84
Views
0
CrossRef citations to date
0
Altmetric
Review

The autophagosome: current understanding of formation and maturation

&
Pages 39-58 | Published online: 16 Feb 2015

References

  • Klionsky DJ, Baehrecke EH, Brumell JH, et al. A comprehensive glossary of autophagy-related molecules and processes (2nd edition). Autophagy. 2011;7(11):1273–1294. PubMed PMID: 21997368. Epub 2011/10/15. eng.
  • Mukaiyama H, Baba M, Osumi M, et al. Modification of a ubiquitin-like protein Paz2 conducted micropexophagy through formation of a novel membrane structure. Mol Biol Cell. 2004;15(1):58–70. PubMed PMID: 13679515. Pubmed Central PMCID: 307527.
  • Santambrogio L, Cuervo AM. Chasing the elusive mammalian microautophagy. Autophagy. 2011;7(6):652–654. PubMed PMID: 21460618.
  • Li W, Yang Q, Mao Z. Chaperone-mediated autophagy: machinery, regulation and biological consequences. Cell Mol Life Sci. 2011;68(5):749–763. PubMed PMID: 20976518.
  • Pankiv S, Clausen TH, Lamark T, et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J Biol Chem. 2007;282(33):24131–24145. PubMed PMID: 17580304.
  • Sawa-Makarska J, Abert C, Romanov J, Zens B, Ibiricu I, Martens S. Cargo binding to Atg19 unmasks additional Atg8 binding sites to mediate membrane-cargo apposition during selective autophagy. Nat Cell Biol. 2014;16(5):425–433. PubMed PMID: 24705553. Pubmed Central PMCID: 4009068.
  • Codogno P, Meijer AJ. Autophagy and signaling: their role in cell survival and cell death. Cell Death Differ. 2005;12(Suppl 2):1509–1518. PubMed PMID: 16247498.
  • De Duve C. The lysosome. Sci Am. 1963;208:64–72. PubMed PMID: 14025755.
  • Klionsky DJ, Ohsumi Y. Vacuolar import of proteins and organelles from the cytoplasm. Annu Rev Cell Dev Biol. 1999;15:1–32. PubMed PMID: 10611955.
  • Tsukada M, Ohsumi Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett. 1993;333(1–2):169–174. PubMed PMID: 8224160.
  • Thumm M, Egner R, Koch B, et al. Isolation of autophagocytosis mutants of Saccharomyces cerevisiae. FEBS Lett. 1994;349(2):275–280. PubMed PMID: 8050581.
  • Levine B, Yuan J. Autophagy in cell death: an innocent convict? J Clin Invest. 2005;115(10):2679–2688. PubMed PMID: 16200202. Pubmed Central PMCID: 1236698.
  • Marino G, Niso-Santano M, Baehrecke EH, Kroemer G. Self-consumption: the interplay of autophagy and apoptosis. Nat Rev Mol Cell Biol. 2014;15(2):81–94. PubMed PMID: 24401948. Pubmed Central PMCID: 3970201.
  • Musiwaro P, Smith M, Manifava M, Walker SA, Ktistakis NT. Characteristics and requirements of basal autophagy in HEK 293 cells. Autophagy. 2013;9(9):1407–1417. PubMed PMID: 23800949.
  • Morselli E, Maiuri MC, Markaki M, et al. Caloric restriction and resveratrol promote longevity through the Sirtuin-1-dependent induction of autophagy. Cell Death Dis. 2010;1:e10. PubMed PMID: 21364612. Pubmed Central PMCID: 3032517.
  • Jiang P, Mizushima N. Autophagy and human diseases. Cell Res. 2014;24(1):69–79. PubMed PMID: 24323045. Pubmed Central PMCID: 3879707.
  • Deretic V, Saitoh T, Akira S. Autophagy in infection, inflammation and immunity. Nat Rev Immunol. 2013;13(10):722–737. PubMed PMID: 24064518.
  • Wileman T. Autophagy as a defence against intracellular pathogens. Essays Biochem. 2013;55:153–163. PubMed PMID: 24070478.
  • Banerjee R, Beal MF, Thomas B. Autophagy in neurodegenerative disorders: pathogenic roles and therapeutic implications. Trends Neurosci. 2010;33(12):541–549. PubMed PMID: 20947179. Pubmed Central PMCID: 2981680.
  • Nixon RA. The role of autophagy in neurodegenerative disease. Nat Med. 2013;19(8):983–997. PubMed PMID: 23921753.
  • Guo JY, Xia B, White E. Autophagy-mediated tumor promotion. Cell. 20135;155(6):1216–1219. PubMed PMID: 24315093. Pubmed Central PMCID: 3987898.
  • White E. Deconvoluting the context-dependent role for autophagy in cancer. Nat Rev Cancer. 2012;12(6):401–410. PubMed PMID: 22534666. Pubmed Central PMCID: 3664381.
  • Mathew R, Karantza-Wadsworth V, White E. Role of autophagy in cancer. Nat Rev Cancer. 2007;7(12):961–967. PubMed PMID: 17972889. Pubmed Central PMCID: 2866167. Epub 2007/11/02. eng.
  • Knodler LA, Celli J. Eating the strangers within: host control of intracellular bacteria via xenophagy. Cell Microbiol. 2011;13(9):1319–1327. PubMed PMID: 21740500. Pubmed Central PMCID: 3158265.
  • Lamark T, Johansen T. Aggrephagy: selective disposal of protein aggregates by macroautophagy. Int J Cell Biol. 2012;2012:736905. PubMed PMID: 22518139. Pubmed Central PMCID: 3320095.
  • Sarkar S, Rubinsztein DC. Huntington’s disease: degradation of mutant huntingtin by autophagy. FEBS J. 2008;275(17):4263–4270. PubMed PMID: 18637946.
  • Lemasters JJ. Selective mitochondrial autophagy, or mitophagy, as a targeted defense against oxidative stress, mitochondrial dysfunction, and aging. Rejuvenation Res. 2005;8(1):3–5. PubMed PMID: 15798367. Epub 2005/03/31. eng.
  • MacVicar T. Mitophagy. Essays Biochem. 2013;55:93–104. PubMed PMID: 24070474.
  • Betin VM, Singleton BK, Parsons SF, Anstee DJ, Lane JD. Autophagy facilitates organelle clearance during differentiation of human erythroblasts: evidence for a role for ATG4 paralogs during autophagosome maturation. Autophagy. 2013;9(6):881–893. PubMed PMID: 23508006. Epub 2013/03/20. Eng.
  • Yamano K, Youle RJ. PINK1 is degraded through the N-end rule pathway. Autophagy. 2013;9(11):1758–1769. PubMed PMID: 24121706.
  • MacVicar TD, Lane JD. Impaired OMA1-dependent cleavage of OPA1 and reduced DRP1 fission activity combine to prevent mitophagy in cells that are dependent on oxidative phosphorylation. J Cell Sci. 2014;127(Pt 10):2313–2325. PubMed PMID: 24634514. Pubmed Central PMCID: 4021475.
  • Gomes LC, Benedetto GD, Scorrano L. During autophagy mitochondria elongate, are spared from degradation and sustain cell viability. Nat Cell Biol. 2011;13(5):589–598. PubMed PMID: 21478857. Pubmed Central PMCID: 3088644. Epub 2011/04/12. eng.
  • Tondera D, Grandemange S, Jourdain A, et al. SLP-2 is required for stress-induced mitochondrial hyperfusion. EMBO J. 2009;28(11):1589–1600. PubMed PMID: 19360003. Pubmed Central PMCID: 2693158. Epub 2009/04/11. eng.
  • Bernales S, McDonald KL, Walter P. Autophagy counterbalances endoplasmic reticulum expansion during the unfolded protein response. PLoS Biol. 2006;4(12):e423. PubMed PMID: 17132049. Pubmed Central PMCID: 1661684.
  • Sakai Y, Oku M, van der Klei IJ, Kiel JA. Pexophagy: autophagic degradation of peroxisomes. Biochim Biophys Acta. 2006;1763(12):1767–1775. PubMed PMID: 17005271.
  • Svenning S, Johansen T. Selective autophagy. Essays Biochem. 2013;55:79–92. PubMed PMID: 24070473.
  • Harding TM, Morano KA, Scott SV, Klionsky DJ. Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway. J Cell Biol. 1995;131(3):591–602. PubMed PMID: 7593182. Pubmed Central PMCID: 2120622.
  • Klionsky DJ. Look people, “Atg” is an abbreviation for “autophagy-related.” That’s it. Autophagy. 2012;8(9):1281–1282. PubMed PMID: 22889836. Pubmed Central PMCID: 3442874.
  • Simonsen A, Tooze SA. Coordination of membrane events during autophagy by multiple class III PI3-kinase complexes. J Cell Biol. 2009;186(6):773–782. PubMed PMID: 19797076. Pubmed Central PMCID: 2753151. Epub 2009/10/03. eng.
  • Koyama-Honda I, Itakura E, Fujiwara TK, Mizushima N. Temporal analysis of recruitment of mammalian ATG proteins to the autophagosome formation site. Autophagy. 2013;9(10):1491–1499. PubMed PMID: 23884233.
  • Suzuki K, Kubota Y, Sekito T, Ohsumi Y. Hierarchy of Atg proteins in pre-autophagosomal structure organization. Genes Cells. 2007;12(2):209–218. PubMed PMID: 17295840.
  • Itakura E, Mizushima N. Characterization of autophagosome formation site by a hierarchical analysis of mammalian Atg proteins. Autophagy. 2010;6(6):764–776. PubMed PMID: 20639694. Pubmed Central PMCID: 3321844.
  • Karanasios E, Stapleton E, Manifava M, et al. Dynamic association of the ULK1 complex with omegasomes during autophagy induction. J Cell Sci. 2013;126(Pt 22):5224–5238. PubMed PMID: 24013547.
  • Ktistakis NT, Karanasios E, Manifava M. Dynamics of autophagosome formation: a pulse and a sequence of waves. Biochem Soc Trans. 2014;42(5):1389–1395. PubMed PMID: 25233420.
  • Gallagher LE, Chan EY. Early signalling events of autophagy. Essays Biochem. 2013;55:1–15. PubMed PMID: 24070467.
  • Kim E, Goraksha-Hicks P, Li L, Neufeld TP, Guan KL. Regulation of TORC1 by Rag GTPases in nutrient response. Nat Cell Biol. 2008;10(8):935–945. PubMed PMID: 18604198. Pubmed Central PMCID: 2711503.
  • Sancak Y, Peterson TR, Shaul YD, et al. The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1. Science. 2008;320(5882):1496–1501. PubMed PMID: 18497260. Pubmed Central PMCID: 2475333.
  • Bar-Peled L, Schweitzer LD, Zoncu R, Sabatini DM. Ragulator is a GEF for the rag GTPases that signal amino acid levels to mTORC1. Cell. 2012;150(6):1196–1208. PubMed PMID: 22980980. Pubmed Central PMCID: 3517996.
  • Inoki K, Kim J, Guan KL. AMPK and mTOR in cellular energy homeostasis and drug targets. Annu Rev Pharmacol Toxicol. 2012;52:381–400. PubMed PMID: 22017684.
  • Kim J, Kundu M, Viollet B, Guan KL. AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1. Nat Cell Biol. 2011;13(2):132–141. PubMed PMID: 21258367. Pubmed Central PMCID: 3987946.
  • He C, Klionsky DJ. Regulation mechanisms and signaling pathways of autophagy. Annu Rev Genet. 2009;43:67–93. PubMed PMID: 19653858. Pubmed Central PMCID: 2831538.
  • Budovskaya YV, Stephan JS, Deminoff SJ, Herman PK. An evolutionary proteomics approach identifies substrates of the cAMP-dependent protein kinase. Proc Natl Acad Sci U S A. 2005;102(39):13933–13938. PubMed PMID: 16172400. Pubmed Central PMCID: 1236527.
  • Cherra SJ 3rd, Kulich SM, Uechi G, et al. Regulation of the autophagy protein LC3 by phosphorylation. J Cell Biol. 2010;190(4):533–539. PubMed PMID: 20713600. Pubmed Central PMCID: 2928022.
  • Jacinto E. What controls TOR? IUBMB Life. 2008;60(8):483–496. PubMed PMID: 18493947.
  • Hosokawa N, Hara T, Kaizuka T, et al. Nutrient-dependent mTORC1 association with the ULK1-Atg13-FIP200 complex required for autophagy. Mol Biol Cell. 2009;20(7):1981–1991. PubMed PMID: 19211835. Pubmed Central PMCID: 2663915. Epub 2009/02/13. eng.
  • Ganley IG, Wong PM, Gammoh N, Jiang X. Distinct autophagosomal-lysosomal fusion mechanism revealed by thapsigargin-induced autophagy arrest. Mol Cell. 2011;42(6):731–743. PubMed PMID: 21700220. Pubmed Central PMCID: 3124681.
  • Jung CH, Jun CB, Ro SH, et al. ULK-Atg13-FIP200 complexes mediate mTOR signaling to the autophagy machinery. Mol Biol Cell. 2009;20(7):1992–2003. PubMed PMID: 19225151. Pubmed Central PMCID: 2663920.
  • Mercer CA, Kaliappan A, Dennis PB. A novel, human Atg13 binding protein, Atg101, interacts with ULK1 and is essential for macroautophagy. Autophagy. 2009;5(5):649–662. PubMed PMID: 19287211. Epub 2009/03/17. eng.
  • Matsunaga K, Morita E, Saitoh T, et al. Autophagy requires endoplasmic reticulum targeting of the PI3-kinase complex via Atg14L. J Cell Biol. 2010;190(4):511–521. PubMed PMID: 20713597. Pubmed Central PMCID: 2928018.
  • Di Bartolomeo S, Corazzari M, Nazio F, et al. The dynamic interaction of AMBRA1 with the dynein motor complex regulates mammalian autophagy. J Cell Biol. 2010;191(1):155–168. PubMed PMID: 20921139. Pubmed Central PMCID: 2953445.
  • Russell RC, Tian Y, Yuan H, et al. ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase. Nat Cell Biol. 2013;15(7):741–750. PubMed PMID: 23685627. Pubmed Central PMCID: 3885611.
  • Jung CH, Seo M, Otto NM, Kim DH. ULK1 inhibits the kinase activity of mTORC1 and cell proliferation. Autophagy. 2011;7(10):1212–1221. PubMed PMID: 21795849. Pubmed Central PMCID: 3210307.
  • Hara T, Takamura A, Kishi C, et al. FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells. J Cell Biol. 2008;181(3):497–510. PubMed PMID: 18443221. Pubmed Central PMCID: 2364687.
  • Ragusa MJ, Stanley RE, Hurley JH. Architecture of the Atg17 complex as a scaffold for autophagosome biogenesis. Cell. 2012;151(7):1501–1512. PubMed PMID: 23219485. Pubmed Central PMCID: 3806636.
  • Cheong H, Nair U, Geng J, Klionsky DJ. The Atg1 kinase complex is involved in the regulation of protein recruitment to initiate sequestering vesicle formation for nonspecific autophagy in Saccharomyces cerevisiae. Mol Biol Cell. 2008;19(2):668–681. PubMed PMID: 18077553. Pubmed Central PMCID: 2230592.
  • Kraft C, Kijanska M, Kalie E, et al. Binding of the Atg1/ULK1 kinase to the ubiquitin-like protein Atg8 regulates autophagy. EMBO J. 2012;31(18):3691–3703. PubMed PMID: 22885598. Pubmed Central PMCID: 3442273.
  • Longatti A, Tooze SA. Recycling endosomes contribute to autophagosome formation. Autophagy. 2012;8(11):1682–1683. PubMed PMID: 22874560. Pubmed Central PMCID: 3494599.
  • Hutagalung AH, Novick PJ. Role of Rab GTPases in membrane traffic and cell physiology. Physiol Rev. 2011;91(1):119–149. PubMed PMID: 21248164. Pubmed Central PMCID: 3710122.
  • Chan EY, Tooze SA. Evolution of Atg1 function and regulation. Autophagy. 2009;5(6):758–765. PubMed PMID: 19411825.
  • Wirth M, Joachim J, Tooze SA. Autophagosome formation – the role of ULK1 and Beclin1-PI3KC3 complexes in setting the stage. Semin Cancer Biol. 2013;23(5):301–309. PubMed PMID: 23727157.
  • Di Paolo G, De Camilli P. Phosphoinositides in cell regulation and membrane dynamics. Nature. 2006;443(7112):651–657. PubMed PMID: 17035995.
  • Axe EL, Walker SA, Manifava M, et al. Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J Cell Biol. 2008;182(4):685–701. PubMed PMID: 18725538.
  • Behnia R, Munro S. Organelle identity and the signposts for membrane traffic. Nature. 2005;438(7068):597–604. PubMed PMID: 16319879.
  • Dall’Armi C, Devereaux KA, Di Paolo G. The role of lipids in the control of autophagy. Curr Biol. 2013;23(1):R33–R45. PubMed PMID: 23305670. Pubmed Central PMCID: 3587843.
  • Itakura E, Kishi C, Inoue K, Mizushima N. Beclin 1 forms two distinct phosphatidylinositol 3-kinase complexes with mammalian Atg14 and UVRAG. Mol Biol Cell. 2008;19(12):5360–5372. PubMed PMID: 18843052. Pubmed Central PMCID: 2592660.
  • Fan W, Nassiri A, Zhong Q. Autophagosome targeting and membrane curvature sensing by Barkor/Atg14(L). Proc Natl Acad Sci U S A. 2011;108(19):7769–7774. PubMed PMID: 21518905. Pubmed Central PMCID: 3093500.
  • Backer JM. The regulation and function of Class III PI3Ks: novel roles for Vps34. Biochem J. 2008;410(1):1–17. PubMed PMID: 18215151.
  • Liang C, Feng P, Ku B, et al. Autophagic and tumour suppressor activity of a novel Beclin1-binding protein UVRAG. Nat Cell Biol. 2006;8(7):688–699. PubMed PMID: 16799551.
  • Takahashi Y, Coppola D, Matsushita N, et al. Bif-1 interacts with Beclin 1 through UVRAG and regulates autophagy and tumorigenesis. Nat Cell Biol. 2007;9(10):1142–1151. PubMed PMID: 17891140. Pubmed Central PMCID: 2254521.
  • Matsunaga K, Saitoh T, Tabata K, et al. Two Beclin 1-binding proteins, Atg14L and Rubicon, reciprocally regulate autophagy at different stages. Nat Cell Biol. 2009;11(4):385–396. PubMed PMID: 19270696.
  • Kang R, Zeh HJ, Lotze MT, Tang D. The Beclin 1 network regulates autophagy and apoptosis. Cell Death Differ. 2011;18(4):571–580. PubMed PMID: 21311563. Pubmed Central PMCID: 3131912.
  • Fimia GM, Stoykova A, Romagnoli A, et al. Ambra1 regulates autophagy and development of the nervous system. Nature. 2007;447(7148):1121–1125. PubMed PMID: 17589504.
  • Nazio F, Strappazzon F, Antonioli M, et al. mTOR inhibits autophagy by controlling ULK1 ubiquitylation, self-association and function through AMBRA1 and TRAF6. Nat Cell Biol. 2013;15(4):406–416. PubMed PMID: 23524951.
  • Vergne I, Roberts E, Elmaoued RA, et al. Control of autophagy initiation by phosphoinositide 3-phosphatase Jumpy. EMBO J. 2009;28(15):2244–2258. PubMed PMID: 19590496. Pubmed Central PMCID: 2726690.
  • Cebollero E, van der Vaart A, Zhao M, et al. Phosphatidylinositol-3-phosphate clearance plays a key role in autophagosome completion. Curr Biol. 2012;22(17):1545–1553. PubMed PMID: 22771041. Pubmed Central PMCID: 3615650.
  • Cheng J, Fujita A, Yamamoto H, et al. Yeast and mammalian autophagosomes exhibit distinct phosphatidylinositol 3-phosphate asymmetries. Nat Commun. 2014;5:3207. PubMed PMID: 24492518.
  • Blommaart EF, Krause U, Schellens JP, Vreeling-Sindelarova H, Meijer AJ. The phosphatidylinositol 3-kinase inhibitors wortmannin and LY294002 inhibit autophagy in isolated rat hepatocytes. Eur J Biochem. 1997;243(1–2):240–246. PubMed PMID: 9030745.
  • Seglen PO, Gordon PB. 3-Methyladenine: specific inhibitor of autophagic/lysosomal protein degradation in isolated rat hepatocytes. Proc Natl Acad Sci U S A. 1982;79(6):1889–1892. PubMed PMID: 6952238.
  • Lu Q, Yang P, Huang X, et al. The WD40 repeat PtdIns(3)P-binding protein EPG-6 regulates progression of omegasomes to autophagosomes. Dev Cell. 2011;21(2):343–357. PubMed PMID: 21802374.
  • Polson HE, de Lartigue J, Rigden DJ, et al. Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation. Autophagy. 2010;6(4):506–522. PubMed PMID: 20505359.
  • Proikas-Cezanne T, Waddell S, Gaugel A, Frickey T, Lupas A, Nordheim A. WIPI-1alpha (WIPI49), a member of the novel 7-bladed WIPI protein family, is aberrantly expressed in human cancer and is linked to starvation-induced autophagy. Oncogene. 2004;23(58):9314–9325. PubMed PMID: 15602573.
  • Dooley HC, Razi M, Polson HE, Girardin SE, Wilson MI, Tooze SA. WIPI2 links LC3 conjugation with PI3P, autophagosome formation, and pathogen clearance by recruiting Atg12-5-16L1. Mol Cell. 2014;55(2):238–252. PubMed PMID: 24954904. Pubmed Central PMCID: 4104028.
  • Fujita N, Itoh T, Omori H, Fukuda M, Noda T, Yoshimori T. The Atg16L complex specifies the site of LC3 lipidation for membrane biogenesis in autophagy. Mol Biol Cell. 2008;19(5):2092–2100. PubMed PMID: 18321988. Pubmed Central PMCID: 2366860.
  • Kaufmann A, Beier V, Franquelim HG, Wollert T. Molecular mechanism of autophagic membrane-scaffold assembly and disassembly. Cell. 2014;156(3):469–481. PubMed PMID: 24485455.
  • Romanov J, Walczak M, Ibiricu I, et al. Mechanism and functions of membrane binding by the Atg5-Atg12/Atg16 complex during autophagosome formation. EMBO J. 2012;31(22):4304–4317. PubMed PMID: 23064152. Pubmed Central PMCID: 3501226.
  • Mizushima N, Yamamoto A, Hatano M, et al. Dissection of autophagosome formation using Apg5-deficient mouse embryonic stem cells. J Cell Biol. 2001;152(4):657–668. PubMed PMID: 11266458.
  • Nishimura T, Kaizuka T, Cadwell K, et al. FIP200 regulates targeting of Atg16L1 to the isolation membrane. EMBO Rep. 2013;14(3):284–291. PubMed PMID: 23392225. Pubmed Central PMCID: 3589088.
  • Ravikumar B, Moreau K, Jahreiss L, Puri C, Rubinsztein DC. Plasma membrane contributes to the formation of pre-autophagosomal structures. Nat Cell Biol. 2010;12(8):747–757. PubMed PMID: 20639872. Pubmed Central PMCID: 2923063.
  • Moreau K, Ravikumar B, Renna M, Puri C, Rubinsztein DC. Autophagosome precursor maturation requires homotypic fusion. Cell. 2011;146(2):303–317. PubMed PMID: 21784250. Pubmed Central PMCID: 3171170.
  • Puri C, Renna M, Bento CF, Moreau K, Rubinsztein DC. Diverse autophagosome membrane sources coalesce in recycling endosomes. Cell. 2013;154(6):1285–1299. PubMed PMID: 24034251. Pubmed Central PMCID: 3791395.
  • Itoh T, Fujita N, Kanno E, Yamamoto A, Yoshimori T, Fukuda M. Golgi-resident small GTPase Rab33B interacts with Atg16L and modulates autophagosome formation. Mol Biol Cell. 2008;19(7):2916–2925. PubMed PMID: 18448665. Pubmed Central PMCID: 2441679.
  • Longatti A, Lamb CA, Razi M, Yoshimura S, Barr FA, Tooze SA. TBC1D14 regulates autophagosome formation via Rab11- and ULK1-positive recycling endosomes. J Cell Biol. 2012;197(5):659–675. PubMed PMID: 22613832. Pubmed Central PMCID: 3365497.
  • Geng J, Klionsky DJ. The Atg8 and Atg12 ubiquitin-like conjugation systems in macroautophagy. ‘Protein modifications: beyond the usual suspects’ review series. EMBO Rep. 2008;9(9):859–864. PubMed PMID: 18704115. Pubmed Central PMCID: 2529362.
  • Tanida I, Komatsu M, Ueno T, Kominami E. GATE-16 and GABARAP are authentic modifiers mediated by Apg7 and Apg3. Biochem Biophys Res Commun. 2003;300(3):637–644. PubMed PMID: 12507496.
  • Tanida I, Ueno T, Kominami E. LC3 conjugation system in mammalian autophagy. Int J Biochem Cell Biol. 2004;36(12):2503–2518. PubMed PMID: 15325588.
  • Kabeya Y, Mizushima N, Yamamoto A, Oshitani-Okamoto S, Ohsumi Y, Yoshimori T. LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation. J Cell Sci. 2004;117(Pt 13):2805–2812. PubMed PMID: 15169837.
  • Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway. J Cell Biol. 2000;151(2):263–276. PubMed PMID: 11038174. Pubmed Central PMCID: 2192639.
  • Tanida I, Tanida-Miyake E, Ueno T, Kominami E. The human homolog of Saccharomyces cerevisiae Apg7p is a Protein-activating enzyme for multiple substrates including human Apg12p, GATE-16, GABARAP, and MAP-LC3. J Biol Chem. 2001;276(3):1701–1706. PubMed PMID: 11096062.
  • Tanida I, Tanida-Miyake E, Komatsu M, Ueno T, Kominami E. Human Apg3p/Aut1p homologue is an authentic E2 enzyme for multiple substrates, GATE-16, GABARAP, and MAP-LC3, and facilitates the conjugation of hApg12p to hApg5p. J Biol Chem. 2002;277(16):13739–13744. PubMed PMID: 11825910.
  • Noda NN, Ohsumi Y, Inagaki F. ATG systems from the protein structural point of view. Chem Rev. 2009;109(4):1587–1598. PubMed PMID: 19236009.
  • Kaiser SE, Mao K, Taherbhoy AM, et al. Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures. Nat Struct Mol Biol. 2012;19(12):1242–1249. PubMed PMID: 23142976. Pubmed Central PMCID: 3515690.
  • Mizushima N, Yoshimori T, Ohsumi Y. Role of the Apg12 conjugation system in mammalian autophagy. Int J Biochem Cell Biol. 2003;35(5):553–561. PubMed PMID: 12672448.
  • Hanada T, Noda NN, Satomi Y, et al. The Atg12-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy. J Biol Chem. 2007;282(52):37298–37302. PubMed PMID: 17986448.
  • Mari M, Griffith J, Rieter E, Krishnappa L, Klionsky DJ, Reggiori F. An Atg9-containing compartment that functions in the early steps of autophagosome biogenesis. J Cell Biol. 2010;190(6):1005–1022. PubMed PMID: 20855505. Pubmed Central PMCID: 3101592.
  • Young AR, Chan EY, Hu XW, et al. Starvation and ULK1-dependent cycling of mammalian Atg9 between the TGN and endosomes. J Cell Sci. 2006;119(Pt 18):3888–3900. PubMed PMID: 16940348. Epub 2006/08/31. eng.
  • Reggiori F, Shintani T, Nair U, Klionsky DJ. Atg9 cycles between mitochondria and the pre-autophagosomal structure in yeasts. Autophagy. 2005;1(2):101–109. PubMed PMID: 16874040. Pubmed Central PMCID: 1762033.
  • Monastyrska I, He C, Geng J, Hoppe AD, Li Z, Klionsky DJ. Arp2 links autophagic machinery with the actin cytoskeleton. Mol Biol Cell. 2008;19(5):1962–1975. PubMed PMID: 18287533. Pubmed Central PMCID: 2366845.
  • Tang HW, Wang YB, Wang SL, Wu MH, Lin SY, Chen GC. Atg1-mediated myosin II activation regulates autophagosome formation during starvation-induced autophagy. EMBO J. 2011;30(4):636–651. PubMed PMID: 21169990. Pubmed Central PMCID: 3041946.
  • Bialik S, Pietrokovski S, Kimchi A. Myosin drives autophagy in a pathway linking Atg1 to Atg9. EMBO J. 2011;30(4):629–630. PubMed PMID: 21326172. Pubmed Central PMCID: 3041959.
  • Reggiori F, Tucker KA, Stromhaug PE, Klionsky DJ. The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure. Dev Cell. 2004;6(1):79–90. PubMed PMID: 14723849.
  • Orsi A, Razi M, Dooley HC, et al. Dynamic and transient interactions of Atg9 with autophagosomes, but not membrane integration, are required for autophagy. Mol Biol Cell. 2012;23(10):1860–1873. PubMed PMID: 22456507. Pubmed Central PMCID: 3350551.
  • Papinski D, Schuschnig M, Reiter W, et al. Early steps in autophagy depend on direct phosphorylation of Atg9 by the Atg1 kinase. Mol Cell. 2014;53(3):471–483. PubMed PMID: 24440502. Pubmed Central PMCID: 3978657.
  • Webber JL, Tooze SA. Coordinated regulation of autophagy by p38alpha MAPK through mAtg9 and p38IP. EMBO J. 2010;29(1):27–40. PubMed PMID: 19893488. Pubmed Central PMCID: 2808369.
  • Nair U, Jotwani A, Geng J, et al. SNARE proteins are required for macroautophagy. Cell. 2011;146(2):290–302. PubMed PMID: 21784249. Pubmed Central PMCID: 3143362.
  • Puri C, Renna M, Bento CF, Moreau K, Rubinsztein DC. ATG16L1 meets ATG9 in recycling endosomes: additional roles for the plasma membrane and endocytosis in autophagosome biogenesis. Autophagy. 2014;10(1):182–184. PubMed PMID: 24257061.
  • Shpilka T, Weidberg H, Pietrokovski S, Elazar Z. Atg8: an autophagy-related ubiquitin-like protein family. Genome Biol. 2011;12(7):226. PubMed PMID: 21867568. Pubmed Central PMCID: 3218822. Epub 2011/08/27. eng.
  • Tanida I, Sou YS, Minematsu-Ikeguchi N, Ueno T, Kominami E. Atg8L/Apg8L is the fourth mammalian modifier of mammalian Atg8 conjugation mediated by human Atg4B, Atg7 and Atg3. FEBS J. 2006;273(11):2553–2562. PubMed PMID: 16704426.
  • Tanida I, Sou YS, Ezaki J, Minematsu-Ikeguchi N, Ueno T, Kominami E. HsAtg4B/HsApg4B/autophagin-1 cleaves the carboxyl termini of three human Atg8 homologues and delipidates microtubule-associated protein light chain 3- and GABAA receptor-associated protein-phospholipid conjugates. J Biol Chem. 2004;279(35):36268–36276. PubMed PMID: 15187094.
  • Klionsky DJ, Abdalla FC, Abeliovich H, et al. Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy. 2012;8(4):445–544. PubMed PMID: 22966490. Pubmed Central PMCID: 3404883.
  • Coyle JE, Qamar S, Rajashankar KR, Nikolov DB. Structure of GABARAP in two conformations: implications for GABA(A) receptor localization and tubulin binding. Neuron. 2002;33(1):63–74. PubMed PMID: 11779480.
  • Kouno T, Mizuguchi M, Tanida I, et al. Solution structure of microtubule-associated protein light chain 3 and identification of its functional subdomains. J Biol Chem. 2005;280(26):24610–24617. PubMed PMID: 15857831.
  • Mann SS, Hammarback JA. Molecular characterization of light chain 3. A microtubule binding subunit of MAP1A and MAP1B. J Biol Chem. 1994;269(15):11492–11497. PubMed PMID: 7908909.
  • Wang H, Bedford FK, Brandon NJ, Moss SJ, Olsen RW. GABA(A)-receptor-associated protein links GABA(A) receptors and the cytoskeleton. Nature. 1999;397(6714):69–72. PubMed PMID: 9892355.
  • Nakatogawa H, Ichimura Y, Ohsumi Y. Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusion. Cell. 2007;130(1):165–178. PubMed PMID: 17632063. Epub 2007/07/17. eng.
  • Weidberg H, Shpilka T, Shvets E, Abada A, Shimron F, Elazar Z. LC3 and GATE-16 N termini mediate membrane fusion processes required for autophagosome biogenesis. Dev Cell. 2011;20(4):444–454. PubMed PMID: 21497758. Epub 2011/04/19. eng.
  • Morvan J, Kochl R, Watson R, Collinson LM, Jefferies HB, Tooze SA. In vitro reconstitution of fusion between immature autophagosomes and endosomes. Autophagy. 2009;5(5):676–689. PubMed PMID: 19337031. Epub 2009/04/02. eng.
  • Xie Z, Nair U, Klionsky DJ. Atg8 controls phagophore expansion during autophagosome formation. Mol Biol Cell. 2008;19(8):3290–3298. PubMed PMID: 18508918. Pubmed Central PMCID: 2488302. Epub 2008/05/30. eng.
  • Xie Z, Nair U, Geng J, Szefler MB, Rothman ED, Klionsky DJ. Indirect estimation of the area density of Atg8 on the phagophore. Autophagy. 2009;5(2):217–220. PubMed PMID: 19088501. Pubmed Central PMCID: 2941343.
  • Alemu EA, Lamark T, Torgersen KM, et al. ATG8 family proteins act as scaffolds for assembly of the ULK complex: sequence requirements for LC3-interacting region (LIR) motifs. J Biol Chem. 2012;287(47):39275–39290. PubMed PMID: 23043107. Pubmed Central PMCID: 3501051.
  • Weidberg H, Shvets E, Shpilka T, Shimron F, Shinder V, Elazar Z. LC3 and GATE-16/GABARAP subfamilies are both essential yet act differently in autophagosome biogenesis. EMBO J. 2010;29(11):1792–1802. PubMed PMID: 20418806. Pubmed Central PMCID: 2885923.
  • Maruyama Y, Sou YS, Kageyama S, et al. LC3B is indispensable for selective autophagy of p62 but not basal autophagy. Biochem Biophys Res Commun. 2014;446(1):309–315. PubMed PMID: 24582747.
  • Lamark T, Kirkin V, Dikic I, Johansen T. NBR1 and p62 as cargo receptors for selective autophagy of ubiquitinated targets. Cell Cycle. 2009;8(13):1986–1990. PubMed PMID: 19502794.
  • Behrends C, Sowa ME, Gygi SP, Harper JW. Network organization of the human autophagy system. Nature. 2010;466(7302):68–76. PubMed PMID: 20562859. Pubmed Central PMCID: 2901998.
  • Novak I, Kirkin V, McEwan DG, et al. Nix is a selective autophagy receptor for mitochondrial clearance. EMBO Rep. 2009;11(1):45–51. PubMed PMID: 20010802. Pubmed Central PMCID: 2816619. Epub 2009/12/17. eng.
  • Noda NN, Kumeta H, Nakatogawa H, et al. Structural basis of target recognition by Atg8/LC3 during selective autophagy. Genes Cells. 2008;13(12):1211–1218. PubMed PMID: 19021777.
  • Rozenknop A, Rogov VV, Rogova NY, et al. Characterization of the interaction of GABARAPL-1 with the LIR motif of NBR1. J Mol Biol. 2011;410(3):477–487. PubMed PMID: 21620860.
  • von Muhlinen N, Akutsu M, Ravenhill BJ, et al. An essential role for the ATG8 ortholog LC3C in antibacterial autophagy. Autophagy. 2013;9(5):784–786. PubMed PMID: 23434839. Pubmed Central PMCID: 3669188.
  • Liu L, Feng D, Chen G, et al. Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells. Nat Cell Biol. 2012;14(2):177–185. PubMed PMID: 22267086. Epub 2012/01/24. eng.
  • Chen G, Han Z, Feng D, et al. A regulatory signaling loop comprising the PGAM5 phosphatase and CK2 controls receptor-mediated mitophagy. Mol Cell. 2014;54(3):362–377. PubMed PMID: 24746696.
  • Wu W, Tian W, Hu Z, et al. ULK1 translocates to mitochondria and phosphorylates FUNDC1 to regulate mitophagy. EMBO Rep. 2014;15(5):566–575. PubMed PMID: 24671035.
  • Popovic D, Akutsu M, Novak I, Harper JW, Behrends C, Dikic I. Rab GTPase-activating proteins in autophagy: regulation of endocytic and autophagy pathways by direct binding to human ATG8 modifiers. Mol Cell Biol. 2012;32(9):1733–1744. PubMed PMID: 22354992. Pubmed Central PMCID: 3347240.
  • Itoh T, Kanno E, Uemura T, Waguri S, Fukuda M. OATL1, a novel autophagosome-resident Rab33B-GAP, regulates autophagosomal maturation. J Cell Biol. 2011;192(5):839–853. PubMed PMID: 21383079. Pubmed Central PMCID: 3051816. Epub 2011/03/09. eng.
  • Pankiv S, Alemu EA, Brech A, et al. FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport. J Cell Biol. 2010;188(2):253–269. PubMed PMID: 20100911. Pubmed Central PMCID: 2812517.
  • Jager S, Bucci C, Tanida I, et al. Role for Rab7 in maturation of late autophagic vacuoles. J Cell Sci. 2004;117(Pt 20):4837–4848. PubMed PMID: 15340014. Epub 2004/09/02. eng.
  • Ichimura Y, Kirisako T, Takao T, et al. A ubiquitin-like system mediates protein lipidation. Nature. 2000;408(6811):488–492. PubMed PMID: 11100732.
  • Nair U, Yen WL, Mari M, et al. A role for Atg8-PE deconjugation in autophagosome biogenesis. Autophagy. 2012;8(5):780–793. PubMed PMID: 22622160. Epub 2012/05/25. Eng.
  • Yu ZQ, Ni T, Hong B, et al. Dual roles of Atg8-PE deconjugation by Atg4 in autophagy. Autophagy. 2012;8(6):883–892. PubMed PMID: 22652539. Pubmed Central PMCID: 3427254.
  • Marino G, Uria JA, Puente XS, Quesada V, Bordallo J, Lopez-Otin C. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy. J Biol Chem. 2003;278(6):3671–3678. PubMed PMID: 12446702.
  • Kumanomidou T, Mizushima T, Komatsu M, et al. The crystal structure of human Atg4b, a processing and de-conjugating enzyme for autophagosome-forming modifiers. J Mol Biol. 2006;355(4):612–618. PubMed PMID: 16325851.
  • Sugawara K, Suzuki NN, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F. Structural basis for the specificity and catalysis of human Atg4B responsible for mammalian autophagy. J Biol Chem. 2005;280(48):40058–40065. PubMed PMID: 16183633.
  • Betin VM, Lane JD. Caspase cleavage of Atg4D stimulates Atg8 processing and triggers mitochondrial targeting and apoptosis. J Cell Sci. 2009;122(Pt 14):2554–2566.
  • Hemelaar J, Lelyveld VS, Kessler BM, Ploegh HL. A single protease, Apg4B, is specific for the autophagy-related ubiquitin-like proteins GATE-16, MAP1-LC3, GABARAP, and Apg8L. J Biol Chem. 2003;278(51):51841–51850. PubMed PMID: 14530254.
  • Li M, Hou Y, Wang J, Chen X, Shao ZM, Yin XM. Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8 substrates. J Biol Chem. 2011;286(9):7327–7338. PubMed PMID: 21177865. Pubmed Central PMCID: 3044989.
  • Shu CW, Drag M, Bekes M, Zhai D, Salvesen GS, Reed JC. Synthetic substrates for measuring activity of autophagy proteases: autophagins (Atg4). Autophagy. 2010;6(7):936–947. PubMed PMID: 20818167. Pubmed Central PMCID: 3039740. Epub 2010/09/08. eng.
  • Scherz-Shouval R, Sagiv Y, Shorer H, Elazar Z. The COOH terminus of GATE-16, an intra-Golgi transport modulator, is cleaved by the human cysteine protease HsApg4A. J Biol Chem. 2003;278(16):14053–14058. PubMed PMID: 12473658.
  • Kuang E, Okumura CY, Sheffy-Levin S, et al. Regulation of ATG4B stability by RNF5 limits basal levels of autophagy and influences susceptibility to bacterial infection. PLoS Genet. 2012;8(10):e1003007. PubMed PMID: 23093945. Pubmed Central PMCID: 3475677.
  • Scherz-Shouval R, Shvets E, Fass E, Shorer H, Gil L, Elazar Z. Reactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4. EMBO J. 2007;26(7):1749–1760. PubMed PMID: 17347651.
  • Betin VMS, MacVicar TDB, Parsons SF, Anstee DJ, Lane JD. A cryptic mitochondrial targeting motif in Atg4D links caspase cleavage with mitochonrial import and oxidative stress. Autophagy. 2012;8(4):664–676.
  • Marino G, Fernandez AF, Cabrera S, et al. Autophagy is essential for mouse sense of balance. J Clin Invest. 2010;120(7):2331–2344. PubMed PMID: 20577052. Pubmed Central PMCID: 2898610. Epub 2010/06/26. eng.
  • Marino G, Salvador-Montoliu N, Fueyo A, Knecht E, Mizushima N, Lopez-Otin C. Tissue-specific autophagy alterations and increased tumorigenesis in mice deficient in ATG4C/autophagin-3. J Biol Chem. 2007;282(25):18573–18583. PubMed PMID: 17442669.
  • Read R, Savelieva K, Baker K, Hansen G, Vogel P. Histopathological and neurological features of Atg4b knockout mice. Vet Pathol. 2011;48(2):486–494. PubMed PMID: 20634410.
  • Nakatogawa H, Ishii J, Asai E, Ohsumi Y. Atg4 recycles inappropriately lipidated Atg8 to promote autophagosome biogenesis. Autophagy. 2012;8(2):177–186. PubMed PMID: 22240591. Epub 2012/01/14. eng.
  • Takeshige K, Baba M, Tsuboi S, Noda T, Ohsumi Y. Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction. J Cell Biol. 1992;119(2):301–311. PubMed PMID: 1400575. Pubmed Central PMCID: 2289660.
  • Fujita N, Hayashi-Nishino M, Fukumoto H, et al. An Atg4B mutant hampers the lipidation of LC3 paralogues and causes defects in autophagosome closure. Mol Biol Cell. 2008;19(11):4651–4659. PubMed PMID: 18768752.
  • Molejon MI, Ropolo A, Re AL, Boggio V, Vaccaro MI. The VMP1-Beclin 1 interaction regulates autophagy induction. Sci Rep. 2013;3:1055. PubMed PMID: 23316280. Pubmed Central PMCID: 3542764.
  • De Antoni A, Schmitzova J, Trepte HH, Gallwitz D, Albert S. Significance of GTP hydrolysis in Ypt1p-regulated endoplasmic reticulum to Golgi transport revealed by the analysis of two novel Ypt1-GAPs. J Biol Chem. 2002;277(43):41023–41031. PubMed PMID: 12189143.
  • Lynch-Day MA, Bhandari D, Menon S, et al. Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy. Proc Natl Acad Sci U S A. 2010;107(17):7811–7816. PubMed PMID: 20375281. Pubmed Central PMCID: 2867920.
  • Kakuta S, Yamamoto H, Negishi L, Kondo-Kakuta C, Hayashi N, Ohsumi Y. Atg9 vesicles recruit vesicle-tethering proteins Trs85 and Ypt1 to the autophagosome formation site. J Biol Chem. 2012;287(53):44261–44269. PubMed PMID: 23129774. Pubmed Central PMCID: 3531741.
  • Dunn WA Jr. Studies on the mechanisms of autophagy: formation of the autophagic vacuole. J Cell Biol. 1990;110(6):1923–1933. PubMed PMID: 2351689.
  • Liou W, Geuze HJ, Geelen MJ, Slot JW. The autophagic and endocytic pathways converge at the nascent autophagic vacuoles. J Cell Biol. 1997;136(1):61–70. PubMed PMID: 9008703.
  • Tooze J, Hollinshead M, Ludwig T, Howell K, Hoflack B, Kern H. In exocrine pancreas, the basolateral endocytic pathway converges with the autophagic pathway immediately after the early endosome. J Cell Biol. 1990;111(2):329–345. PubMed PMID: 2166050.
  • Razi M, Chan EY, Tooze SA. Early endosomes and endosomal coatomer are required for autophagy. J Cell Biol. 2009;185(2):305–321. PubMed PMID: 19364919. Pubmed Central PMCID: 2700373. Epub 2009/04/15. eng.
  • Gutierrez MG, Munafo DB, Beron W, Colombo MI. Rab7 is required for the normal progression of the autophagic pathway in mammalian cells. J Cell Sci. 2004;117(Pt 13):2687–2697. PubMed PMID: 15138286. Epub 2004/05/13. eng.
  • Fader CM, Sanchez D, Furlan M, Colombo MI. Induction of autophagy promotes fusion of multivesicular bodies with autophagic vacuoles in k562 cells. Traffic. 2008;9(2):230–250. PubMed PMID: 17999726.
  • Liang C, Lee JS, Inn KS, et al. Beclin1-binding UVRAG targets the class C Vps complex to coordinate autophagosome maturation and endocytic trafficking. Nat Cell Biol. 2008;10(7):776–787. PubMed PMID: 18552835. Pubmed Central PMCID: 2878716.
  • Nickerson DP, Brett CL, Merz AJ. Vps-C complexes: gatekeepers of endolysosomal traffic. Curr Opin Cell Biol. 2009;21(4):543–551. PubMed PMID: 19577915. Pubmed Central PMCID: 2807627.
  • Fader CM, Sanchez DG, Mestre MB, Colombo MI. TI-VAMP/VAMP7 and VAMP3/cellubrevin: two v-SNARE proteins involved in specific steps of the autophagy/multivesicular body pathways. Biochim Biophys Acta. 2009;1793(12):1901–1916. PubMed PMID: 19781582.
  • Dove SK, Dong K, Kobayashi T, Williams FK, Michell RH. Phosphatidylinositol 3,5-bisphosphate and Fab1p/PIKfyve underPPIn endo-lysosome function. Biochem J. 2009;419(1):1–13. PubMed PMID: 19272020.
  • Munafo DB, Colombo MI. Induction of autophagy causes dramatic changes in the subcellular distribution of GFP-Rab24. Traffic. 2002;3(7):472–482. PubMed PMID: 12047555.
  • Tambe Y, Yamamoto A, Isono T, Chano T, Fukuda M, Inoue H. The drs tumor suppressor is involved in the maturation process of autophagy induced by low serum. Cancer Lett. 2009;283(1):74–83. PubMed PMID: 19368996.
  • Rieder SE, Emr SD. A novel RING finger protein complex essential for a late step in protein transport to the yeast vacuole. Mol Biol Cell. 1997;8(11):2307–2327. PubMed PMID: 9362071. Pubmed Central PMCID: 25710.
  • Seals DF, Eitzen G, Margolis N, Wickner WT, Price A. A Ypt/Rab effector complex containing the Sec1 homolog Vps33p is required for homotypic vacuole fusion. Proc Natl Acad Sci U S A. 2000;97(17):9402–9407. PubMed PMID: 10944212. Pubmed Central PMCID: 16876.
  • Wurmser AE, Sato TK, Emr SD. New component of the vacuolar class C-Vps complex couples nucleotide exchange on the Ypt7 GTPase to SNARE-dependent docking and fusion. J Cell Biol. 2000;151(3):551–562. PubMed PMID: 11062257. Pubmed Central PMCID: 2185595.
  • Filimonenko M, Stuffers S, Raiborg C, et al. Functional multivesicular bodies are required for autophagic clearance of protein aggregates associated with neurodegenerative disease. J Cell Biol. 2007;179(3):485–500. PubMed PMID: 17984323. Pubmed Central PMCID: 2064794.
  • Lee JA, Beigneux A, Ahmad ST, Young SG, Gao FB. ESCRT-III dysfunction causes autophagosome accumulation and neurodegeneration. Curr Biol. 2007;17(18):1561–1567. PubMed PMID: 17683935.
  • Rusten TE, Vaccari T, Lindmo K, et al. ESCRTs and Fab1 regulate distinct steps of autophagy. Curr Biol. 2007;17(20):1817–1825. PubMed PMID: 17935992.
  • Hurley JH. The ESCRT complexes. Crit Rev Biochem Mol Biol. 2010;45(6):463–487. PubMed PMID: 20653365. Pubmed Central PMCID: 2988974.
  • Eskelinen EL, Illert AL, Tanaka Y, et al. Role of LAMP-2 in lysosome biogenesis and autophagy. Mol Biol Cell. 2002;13(9):3355–3368. PubMed PMID: 12221139. Pubmed Central PMCID: 124165. Epub 2002/09/11. eng.
  • Eskelinen EL, Schmidt CK, Neu S, et al. Disturbed cholesterol traffic but normal proteolytic function in LAMP-1/LAMP-2 double-deficient fibroblasts. Mol Biol Cell. 2004;15(7):3132–3145. PubMed PMID: 15121881. Pubmed Central PMCID: 452571. Epub 2004/05/04. eng.
  • Huynh KK, Eskelinen EL, Scott CC, Malevanets A, Saftig P, Grinstein S. LAMP proteins are required for fusion of lysosomes with phagosomes. EMBO J. 2007;26(2):313–324. PubMed PMID: 17245426. Pubmed Central PMCID: 1783450.
  • Darsow T, Rieder SE, Emr SD. A multispecificity syntaxin homologue, Vam3p, essential for autophagic and biosynthetic protein transport to the vacuole. J Cell Biol. 1997;138(3):517–529. PubMed PMID: 9245783.
  • Itakura E, Kishi-Itakura C, Mizushima N. The hairpin-type tail-anchored SNARE syntaxin 17 targets to autophagosomes for fusion with endosomes/lysosomes. Cell. 2012;151(6):1256–1269. PubMed PMID: 23217709.
  • Furuta N, Fujita N, Noda T, Yoshimori T, Amano A. Combinational soluble N-ethylmaleimide-sensitive factor attachment protein receptor proteins VAMP8 and Vti1b mediate fusion of antimicrobial and canonical autophagosomes with lysosomes. Mol Biol Cell. 2010;21(6):1001–1010. PubMed PMID: 20089838. Pubmed Central PMCID: 2836953.
  • Atlashkin V, Kreykenbohm V, Eskelinen EL, Wenzel D, Fayyazi A, Fischer von Mollard G. Deletion of the SNARE vti1b in mice results in the loss of a single SNARE partner, syntaxin 8. Mol Cell Biol. 2003;23(15):5198–5207. PubMed PMID: 12861006. Pubmed Central PMCID: 165714.
  • Jiang P, Nishimura T, Sakamaki Y, et al. The HOPS complex mediates autophagosome-lysosome fusion through interaction with syntaxin 17. Mol Biol Cell. 2014;25(8):1327–1337. PubMed PMID: 24554770. Pubmed Central PMCID: 3982997.
  • Chen D, Fan W, Lu Y, Ding X, Chen S, Zhong Q. A mammalian autophagosome maturation mechanism mediated by TECPR1 and the Atg12-Atg5 conjugate. Mol Cell. 2012;45(5):629–641. PubMed PMID: 22342342. Pubmed Central PMCID: 3299828.
  • Burman C, Ktistakis NT. Autophagosome formation in mammalian cells. Semin Immunopathol. 2010;32(4):397–413. PubMed PMID: 20740284.
  • Longatti A, Tooze SA. Vesicular trafficking and autophagosome formation. Cell Death Differ. 2009;16(7):956–965. PubMed PMID: 19373247.
  • Hayashi-Nishino M, Fujita N, Noda T, Yamaguchi A, Yoshimori T, Yamamoto A. A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation. Nat Cell Biol. 2009;11(12):1433–1437. PubMed PMID: 19898463.
  • Yla-Anttila P, Vihinen H, Jokitalo E, Eskelinen EL. 3D tomography reveals connections between the phagophore and endoplasmic reticulum. Autophagy. 2009;5(8):1180–1185. PubMed PMID: 19855179.
  • Yamamoto A, Masaki R, Tashiro Y. Characterization of the isolation membranes and the limiting membranes of autophagosomes in rat hepatocytes by lectin cytochemistry. J Histochem Cytochem. 1990;38(4):573–580. PubMed PMID: 2319125.
  • Suzuki K, Akioka M, Kondo-Kakuta C, Yamamoto H, Ohsumi Y. Fine mapping of autophagy-related proteins during autophagosome formation in Saccharomyces cerevisiae. J Cell Sci. 2013;126(Pt 11):2534–2544. PubMed PMID: 23549786.
  • Graef M, Friedman JR, Graham C, Babu M, Nunnari J. ER exit sites are physical and functional core autophagosome biogenesis components. Mol Biol Cell. 2013;24(18):2918–2931. PubMed PMID: 23904270. Pubmed Central PMCID: 3771953.
  • Ge L, Melville D, Zhang M, Schekman R. The ER-Golgi intermediate compartment is a key membrane source for the LC3 lipidation step of autophagosome biogenesis. eLife. 2013;2:e00947. PubMed PMID: 23930225. Pubmed Central PMCID: 3736544.
  • Reggiori F, Wang CW, Nair U, Shintani T, Abeliovich H, Klionsky DJ. Early stages of the secretory pathway, but not endosomes, are required for Cvt vesicle and autophagosome assembly in Saccharomyces cerevisiae. Mol Biol Cell. 2004;15(5):2189–2204. PubMed PMID: 15004240. Pubmed Central PMCID: 404015.
  • Ohashi Y, Munro S. Membrane delivery to the yeast autophagosome from the Golgi-endosomal system. Mol Biol Cell. 2010;21(22):3998–4008. PubMed PMID: 20861302. Pubmed Central PMCID: 2982105.
  • Hailey DW, Rambold AS, Satpute-Krishnan P, et al. Mitochondria supply membranes for autophagosome biogenesis during starvation. Cell. 2010;141(4):656–667. PubMed PMID: 20478256. Pubmed Central PMCID: 3059894.
  • Hamasaki M, Furuta N, Matsuda A, et al. Autophagosomes form at ER-mitochondria contact sites. Nature. 2013;495(7441):389–393. PubMed PMID: 23455425. Epub 2013/03/05. eng.
  • Lamb CA, Yoshimori T, Tooze SA. The autophagosome: origins unknown, biogenesis complex. Nat Rev Mol Cell Biol. 2013;14(12):759–774. PubMed PMID: 24201109.
  • Knaevelsrud H, Soreng K, Raiborg C, et al. Membrane remodeling by the PX-BAR protein SNX18 promotes autophagosome formation. J Cell Biol. 2013;202(2):331–349. PubMed PMID: 23878278. Pubmed Central PMCID: 3718966.
  • Moreau K, Ravikumar B, Puri C, Rubinsztein DC. Arf6 promotes autophagosome formation via effects on phosphatidylinositol 4,5-bisphosphate and phospholipase D. J Cell Biol. 2012;196(4):483–496. PubMed PMID: 22351926. Pubmed Central PMCID: 3283994.
  • Dupont N, Chauhan S, Arko-Mensah J, et al. Neutral lipid stores and lipase PNPLA5 contribute to autophagosome biogenesis. Curr Biol. 2014;24(6):609–620. PubMed PMID: 24613307. Pubmed Central PMCID: 4016984.
  • Bejarano E, Yuste A, Patel B, Stout RF Jr, Spray DC, Cuervo AM. Connexins modulate autophagosome biogenesis. Nat Cell Biol. 2014;16(5):401–414. PubMed PMID: 24705551. Pubmed Central PMCID: 4008708.