The big and intricate dreams of little organelles: Embracing complexity in the study of membrane traffic
dc.contributor.author | Liu, Allen P. | |
dc.contributor.author | Botelho, Roberto J. | |
dc.contributor.author | Antonescu, Costin N. | |
dc.date.accessioned | 2017-10-05T18:20:27Z | |
dc.date.available | 2018-12-03T15:34:04Z | en |
dc.date.issued | 2017-09 | |
dc.identifier.citation | Liu, Allen P.; Botelho, Roberto J.; Antonescu, Costin N. (2017). "The big and intricate dreams of little organelles: Embracing complexity in the study of membrane traffic." Traffic 18(9): 567-579. | |
dc.identifier.issn | 1398-9219 | |
dc.identifier.issn | 1600-0854 | |
dc.identifier.uri | https://hdl.handle.net/2027.42/138421 | |
dc.publisher | John Wiley & Sons A/S | |
dc.subject.other | phosphoinositides | |
dc.subject.other | signaling | |
dc.subject.other | transcription | |
dc.subject.other | systems biology | |
dc.subject.other | adaptation | |
dc.subject.other | clathrin‐mediated endocytosis | |
dc.subject.other | computational modeling | |
dc.subject.other | heterogeneity | |
dc.subject.other | lipids | |
dc.subject.other | lysosomes | |
dc.title | The big and intricate dreams of little organelles: Embracing complexity in the study of membrane traffic | |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | |
dc.subject.hlbsecondlevel | Molecular, Cellular and Developmental Biology | |
dc.subject.hlbtoplevel | Health Sciences | |
dc.description.peerreviewed | Peer Reviewed | |
dc.description.bitstreamurl | https://deepblue.lib.umich.edu/bitstream/2027.42/138421/1/tra12497_am.pdf | |
dc.description.bitstreamurl | https://deepblue.lib.umich.edu/bitstream/2027.42/138421/2/tra12497-sup-0001-EditorialProcess.pdf | |
dc.description.bitstreamurl | https://deepblue.lib.umich.edu/bitstream/2027.42/138421/3/tra12497.pdf | |
dc.identifier.doi | 10.1111/tra.12497 | |
dc.identifier.source | Traffic | |
dc.identifier.citedreference | Pin CL, Rukstalis JM, Johnson C, Konieczny SF. The bHLH transcription factor Mist1 is required to maintain exocrine pancreas cell organization and acinar cell identity. J Cell Biol. 2001; 155: 519 ‐ 530. | |
dc.identifier.citedreference | Boulant S, Kural C, Zeeh JC, Ubelmann F, Kirchhausen T. Actin dynamics counteract membrane tension during clathrin‐mediated endocytosis. Nat Cell Biol. 2011; 13: 1124 ‐ 1158. | |
dc.identifier.citedreference | Tan X, Heureaux J, Liu AP. Cell spreading area regulates clathrin‐coated pit dynamics on micropatterned substrate. Integr Biol. 2015; 7: 1033 ‐ 1043. | |
dc.identifier.citedreference | Hassinger JE, Oster G, Drubin DG, Rangamani P. Design principles for robust vesiculation in clathrin‐mediated endocytosis. Proc Natl Acad Sci USA. 2017; 114: E1118 ‐ E1127. | |
dc.identifier.citedreference | Walani N, Torres J, Agrawal A. Endocytic proteins drive vesicle growth via instability in high membrane tension environment. Proc Natl Acad Sci USA. 2015; 112: E1423 ‐ E1432. | |
dc.identifier.citedreference | Irajizad E, Walani N, Veatch SL, Liu AP, Agrawal A. Clathrin polymerization exhibits high mechano‐geometric sensitivity. Soft Matter. 2017; 13: 1455 ‐ 1462. | |
dc.identifier.citedreference | Tourdot RW, Bradley RP, Ramakrishnan N, Radhakrishnan R. Multiscale computational models in physical systems biology of intracellular trafficking. IET Syst Biol. 2014; 8: 198 ‐ 213. | |
dc.identifier.citedreference | Scita G, Di Fiore PP. The endocytic matrix. Nature. 2010; 463: 464 ‐ 473. | |
dc.identifier.citedreference | Dai J, Sheetz MP. Regulation of endocytosis, exocytosis, and shape by membrane tension. Cold Spring Harb Symp Quant Biol. 1995; 60: 567 ‐ 571. | |
dc.identifier.citedreference | Bretscher MS. Getting membrane flow and the cytoskeleton to cooperate in moving cells. Cell. 1996; 87: 601 ‐ 606. | |
dc.identifier.citedreference | Gauthier NC, Fardin MA, Roca‐Cusachs P, Sheetz MP. Temporary increase in plasma membrane tension coordinates the activation of exocytosis and contraction during cell spreading. Proc Natl Acad Sci USA. 2011; 108: 14467 ‐ 14472. | |
dc.identifier.citedreference | Sinha B, Koster D, Ruez R, et al. Cells respond to mechanical stress by rapid disassembly of caveolae. Cell. 2011; 144: 402 ‐ 413. | |
dc.identifier.citedreference | Houk AR, Jilkine A, Mejean CO, et al. Membrane tension maintains cell polarity by confining signals to the leading edge during neutrophil migration. Cell. 2012; 148: 175 ‐ 188. | |
dc.identifier.citedreference | Rappoport JZ, Simon SM. Real‐time analysis of clathrin‐mediated endocytosis during cell migration. J Cell Sci. 2003; 116: 847 ‐ 855. | |
dc.identifier.citedreference | Kural C, Akatay AA, Gaudin R, et al. Asymmetric formation of coated pits on dorsal and ventral surfaces at the leading edges of motile cells and on protrusions of immobile cells. Mol Biol Cell. 2015; 26: 2044 ‐ 2053. | |
dc.identifier.citedreference | Ferguson JP, Willy NM, Heidotting SP, Huber SD, Webber MJ, Kural C. Deciphering dynamics of clathrin‐mediated endocytosis in a living organism. J Cell Biol. 2016; 214: 347 ‐ 358. | |
dc.identifier.citedreference | Jimenez AJ, Maiuri P, Lafaurie‐Janvore J, Divoux S, Piel M, Perez F. ESCRT machinery is required for plasma membrane repair. Science. 2014; 343: 1247136. | |
dc.identifier.citedreference | Raab M, Gentili M, de Belly H, et al. ESCRT III repairs nuclear envelope ruptures during cell migration to limit DNA damage and cell death. Science. 2016; 352: 359 ‐ 362. | |
dc.identifier.citedreference | Denais CM, Gilbert RM, Isermann P, et al. Nuclear envelope rupture and repair during cancer cell migration. Science. 2016; 352: 353 ‐ 358. | |
dc.identifier.citedreference | Boucrot E, Kirchhausen T. Endosomal recycling controls plasma membrane area during mitosis. Proc Natl Acad Sci USA. 2007; 104: 7939 ‐ 7944. | |
dc.identifier.citedreference | Fielding AB, Willox AK, Okeke E, Royle SJ. Clathrin‐mediated endocytosis is inhibited during mitosis. Proc Natl Acad Sci USA. 2012; 109: 6572 ‐ 6577. | |
dc.identifier.citedreference | 190. Tacheva‐Grigorova SK, Santos AJ, Boucrot E, Kirchhausen T. Clathrin‐mediated endocytosis persists during unperturbed mitosis. Cell Rep. 2013; 4: 659 ‐ 668. | |
dc.identifier.citedreference | Kaur S, Fielding AB, Gassner G, Carter NJ, Royle SJ. An unmet actin requirement explains the mitotic inhibition of clathrin‐mediated endocytosis. Elife. 2014; 3: e00829. | |
dc.identifier.citedreference | Schmid EM, McMahon HT. Integrating molecular and network biology to decode endocytosis. Nature. 2007; 448: 883 ‐ 888. | |
dc.identifier.citedreference | Smith CM, Chircop M. Clathrin‐mediated endocytic proteins are involved in regulating mitotic progression and completion. Traffic. 2012; 13: 1628 ‐ 1641. | |
dc.identifier.citedreference | Klinkert K, Rocancourt M, Houdusse A, Echard A. Rab35 GTPase couples cell division with initiation of epithelial apico‐basal polarity and lumen opening. Nat Commun. 2016; 7: 11166. | |
dc.identifier.citedreference | Maxfield FR, McGraw TE. Endocytic recycling. Nat Rev Mol Cell Biol. 2004; 5: 121 ‐ 132. | |
dc.identifier.citedreference | Hutagalung AH, Novick PJ. Role of Rab GTPases in membrane traffic and cell physiology. Physiol Rev. 2011; 91: 119 – 149. | |
dc.identifier.citedreference | Maxfield FR. Role of endosomes and lysosomes in human disease. Cold Spring Harb Perspect Biol. 2014; 6: a016931. | |
dc.identifier.citedreference | Antonescu CN, McGraw TE, Klip A. Reciprocal regulation of endocytosis and metabolism. Cold Spring Harb Perspect Biol. 2013; 6: a016964. | |
dc.identifier.citedreference | Maritzen T, Schachtner H, Legler DF. On the move: endocytic trafficking in cell migration. Cell Mol Life Sci. 2015; 72: 2119 ‐ 2134. | |
dc.identifier.citedreference | Mazzocchi F. Complexity and the reductionism‐holism debate in systems biology. Wiley Interdiscip Rev Syst Biol Med. 2012; 4: 413 ‐ 427. | |
dc.identifier.citedreference | Tartakoff AM. George Emil Palade: charismatic virtuoso of cell biology. Nat Rev Mol Cell Biol. 2002; 3: 871 ‐ 876. | |
dc.identifier.citedreference | Opperdoes F. A feeling for the cell: Christian de Duve (1917–2013). PLoS Biol. 2013; 11: e1001671. | |
dc.identifier.citedreference | Novick P, Field C, Schekman R. Identification of 23 complementation groups required for post‐translational events in the yeast secretory pathway. Cell. 1980; 21: 205 ‐ 215. | |
dc.identifier.citedreference | Islamaj Dogan R, Kim S, Chatr‐Aryamontri A, et al. The BioC‐BioGRID corpus: full text articles annotated for curation of protein‐protein and genetic interactions. Database. 2017; 2017: baw147. | |
dc.identifier.citedreference | Hein MY, Hubner NC, Poser I, et al. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell. 2015; 163: 712 ‐ 723. | |
dc.identifier.citedreference | Rolland T, Taşan M, Charloteaux B, et al. A proteome‐scale map of the human interactome network. Cell. 2014; 159: 1212 ‐ 1226. | |
dc.identifier.citedreference | Thul PJ, Åkesson L, Wiking M, et al. A subcellular map of the human proteome. Science. 2017; 356: eaal3321. | |
dc.identifier.citedreference | Walther TC, Mann M. Mass spectrometry‐based proteomics in cell biology. J Cell Biol. 2010; 190: 491 ‐ 500. | |
dc.identifier.citedreference | Yates JR III, Gilchrist A, Howell KE, Bergeron JJM. Proteomics of organelles and large cellular structures. Nat Rev Mol Cell Biol. 2005; 6: 702 ‐ 714. | |
dc.identifier.citedreference | Forner F, Foster LJ, Campanaro S, Valle G, Mann M. Quantitative proteomic comparison of rat mitochondria from muscle, heart, and liver. Mol Cell Proteomics. 2005; 5: 608 ‐ 619. | |
dc.identifier.citedreference | Foster LJ, de Hoog CL, Zhang Y, et al. A mammalian organelle map by protein correlation profiling. Cell. 2006; 125: 187 ‐ 199. | |
dc.identifier.citedreference | Boisvert F‐M, Lam YW, Lamont D, Lamond AI. A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage. Mol Cell Proteomics. 2010; 9: 457 ‐ 470. | |
dc.identifier.citedreference | Huh W‐K, Falvo JV, Gerke LC, et al. Global analysis of protein localization in budding yeast. Nature. 2003; 425: 686 ‐ 691. | |
dc.identifier.citedreference | Williams CC, Jan CH, Weissman JS. Targeting and plasticity of mitochondrial proteins revealed by proximity‐specific ribosome profiling. Science. 2014; 346: 748 ‐ 751. | |
dc.identifier.citedreference | Roux KJ, Kim DI, Raida M, Burke B. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J Cell Biol. 2012; 196: 801 ‐ 810. | |
dc.identifier.citedreference | Steel E, Murray VL, Liu AP. Multiplex detection of homo‐ and heterodimerization of g protein‐coupled receptors by proximity biotinylation. PLoS One. 2014; 9: e93646. | |
dc.identifier.citedreference | Zou P, Ting AY. Imaging LDL receptor oligomerization during endocytosis using a co‐internalization assay. ACS Chem Biol. 2011; 6: 308 ‐ 313. | |
dc.identifier.citedreference | Choi‐Rhee E, Schulman H, Cronan JE. Promiscuous protein biotinylation by Escherichia coli biotin protein ligase. Protein Sci. 2004; 13: 3043 ‐ 3050. | |
dc.identifier.citedreference | Rhee HW, Zou P, Udeshi ND, et al. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science. 2013; 339: 1328 ‐ 1331. | |
dc.identifier.citedreference | Lam SS, Martell JD, Kamer KJ, et al. Directed evolution of APEX2 for electron microscopy and proximity labeling. Nat Methods. 2015; 12: 51 ‐ 54. | |
dc.identifier.citedreference | Perez White BE, Ventrella R, Kaplan N, Cable CJ, Thomas PM, Getsios S. EphA2 proteomics in human keratinocytes reveals a novel association with afadin and epidermal tight junctions. J Cell Sci. 2017; 130: 111 ‐ 118. | |
dc.identifier.citedreference | Fredriksson K, Van Itallie CM, Aponte A, Gucek M, Tietgens AJ, Anderson JM. Proteomic analysis of proteins surrounding occludin and claudin‐4 reveals their proximity to signaling and trafficking networks. PLoS One. 2015; 10: e0117074. | |
dc.identifier.citedreference | Haugsten EM, Sorensen V, Kunova Bosakova M, et al. Proximity labeling reveals molecular determinants of FGFR4 endosomal transport. J Proteome Res. 2016; 15: 3841 ‐ 3855. | |
dc.identifier.citedreference | Marx V. Mapping proteins with spatial proteomics. Nat Methods. 2015; 12: 815 ‐ 819. | |
dc.identifier.citedreference | Hung V, Zou P, Rhee HW, et al. Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging. Mol Cell. 2014; 55: 332 ‐ 341. | |
dc.identifier.citedreference | Mick DU, Rodrigues RB, Leib RD, et al. Proteomics of primary cilia by proximity labeling. Dev Cell. 2015; 35: 497 ‐ 512. | |
dc.identifier.citedreference | Lobingier BT, Hüttenhain R, Eichel K, et al. An approach to spatiotemporally resolve protein interaction networks in living cells. Cell. 2017; 169: 350 ‐ 360.e12. | |
dc.identifier.citedreference | Starkuviene V, Liebel U, Simpson JC, et al. High‐content screening microscopy identifies novel proteins with a putative role in secretory membrane traffic. Genome Res. 2004; 14: 1948 ‐ 1956. | |
dc.identifier.citedreference | Simpson JC, Joggerst B, Laketa V, et al. Genome‐wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway. Nat Cell Biol. 2012; 14: 764 ‐ 774. | |
dc.identifier.citedreference | Snijder B, Sacher R, Rämö P, Damm E‐M, Liberali P, Pelkmans L. Population context determines cell‐to‐cell variability in endocytosis and virus infection. Nature. 2009; 461: 520 ‐ 523. | |
dc.identifier.citedreference | Liberali P, Snijder B, Pelkmans L. A hierarchical map of regulatory genetic interactions in membrane trafficking. Cell. 2014; 157: 1473 ‐ 1487. | |
dc.identifier.citedreference | Kozik P, Hodson NA, Sahlender DA, et al. A human genome‐wide screen for regulators of clathrin‐coated vesicle formation reveals an unexpected role for the V‐ATPase. Nat Cell Biol. 2012; 15: 50 ‐ 60. | |
dc.identifier.citedreference | Orvedahl A, Jr RS, Xiao G, et al. Image‐based genome‐wide siRNA screen identifies selective autophagy factors. Nature. 2011; 480: 113 ‐ 117. | |
dc.identifier.citedreference | Chong YT, Koh JLY, Friesen H, et al. Yeast proteome dynamics from single cell imaging and automated analysis. Cell. 2015; 161: 1413 ‐ 1424. | |
dc.identifier.citedreference | Peng J, Zhou Y, Zhu S, Wei W. High‐throughput screens in mammalian cells using the CRISPR‐Cas9 system. FEBS J. 2015; 282: 2089 ‐ 2096. | |
dc.identifier.citedreference | Lievens S, Van der Heyden J, Masschaele D, et al. Proteome‐scale binary interactomics in human cells. Mol Cell Proteomics. 2016; 15: 3624 ‐ 3639. | |
dc.identifier.citedreference | Snijder B, Pelkmans L. Origins of regulated cell‐to‐cell variability. Nat Rev Mol Cell Biol. 2011; 12: 119 ‐ 125. | |
dc.identifier.citedreference | Di Paolo G, De Camilli P. Phosphoinositides in cell regulation and membrane dynamics. Nature. 2006; 443: 651 ‐ 657. | |
dc.identifier.citedreference | Balla T. Phosphoinositides: tiny lipids with giant impact on cell regulation. Physiol Rev. 2013; 93: 1019 ‐ 1137. | |
dc.identifier.citedreference | Cremona O, Di Paolo G, Wenk MR, et al. Essential role of phosphoinositide metabolism in synaptic vesicle recycling. Cell. 1999; 99: 179 ‐ 188. | |
dc.identifier.citedreference | Perera RM, Zoncu R, Lucast L, De Camilli P, Toomre D. Two synaptojanin 1 isoforms are recruited to clathrin‐coated pits at different stages. Proc Natl Acad Sci USA. 2006; 103: 19332 ‐ 19337. | |
dc.identifier.citedreference | Antonescu CN, Aguet F, Danuser G, Schmid SL. Phosphatidylinositol‐(4,5)‐bisphosphate regulates clathrin‐coated pit initiation, stabilization, and size. Mol Biol Cell. 2011; 22: 2588 ‐ 2600. | |
dc.identifier.citedreference | Lawe DC, Chawla A, Merithew E, et al. Sequential roles for phosphatidylinositol 3‐phosphate and Rab5 in tethering and fusion of early endosomes via their interaction with EEA1. J Biol Chem. 2002; 277: 8611 ‐ 8617. | |
dc.identifier.citedreference | Simonsen A, Lippé R, Christoforidis S, et al. EEA1 links PI(3)K function to Rab5 regulation of endosome fusion. Nature. 1998; 394: 494 ‐ 498. | |
dc.identifier.citedreference | Schink KO, Raiborg C, Stenmark H. Phosphatidylinositol 3‐phosphate, a lipid that regulates membrane dynamics, protein sorting and cell signalling. Bioessays. 2013; 35: 900 ‐ 912. | |
dc.identifier.citedreference | Holub BJ, Kuksis A. Structural and metabolic interrelationships among glycerophosphatides of rat liver in vivo. Can J Biochem. 1971; 49: 1347 ‐ 1356. | |
dc.identifier.citedreference | Baker RR, Thompson W. Positional distribution and turnover of fatty acids in phosphatidic acid, phosphoinositides, phosphatidylcholine and phosphatidylethanolamine in rat brain in vivo. Biochim Biophys Acta. 1972; 270: 489 ‐ 503. | |
dc.identifier.citedreference | Imae R, Inoue T, Nakasaki Y, et al. LYCAT, a homologue of C. elegans acl‐8, acl‐9 and acl‐10, determines the fatty acid composition of phosphatidylinositol in mice. J Lipid Res. 2011; 53: 335 ‐ 347. | |
dc.identifier.citedreference | Bone LN, Dayam RM, Lee M, et al. The acyltransferase LYCAT controls specific phosphoinositides and related membrane traffic. Mol Biol Cell. 2017; 28: 161 ‐ 172. | |
dc.identifier.citedreference | Shevchenko A, Simons K. Lipidomics: coming to grips with lipid diversity. Nat Rev Mol Cell Biol. 2010; 11: 593 ‐ 598. | |
dc.identifier.citedreference | Anderson KE, Kielkowska A, Durrant TN, et al. Lysophosphatidylinositol‐acyltransferase‐1 (LPIAT1) is required to maintain physiological levels of PtdIns and PtdInsP2 in the mouse. PLoS One. 2013; 8: e58425. | |
dc.identifier.citedreference | Lee H‐C, Inoue T, Sasaki J, et al. LPIAT1 regulates arachidonic acid content in phosphatidylinositol and is required for cortical lamination in mice. Mol Biol Cell. 2012; 23: 4689 ‐ 4700. | |
dc.identifier.citedreference | Lung M, Shulga YV, Ivanova PT, et al. Diacylglycerol kinase epsilon is selective for both acyl chains of phosphatidic acid or diacylglycerol. J Biol Chem. 2009; 284: 31062 ‐ 31073. | |
dc.identifier.citedreference | Abbott SK, Else PL, Atkins TA, Hulbert AJ. Fatty acid composition of membrane bilayers: Importance of diet polyunsaturated fat balance. Biochim Biophys Acta. E1818; 2012: 1309 ‐ 1317. | |
dc.identifier.citedreference | Naguib A, Bencze G, Engle DD, et al. P53 mutations change phosphatidylinositol acyl chain composition. Cell Rep. 2015; 10: 8 ‐ 19. | |
dc.identifier.citedreference | Oliveira TG, Chan RB, Bravo FV, et al. The impact of chronic stress on the rat brain lipidome. Mol Psychiatry. 2016; 21: 80 ‐ 88. | |
dc.identifier.citedreference | Frechin M, Stoeger T, Daetwyler S, et al. Cell‐intrinsic adaptation of lipid composition to local crowding drives social behaviour. Nature. 2015; 523: 88 ‐ 91. | |
dc.identifier.citedreference | Kolarich D, Jensen PH, Altmann F, Packer NH. Determination of site‐specific glycan heterogeneity on glycoproteins. Nat Protoc. 2012; 7: 1285 ‐ 1298. | |
dc.identifier.citedreference | Lau KS, Partridge EA, Grigorian A, et al. Complex N‐glycan number and degree of branching cooperate to regulate cell proliferation and differentiation. Cell. 2007; 129: 123 ‐ 134. | |
dc.identifier.citedreference | McMahon HT, Boucrot E. Molecular mechanism and physiological functions of clathrin‐mediated endocytosis. Nat Rev Mol Cell Biol. 2011; 12: 517 ‐ 533. | |
dc.identifier.citedreference | Conner SD, Schmid SL. Regulated portals of entry into the cell. Nature. 2003; 422: 37 ‐ 44. | |
dc.identifier.citedreference | Tosoni D, Puri C, Confalonieri S, et al. TTP specifically regulates the internalization of the transferrin receptor. Cell. 2005; 123: 875 ‐ 888. | |
dc.identifier.citedreference | Johannessen LE, Pedersen NM, Pedersen KW, Madshus IH, Stang E. Activation of the epidermal growth factor (EGF) receptor induces formation of EGF receptor‐ and Grb2‐containing clathrin‐coated pits. Mol Cell Biol. 2006; 26: 389 ‐ 401. | |
dc.identifier.citedreference | Antonescu CN, Danuser G, Schmid SL. Phosphatidic acid plays a regulatory role in clathrin‐mediated endocytosis. Mol Biol Cell. 2010; 21: 2944 ‐ 2952. | |
dc.identifier.citedreference | Confalonieri S, Salcini AE, Puri C, Tacchetti C, Di Fiore PP. Tyrosine phosphorylation of Eps15 is required for ligand‐regulated, but not constitutive, endocytosis. J Cell Biol. 2000; 150: 905 ‐ 912. | |
dc.identifier.citedreference | Motley A, Bright NA, Seaman MNJ, Robinson MS. Clathrin‐mediated endocytosis in AP‐2‐depleted cells. J Cell Biol. 2003; 162: 909 ‐ 918. | |
dc.identifier.citedreference | Conner SD, Schmid SL. Differential requirements for AP‐2 in clathrin‐mediated endocytosis. J Cell Biol. 2003; 162: 773 ‐ 779. | |
dc.identifier.citedreference | Huang F, Khvorova A, Marshall W, Sorkin A. Analysis of clathrin‐mediated endocytosis of epidermal growth factor receptor by RNA interference. J Biol Chem. 2004; 279: 16657 ‐ 16661. | |
dc.identifier.citedreference | Reis CR, Chen P‐H, Bendris N, Schmid SL. TRAIL‐death receptor endocytosis and apoptosis are selectively regulated by dynamin‐1 activation. Proc Natl Acad Sci USA. 2017; 114: 504 ‐ 509. | |
dc.identifier.citedreference | Taylor MJ, Perrais D, Merrifield CJ. A high precision survey of the molecular dynamics of Mammalian clathrin‐mediated endocytosis. PLoS Biol. 2011; 9: e1000604. | |
dc.identifier.citedreference | Liu AP, Loerke D, Schmid SL, Danuser G. Global and local regulation of clathrin‐coated pit dynamics detected on patterned substrates. Biophys J. 2009; 97: 1038 ‐ 1047. | |
dc.identifier.citedreference | Mettlen M, Loerke D, Yarar D, Danuser G, Schmid SL. Cargo‐ and adaptor‐specific mechanisms regulate clathrin‐mediated endocytosis. J Cell Biol. 2010; 188: 919 ‐ 933. | |
dc.identifier.citedreference | Mettlen M, Stoeber M, Loerke D, Antonescu CN, Danuser G, Schmid SL. Endocytic accessory proteins are functionally distinguished by their differential effects on the maturation of clathrin‐coated pits. Mol Biol Cell. 2009; 20: 3251 ‐ 3260. | |
dc.identifier.citedreference | Liu AP, Aguet F, Danuser G, Schmid SL. Local clustering of transferrin receptors promotes clathrin‐coated pit initiation. J Cell Biol. 2010; 191: 1381 ‐ 1393. | |
dc.identifier.citedreference | Loerke D, Mettlen M, Schmid SL, Danuser G. Measuring the hierarchy of molecular events during clathrin‐mediated endocytosis. Traffic. 2011; 12: 815 ‐ 825. | |
dc.identifier.citedreference | Nunez D, Antonescu C, Mettlen M, et al. Hotspots organize clathrin‐mediated endocytosis by efficient recruitment and retention of nucleating resources. Traffic. 2011; 12: 1868 ‐ 1878. | |
dc.identifier.citedreference | Loerke D, Mettlen M, Yarar D, et al. Cargo and dynamin regulate clathrin‐coated pit maturation. PLoS Biol. 2009; 7: e57. | |
dc.identifier.citedreference | Aguet F, Antonescu CN, Mettlen M, Schmid SL, Danuser G. Advances in analysis of low signal‐to‐noise images link dynamin and AP2 to the functions of an endocytic checkpoint. Dev Cell. 2013; 26: 279 ‐ 291. | |
dc.identifier.citedreference | Puthenveedu MA, von Zastrow M. Cargo regulates clathrin‐coated pit dynamics. Cell. 2006; 127: 113 ‐ 124. | |
dc.identifier.citedreference | Rosselli‐Murai LK, Yates JA, Yoshida S, et al. Loss of PTEN promotes formation of signaling‐specific clathrin‐coated pits. bioRxiv. 2017; 137760. https://doi.org/10.1101/137760. | |
dc.identifier.citedreference | Banerjee A, Berezhkovskii A, Nossal R. Stochastic model of clathrin‐coated pit assembly. Biophys J. 2012; 102: 2725 ‐ 2730. | |
dc.identifier.citedreference | McGough IJ, Steinberg F, Gallon M, et al. Identification of molecular heterogeneity in SNX27‐retromer‐mediated endosome‐to‐plasma‐membrane recycling. J Cell Sci. 2014; 127: 4940 ‐ 4953. | |
dc.identifier.citedreference | Chang AY, Marshall WF. Organelles—understanding noise and heterogeneity in cell biology at an intermediate scale. J Cell Sci. 2017; 130: 819 ‐ 826. | |
dc.identifier.citedreference | Kelly BM, Waheed A, Van Etten R, Chang PL. Heterogeneity of lysosomes in human fibroblasts. Mol Cell Biochem. 1989; 87: 171 ‐ 183. | |
dc.identifier.citedreference | Johnson DE, Ostrowski P, Jaumouillé V, Grinstein S. The position of lysosomes within the cell determines their luminal pH. J Cell Biol. 2016; 212: 677 ‐ 692. | |
dc.identifier.citedreference | Hollenbeck PJ, Swanson JA. Radial extension of macrophage tubular lysosomes supported by kinesin. Nature. 1990; 346: 864 ‐ 866. | |
dc.identifier.citedreference | Mrakovic A, Kay JG, Furuya W, Brumell JH, Botelho RJ. Rab7 and Arl8 GTPases are necessary for lysosome tubulation in macrophages. Traffic. 2012; 13: 1667 ‐ 1679. | |
dc.identifier.citedreference | Saric A, Hipolito VEB, Kay JG, Canton J, Antonescu CN, Botelho RJ. mTOR controls lysosome tubulation and antigen presentation in macrophages and dendritic cells. Mol Biol Cell. 2016; 27: 321 ‐ 333. | |
dc.identifier.citedreference | Lowrie DB, Andrew PW, Peters TJ. Analytical subcellular fractionation of alveolar macrophages from normal and BCG‐vaccinated rabbits with particular reference to heterogeneity of hydrolase‐containing granules. Biochem J. 1979; 178: 761 ‐ 767. | |
dc.identifier.citedreference | Pu J, Schindler C, Jia R, Jarnik M, Backlund P, Bonifacino JS. BORC, a multisubunit complex that regulates lysosome positioning. Dev Cell. 2015; 33: 176 ‐ 188. | |
dc.identifier.citedreference | Pelkmans L, Fava E, Grabner H, et al. Genome‐wide analysis of human kinases in clathrin‐ and caveolae/raft‐mediated endocytosis. Nature. 2005; 436: 78 ‐ 86. | |
dc.identifier.citedreference | Schauer K, Duong T, Bleakley K, Bardin S, Bornens M, Goud B. Probabilistic density maps to study global endomembrane organization. Nat Methods. 2010; 7: 560 ‐ 566. | |
dc.identifier.citedreference | Battich N, Stoeger T, Pelkmans L. Control of transcript variability in single mammalian cells. Cell. 2015; 163: 1596 ‐ 1610. | |
dc.identifier.citedreference | Thattai M, van Oudenaarden A. Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci USA. 2001; 98: 8614 ‐ 8619. | |
dc.identifier.citedreference | Raj A, van Oudenaarden A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell. 2008; 135: 216 ‐ 226. | |
dc.identifier.citedreference | Hooshangi S, Thiberge S, Weiss R. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc Natl Acad Sci USA. 2005; 102: 3581 ‐ 3586. | |
dc.identifier.citedreference | Mugler A, Tostevin F, ten Wolde PR. Spatial partitioning improves the reliability of biochemical signaling. Proc Natl Acad Sci USA. 2013; 110: 5927 ‐ 5932. | |
dc.identifier.citedreference | Stoeger T, Battich N, Pelkmans L. Passive noise filtering by cellular compartmentalization. Cell. 2016; 164: 1151 ‐ 1161. | |
dc.identifier.citedreference | Mills JC, Taghert PH. Scaling factors: transcription factors regulating subcellular domains. Bioessays. 2012; 34: 10 ‐ 16. | |
dc.identifier.citedreference | Mullins C, Bonifacino JS. The molecular machinery for lysosome biogenesis. Bioessays. 2001; 23: 333 ‐ 343. | |
dc.identifier.citedreference | Luzio JP, Parkinson MDJ, Gray SR, Bright NA. The delivery of endocytosed cargo to lysosomes. Biochem Soc Trans. 2009; 37: 1019 ‐ 1021. | |
dc.identifier.citedreference | Settembre C, Ballabio A. Lysosome: regulator of lipid degradation pathways. Trends Cell Biol. 2014; 24: 743 ‐ 750. | |
dc.identifier.citedreference | Palmieri M, Impey S, Kang H, et al. Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways. Hum Mol Genet. 2011; 20: 3852 ‐ 3866. | |
dc.identifier.citedreference | Luzio JP, Pryor PR, Bright NA. Lysosomes: fusion and function. Nat Rev Mol Cell Biol. 2007; 8: 622 ‐ 632. | |
dc.identifier.citedreference | Medina DL, Di Paola S, Peluso I, et al. Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB. Nat Cell Biol. 2015; 17: 288 ‐ 299. | |
dc.identifier.citedreference | Settembre C, Ballabio A. Lysosomal adaptation: how the lysosome responds to external cues. Cold Spring Harb Perspect Biol. 2014; 6: a016907. | |
dc.identifier.citedreference | Huber LA, Teis D. Lysosomal signaling in control of degradation pathways. Curr Opin Cell Biol. 2016; 39: 8 ‐ 14. | |
dc.identifier.citedreference | Martina JA, Puertollano R. Rag GTPases mediate amino acid‐dependent recruitment of TFEB and MITF to lysosomes. J Cell Biol. 2013; 200: 475 ‐ 491. | |
dc.identifier.citedreference | Roczniak‐Ferguson A, Petit CS, Froehlich F, Qian S, Ky J, Angarola B, Walther TC, Ferguson SM. The transcription factor TFEB links mTORC1 signaling to transcriptional control of lysosome homeostasis. Sci Signal. 2012; 5: ra42. | |
dc.identifier.citedreference | Sardiello M, Palmieri M, di Ronza A, et al. A gene network regulating lysosomal biogenesis and function. Science. 2009; 325: 473 ‐ 477. | |
dc.identifier.citedreference | Settembre C, Di Malta C, Polito VA, et al. TFEB links autophagy to lysosomal biogenesis. Science. 2011; 332: 1429 ‐ 1433. | |
dc.identifier.citedreference | Martina JA, Diab HI, Li H, Puertollano R. Novel roles for the MiTF/TFE family of transcription factors in organelle biogenesis, nutrient sensing, and energy homeostasis. Cell Mol Life Sci. 2014; 71: 2483 ‐ 2497. | |
dc.identifier.citedreference | Raben N, Puertollano R. TFEB and TFE3: linking lysosomes to cellular adaptation to stress. Annu Rev Cell Dev Biol. 2016; 32: 255 ‐ 278. | |
dc.identifier.citedreference | Ploper D, De Robertis EM. The MITF family of transcription factors: role in endolysosomal biogenesis, Wnt signaling, and oncogenesis. Pharmacol Res. 2015; 99: 36 ‐ 43. | |
dc.identifier.citedreference | Zoncu R, Bar‐Peled L, Efeyan A, Wang S, Sancak Y, Sabatini DM. mTORC1 senses lysosomal amino acids through an inside‐out mechanism that requires the vacuolar H(+)‐ATPase. Science. 2011; 334: 678 ‐ 683. | |
dc.identifier.citedreference | Efeyan A, Zoncu R, Sabatini DM. Amino acids and mTORC1: from lysosomes to disease. Trends Mol Med. 2012; 18: 524 ‐ 533. | |
dc.identifier.citedreference | Sancak Y, Bar‐Peled L, Zoncu R, Markhard AL, Nada S, Sabatini DM. Ragulator‐Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids. Cell. 2010; 141: 290 ‐ 303. | |
dc.identifier.citedreference | Han JM, Jeong SJ, Park MC, et al. Leucyl‐tRNA synthetase is an intracellular leucine sensor for the mTORC1‐signaling pathway. Cell. 2012; 149: 410 ‐ 424. | |
dc.identifier.citedreference | Peña‐Llopis S, Vega‐Rubin‐de‐Celis S, Schwartz JC, et al. Regulation of TFEB and V‐ATPases by mTORC1. EMBO J. 2011; 30: 3242 ‐ 3258. | |
dc.identifier.citedreference | Settembre C, Zoncu R, Medina DL, et al. A lysosome‐to‐nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB. EMBO J. 2012; 31: 1095 ‐ 1108. | |
dc.identifier.citedreference | Martina JA, Diab HI, Lishu L, et al. The nutrient‐responsive transcription factor TFE3 promotes autophagy, lysosomal biogenesis, and clearance of cellular debris. Sci Signal. 2014; 7: ra9. | |
dc.identifier.citedreference | Settembre C, De Cegli R, Mansueto G, et al. TFEB controls cellular lipid metabolism through a starvation‐induced autoregulatory loop. Nat Cell Biol. 2013; 15: 647 ‐ 658. | |
dc.identifier.citedreference | O’Rourke EJ, Ruvkun G. MXL‐3 and HLH‐30 transcriptionally link lipolysis and autophagy to nutrient availability. Nat Cell Biol. 2013; 15: 668 ‐ 676. | |
dc.identifier.citedreference | Tsunemi T, Ashe TD, Morrison BE, et al. PGC‐1 rescues huntington’s disease proteotoxicity by preventing oxidative stress and promoting TFEB function. Sci Transl Med. 2012; 4: 142ra97. | |
dc.identifier.citedreference | Nezich CL, Wang C, Fogel AI, Youle RJ. MiT/TFE transcription factors are activated during mitophagy downstream of Parkin and Atg5. J Cell Biol. 2015; 210: 435 ‐ 450. | |
dc.identifier.citedreference | Settembre C, Ballabio A. TFEB regulates autophagy: an integrated coordination of cellular degradation and recycling processes. Autophagy. 2011; 7: 1379 ‐ 1381. | |
dc.identifier.citedreference | Martina JA, Diab HI, Brady OA, Puertollano R. TFEB and TFE3 are novel components of the integrated stress response. EMBO J. 2016; 35: 479 ‐ 495. | |
dc.identifier.citedreference | Visvikis O, Ihuegbu N, Labed SAA, et al. Innate host defense requires TFEB‐mediated transcription of cytoprotective and antimicrobial genes. Immunity. 2014; 40: 896 ‐ 909. | |
dc.identifier.citedreference | Pastore N, Brady OA, Diab HI, et al. TFEB and TFE3 cooperate in the regulation of the innate immune response in activated macrophages. Autophagy. 2016; 12: 1240 ‐ 1258. | |
dc.identifier.citedreference | Gray MA, Choy CH, Dayam RM, et al. Phagocytosis enhances lysosomal and bactericidal properties by activating the transcription factor TFEB. Curr Biol. 2016; 26: 1955 ‐ 1964. | |
dc.identifier.citedreference | Ferron M, Settembre C, Shimazu J, et al. A RANKL‐PKC ‐TFEB signaling cascade is necessary for lysosomal biogenesis in osteoclasts. Genes Dev. 2013; 27: 955 ‐ 969. | |
dc.identifier.citedreference | Li Y, Xu M, Ding X, et al. Protein kinase C controls lysosome biogenesis independently of mTORC1. Nat Cell Biol. 2016; 18: 1065 ‐ 1077. | |
dc.identifier.citedreference | Ouimet M, Koster S, Sakowski E, et al. Mycobacterium tuberculosis induces the miR‐33 locus to reprogram autophagy and host lipid metabolism. Nat Immunol. 2016; 17: 677 ‐ 686. | |
dc.identifier.citedreference | Slack JM. Developmental biology of the pancreas. Development. 1995; 121: 1569 ‐ 1580. | |
dc.identifier.citedreference | Williams JA. Regulation of acinar cell function in the pancreas. Curr Opin Gastroenterol. 2010; 26: 478 ‐ 483. | |
dc.identifier.citedreference | Metzler MA, Venkatesh SG, Lakshmanan J, et al. A systems biology approach identifies a regulatory network in parotid acinar cell terminal differentiation. PLoS One. 2015; 10: e0125153. | |
dc.identifier.citedreference | Jiang M, Azevedo‐Pouly AC, Deering TG, et al. MIST1 and PTF1 collaborate in feed‐forward regulatory loops that maintain the pancreatic acinar phenotype in adult mice. Mol Cell Biol. 2016; 36: 2945 ‐ 2955. | |
dc.identifier.citedreference | Huh WJ, Esen E, Geahlen JH, et al. XBP1 controls maturation of gastric zymogenic cells by induction of MIST1 and expansion of the rough endoplasmic reticulum. Gastroenterology. 2010; 139: 2038 ‐ 2049. | |
dc.identifier.citedreference | Hess DA, Strelau KM, Karki A, et al. MIST1 links secretion and stress as both target and regulator of the unfolded protein response. Mol Cell Biol. 2016; 36: 2931 ‐ 2944. | |
dc.identifier.citedreference | Lee A‐H, Chu GC, Iwakoshi NN, Glimcher LH. XBP‐1 is required for biogenesis of cellular secretory machinery of exocrine glands. EMBO J. 2005; 24: 4368 ‐ 4380. | |
dc.identifier.citedreference | Hoang CQ, Hale MA, Azevedo‐Pouly AC, et al. Transcriptional maintenance of pancreatic acinar identity, differentiation, and homeostasis by PTF1A. Mol Cell Biol. 2016; 36: 3033 ‐ 3047. | |
dc.identifier.citedreference | Ramsey VG, Doherty JM, Chen CC, Stappenbeck TS, Konieczny SF, Mills JC. The maturation of mucus‐secreting gastric epithelial progenitors into digestive‐enzyme secreting zymogenic cells requires Mist1. Development. 2007; 134: 211 ‐ 222. | |
dc.identifier.citedreference | Pin CL, Bonvissuto AC, Konieczny SF. Mist1 expression is a common link among serous exocrine cells exhibiting regulated exocytosis. Anat Rec. 2000; 259: 157 ‐ 167. | |
dc.identifier.citedreference | Zhu L, Tran T, Rukstalis JM, Sun P, Damsz B, Konieczny SF. Inhibition of Mist1 homodimer formation induces pancreatic acinar‐to‐ductal metaplasia. Mol Cell Biol. 2004; 24: 2673 ‐ 2681. | |
dc.identifier.citedreference | Johnson CL, Kowalik AS, Rajakumar N, Pin CL. Mist1 is necessary for the establishment of granule organization in serous exocrine cells of the gastrointestinal tract. Mech Dev. 2004; 121: 261 ‐ 272. | |
dc.identifier.citedreference | Direnzo D, Hess DA, Damsz B, et al. Induced Mist1 expression promotes remodeling of mouse pancreatic acinar cells. Gastroenterology. 2012; 143: 469 ‐ 480. | |
dc.identifier.citedreference | Garside VC, Kowalik AS, Johnson CL, DiRenzo D, Konieczny SF, Pin CL. MIST1 regulates the pancreatic acinar cell expression of Atp2c2, the gene encoding secretory pathway calcium ATPase 2. Exp Cell Res. 2010; 316: 2859 ‐ 2870. | |
dc.identifier.citedreference | Luo X, Shin DM, Wang X, Konieczny SF, Muallem S. Aberrant localization of intracellular organelles, Ca2+ signaling, and exocytosis in Mist1 null mice. J Biol Chem. 2005; 280: 12668 ‐ 12675. | |
dc.identifier.citedreference | Tian X, Jin RU, Bredemeyer AJ, et al. RAB26 and RAB3D are direct transcriptional targets of MIST1 that regulate exocrine granule maturation. Mol Cell Biol. 2010; 30: 1269 ‐ 1284. | |
dc.identifier.citedreference | Jin RU, Mills JC. RAB26 coordinates lysosome traffic and mitochondrial localization. J Cell Sci. 2014; 127: 1018 ‐ 1032. | |
dc.identifier.citedreference | Jegga AG, Schneider L, Ouyang X, Zhang J. Systems biology of the autophagy‐lysosomal pathway. Autophagy. 2011; 7: 477 ‐ 489. | |
dc.identifier.citedreference | Mazzocchi F. Complexity in biology. Exceeding the limits of reductionism and determinism using complexity theory. EMBO Rep. 2008; 9: 10 ‐ 14. | |
dc.identifier.citedreference | Bartocci E, Lió P. Computational modeling, formal analysis, and tools for systems biology. PLoS Comput Biol. 2016; 12: e1004591. | |
dc.identifier.citedreference | Yang Q, Ferrell JE. The Cdk1‐APC/C cell cycle oscillator circuit functions as a time‐delayed, ultrasensitive switch. Nat Cell Biol. 2013; 15: 519 ‐ 525. | |
dc.identifier.citedreference | Kauffman SA. Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol. 1969; 22: 437 ‐ 467. | |
dc.identifier.citedreference | Wynn ML, Consul N, Merajver SD, Schnell S. Logic‐based models in systems biology: a predictive and parameter‐free network analysis method. Integr Biol (Camb). 2012; 4: 1323 ‐ 1337. | |
dc.identifier.citedreference | Li S, Assmann SM, Albert R. Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling. PLoS Biol. 2006; 4: e312. | |
dc.identifier.citedreference | Chylek LA, Akimov V, Dengjel J, et al. Phosphorylation site dynamics of early T‐cell receptor signaling. PLoS One. 2014; 9: e10424. | |
dc.identifier.citedreference | Börlin CS, Lang V, Hamacher‐Brady A, Brady NR. Agent‐based modeling of autophagy reveals emergent regulatory of spatio‐temporal autophagy dynamics. Cell Commun Signal. 2014; 12: 56. | |
dc.identifier.citedreference | Pogson M, Smallwood R, Qwarnstrom E, Holcombe M. Formal agent‐based modelling of intracellular chemical interactions. Biosystems. 2006; 85: 37 ‐ 45. | |
dc.identifier.citedreference | Helfrich W. Elastic properties of lipid bilayers: theory and possible experiments. Z Naturforsch C. 1973; 28: 693 ‐ 703. | |
dc.identifier.citedreference | Ramanan V, Agrawal NJ, Liu J, Engles S, Toy R, Radhakrishnan R. Systems biology and physical biology of clathrin‐mediated endocytosis. Integr Biol. 2011; 3: 803 ‐ 815. | |
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