Spatial and functional separation of mTORC1 signalling in response to different amino acid sources.
Journal
Nature cell biology
ISSN: 1476-4679
Titre abrégé: Nat Cell Biol
Pays: England
ID NLM: 100890575
Informations de publication
Date de publication:
09 Oct 2024
09 Oct 2024
Historique:
received:
01
02
2024
accepted:
09
09
2024
medline:
10
10
2024
pubmed:
10
10
2024
entrez:
9
10
2024
Statut:
aheadofprint
Résumé
Amino acid (AA) availability is a robust determinant of cell growth through controlling mechanistic/mammalian target of rapamycin complex 1 (mTORC1) activity. According to the predominant model in the field, AA sufficiency drives the recruitment and activation of mTORC1 on the lysosomal surface by the heterodimeric Rag GTPases, from where it coordinates the majority of cellular processes. Importantly, however, the teleonomy of the proposed lysosomal regulation of mTORC1 and where mTORC1 acts on its effector proteins remain enigmatic. Here, by using multiple pharmacological and genetic means to perturb the lysosomal AA-sensing and protein recycling machineries, we describe the spatial separation of mTORC1 regulation and downstream functions in mammalian cells, with lysosomal and non-lysosomal mTORC1 phosphorylating distinct substrates in response to different AA sources. Moreover, we reveal that a fraction of mTOR localizes at lysosomes owing to basal lysosomal proteolysis that locally supplies new AAs, even in cells grown in the presence of extracellular nutrients, whereas cytoplasmic mTORC1 is regulated by exogenous AAs. Overall, our study substantially expands our knowledge about the topology of mTORC1 regulation by AAs and hints at the existence of distinct, Rag- and lysosome-independent mechanisms that control its activity at other subcellular locations. Given the importance of mTORC1 signalling and AA sensing for human ageing and disease, our findings will probably pave the way towards the identification of function-specific mTORC1 regulators and thus highlight more effective targets for drug discovery against conditions with dysregulated mTORC1 activity in the future.
Identifiants
pubmed: 39385049
doi: 10.1038/s41556-024-01523-7
pii: 10.1038/s41556-024-01523-7
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
ID : 757729
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : DE 3170/1-1
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : DE 3170/1-1
Informations de copyright
© 2024. The Author(s).
Références
Laplante, M. & Sabatini, D. M. mTOR signaling in growth control and disease. Cell 149, 274–293 (2012).
pubmed: 22500797
pmcid: 3331679
doi: 10.1016/j.cell.2012.03.017
Proud, C. G. mTOR Signalling in health and disease. Biochem. Soc. Trans. 39, 431–436 (2011).
pubmed: 21428914
doi: 10.1042/BST0390431
Liko, D. & Hall, M. N. mTOR in health and in sickness. J. Mol. Med. 93, 1061–1073 (2015).
pubmed: 26391637
doi: 10.1007/s00109-015-1326-7
Valvezan, A. J. & Manning, B. D. Molecular logic of mTORC1 signalling as a metabolic rheostat. Nat. Metab. 1, 321–333 (2019).
pubmed: 32694720
doi: 10.1038/s42255-019-0038-7
Kennedy, B. K. & Lamming, D. W. The mechanistic target of rapamycin: the grand conductor of metabolism and aging. Cell Metab. 23, 990–1003 (2016).
pubmed: 27304501
pmcid: 4910876
doi: 10.1016/j.cmet.2016.05.009
Gonzalez, A. & Hall, M. N. Nutrient sensing and TOR signaling in yeast and mammals. EMBO J. 36, 397–408 (2017).
pubmed: 28096180
pmcid: 5694944
doi: 10.15252/embj.201696010
Liu, G. Y. & Sabatini, D. M. mTOR at the nexus of nutrition, growth, ageing and disease. Nat. Rev. Mol. Cell Biol. 21, 183–203 (2020).
pubmed: 31937935
pmcid: 7102936
doi: 10.1038/s41580-019-0199-y
Rabanal-Ruiz, Y. & Korolchuk, V. I. mTORC1 and nutrient homeostasis: the central role of the lysosome. Int. J. Mol. Sci. 19, 818 (2018).
pubmed: 29534520
pmcid: 5877679
doi: 10.3390/ijms19030818
Blommaart, E. F., Luiken, J. J., Blommaart, P. J., van Woerkom, G. M. & Meijer, A. J. Phosphorylation of ribosomal protein S6 is inhibitory for autophagy in isolated rat hepatocytes. J. Biol. Chem. 270, 2320–2326 (1995).
pubmed: 7836465
doi: 10.1074/jbc.270.5.2320
Hara, K. et al. Amino acid sufficiency and mTOR regulate p70 S6 kinase and eIF-4E BP1 through a common effector mechanism. J. Biol. Chem. 273, 14484–14494 (1998).
pubmed: 9603962
doi: 10.1074/jbc.273.23.14484
Efeyan, A., Zoncu, R. & Sabatini, D. M. Amino acids and mTORC1: from lysosomes to disease. Trends Mol. Med. 18, 524–533 (2012).
pubmed: 22749019
pmcid: 3432651
doi: 10.1016/j.molmed.2012.05.007
Jewell, J. L., Russell, R. C. & Guan, K. L. Amino acid signalling upstream of mTOR. Nat. Rev. Mol. Cell Biol. 14, 133–139 (2013).
pubmed: 23361334
pmcid: 3988467
doi: 10.1038/nrm3522
Fernandes, S. A. & Demetriades, C. The multifaceted role of nutrient sensing and mTORC1 signaling in physiology and aging. Front. Aging 2, 707372 (2021).
pubmed: 35822019
pmcid: 9261424
doi: 10.3389/fragi.2021.707372
Johnson, S. C., Rabinovitch, P. S. & Kaeberlein, M. mTOR is a key modulator of ageing and age-related disease. Nature 493, 338–345 (2013).
pubmed: 23325216
pmcid: 3687363
doi: 10.1038/nature11861
Cornu, M., Albert, V. & Hall, M. N. mTOR in aging, metabolism, and cancer. Curr. Opin. Genet. Dev. 23, 53–62 (2013).
pubmed: 23317514
doi: 10.1016/j.gde.2012.12.005
Tsang, C. K., Qi, H., Liu, L. F. & Zheng, X. F. Targeting mammalian target of rapamycin (mTOR) for health and diseases. Drug Discov. Today 12, 112–124 (2007).
pubmed: 17275731
doi: 10.1016/j.drudis.2006.12.008
Um, S. H., D’Alessio, D. & Thomas, G. Nutrient overload, insulin resistance, and ribosomal protein S6 kinase 1, S6K1. Cell Metab. 3, 393–402 (2006).
pubmed: 16753575
doi: 10.1016/j.cmet.2006.05.003
Sancak, Y. et al. The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1. Science 320, 1496–1501 (2008).
pubmed: 18497260
pmcid: 2475333
doi: 10.1126/science.1157535
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).
pubmed: 18604198
pmcid: 2711503
doi: 10.1038/ncb1753
Zoncu, R. et al. mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H(
pubmed: 22053050
pmcid: 3211112
doi: 10.1126/science.1207056
Gollwitzer, P., Grutzmacher, N., Wilhelm, S., Kummel, D. & Demetriades, C. A Rag GTPase dimer code defines the regulation of mTORC1 by amino acids. Nat. Cell Biol. 24, 1394–1406 (2022).
pubmed: 36097072
pmcid: 9481461
doi: 10.1038/s41556-022-00976-y
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).
pubmed: 20381137
pmcid: 3024592
doi: 10.1016/j.cell.2010.02.024
Demetriades, C., Doumpas, N. & Teleman, A. A. Regulation of TORC1 in response to amino acid starvation via lysosomal recruitment of TSC2. Cell 156, 786–799 (2014).
pubmed: 24529380
pmcid: 4346203
doi: 10.1016/j.cell.2014.01.024
Powis, K. & De Virgilio, C. Conserved regulators of Rag GTPases orchestrate amino acid-dependent TORC1 signaling. Cell Discov. 2, 15049 (2016).
pubmed: 27462445
pmcid: 4860963
doi: 10.1038/celldisc.2015.49
Lim, C. Y. & Zoncu, R. The lysosome as a command-and-control center for cellular metabolism. J. Cell Biol. 214, 653–664 (2016).
pubmed: 27621362
pmcid: 5021098
doi: 10.1083/jcb.201607005
Betz, C. & Hall, M. N. Where is mTOR and what is it doing there? J. Cell Biol. 203, 563–574 (2013).
pubmed: 24385483
pmcid: 3840941
doi: 10.1083/jcb.201306041
Manifava, M. et al. Dynamics of mTORC1 activation in response to amino acids. eLife 5, e19960 (2016).
pubmed: 27725083
pmcid: 5059141
doi: 10.7554/eLife.19960
Lawrence, R. E. et al. A nutrient-induced affinity switch controls mTORC1 activation by its Rag GTPase–Ragulator lysosomal scaffold. Nat. Cell Biol. 20, 1052–1063 (2018).
pubmed: 30061680
pmcid: 6279252
doi: 10.1038/s41556-018-0148-6
Mauvezin, C. & Neufeld, T. P. Bafilomycin A1 disrupts autophagic flux by inhibiting both V-ATPase-dependent acidification and Ca-P60A/SERCA-dependent autophagosome-lysosome fusion. Autophagy 11, 1437–1438 (2015).
pubmed: 26156798
pmcid: 4590655
doi: 10.1080/15548627.2015.1066957
Musiwaro, P., Smith, M., Manifava, M., Walker, S. A. & Ktistakis, N. T. Characteristics and requirements of basal autophagy in HEK 293 cells. Autophagy 9, 1407–1417 (2013).
pubmed: 23800949
doi: 10.4161/auto.25455
Abu-Remaileh, M. et al. Lysosomal metabolomics reveals V-ATPase- and mTOR-dependent regulation of amino acid efflux from lysosomes. Science 358, 807–813 (2017).
pubmed: 29074583
pmcid: 5704967
doi: 10.1126/science.aan6298
Efeyan, A. et al. RagA, but not RagB, is essential for embryonic development and adult mice. Dev. Cell 29, 321–329 (2014).
pubmed: 24768164
pmcid: 4035553
doi: 10.1016/j.devcel.2014.03.017
Laqtom, N. N. et al. CLN3 is required for the clearance of glycerophosphodiesters from lysosomes. Nature 609, 1005–1011 (2022).
pubmed: 36131016
pmcid: 10510443
doi: 10.1038/s41586-022-05221-y
Rosner, M., Schipany, K. & Hengstschlager, M. p70 S6K1 nuclear localization depends on its mTOR-mediated phosphorylation at T389, but not on its kinase activity towards S6. Amino Acids 42, 2251–2256 (2012).
pubmed: 21710263
doi: 10.1007/s00726-011-0965-4
Pavan, I. C. et al. Different interactomes for p70-S6K1 and p54-S6K2 revealed by proteomic analysis. Proteomics 16, 2650–2666 (2016).
pubmed: 27493124
doi: 10.1002/pmic.201500249
Nuchel, J. et al. An mTORC1-GRASP55 signaling axis controls unconventional secretion to reshape the extracellular proteome upon stress. Mol. Cell. 81, 3275–3293 (2021).
pubmed: 34245671
pmcid: 8382303
doi: 10.1016/j.molcel.2021.06.017
Yang, G. et al. RagC phosphorylation autoregulates mTOR complex 1. EMBO J. 38, e99548 (2019).
pubmed: 30552228
doi: 10.15252/embj.201899548
Bar-Peled, L., Schweitzer, L. D., Zoncu, R. & Sabatini, D. M. Ragulator is a GEF for the rag GTPases that signal amino acid levels to mTORC1. Cell 150, 1196–1208 (2012).
pubmed: 22980980
pmcid: 3517996
doi: 10.1016/j.cell.2012.07.032
Demetriades, C., Plescher, M. & Teleman, A. A. Lysosomal recruitment of TSC2 is a universal response to cellular stress. Nat. Commun. 7, 10662 (2016).
pubmed: 26868506
pmcid: 4754342
doi: 10.1038/ncomms10662
Plescher, M., Teleman, A. A. & Demetriades, C. TSC2 mediates hyperosmotic stress-induced inactivation of mTORC1. Sci. Rep. 5, 13828 (2015).
pubmed: 26345496
pmcid: 4642562
doi: 10.1038/srep13828
Carroll, B. et al. Control of TSC2-Rheb signaling axis by arginine regulates mTORC1 activity. eLife 5, e11058 (2016).
pubmed: 26742086
pmcid: 4764560
doi: 10.7554/eLife.11058
Chantranupong, L. et al. The Sestrins interact with GATOR2 to negatively regulate the amino-acid-sensing pathway upstream of mTORC1. Cell Rep. 9, 1–8 (2014).
pubmed: 25263562
pmcid: 4223866
doi: 10.1016/j.celrep.2014.09.014
Chantranupong, L. et al. The CASTOR proteins are arginine sensors for the mTORC1 pathway. Cell 165, 153–164 (2016).
pubmed: 26972053
pmcid: 4808398
doi: 10.1016/j.cell.2016.02.035
Saxton, R. A. et al. Structural basis for leucine sensing by the Sestrin2-mTORC1 pathway. Science 351, 53–58 (2016).
pubmed: 26586190
doi: 10.1126/science.aad2087
Saxton, R. A., Chantranupong, L., Knockenhauer, K. E., Schwartz, T. U. & Sabatini, D. M. Mechanism of arginine sensing by CASTOR1 upstream of mTORC1. Nature 536, 229–233 (2016).
pubmed: 27487210
pmcid: 4988899
doi: 10.1038/nature19079
Parmigiani, A. et al. Sestrins inhibit mTORC1 kinase activation through the GATOR complex. Cell Rep. 9, 1281–1291 (2014).
pubmed: 25457612
pmcid: 4303546
doi: 10.1016/j.celrep.2014.10.019
Wolfson, R. L. et al. Sestrin2 is a leucine sensor for the mTORC1 pathway. Science 351, 43–48 (2016).
pubmed: 26449471
doi: 10.1126/science.aab2674
Chen, J. et al. SAR1B senses leucine levels to regulate mTORC1 signalling. Nature 596, 281–284 (2021).
pubmed: 34290409
doi: 10.1038/s41586-021-03768-w
Bar-Peled, L. 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).
pubmed: 23723238
pmcid: 3728654
doi: 10.1126/science.1232044
Panchaud, N., Peli-Gulli, M. P. & De Virgilio, C. Amino acid deprivation inhibits TORC1 through a GTPase-activating protein complex for the Rag family GTPase Gtr1. Sci. Signal 6, ra42 (2013).
pubmed: 23716719
doi: 10.1126/scisignal.2004112
Jewell, J. L. et al. Differential regulation of mTORC1 by leucine and glutamine. Science 347, 194–198 (2015).
pubmed: 25567907
pmcid: 4384888
doi: 10.1126/science.1259472
Meng, D. et al. Glutamine and asparagine activate mTORC1 independently of Rag GTPases. J. Biol. Chem. 295, 2890–2899 (2020).
pubmed: 32019866
pmcid: 7062167
doi: 10.1074/jbc.AC119.011578
Stracka, D., Jozefczuk, S., Rudroff, F., Sauer, U. & Hall, M. N. Nitrogen source activates TOR (target of rapamycin) complex 1 via glutamine and independently of Gtr/Rag proteins. J. Biol. Chem. 289, 25010–25020 (2014).
pubmed: 25063813
pmcid: 4155668
doi: 10.1074/jbc.M114.574335
Sardiello, M. et al. A gene network regulating lysosomal biogenesis and function. Science 325, 473–477 (2009).
pubmed: 19556463
doi: 10.1126/science.1174447
Settembre, C. et al. TFEB links autophagy to lysosomal biogenesis. Science 332, 1429–1433 (2011).
pubmed: 21617040
pmcid: 3638014
doi: 10.1126/science.1204592
Martina, J. A. et al. The nutrient-responsive transcription factor TFE3 promotes autophagy, lysosomal biogenesis, and clearance of cellular debris. Sci. Signal 7, ra9 (2014).
pubmed: 24448649
pmcid: 4696865
doi: 10.1126/scisignal.2004754
Puertollano, R., Ferguson, S. M., Brugarolas, J. & Ballabio, A. The complex relationship between TFEB transcription factor phosphorylation and subcellular localization. EMBO J. 37, e98804 (2018).
pubmed: 29764979
pmcid: 5983138
doi: 10.15252/embj.201798804
Duvel, K. et al. Activation of a metabolic gene regulatory network downstream of mTOR complex 1. Mol. Cell 39, 171–183 (2010).
pubmed: 20670887
pmcid: 2946786
doi: 10.1016/j.molcel.2010.06.022
Ben-Sahra, I., Hoxhaj, G., Ricoult, S. J. H., Asara, J. M. & Manning, B. D. mTORC1 induces purine synthesis through control of the mitochondrial tetrahydrofolate cycle. Science 351, 728–733 (2016).
pubmed: 26912861
pmcid: 4786372
doi: 10.1126/science.aad0489
Artoni, F., Grutzmacher, N. & Demetriades, C. Unbiased evaluation of rapamycin’s specificity as an mTOR inhibitor. Aging Cell 22, e13888 (2023).
pubmed: 37222020
pmcid: 10410055
doi: 10.1111/acel.13888
Settembre, C. et al. A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB. EMBO J. 31, 1095–1108 (2012).
pubmed: 22343943
pmcid: 3298007
doi: 10.1038/emboj.2012.32
Thedieck, K. et al. Inhibition of mTORC1 by astrin and stress granules prevents apoptosis in cancer cells. Cell 154, 859–874 (2013).
pubmed: 23953116
doi: 10.1016/j.cell.2013.07.031
Averous, J. et al. Requirement for lysosomal localization of mTOR for its activation differs between leucine and other amino acids. Cell Signal 26, 1918–1927 (2014).
pubmed: 24793303
doi: 10.1016/j.cellsig.2014.04.019
Wang, A. et al. Activity-independent targeting of mTOR to lysosomes in primary osteoclasts. Sci. Rep. 7, 3005 (2017).
pubmed: 28592812
pmcid: 5462732
doi: 10.1038/s41598-017-03494-2
Oshiro, N., Rapley, J. & Avruch, J. Amino acids activate mammalian target of rapamycin (mTOR) complex 1 without changing Rag GTPase guanyl nucleotide charging. J. Biol. Chem. 289, 2658–2674 (2014).
pubmed: 24337580
doi: 10.1074/jbc.M113.528505
Buerger, C., DeVries, B. & Stambolic, V. Localization of Rheb to the endomembrane is critical for its signaling function. Biochem. Biophys. Res. Commun. 344, 869–880 (2006).
pubmed: 16631613
doi: 10.1016/j.bbrc.2006.03.220
Hanker, A. B. et al. Differential requirement of CAAX-mediated posttranslational processing for Rheb localization and signaling. Oncogene 29, 380–391 (2010).
pubmed: 19838215
doi: 10.1038/onc.2009.336
Yadav, R. B. et al. mTOR direct interactions with Rheb-GTPase and raptor: subcellular localization using fluorescence lifetime imaging. BMC Cell Biol. 14, 3 (2013).
pubmed: 23311891
pmcid: 3549280
doi: 10.1186/1471-2121-14-3
Hao, F. et al. Rheb localized on the Golgi membrane activates lysosome-localized mTORC1 at the Golgi–lysosome contact site. J. Cell Sci. 131, jcs208017 (2018).
pubmed: 29222112
doi: 10.1242/jcs.208017
Gosavi, P., Houghton, F. J., McMillan, P. J., Hanssen, E. & Gleeson, P. A. The Golgi ribbon in mammalian cells negatively regulates autophagy by modulating mTOR activity. J. Cell Sci. 131, jcs211987 (2018).
pubmed: 29361552
doi: 10.1242/jcs.211987
Angarola, B. & Ferguson, S. M. Weak membrane interactions allow Rheb to activate mTORC1 signaling without major lysosome enrichment. Mol. Biol. Cell 30, 2750–2760 (2019).
pubmed: 31532697
pmcid: 6789162
doi: 10.1091/mbc.E19-03-0146
Holz, M. K., Ballif, B. A., Gygi, S. P. & Blenis, J. mTOR and S6K1 mediate assembly of the translation preinitiation complex through dynamic protein interchange and ordered phosphorylation events. Cell 123, 569–580 (2005).
pubmed: 16286006
doi: 10.1016/j.cell.2005.10.024
Zhou, X. et al. Dynamic visualization of mTORC1 activity in living cells. Cell Rep. 10, 1767–1777 (2015).
pubmed: 25772363
pmcid: 4567530
doi: 10.1016/j.celrep.2015.02.031
Ahmed, A. R. et al. Direct imaging of the recruitment and phosphorylation of S6K1 in the mTORC1 pathway in living cells. Sci. Rep. 9, 3408 (2019).
pubmed: 30833605
pmcid: 6399282
doi: 10.1038/s41598-019-39410-z
Drenan, R. M., Liu, X., Bertram, P. G. & Zheng, X. F. FKBP12-rapamycin-associated protein or mammalian target of rapamycin (FRAP/mTOR) localization in the endoplasmic reticulum and the Golgi apparatus. J. Biol. Chem. 279, 772–778 (2004).
pubmed: 14578359
doi: 10.1074/jbc.M305912200
Liu, X. & Zheng, X. F. Endoplasmic reticulum and Golgi localization sequences for mammalian target of rapamycin. Mol. Biol. Cell 18, 1073–1082 (2007).
pubmed: 17215520
pmcid: 1805082
doi: 10.1091/mbc.e06-05-0406
Tsokanos, F. F. et al. eIF4A inactivates TORC1 in response to amino acid starvation. EMBO J. 35, 1058–1076 (2016).
pubmed: 26988032
pmcid: 4868951
doi: 10.15252/embj.201593118
Schieke, S. M. et al. The mammalian target of rapamycin (mTOR) pathway regulates mitochondrial oxygen consumption and oxidative capacity. J. Biol. Chem. 281, 27643–27652 (2006).
pubmed: 16847060
doi: 10.1074/jbc.M603536200
Mutvei, A. P. et al. Rap1-GTPases control mTORC1 activity by coordinating lysosome organization with amino acid availability. Nat. Commun. 11, 1416 (2020).
pubmed: 32184389
pmcid: 7078236
doi: 10.1038/s41467-020-15156-5
Lindquist, R. A. et al. Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1-S6K pathway signaling. Genome Res. 21, 433–446 (2011).
pubmed: 21239477
pmcid: 3044857
doi: 10.1101/gr.111492.110
Teis, D. et al. p14-MP1-MEK1 signaling regulates endosomal traffic and cellular proliferation during tissue homeostasis. J. Cell Biol. 175, 861–868 (2006).
pubmed: 17178906
pmcid: 2064696
doi: 10.1083/jcb.200607025
Gangloff, Y. G. et al. Disruption of the mouse mTOR gene leads to early postimplantation lethality and prohibits embryonic stem cell development. Mol. Cell. Biol. 24, 9508–9516 (2004).
pubmed: 15485918
pmcid: 522282
doi: 10.1128/MCB.24.21.9508-9516.2004
Murakami, M. et al. mTOR is essential for growth and proliferation in early mouse embryos and embryonic stem cells. Mol. Cell. Biol. 24, 6710–6718 (2004).
pubmed: 15254238
pmcid: 444840
doi: 10.1128/MCB.24.15.6710-6718.2004
Guertin, D. A. et al. Ablation in mice of the mTORC components raptor, rictor, or mLST8 reveals that mTORC2 is required for signaling to Akt-FOXO and PKCalpha, but not S6K1. Dev. Cell 11, 859–871 (2006).
pubmed: 17141160
doi: 10.1016/j.devcel.2006.10.007
Kim, Y. C. et al. Rag GTPases are cardioprotective by regulating lysosomal function. Nat. Commun. 5, 4241 (2014).
pubmed: 24980141
doi: 10.1038/ncomms5241
Shen, K., Sidik, H. & Talbot, W. S. The Rag–Ragulator complex regulates lysosome function and phagocytic flux in microglia. Cell Rep. 14, 547–559 (2016).
pubmed: 26774477
pmcid: 4731305
doi: 10.1016/j.celrep.2015.12.055
Settembre, C. et al. TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop. Nat. Cell Biol. 15, 647–658 (2013).
pubmed: 23604321
pmcid: 3699877
doi: 10.1038/ncb2718
Pastore, N. et al. TFE3 regulates whole-body energy metabolism in cooperation with TFEB. EMBO Mol. Med. 9, 605–621 (2017).
pubmed: 28283651
pmcid: 5412821
doi: 10.15252/emmm.201607204
Lawrence, R. E. et al. Structural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complex. Science 366, 971–977 (2019).
pubmed: 31672913
pmcid: 6945816
doi: 10.1126/science.aax0364
Napolitano, G. et al. A substrate-specific mTORC1 pathway underlies Birt–Hogg–Dube syndrome. Nature 585, 597–602 (2020).
pubmed: 32612235
pmcid: 7610377
doi: 10.1038/s41586-020-2444-0
Alesi, N. et al. TSC2 regulates lysosome biogenesis via a non-canonical RAGC and TFEB-dependent mechanism. Nat. Commun. 12, 4245 (2021).
pubmed: 34253722
pmcid: 8275687
doi: 10.1038/s41467-021-24499-6
Hatakeyama, R. et al. Spatially distinct pools of TORC1 balance protein homeostasis. Mol. Cell 73, 325–338 e328 (2019).
pubmed: 30527664
doi: 10.1016/j.molcel.2018.10.040
Mane, S. M. et al. Purification and characterization of human lysosomal membrane glycoproteins. Arch. Biochem. Biophys. 268, 360–378 (1989).
pubmed: 2912382
doi: 10.1016/0003-9861(89)90597-3
Chen, J. W., Murphy, T. L., Willingham, M. C., Pastan, I. & August, J. T. Identification of two lysosomal membrane glycoproteins. J. Cell Biol. 101, 85–95 (1985).
pubmed: 2409098
doi: 10.1083/jcb.101.1.85
Nuchel, J. et al. TGFB1 is secreted through an unconventional pathway dependent on the autophagic machinery and cytoskeletal regulators. Autophagy 14, 465–486 (2018).
pubmed: 29297744
pmcid: 5915026
doi: 10.1080/15548627.2017.1422850
Kowarz, E., Loscher, D. & Marschalek, R. Optimized Sleeping Beauty transposons rapidly generate stable transgenic cell lines. Biotechnol. J. 10, 647–653 (2015).
pubmed: 25650551
doi: 10.1002/biot.201400821
Ran, F. A. et al. Genome engineering using the CRISPR–Cas9 system. Nat. Protoc. 8, 2281–2308 (2013).
pubmed: 24157548
pmcid: 3969860
doi: 10.1038/nprot.2013.143
Wyant, G. A. et al. mTORC1 activator SLC38A9 is required to efflux essential amino acids from lysosomes and use protein as a nutrient. Cell 171, 642–654 e612 (2017).
pubmed: 29053970
pmcid: 5704964
doi: 10.1016/j.cell.2017.09.046
Mahoney, S. J. et al. A small molecule inhibitor of Rheb selectively targets mTORC1 signaling. Nat. Commun. 9, 548 (2018).
pubmed: 29416044
pmcid: 5803267
doi: 10.1038/s41467-018-03035-z
Sancak, Y. et al. PRAS40 is an insulin-regulated inhibitor of the mTORC1 protein kinase. Mol. Cell 25, 903–915 (2007).
pubmed: 17386266
doi: 10.1016/j.molcel.2007.03.003
Nicastro, R. et al. Malonyl-CoA is a conserved endogenous ATP-competitive mTORC1 inhibitor. Nat. Cell Biol. 25, 1303–1318 (2023).
pubmed: 37563253
pmcid: 10495264
doi: 10.1038/s41556-023-01198-6
Fitzian, K. et al. TSC1 binding to lysosomal PIPs is required for TSC complex translocation and mTORC1 regulation. Mol. Cell 81, 2705–2721 e2708 (2021).
pubmed: 33974911
doi: 10.1016/j.molcel.2021.04.019
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
pubmed: 22743772
doi: 10.1038/nmeth.2019
Manders, E. M. M., Verbeek, F. J. & Aten, J. A. Measurement of co-localization of objects in dual-colour confocal images. J. Microsc. 169, 375–382 (1993).
pubmed: 33930978
doi: 10.1111/j.1365-2818.1993.tb03313.x
Costes, S. V. et al. Automatic and quantitative measurement of protein-protein colocalization in live cells. Biophys. J. 86, 3993–4003 (2004).
pubmed: 15189895
pmcid: 1304300
doi: 10.1529/biophysj.103.038422
Dunn, K. W., Kamocka, M. M. & McDonald, J. H. A practical guide to evaluating colocalization in biological microscopy. Am. J. Physiol. Cell Physiol. 300, C723–C742 (2011).
pubmed: 21209361
pmcid: 3074624
doi: 10.1152/ajpcell.00462.2010
Stirling, J. W. & Graff, P. S. Antigen unmasking for immunoelectron microscopy: labeling is improved by treating with sodium ethoxide or sodium metaperiodate, then heating on retrieval medium. J. Histochem. Cytochem. 43, 115–123 (1995).
pubmed: 7529784
doi: 10.1177/43.2.7529784
Rouillard, A. D. et al. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database 2016, baw100 (2016).
pubmed: 27374120
pmcid: 4930834
doi: 10.1093/database/baw100
Igarashi, T. et al. Clock and ATF4 transcription system regulates drug resistance in human cancer cell lines. Oncogene 26, 4749–4760 (2007).
pubmed: 17297441
doi: 10.1038/sj.onc.1210289
Torrence, M. E. et al. The mTORC1-mediated activation of ATF4 promotes protein and glutathione synthesis downstream of growth signals. eLife 10, e63326 (2021).
pubmed: 33646118
pmcid: 7997658
doi: 10.7554/eLife.63326
Iqbal, A. et al. Flaski toolbox. GitHub https://flaski.age.mpg.de (2021).