Ultrastructural relationship of the phagophore with surrounding organelles

References

• Chan DC. Mitochondrial fusion and fission in mammals. Annu Rev Cell Dev Biol 2006; 22:79-99; PMID:16704336
   PubMed Web of Science ®Google Scholar
• Suzuki K, Kirisako T, Kamada Y, Mizushima N, Noda T, Ohsumi Y. The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. EMBO J 2001; 20:5971-81; PMID:11689437; http://dx.doi.org/10.1093/emboj/20.21.5971
   PubMed Web of Science ®Google Scholar
• Suzuki K, Ohsumi Y. Current knowledge of the pre-autophagosomal structure (PAS). FEBS Lett 2010; 584:1280-6; PMID:20138172; http://dx.doi.org/10.1016/j.febslet.2010.02.001
   PubMed Web of Science ®Google Scholar
• Abounit K, Scarabelli TM, McCauley RB. Autophagy in mammalian cells. World J Biol Chem 2012; 3:1-6; PMID:22312452
   PubMedGoogle Scholar
• Klionsky DJ. The molecular machinery of autophagy: unanswered questions. J Cell Sci 2005; 118:7-18; PMID:15615779; http://dx.doi.org/10.1242/jcs.01620
   PubMed Web of Science ®Google Scholar
• Longatti A, Tooze SA. Vesicular trafficking and autophagosome formation. Cell Death Differ 2009; 16:956-65; PMID:19373247; http://dx.doi.org/10.1038/cdd.2009.39
   PubMed Web of Science ®Google Scholar
• Juhasz G, Neufeld TP. Autophagy: a forty-year search for a missing membrane source. PLoS Biol 2006; 4:e36; PMID:16464128
   PubMedGoogle Scholar
• Axe EL, Walker SA, Manifava M, Chandra P, Roderick HL, Habermann A, Griffiths G, Ktistakis NT. Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J Cell Biol 2008; 182:685-701; PMID:18725538; http://dx.doi.org/10.1083/jcb.200803137
   PubMed Web of Science ®Google Scholar
• Ktistakis NT, Andrews S, Long J. What is the advantage of a transient precursor in autophagosome biogenesis? Autophagy 2011; 7:118-22; PMID:20935487; http://dx.doi.org/10.4161/auto.7.1.13697
   PubMed Web of Science ®Google Scholar
• Friedman JR, Voeltz GK. The ER in 3D: a multifunctional dynamic membrane network. Trends Cell Biol 2011; 21:709-17; PMID:21900009; http://dx.doi.org/10.1016/j.tcb.2011.07.004
   PubMed Web of Science ®Google Scholar
• Helle SC, Kanfer G, Kolar K, Lang A, Michel AH, Kornmann B. Organization and function of membrane contact sites. Biochim Biophys Acta 2013; 1833:2526-41; PMID:23380708; http://dx.doi.org/10.1016/j.bbamcr.2013.01.028
   PubMed Web of Science ®Google Scholar
• Levine T. Short-range intracellular trafficking of small molecules across endoplasmic reticulum junctions. Trends Cell Biol 2004; 14:483-90; PMID:15350976
   PubMed Web of Science ®Google Scholar
• Kornmann B. The molecular hug between the ER and the mitochondria. Curr Opin Cell Biol 2013; 25:443-8; PMID:23478213
   PubMed Web of Science ®Google Scholar
• Uemura T, Yamamoto M, Kametaka A, Sou YS, Yabashi A, Yamada A, Annoh H, Kametaka S, Komatsu M, Waguri S. A cluster of thin tubular structures mediates transformation of the endoplasmic reticulum to autophagic isolation membrane. Mol Cell Biol 2014; 34:1695-706; PMID:24591649; http://dx.doi.org/10.1128/MCB.01327-13
   PubMed Web of Science ®Google Scholar
• Hayashi-Nishino M, Fujita N, Noda T, Yamaguchi A, Yoshimori T, Yamamoto A. Electron tomography reveals the endoplasmic reticulum as a membrane source for autophagosome formation. Autophagy 2010; 6:301-3; PMID:20104025; http://dx.doi.org/10.4161/auto.6.2.11134
   PubMed Web of Science ®Google Scholar
• Yla-Anttila P, Vihinen H, Jokitalo E, Eskelinen EL. 3D tomography reveals connections between the phagophore and endoplasmic reticulum. Autophagy 2009a; 5:1180-5; PMID:19855179; http://dx.doi.org/10.4161/auto.5.8.10274
   PubMed Web of Science ®Google Scholar
• Yorimitsu T, Klionsky DJ. Eating the endoplasmic reticulum: quality control by autophagy. Trends Cell Biol 2007; 17:279-85; PMID:17481899; http://dx.doi.org/10.1016/j.tcb.2007.04.005
   PubMed Web of Science ®Google Scholar
• Kovacs AL, Palfia Z, Rez G, Vellai T, Kovacs J. Sequestration revisited: integrating traditional electron microscopy, de novo assembly and new results. Autophagy 2007; 3:655-62; PMID:17603297; http://dx.doi.org/10.4161/auto.4590
   PubMed Web of Science ®Google Scholar
• van der Vaart A, Griffith J, Reggiori F. Exit from the Golgi is required for the expansion of the autophagosomal phagophore in yeast Saccharomyces cerevisiae. Mol Biol Cell; 21:2270-84; PMID:20444982
   PubMedGoogle Scholar
• van der Vaart A, Reggiori F. The Golgi complex as a source for yeast autophagosomal membranes. Autophagy; 6:800-1; PMID:20714226
   PubMedGoogle Scholar
• Cuervo AM. The plasma membrane brings autophagosomes to life. Nat Cell Biol 2010; 12:735-7; PMID:20680002; http://dx.doi.org/10.1038/ncb0810-735
   PubMed Web of Science ®Google Scholar
• Ravikumar B, Moreau K, Rubinsztein DC. Plasma membrane helps autophagosomes grow. Autophagy 2010; 6:1184-6; PMID:20861674; http://dx.doi.org/10.4161/auto.6.8.13428
   PubMed Web of Science ®Google Scholar
• Ravikumar B, Moreau K, Jahreiss L, Puri C, Rubinsztein DC. Plasma membrane contributes to the formation of pre-autophagosomal structures. Nat Cell Biol 2010; 12:747-57; PMID:20639872; http://dx.doi.org/10.1038/ncb2078
   PubMed Web of Science ®Google Scholar
• Hailey DW, Rambold AS, Satpute-Krishnan P, Mitra K, Sougrat R, Kim PK, Lippincott-Schwartz J. Mitochondria supply membranes for autophagosome biogenesis during starvation. Cell 2010; 141:656-67; PMID:20478256; http://dx.doi.org/10.1016/j.cell.2010.04.009
   PubMed Web of Science ®Google Scholar
• Rambold AS, Lippincott-Schwartz J. Starved cells use mitochondria for autophagosome biogenesis. Cell Cycle 2010; 9:3633-4; PMID:20855967; http://dx.doi.org/10.4161/cc.9.18.13170
   PubMed Web of Science ®Google Scholar
• Luo S, Chen Q, Cebollero E, Xing D. Mitochondria: one of the origins for autophagosomal membranes? Mitochondrion 2009; 9:227-31; PMID:19398041; http://dx.doi.org/10.1016/j.mito.2009.04.004
   PubMed Web of Science ®Google Scholar
• Puri C, Renna M, Bento CF, Moreau K, Rubinsztein DC. Diverse autophagosome membrane sources coalesce in recycling endosomes. Cell 2013; 154:1285-99; PMID:24034251; http://dx.doi.org/10.1016/j.cell.2013.08.044
   PubMed Web of Science ®Google Scholar
• Longatti A, Tooze SA. Recycling endosomes contribute to autophagosome formation. Autophagy 2012; 8:1682-3; PMID:22874560; http://dx.doi.org/10.4161/auto.21486
   PubMed Web of Science ®Google Scholar
• Bockler S, Westermann B. ER-mitochondria contacts as sites of mitophagosome formation. Autophagy 2014; 10:1346-7; PMID:24905224; http://dx.doi.org/10.4161/auto.28981
   PubMed Web of Science ®Google Scholar
• Hamasaki M, Furuta N, Matsuda A, Nezu A, Yamamoto A, Fujita N, Oomori H, Noda T, Haraguchi T, Hiraoka Y, et al. Autophagosomes form at ER-mitochondria contact sites. Nature 2013; 495:389-93; PMID:23455425; http://dx.doi.org/10.1038/nature11910
   PubMed Web of Science ®Google Scholar
• 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; 24:2918-31; PMID:23904270; http://dx.doi.org/10.1091/mbc.E13-07-0381
   PubMed Web of Science ®Google Scholar
• Tan D, Cai Y, Wang J, Zhang J, Menon S, Chou HT, Ferro-Novick S, Reinisch KM, Walz T. The EM structure of the TRAPPIII complex leads to the identification of a requirement for COPII vesicles on the macroautophagy pathway. Proc Natl Acad Sci U S A 2013; 110:19432-7; PMID:24218626; http://dx.doi.org/10.1073/pnas.1316356110
   PubMed Web of Science ®Google Scholar
• 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; PMID:23930225; http://dx.doi.org/10.7554/eLife.00947
   PubMed Web of Science ®Google Scholar
• Mijaljica D, Prescott M, Devenish RJ. Endoplasmic reticulum and Golgi complex: Contributions to, and turnover by, autophagy. Traffic 2006; 7:1590-5; PMID:17040485; http://dx.doi.org/10.1111/j.1600-0854.2006.00495.x
   PubMed Web of Science ®Google Scholar
• Eskelinen EL, Reggiori F, Baba M, Kovacs AL, Seglen PO. Seeing is believing: the impact of electron microscopy on autophagy research. Autophagy 2011; 7:935-56; PMID:21566462; http://dx.doi.org/10.4161/auto.7.9.15760
   PubMed Web of Science ®Google Scholar
• Klionsky DJ, Cregg JM, Dunn WA, Jr., Emr SD, Sakai Y, Sandoval IV, Sibirny A, Subramani S, Thumm M, Veenhuis M, et al. A unified nomenclature for yeast autophagy-related genes. Dev Cell 2003; 5:539-45; PMID:14536056; http://dx.doi.org/10.1016/S1534-5807(03)00296-X
   PubMed Web of Science ®Google Scholar
• Koyama-Honda I, Itakura E, Fujiwara TK, Mizushima N. Temporal analysis of recruitment of mammalian ATG proteins to the autophagosome formation site. Autophagy 2013; 9:1491-9; PMID:23884233; http://dx.doi.org/10.4161/auto.25529
   PubMed Web of Science ®Google Scholar
• Orsi A, Razi M, Dooley HC, Robinson D, Weston AE, Collinson LM, Tooze SA. Dynamic and transient interactions of Atg9 with autophagosomes, but not membrane integration, are required for autophagy. Mol Biol Cell 2012; 23:1860-73; PMID:22456507; http://dx.doi.org/10.1091/mbc.E11-09-0746
   PubMed Web of Science ®Google Scholar
• Longatti A, Orsi A, Tooze SA. Autophagosome formation: not necessarily an inside job. Cell Res 2010; 20:1181-4; PMID:20838417; http://dx.doi.org/10.1038/cr.2010.132
   PubMed Web of Science ®Google Scholar
• Kabeya Y, Mizushima N, Ueno T, Yamamoto A, Kirisako T, Noda T, Kominami E, Ohsumi Y, Yoshimori T. LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J 2000; 19:5720-8; PMID:11060023; http://dx.doi.org/10.1093/emboj/19.21.5720
   PubMed Web of Science ®Google Scholar
• Polson HE, de Lartigue J, Rigden DJ, Reedijk M, Urbe S, Clague MJ, Tooze SA. Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation. Autophagy 2010; 6:506-22; PMID:20505359; http://dx.doi.org/10.4161/auto.6.4.11863
   PubMed Web of Science ®Google Scholar
• 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; 11:1433-7; PMID:19898463; http://dx.doi.org/10.1038/ncb1991
   PubMed Web of Science ®Google Scholar
• Puhka M, Joensuu M, Vihinen H, Belevich I, Jokitalo E. Progressive sheet-to-tubule transformation is a general mechanism for endoplasmic reticulum partitioning in dividing mammalian cells. Mol Biol Cell 2012; 23:2424-32; PMID:22573885; http://dx.doi.org/10.1091/mbc.E10-12-0950
   PubMed Web of Science ®Google Scholar
• Achleitner G, Gaigg B, Krasser A, Kainersdorfer E, Kohlwein SD, Perktold A, Zellnig G, Daum G. Association between the endoplasmic reticulum and mitochondria of yeast facilitates interorganelle transport of phospholipids through membrane contact. Eur J Biochem 1999; 264:545-53; PMID:10491102; http://dx.doi.org/10.1046/j.1432-1327.1999.00658.x
   PubMedGoogle Scholar
• 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; 197:659-75; PMID:22613832; http://dx.doi.org/10.1083/jcb.201111079
   PubMed Web of Science ®Google Scholar
• Horl G, Wagner A, Cole LK, Malli R, Reicher H, Kotzbeck P, Kofeler H, Hofler G, Frank S, Bogner-Strauss JG, et al. Sequential synthesis and methylation of phosphatidylethanolamine promote lipid droplet biosynthesis and stability in tissue culture and in vivo. J Biol Chem 2011; 286:17338-50; PMID:21454708; http://dx.doi.org/10.1074/jbc.M111.234534
   PubMedGoogle Scholar
• Vance JE. The use of newly synthesized phospholipids for assembly into secreted hepatic lipoproteins. Biochim Biophys Acta 1989; 1006:59-69; PMID:2508747
   PubMed Web of Science ®Google Scholar
• Girardi JP, Pereira L, Bakovic M. De novo synthesis of phospholipids is coupled with autophagosome formation. Med Hypotheses 2011; 77:1083-7; PMID:21963355; http://dx.doi.org/10.1016/j.mehy.2011.09.008
   PubMed Web of Science ®Google Scholar
• Gaspar ML, Jesch SA, Viswanatha R, Antosh AL, Brown WJ, Kohlwein SD, Henry SA. A block in endoplasmic reticulum-to-Golgi trafficking inhibits phospholipid synthesis and induces neutral lipid accumulation. J Biol Chem 2008; 283:25735-51; PMID:18614533; http://dx.doi.org/10.1074/jbc.M802685200
   PubMedGoogle Scholar
• Zoppino FC, Militello RD, Slavin I, Alvarez C, Colombo MI. Autophagosome formation depends on the small GTPase Rab1 and functional ER exit sites. Traffic 2010; 11:1246-61; PMID:20545908; http://dx.doi.org/10.1111/j.1600-0854.2010.01086.x
   PubMed Web of Science ®Google Scholar
• Zeuschner D, Geerts WJ, van Donselaar E, Humbel BM, Slot JW, Koster AJ, Klumperman J. Immuno-electron tomography of ER exit sites reveals the existence of free COPII-coated transport carriers. Nat Cell Biol 2006; 8:377-83; PMID:16531996; http://dx.doi.org/10.1038/ncb1371
   PubMed Web of Science ®Google Scholar
• Novikoff AB, Shin WY. Endoplasmic reticulum and autophagy in rat hepatocytes. Proc Natl Acad Sci U S A 1978; 75:5039-42; PMID:283412; http://dx.doi.org/10.1073/pnas.75.10.5039
   PubMed Web of Science ®Google Scholar
• Seglen PO. Regulation of autophagic protein degradation in isolated liver cells. In: Glaumann H, Ballard FJ, editors. Lysosomes: their role in protein breakdown. London Academic Press, 1987, pp. 371-414
   Google Scholar
• Knaevelsrud H, Carlsson SR, Simonsen A. SNX18 tubulates recycling endosomes for autophagosome biogenesis. Autophagy 2013; 9:1639-41; PMID:24113029
   PubMed Web of Science ®Google Scholar
• 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 2013; 10:182-4; PMID:24257061
   PubMed Web of Science ®Google Scholar
• Cook KL, Soto-Pantoja DR, Abu-Asab M, Clarke PA, Roberts DD, Clarke R. Mitochondria directly donate their membrane to form autophagosomes during a novel mechanism of parkin-associated mitophagy. Cell Biosci 2014; 4:16; PMID:24669863; http://dx.doi.org/10.1186/2045-3701-4-16
   PubMedGoogle Scholar
• Ding WX, Li M, Biazik JM, Morgan DG, Guo F, Ni HM, Goheen M, Eskelinen EL, Yin XM. Electron microscopic analysis of a spherical mitochondrial structure. J Biol Chem 2012; 287:42373-8; PMID:23093403; http://dx.doi.org/10.1074/jbc.M112.413674
   PubMed Web of Science ®Google Scholar
• Rowland AA, Voeltz GK. Endoplasmic reticulum-mitochondria contacts: function of the junction. Nat Rev Mol Cell Biol 2012; 13:607-25; PMID:22992592; http://dx.doi.org/10.1038/nrm3440
   PubMed Web of Science ®Google Scholar
• Bozidis P, Williamson CD, Colberg-Poley AM. Mitochondrial and secretory human cytomegalovirus UL37 proteins traffic into mitochondrion-associated membranes of human cells. J Virol 2008; 82:2715-26; PMID:18199645; http://dx.doi.org/10.1128/JVI.02456-07
   PubMedGoogle Scholar
• Marsh BJ, Mastronarde DN, Buttle KF, Howell KE, McIntosh JR. Organellar relationships in the Golgi region of the pancreatic beta cell line, HIT-T15, visualized by high resolution electron tomography. Proc Natl Acad Sci U S A 2001; 98:2399-406; PMID:11226251; http://dx.doi.org/10.1073/pnas.051631998
   PubMed Web of Science ®Google Scholar
• Kornmann B, Currie E, Collins SR, Schuldiner M, Nunnari J, Weissman JS, Walter P. An ER-mitochondria tethering complex revealed by a synthetic biology screen. Science 2009; 325:477-81; PMID:19556461; http://dx.doi.org/10.1126/science.1175088
   PubMed Web of Science ®Google Scholar
• Kim S, Naylor SA, DiAntonio A. Drosophila Golgi membrane protein Ema promotes autophagosomal growth and function. Proc Natl Acad Sci U S A 2012; 109:E1072-81; PMID:22493244; http://dx.doi.org/10.1073/pnas.1120320109
   PubMed Web of Science ®Google Scholar
• Germain M, Nguyen AP, Le Grand JN, Arbour N, Vanderluit JL, Park DS, Opferman JT, Slack RS. MCL-1 is a stress sensor that regulates autophagy in a developmentally regulated manner. EMBO J 2011; 30:395-407; PMID:21139567; http://dx.doi.org/10.1038/emboj.2010.327
   PubMed Web of Science ®Google Scholar
• Takahashi Y, Meyerkord CL, Hori T, Runkle K, Fox TE, Kester M, Loughran TP, Wang HG. Bif-1 regulates Atg9 trafficking by mediating the fission of Golgi membranes during autophagy. Autophagy 2011; 7:61-73; PMID:21068542; http://dx.doi.org/10.4161/auto.7.1.14015
   PubMed Web of Science ®Google Scholar
• 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; 190:1005-22; PMID:20855505; http://dx.doi.org/10.1083/jcb.200912089
   PubMed Web of Science ®Google Scholar
• Yamamoto H, Kakuta S, Watanabe TM, Kitamura A, Sekito T, Kondo-Kakuta C, Ichikawa R, Kinjo M, Ohsumi Y. Atg9 vesicles are an important membrane source during early steps of autophagosome formation. J Cell Biol 2012; 198:219-33; PMID:22826123; http://dx.doi.org/10.1083/jcb.201202061
   PubMed Web of Science ®Google Scholar
• Guo Y, Chang C, Huang R, Liu B, Bao L, Liu W. AP1 is essential for generation of autophagosomes from the trans-Golgi network. J Cell Sci 2012; 125:1706-15; PMID:22328508; http://dx.doi.org/10.1242/jcs.093203
   PubMed Web of Science ®Google Scholar
• Young AR, Chan EY, Hu XW, Kochl R, Crawshaw SG, High S, Hailey DW, Lippincott-Schwartz J, Tooze SA. Starvation and ULK1-dependent cycling of mammalian Atg9 between the TGN and endosomes. J Cell Sci 2006; 119:3888-900; PMID:16940348; http://dx.doi.org/10.1242/jcs.03172
   PubMed Web of Science ®Google Scholar
• Moreau K, Renna M, Rubinsztein DC. Connections between SNAREs and autophagy. Trends Biochem Sci 2013; 38:57-63; PMID:23306003; http://dx.doi.org/10.1016/j.tibs.2012.11.004
   PubMed Web of Science ®Google Scholar
• Lev S. Nonvesicular lipid transfer from the endoplasmic reticulum. Cold Spring Harb Perspect Biol 2012; 4:a013300; PMID:23028121
   PubMedGoogle Scholar
• Lev S. Non-vesicular lipid transport by lipid-transfer proteins and beyond. Nat Rev Mol Cell Biol 2010; 11:739-50; PMID:20823909; http://dx.doi.org/10.1038/nrm2971
   PubMed Web of Science ®Google Scholar
• Perkins G, Renken C, Martone ME, Young SJ, Ellisman M, Frey T. Electron tomography of neuronal mitochondria: three-dimensional structure and organization of cristae and membrane contacts. J Struct Biol 1997; 119:260-72; PMID:9245766; http://dx.doi.org/10.1006/jsbi.1997.3885
   PubMed Web of Science ®Google Scholar
• Sleight RG. Intracellular lipid transport in eukaryotes. Annu Rev Physiol 1987; 49:193-208; PMID:3551798
   PubMed Web of Science ®Google Scholar
• Kawano M, Kumagai K, Nishijima M, Hanada K. Efficient trafficking of ceramide from the endoplasmic reticulum to the Golgi apparatus requires a VAMP-associated protein-interacting FFAT motif of CERT. J Biol Chem 2006; 281:30279-88; PMID:16895911; http://dx.doi.org/10.1074/jbc.M605032200
   PubMed Web of Science ®Google Scholar
• Starborg T, Kalson NS, Lu Y, Mironov A, Cootes TF, Holmes DF, Kadler KE. Using transmission electron microscopy and 3View to determine collagen fibril size and three-dimensional organization. Nat Protoc 2013; 8:1433-48; PMID:23807286; http://dx.doi.org/10.1038/nprot.2013.086
   PubMedGoogle Scholar
• Yla-Anttila P, Vihinen H, Jokitalo E, Eskelinen EL. Monitoring autophagy by electron microscopy in Mammalian cells. Methods Enzymol 2009b; 452:143-64; PMID:19200881; http://dx.doi.org/10.1016/S0076-6879(08)03610-0
   PubMed Web of Science ®Google Scholar
• Mastronarde DN. Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol 2005; 152:36-51; PMID:16182563
   PubMed Web of Science ®Google Scholar
• Kremer JR, Mastronarde DN, McIntosh JR. Computer visualization of three-dimensional image data using IMOD. J Struct Biol 1996; 116:71-6; PMID:8742726; http://dx.doi.org/10.1006/jsbi.1996.0013
   PubMed Web of Science ®Google Scholar