Tsien (University of California at San Diego; mCherry), T. Kouno (Toyama Medical and Pharmaceutical University; hLC3B) and K-L. Guan (University of California at San Diego; Rheb); B. Ravikumar, S. Luo and B. Underwood (University of Cambridge) for suggestions, M. Gratian and M. Bowen (University of Cambridge) for microscopy assistance, and the Bloomington Drosophila Stock Center. We are grateful for financial support from a Hughes Hall Research Fellowship (V.I.K. and S. Sarkar), a 2005 Pergolide Fellowship from Eli Lilly Japan (S. Saiki), the British Council Japan Association (S. Saiki), MRC studentships (M.L. and L.J.), a Daphne Jackson Trust Fellowship funded by the MRC (F.H.S.), a Heiser Foundation Postdoctoral Fellowship in Tuberculosis and Leprosy Research (E.A.R.), NIH grant AI069345, and in part NIH grants AI045148 and AI042999 (V.D.), a Wellcome Trust Senior Fellowship in Clinical Science (D.C.R.), an MRC programme grant (D.C.R., C.J.O’K.) and an EU Framework VI (EUROSCA) grant (D.C.R.).
The authors declare no competing financial interests.
About this article
Cite this article
Korolchuk, V., Saiki, S., Lichtenberg, M. et al. Lysosomal positioning coordinates cellular nutrient responses. Nat Cell Biol 13, 453–460 (2011). https://doi.org/10.1038/ncb2204
This article is cited by
Functional defects in hiPSCs-derived cardiomyocytes from patients with a PLEKHM2-mutation associated with dilated cardiomyopathy and left ventricular non-compaction
Biological Research (2023)
Nature Reviews Molecular Cell Biology (2023)
RUFY3 regulates endolysosomes perinuclear positioning, antigen presentation and migration in activated phagocytes
Nature Communications (2023)
Nature Chemical Biology (2023)
HDAC6-G3BP2 promotes lysosomal-TSC2 and suppresses mTORC1 under ETV4 targeting-induced low-lactate stress in non-small cell lung cancer