Location and membrane sources for autophagosome formation – from ER-mitochondria contact sites to Golgi-endosome-derived carriers

References

• Axe EL, Walker SA, Manifava M, Chandra P, Roderick HL, Habermann A, et al. 2008. Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J Cell Biol 182:685–701.
   PubMed Web of Science ®Google Scholar
• Backues SK, Klionsky DJ. 2012. Atg11: A Rab-dependent, coiled-coil membrane protein that acts as a tether for autophagy. Autophagy 8:1275–1278.
   PubMed Web of Science ®Google Scholar
• Banerjee R, Beal MF, Thomas B. 2010. Autophagy in neurodegenerative disorders: Pathogenic roles and therapeutic implications. Trends Neurosci 33:541–549.
   PubMed Web of Science ®Google Scholar
• Bannykh SI, Rowe T, Balch WE. 1996. The organization of endoplasmic reticulum export complexes. J Cell Biol 135:19–35.
   PubMed Web of Science ®Google Scholar
• Bui M, Gilady SY, Fitzsimmons REB, Benson MD, Lynes EM, Gesson K, et al. 2010. Rab32 modulates apoptosis onset and mitochondria-associated membrane (MAM) properties. J Biol Chem 285:31590–31602.
   PubMed Web of Science ®Google Scholar
• Bultema JJ, Di Pietro SM. 2013. Cell type-specific Rab32 and Rab38 cooperate with the ubiquitous lysosome biogenesis machinery to synthesize specialized lysosome-related organelles. Small GTPases 4:16–21.
   PubMedGoogle Scholar
• Cebollero E, Reggiori F, Kraft C. 2012. Reticulophagy and ribophagy: Regulated degradation of protein production factories. Int J Cell Biol 2012:182834.
   PubMedGoogle Scholar
• Chen Y, Azad MB, Gibson SB. 2009. Superoxide is the major reactive oxygen species regulating autophagy. Cell Death Differ 16:1040–1052.
   PubMed Web of Science ®Google Scholar
• Cheong H, Nair U, Geng J, Klionsky DJ. 2008. 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 19:668–681.
   PubMed Web of Science ®Google Scholar
• de Brito OM, Scorrano L. 2008. Mitofusin 2 tethers endoplasmic reticulum to mitochondria. Nature 456:605–610.
   PubMed Web of Science ®Google Scholar
• Ding WX, Yin XM. 2012. Mitophagy: Mechanisms, pathophysiological roles, and analysis. Biol Chem 393:547–564.
   PubMed Web of Science ®Google Scholar
• Fujita N, Itoh T, Omori H, Fukuda M, Noda T, Yoshimori T. 2008. The Atg16L complex specifies the site of LC3 lipidation for membrane biogenesis in autophagy. Mol Biol Cell 19:2092–2100.
   PubMed Web of Science ®Google Scholar
• Gelino S, Hansen M. 2012. Autophagy – an emerging anti-aging mechanism. J Clin Experim Pathol Suppl 4.
   Google Scholar
• Hailey DW, Rambold AS, Satpute-Krishnan P, Mitra K, Sougrat R, Kim PK, et al. 2010. Mitochondria supply membranes for autophagosome biogenesis during starvation. Cell 141:656–667.
   PubMed Web of Science ®Google Scholar
• Hamasaki M, Furuta N, Matsuda A, Nezu A, Yamamoto A, Fujita N, et al. 2013. Autophagosomes form at ER-mitochondria contact sites. Nature 495:389–393.
   PubMed Web of Science ®Google Scholar
• Hamasaki M, Yoshimori T. 2010. Where do they come from? Insights into autophagosome formation. FEBS Lett 584:1296–1301.
   PubMed Web of Science ®Google Scholar
• Hay JC. 2001. SNARE complex structure and function. Exp Cell Res 271:10–21.
   PubMed Web of Science ®Google Scholar
• Hayashi-Nishino M, Fujita N, Noda T, Yamaguchi A, Yoshimori T, Yamamoto A. 2009. A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation. Nat Cell Biol 11:1433–1437.
   PubMed Web of Science ®Google Scholar
• He C, Song H, Yorimitsu T, Monastyrska I, Yen WL, Legakis JE, et al. 2006. Recruitment of Atg9 to the preautophagosomal structure by Atg11 is essential for selective autophagy in budding yeast. J Cell Biol 175:925–935.
   PubMed Web of Science ®Google Scholar
• Hirota Y, Tanaka Y. 2009. A small GTPase, human Rab32, is required for the formation of autophagic vacuoles under basal conditions. Cell Mol Life Sci 66:2913–2932.
   PubMed Web of Science ®Google Scholar
• Itakura E, Kishi-Itakura C, Mizushima N. 2012. The hairpin-type tail-anchored SNARE syntaxin 17 targets to autophagosomes for fusion with endosomes/lysosomes. Cell 151:1256–1269.
   PubMed Web of Science ®Google Scholar
• Jedd G, Richardson C, Litt R, Segev N. 1995. The Ypt1 GTPase is essential for the first two steps of the yeast secretory pathway. J Cell Biol 131:583–590.
   PubMedGoogle Scholar
• Juenemann K, Reits EA. 2012. Alternative macroautophagic pathways. Int J Cell Biol 2012:189794.
   PubMedGoogle Scholar
• Kakuta S, Yamamoto H, Negishi L, Kondo-Kakuta C, Hayashi N, Ohsumi Y. 2012. Atg9 vesicles recruit vesicle-tethering proteins Trs85 and Ypt1 to the autophagosome formation site. J Biol Chem 287:44261–44269.
   PubMed Web of Science ®Google Scholar
• Kaushik S, Cuervo AM. 2012. Chaperone-mediated autophagy: A unique way to enter the lysosome world. Trends Cell Biol 22:407–417.
   PubMed Web of Science ®Google Scholar
• Klionsky D. 2013. An overview of autophagy: Morphology, mechanism and regulation. Antioxid Redox Signal.
   Google Scholar
• Kornmann B, Currie E, Collins SR, Schuldiner M, Nunnari J, Weissman JS, et al. 2009. An ER-mitochondria tethering complex revealed by a synthetic biology screen. Science 325:477–481.
   PubMed Web of Science ®Google Scholar
• Kraft C, Kijanska M, Kalie E, Siergiejuk E, Lee SS, Semplicio G, et al. 2012. Binding of the Atg1/ULK1 kinase to the ubiquitin-like protein Atg8 regulates autophagy. EMBO J 31:3691–3703.
   PubMed Web of Science ®Google Scholar
• Lang T, Reiche S, Straub M, Bredschneider M, Thumm M. 2000. Autophagy and the cvt pathway both depend on AUT9. J Bacteriol 182:2125–2133.
   PubMed Web of Science ®Google Scholar
• Li L, Chen Y, Gibson SB. 2013. Starvation-induced autophagy is regulated by mitochondrial reactive oxygen species leading to AMPK activation. Cell Signal 25:50–65.
   PubMed Web of Science ®Google Scholar
• Li WW, Li J, Bao JK. 2012. Microautophagy: Lesser-known self-eating. Cell Mol Life Sci 69:1125–1136.
   PubMed Web of Science ®Google Scholar
• Lipatova Z, Belogortseva N, Zhang XQ, Kim J, Taussig D, Segev N. 2012. Regulation of selective autophagy onset by a Ypt/Rab GTPase module. Proc Natl Acad Sci USA 109:6981–6986.
   PubMed Web of Science ®Google Scholar
• Lipatova Z, Segev N. 2012. A Ypt/Rab GTPase module makes a PAS. Autophagy 8:1271–1272.
   PubMed Web of Science ®Google Scholar
• Lynch-Day MA, Bhandari D, Menon S, Huang J, Cai H, Bartholomew CR, et al. 2010. Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy. Proc Natl Acad Sci USA 107:7811–7816.
   PubMed Web of Science ®Google Scholar
• Manjithaya R, Nazarko TY, Farré JC, Subramani S. 2010. Molecular mechanism and physiological role of pexophagy. FEBS Lett 584:1367–1373.
   PubMed Web of Science ®Google Scholar
• Mari M, Griffith J, Rieter E, Krishnappa L, Klionsky DJ, Reggiori F. 2010. An Atg9-containing compartment that functions in the early steps of autophagosome biogenesis. J Cell Biol 190:1005–1022.
   PubMed Web of Science ®Google Scholar
• Matsunaga K, Morita E, Saitoh T, Akira S, Ktistakis NT, Izumi T, et al. 2010. Autophagy requires endoplasmic reticulum targeting of the PI3-kinase complex via Atg14L. J Cell Biol 190:511–521.
   PubMed Web of Science ®Google Scholar
• Muppirala M, Gupta V, Swarup G. 2011. Syntaxin 17 cycles between the ER and ERGIC and is required to maintain the architecture of ERGIC and Golgi. Biol Cell 103:333–350.
   PubMed Web of Science ®Google Scholar
• Nishida Y, Arakawa S, Fujitani K, Yamaguchi H, Mizuta T, Kanaseki T, et al. 2009. Discovery of Atg5/Atg7-independent alternative macroautophagy. Nature 461:654–658.
   PubMed Web of Science ®Google Scholar
• Noda T, Fujita N, Yoshimori T. 2008. The Ubi brothers reunited. Autophagy 4:540–541.
   PubMed Web of Science ®Google Scholar
• Ohashi Y, Munro S. 2010. Membrane delivery to the yeast autophagosome from the Golgi-endosomal system. Mol Biol Cell 21:3998–4008.
   PubMed Web of Science ®Google Scholar
• Orsi A, Razi M, Dooley HC, Robinson D, Weston AE, Collinson LM, et al. 2012. Dynamic and transient interactions of Atg9 with autophagosomes, but not membrane integration, are required for autophagy. Mol Biol Cell 23:1860–1873.
   PubMed Web of Science ®Google Scholar
• Ouimet M. 2013. Autophagy in obesity and atherosclerosis: Interrelationships between cholesterol homeostasis, lipoprotein metabolism and autophagy in macrophages and other systems. Biochim Biophys Acta 1831:1124–1133.
   PubMed Web of Science ®Google Scholar
• Polson HEJ, de Lartigue J, Rigden DJ, Reedijk M, Urbé S, Clague MJ, et al. 2010. Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation. Autophagy 6:506–522.
   PubMed Web of Science ®Google Scholar
• Puri C, Renna M, Bento CF, Moreau K, Rubinsztein DC. 2013. Diverse autophagosome membrane sources coalesce in recycling endosomes. Cell 154:1285–1299.
   PubMed Web of Science ®Google Scholar
• Raturi A, Simmen T. 2013. Where the endoplasmic reticulum and the mitochondrion tie the knot: The mitochondria-associated membrane (MAM). Biochim Biophys Acta 1833:213–224.
   PubMed Web of Science ®Google Scholar
• Ravikumar B, Moreau K, Jahreiss L, Puri C, Rubinsztein DC. 2010. Plasma membrane contributes to the formation of pre-autophagosomal structures. Nat Cell Biol 12:747–757.
   PubMed Web of Science ®Google Scholar
• Reggiori F, Klionsky DJ. 2002. Autophagy in the eukaryotic cell. Eukaryot Cell 1:11–21.
   PubMed Web of Science ®Google Scholar
• Reggiori F, Shintani T, Nair U, Klionsky DJ. 2005. Atg9 cycles between mitochondria and the pre-autophagosomal structure in yeasts. Autophagy 1:101–109.
   PubMed Web of Science ®Google Scholar
• Reggiori F, Tucker KA, Stromhaug PE, Klionsky DJ. 2004. The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure. Dev Cell 6:79–90.
   PubMed Web of Science ®Google Scholar
• Rosenfeldt MT, Ryan KM. 2011. The multiple roles of autophagy in cancer. Carcinogenesis.
   PubMed Web of Science ®Google Scholar
• Rowland AA, Voeltz GK. 2012. Endoplasmic reticulum-mitochondria contacts: Function of the junction. Nat Rev Mol Cell Biol 13:607–625.
   PubMed Web of Science ®Google Scholar
• Rubinsztein DC, Shpilka T, Elazar Z. 2012. Mechanisms of autophagosome biogenesis. Curr Biol 22:R29–R34.
   PubMed Web of Science ®Google Scholar
• Russell RC, Tian Y, Yuan H, Park HW, Chang YY, Kim J, et al. 2013. ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase. Nat Cell Biol 15:741–750.
   PubMed Web of Science ®Google Scholar
• Sekito T, Kawamata T, Ichikawa R, Suzuki K, Ohsumi Y. 2009. Atg17 recruits Atg9 to organize the pre-autophagosomal structure. Genes Cells 14:525–538.
   PubMed Web of Science ®Google Scholar
• Simonsen A, Tooze SA. 2009. Coordination of membrane events during autophagy by multiple class III PI3-kinase complexes. J Cell Biol 186:773–782.
   PubMed Web of Science ®Google Scholar
• Strømhaug PE, Berg TO, Fengsrud M, Seglen PO. 1998. Purification and characterization of autophagosomes from rat hepatocytes. Biochem J 335(Pt 2):217–224.
   PubMedGoogle Scholar
• Takahashi Y, Meyerkord CL, Wang HG. 2009. Bif-1/endophilin B1: A candidate for crescent driving force in autophagy. Cell Death Differ 16:947–955.
   PubMed Web of Science ®Google Scholar
• Tanida I. 2011. Autophagosome formation and molecular mechanism of autophagy. Antioxid Redox Signal 14:2201–2214.
   PubMed Web of Science ®Google Scholar
• Tanida I, Ueno T, Kominami E. 2008. LC3 and autophagy. Meth Mol Biol 445:77–88.
   PubMedGoogle Scholar
• Tooze SA, Yoshimori T. 2010. The origin of the autophagosomal membrane. Nat Cell Biol 12:831–835.
   PubMed Web of Science ®Google Scholar
• Walker S, Chandra P, Manifava M, Axe E, Ktistakis NT. 2008. Making autophagosomes: Localized synthesis of phosphatidylinositol 3-phosphate holds the clue. Autophagy 4:1093–1096.
   PubMed Web of Science ®Google Scholar
• Wang C, Liu Z, Huang X. 2012. Rab32 is important for autophagy and lipid storage in Drosophila. PLoS ONE 7:e32086.
   PubMed Web of Science ®Google Scholar
• Wong PM, Puente C, Ganley IG, Jiang X. 2013. The ULK1 complex: Sensing nutrient signals for autophagy activation. Autophagy 9:124–137.
   PubMed Web of Science ®Google Scholar
• Yamamoto H, Kakuta S, Watanabe TM, Kitamura A, Sekito T, Kondo-Kakuta C, et al. 2012. Atg9 vesicles are an important membrane source during early steps of autophagosome formation. J Cell Biol 198:219–233.
   PubMed Web of Science ®Google Scholar
• Yang Z, Klionsky DJ. 2010a. Eaten alive: A history of macroautophagy. Nat Cell Biol 12:814–822.
   PubMed Web of Science ®Google Scholar
• Yang Z, Klionsky DJ. 2010b. Mammalian autophagy: Core molecular machinery and signaling regulation. Curr Opin Cell Biol 22:124–131.
   PubMed Web of Science ®Google Scholar
• Yen WL, Legakis JE, Nair U, Klionsky DJ. 2007. Atg27 is required for autophagy-dependent cycling of Atg9. Mol Biol Cell 18:581–593.
   PubMed Web of Science ®Google Scholar
• Ylä-Anttila P, Vihinen H, Jokitalo E, Eskelinen EL. 2009. 3D tomography reveals connections between the phagophore and endoplasmic reticulum. Autophagy 5:1180–1185.
   PubMed Web of Science ®Google Scholar
• Young ARJ, Chan EYW, Hu XW, Köchl R, Crawshaw SG, High S, et al. 2006. Starvation and ULK1-dependent cycling of mammalian Atg9 between the TGN and endosomes. J Cell Sci 119:3888–3900.
   PubMed Web of Science ®Google Scholar
• Yuan HX, Xiong Y, Guan KL. 2013. Nutrient sensing, metabolism, and cell growth control. Mol Cell 49:379–387.
   PubMed Web of Science ®Google Scholar
• Zoncu R, Efeyan A, Sabatini DM. 2011. mTOR: From growth signal integration to cancer, diabetes and ageing. Nat Rev Mol Cell Biol 12:21–35.
   PubMed Web of Science ®Google Scholar