SEARCH

SEARCH BY CITATION

References

  • 1
    Boya P, Reggiori F, Codogno P (2013) Emerging regulation and functions of autophagy. Nat Cell Biol 15: 713720
  • 2
    Choi AM, Ryter SW, Levine B (2013) Autophagy in human health and disease. N Engl J Med 368: 651662
  • 3
    Sato M, Sato K (2013) Dynamic regulation of autophagy and endocytosis for cell remodeling during early development. Traffic 14: 479486
  • 4
    Guan JL, Simon AK, Prescott M, Menendez JA, Liu F, Wang F, Wang C, Wolvetang E, Vazquez-Martin A, Zhang J (2013) Autophagy in stem cells. Autophagy 9: 830849
  • 5
    Weidberg H, Shvets E, Elazar Z (2011) Biogenesis and cargo selectivity of autophagosomes. Annu Rev Biochem 80: 125156
  • 6
    Rubinsztein DC, Shpilka T, Elazar Z (2012) Mechanisms of autophagosome biogenesis. Curr Biol 22: R29R34
  • 7
    Laplante M, Sabatini DM (2012) mTOR signaling in growth control and disease. Cell 149: 274293
  • 8
    Sarkar S (2013) Regulation of autophagy by mTOR-dependent and mTOR-independent pathways: autophagy dysfunction in neurodegenerative diseases and therapeutic application of autophagy enhancers. Biochem Soc Trans 41: 11031130
  • 9
    Shimobayashi M, Hall MN (2014) Making new contacts: the mTOR network in metabolism and signalling crosstalk. Nat Rev Mol Cell Biol 15: 155162
  • 10
    Hundal HS, Taylor PM (2009) Amino acid transceptors: gate keepers of nutrient exchange and regulators of nutrient signaling. Am J Physiol Endocrinol Metab 296: E603E613
  • 11
    Ecker N, Mor A, Journo D, Abeliovich H (2010) Induction of autophagic flux by amino acid deprivation is distinct from nitrogen starvation-induced macroautophagy. Autophagy 6: 879890
  • 12
    Wauson EM, Zaganjor E, Lee AY, Guerra ML, Ghosh AB, Bookout AL, Chambers CP, Jivan A, McGlynn K, Hutchison MR et al (2012) The G protein-coupled taste receptor T1R1/T1R3 regulates mTORC1 and autophagy. Mol Cell 47: 851862
  • 13
    Han JM, Jeong SJ, Park MC, Kim G, Kwon NH, Kim HK, Ha SH, Ryu SH, Kim S (2012) Leucyl-tRNA synthetase is an intracellular leucine sensor for the mTORC1-signaling pathway. Cell 149: 410424
  • 14
    Bonfils G, Jaquenoud M, Bontron S, Ostrowicz C, Ungermann C, De Virgilio C (2012) Leucyl-tRNA synthetase controls TORC1 via the EGO complex. Mol Cell 46: 105110
  • 15
    Lorin S, Tol MJ, Bauvy C, Strijland A, Pous C, Verhoeven AJ, Codogno P, Meijer AJ (2013) Glutamate dehydrogenase contributes to leucine sensing in the regulation of autophagy. Autophagy 9: 850860
  • 16
    Duran RV, Oppliger W, Robitaille AM, Heiserich L, Skendaj R, Gottlieb E, Hall MN (2012) Glutaminolysis activates Rag-mTORC1 signaling. Mol Cell 47: 349358
  • 17
    Nicklin P, Bergman P, Zhang B, Triantafellow E, Wang H, Nyfeler B, Yang H, Hild M, Kung C, Wilson C (2009) Bidirectional transport of amino acids regulates mTOR and autophagy. Cell 136: 521534
  • 18
    Sancak Y, Bar-Peled L, Zoncu R, Markhard AL, Nada S, Sabatini DM (2010) Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids. Cell 141: 290303
  • 19
    Sancak Y, Peterson TR, Shaul YD, Lindquist RA, Thoreen CC, Bar-Peled L, Sabatini DM (2008) The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1. Science 320: 14961501
  • 20
    Zoncu R, Bar-Peled L, Efeyan A, Wang S, Sancak Y, Sabatini DM (2011) mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H(+)-ATPase. Science 334: 678683
  • 21
    Li M, Khambu B, Zhang H, Kang JH, Chen X, Chen D, Vollmer L, Liu PQ, Vogt A, Yin XM (2013) Suppression of lysosome function induces autophagy via a feedback down-regulation of MTOR complex 1 (MTORC1) activity. J Biol Chem 288: 3576935780
  • 22
    Korolchuk VI, Saiki S, Lichtenberg M, Siddiqi FH, Roberts EA, Imarisio S, Jahreiss L, Sarkar S, Futter M, Menzies FM et al (2011) Lysosomal positioning coordinates cellular nutrient responses. Nat Cell Biol 13: 453460
  • 23
    Inoki K, Li Y, Xu T, Guan KL (2003) Rheb GTPase is a direct target of TSC2 GAP activity and regulates mTOR signaling. Genes Dev 17: 18291834
  • 24
    Kim YM, Stone M, Hwang TH, Kim YG, Dunlevy JR, Griffin TJ, Kim DH (2012) SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1 signaling. Mol Cell 46: 833846
  • 25
    Bar-Peled L, Chantranupong L, Cherniack AD, Chen WW, Ottina KA, Grabiner BC, Spear ED, Carter SL, Meyerson M, Sabatini DM (2013) A Tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1. Science 340: 11001106
  • 26
    Hosokawa N, Sasaki T, Iemura S, Natsume T, Hara T, Mizushima N (2009) Atg101, a novel mammalian autophagy protein interacting with Atg13. Autophagy 5: 973979
  • 27
    Mercer CA, Kaliappan A, Dennis PB (2009) A novel, human Atg13 binding protein, Atg101, interacts with ULK1 and is essential for macroautophagy. Autophagy 5: 649662
  • 28
    Hara T, Takamura A, Kishi C, Iemura S, Natsume T, Guan JL, Mizushima N (2008) FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells. J Cell Biol 181: 497510
  • 29
    Jung CH, Jun CB, Ro SH, Kim YM, Otto NM, Cao J, Kundu M, Kim DH (2009) ULK-Atg13-FIP200 complexes mediate mTOR signaling to the autophagy machinery. Mol Biol Cell 20: 19922003
  • 30
    Ganley IG, du Lam H, Wang J, Ding X, Chen S, Jiang X (2009) ULK1.ATG13.FIP200 complex mediates mTOR signaling and is essential for autophagy. J Biol Chem 284: 1229712305
  • 31
    Duran A, Amanchy R, Linares JF, Joshi J, Abu-Baker S, Porollo A, Hansen M, Moscat J, Diaz-Meco MT (2011) p62 is a key regulator of nutrient sensing in the mTORC1 pathway. Mol Cell 44: 134146
  • 32
    Linares JF, Duran A, Yajima T, Pasparakis M, Moscat J, Diaz-Meco MT (2013) K63 polyubiquitination and activation of mTOR by the p62-TRAF6 complex in nutrient-activated cells. Mol Cell 51: 283296
  • 33
    Pattingre S, Tassa A, Qu X, Garuti R, Liang XH, Mizushima N, Packer M, Schneider MD, Levine B (2005) Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy. Cell 122: 927939
  • 34
    Wei Y, Pattingre S, Sinha S, Bassik M, Levine B (2008) JNK1-mediated phosphorylation of Bcl-2 regulates starvation-induced autophagy. Mol Cell 30: 678688
  • 35
    Moruno F, Perez-Jimenez E, Knecht E (2012) Regulation of autophagy by glucose in Mammalian cells. Cells 1: 372395
  • 36
    Manning BD, Tee AR, Logsdon MN, Blenis J, Cantley LC (2002) Identification of the tuberous sclerosis complex-2 tumor suppressor gene product tuberin as a target of the phosphoinositide 3-kinase/akt pathway. Mol Cell 10: 151162
  • 37
    Sarbassov DD, Guertin DA, Ali SM, Sabatini DM (2005) Phosphorylation and regulation of Akt/PKB by the rictor-mTOR complex. Science 307: 10981101
  • 38
    Brozinick JT Jr, Birnbaum MJ (1998) Insulin, but not contraction, activates Akt/PKB in isolated rat skeletal muscle. J Biol Chem 273: 1467914682
  • 39
    Martin TD, Chen XW, Kaplan RE, Saltiel AR, Walker CL, Reiner DJ, Der CJ (2014) Ral and Rheb GTPase activating proteins integrate mTOR and GTPase signaling in aging, autophagy, and tumor cell invasion. Mol Cell 53: 209220
  • 40
    Mammucari C, Milan G, Romanello V, Masiero E, Rudolf R, Del Piccolo P, Burden SJ, Di Lisi R, Sandri C, Zhao J et al (2007) FoxO3 controls autophagy in skeletal muscle in vivo. Cell Metab 6: 458471
  • 41
    Zhao J, Brault JJ, Schild A, Cao P, Sandri M, Schiaffino S, Lecker SH, Goldberg AL (2007) FoxO3 coordinately activates protein degradation by the autophagic/lysosomal and proteasomal pathways in atrophying muscle cells. Cell Metab 6: 472483
  • 42
    Tan SH, Shui G, Zhou J, Shi Y, Huang J, Xia D, Wenk MR, Shen HM (2014) Critical role of SCD1 in autophagy regulation via lipogenesis and lipid rafts-coupled AKT-FOXO1 signaling pathway. Autophagy 10: 226242
  • 43
    Roberts DJ, Tan-Sah VP, Ding EY, Smith JM, Miyamoto S (2014) Hexokinase-II positively regulates glucose starvation-induced autophagy through TORC1 inhibition. Mol Cell 53: 521533
  • 44
    Efeyan A, Zoncu R, Chang S, Gumper I, Snitkin H, Wolfson RL, Kirak O, Sabatini DD, Sabatini DM (2013) Regulation of mTORC1 by the Rag GTPases is necessary for neonatal autophagy and survival. Nature 493: 679683
  • 45
    Naito T, Kuma A, Mizushima N (2013) Differential contribution of insulin and amino acids to the mTORC1-autophagy pathway in the liver and muscle. J Biol Chem 288: 2107421081
  • 46
    Wheeler M, Domin J (2001) Recruitment of the class II phosphoinositide 3-kinase C2beta to the epidermal growth factor receptor: role of Grb2. Mol Cell Biol 21: 66606667
  • 47
    Wei Y, Zou Z, Becker N, Anderson M, Sumpter R, Xiao G, Kinch L, Koduru P, Christudass CS, Veltri RW et al (2013) EGFR-mediated Beclin 1 phosphorylation in autophagy suppression, tumor progression, and tumor chemoresistance. Cell 154: 12691284
  • 48
    Jutten B, Rouschop KM (2014) EGFR signaling and autophagy dependence for growth, survival, and therapy resistance. Cell Cycle 13: 4251
  • 49
    Shen S, Niso-Santano M, Adjemian S, Takehara T, Malik SA, Minoux H, Souquere S, Mariño G, Lachkar S, Senovilla L et al (2012) Cytoplasmic STAT3 represses autophagy by inhibiting PKR activity. Mol Cell 48: 667680
  • 50
    Rouschop KM, van den Beucken T, Dubois L, Niessen H, Bussink J, Savelkouls K, Keulers T, Mujcic H, Landuyt W, Voncken JW et al (2010) The unfolded protein response protects human tumor cells during hypoxia through regulation of the autophagy genes MAP1LC3B and ATG5. J Clin Invest 120: 127141
  • 51
    Guo JY, Chen HY, Mathew R, Fan J, Strohecker AM, Karsli-Uzunbas G, Kamphorst JJ, Chen G, Lemons JM, Karantza V et al (2011) Activated Ras requires autophagy to maintain oxidative metabolism and tumorigenesis. Genes Dev 25: 460470
  • 52
    Lin SY, Li TY, Liu Q, Zhang C, Li X, Chen Y, Zhang SM, Lian G, Liu Q, Ruan K et al (2012) GSK3-TIP60-ULK1 signaling pathway links growth factor deprivation to autophagy. Science 336: 477481
  • 53
    Into T, Inomata M, Takayama E, Takigawa T (2012) Autophagy in regulation of Toll-like receptor signaling. Cell Signal 24: 11501162
  • 54
    O'Neill LA, Bowie AG (2007) The family of five: TIR-domain-containing adaptors in Toll-like receptor signalling. Nat Rev Immunol 7: 353364
  • 55
    Shi CS, Kehrl JH (2010) TRAF6 and A20 regulate lysine 63-linked ubiquitination of Beclin-1 to control TLR4-induced autophagy. Sci Signal 3: ra42
  • 56
    Fujita K, Maeda D, Xiao Q, Srinivasula SM (2011) Nrf2-mediated induction of p62 controls Toll-like receptor-4-driven aggresome-like induced structure formation and autophagic degradation. Proc Natl Acad Sci U S A 108: 14271432
  • 57
    Gomes LC, Dikic I (2014) Autophagy in antimicrobial immunity. Mol Cell 54: 224233
  • 58
    Deretic V, Saitoh T, Akira S (2013) Autophagy in infection, inflammation and immunity. Nat Rev Immunol 13: 722737
  • 59
    Hardie DG, Ross FA, Hawley SA (2012) AMPK: a nutrient and energy sensor that maintains energy homeostasis. Nat Rev Mol Cell Biol 13: 251262
  • 60
    Shaw RJ, Bardeesy N, Manning BD, Lopez L, Kosmatka M, DePinho RA, Cantley LC (2004) The LKB1 tumor suppressor negatively regulates mTOR signaling. Cancer Cell 6: 9199
  • 61
    Inoki K, Ouyang H, Zhu T, Lindvall C, Wang Y, Zhang X, Yang Q, Bennett C, Harada Y, Stankunas K et al (2006) TSC2 integrates Wnt and energy signals via a coordinated phosphorylation by AMPK and GSK3 to regulate cell growth. Cell 126: 955968
  • 62
    Inoki K, Zhu T, Guan KL (2003) TSC2 mediates cellular energy response to control cell growth and survival. Cell 115: 577590
  • 63
    Gwinn DM, Shackelford DB, Egan DF, Mihaylova MM, Mery A, Vasquez DS, Turk BE, Shaw RJ (2008) AMPK phosphorylation of raptor mediates a metabolic checkpoint. Mol Cell 30: 214226
  • 64
    Kim J, Kundu M, Viollet B, Guan KL (2011) AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1. Nat Cell Biol 13: 132141
  • 65
    Kim J, Kim YC, Fang C, Russell RC, Kim JH, Fan W, Liu R, Zhong Q, Guan KL (2013) Differential regulation of distinct Vps34 complexes by AMPK in nutrient stress and autophagy. Cell 152: 290303
  • 66
    Lee SR, Yang KS, Kwon J, Lee C, Jeong W, Rhee SG (2002) Reversible inactivation of the tumor suppressor PTEN by H2O2. J Biol Chem 277: 2033620342
  • 67
    Tang HW, Liao HM, Peng WH, Lin HR, Chen CH, Chen GC (2013) Atg9 interacts with dTRAF2/TRAF6 to regulate oxidative stress-induced JNK activation and autophagy induction. Dev Cell 27: 489503
  • 68
    Adler V, Yin Z, Fuchs SY, Benezra M, Rosario L, Tew KD, Pincus MR, Sardana M, Henderson CJ, Wolf CR et al (1999) Regulation of JNK signaling by GSTp. EMBO J 18: 13211334
  • 69
    Chen K, Vita JA, Berk BC, Keaney JF Jr (2001) c-Jun N-terminal kinase activation by hydrogen peroxide in endothelial cells involves SRC-dependent epidermal growth factor receptor transactivation. J Biol Chem 276: 1604516050
  • 70
    Meng Y, Yong Y, Yang G, Ding H, Fan Z, Tang Y, Luo J, Ke ZJ (2013) Autophagy alleviates neurodegeneration caused by mild impairment of oxidative metabolism. J Neurochem 126: 805818
  • 71
    Sciarretta S, Zhai P, Shao D, Zablocki D, Nagarajan N, Terada LS, Volpe M, Sadoshima J (2013) Activation of NADPH oxidase 4 in the endoplasmic reticulum promotes cardiomyocyte autophagy and survival during energy stress through the protein kinase RNA-activated-like endoplasmic reticulum kinase/eukaryotic initiation factor 2 alpha/activating transcription factor 4 pathway. Circ Res 113: 12531264
  • 72
    Zhang J, Kim J, Alexander A, Cai S, Tripathi DN, Dere R, Tee AR, Tait-Mulder J, Di Nardo A, Han JM et al (2013) A tuberous sclerosis complex signalling node at the peroxisome regulates mTORC1 and autophagy in response to ROS. Nat Cell Biol 15: 11861196
  • 73
    Scherz-Shouval R, Shvets E, Fass E, Shorer H, Gil L, Elazar Z (2007) Reactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4. EMBO J 26: 17491760
  • 74
    Scherz-Shouval R, Elazar Z (2011) Regulation of autophagy by ROS: physiology and pathology. Trends Biochem Sci 36: 3038
  • 75
    Thomas DD, Ridnour LA, Isenberg JS, Flores-Santana W, Switzer CH, Donzelli S, Hussain P, Vecoli C, Paolocci N, Ambs S et al (2008) The chemical biology of nitric oxide: implications in cellular signaling. Free Radic Biol Med 45: 1831
  • 76
    Sarkar S, Korolchuk VI, Renna M, Imarisio S, Fleming A, Williams A, Garcia-Arencibia M, Rose C, Luo S, Underwood BR et al (2011) Complex inhibitory effects of nitric oxide on autophagy. Mol Cell 43: 1932
  • 77
    Tripathi DN, Chowdhury R, Trudel LJ, Tee AR, Slack RS, Walker CL, Wogan GN (2013) Reactive nitrogen species regulate autophagy through ATM-AMPK-TSC2-mediated suppression of mTORC1. Proc Natl Acad Sci U S A 110: E2950E2957
  • 78
    Ito C, Saito Y, Nozawa T, Fujii S, Sawa T, Inoue H, Matsunaga T, Khan S, Akashi S, Hashimoto R et al (2013) Endogenous nitrated nucleotide is a key mediator of autophagy and innate defense against bacteria. Mol Cell 52: 794804
  • 79
    Williams A, Sarkar S, Cuddon P, Ttofi EK, Saiki S, Siddiqi FH, Jahreiss L, Fleming A, Pask D, Goldsmith P et al (2008) Novel targets for Huntington's disease in an mTOR-independent autophagy pathway. Nat Chem Biol 4: 295305
  • 80
    Ganley IG, Wong PM, Gammoh N, Jiang X (2011) Distinct autophagosomal-lysosomal fusion mechanism revealed by thapsigargin-induced autophagy arrest. Mol Cell 42: 731743
  • 81
    East DA, Campanella M (2013) Ca2+ in quality control: an unresolved riddle critical to autophagy and mitophagy. Autophagy 9: 17101719
  • 82
    Kiviluoto S, Vervliet T, Ivanova H, Decuypere JP, De Smedt H, Missiaen L, Bultynck G, Parys JB (2013) Regulation of inositol 1,4,5-trisphosphate receptors during endoplasmic reticulum stress. Biochim Biophys Acta 1833: 16121624
  • 83
    Decuypere JP, Welkenhuyzen K, Luyten T, Ponsaerts R, Dewaele M, Molgó J, Agostinis P, Missiaen L, De Smedt H, Parys JB et al (2011) Ins(1,4,5)P3 receptor-mediated Ca2+ signaling and autophagy induction are interrelated. Autophagy 7: 14721489
  • 84
    Cárdenas C, Miller RA, Smith I, Bui T, Molgó J, Müller M, Vais H, Cheung KH, Yang J, Parker I et al (2010) Essential regulation of cell bioenergetics by constitutive InsP3 receptor Ca2+ transfer to mitochondria. Cell 142: 270283
  • 85
    Axe EL, Walker SA, Manifava M, Chandra P, Roderick HL, Habermann A, Griffiths G, Ktistakis NT (2008) Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J Cell Biol 182: 685701
  • 86
    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: 14331437
  • 87
    Yla-Anttila P, Vihinen H, Jokitalo E, Eskelinen EL (2009) 3D tomography reveals connections between the phagophore and endoplasmic reticulum. Autophagy 5: 11801185
  • 88
    Moreau K, Ravikumar B, Renna M, Puri C, Rubinsztein DC (2011) Autophagosome precursor maturation requires homotypic fusion. Cell 146: 303317
  • 89
    Nair U, Jotwani A, Geng J, Gammoh N, Richerson D, Yen WL, Griffith J, Nag S, Wang K, Moss T et al (2011) SNARE proteins are required for macroautophagy. Cell 146: 290302
  • 90
    Hailey DW, Rambold AS, Satpute-Krishnan P, Mitra K, Sougrat R, Kim PK, Lippincott-Schwartz J (2010) Mitochondria supply membranes for autophagosome biogenesis during starvation. Cell 141: 656667
  • 91
    van der Vaart A, Griffith J, Reggiori F (2010) Exit from the Golgi is required for the expansion of the autophagosomal phagophore in yeast Saccharomyces cerevisiae. Mol Biol Cell 21: 22702284
  • 92
    Ge L, Melville D, Zhang M, Schekman R (2013) The ER-Golgi intermediate compartment is a key membrane source for the LC3 lipidation step of autophagosome biogenesis. Elife 2: e00947
  • 93
    Hamasaki M, Furuta N, Matsuda A, Nezu A, Yamamoto A, Fujita N, Oomori H, Noda T, Haraguchi T, Hiraoka Y et al (2013) Autophagosomes form at ER-mitochondria contact sites. Nature 495: 389393
  • 94
    Graef M, Friedman JR, Graham C, Babu M, Nunnari J (2013) ER exit sites are physical and functional core autophagosome biogenesis components. Mol Biol Cell 24: 29182931
  • 95
    Puri C, Renna M, Bento CF, Moreau K, Rubinsztein DC (2013) Diverse autophagosome membrane sources coalesce in recycling endosomes. Cell 154: 12851299
  • 96
    Lamb CA, Yoshimori T, Tooze SA (2013) The autophagosome: origins unknown, biogenesis complex. Nat Rev Mol Cell Biol 14: 759774
  • 97
    Koyama-Honda I, Itakura E, Fujiwara TK, Mizushima N (2013) Temporal analysis of recruitment of mammalian ATG proteins to the autophagosome formation site. Autophagy 9: 14911499
  • 98
    Suzuki K, Kubota Y, Sekito T, Ohsumi Y (2007) Hierarchy of Atg proteins in pre-autophagosomal structure organization. Genes Cells 12: 209218
  • 99
    Kihara A, Noda T, Ishihara N, Ohsumi Y (2001) Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in autophagy and carboxypeptidase Y sorting in Saccharomyces cerevisiae. J Cell Biol 152: 519530
  • 100
    Cheng J, Fujita A, Yamamoto H, Tatematsu T, Kakuta S, Obara K, Ohsumi Y, Fujimoto T (2014) Yeast and mammalian autophagosomes exhibit distinct phosphatidylinositol 3-phosphate asymmetries. Nat Commun 5: 3207
  • 101
    Proikas-Cezanne T, Waddell S, Gaugel A, Frickey T, Lupas A, Nordheim A (2004) WIPI-1 alpha (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 23: 93149325
  • 102
    Polson HE, de Lartigue J, Rigden DJ, Reedijk M, Urbe S, Clague MJ, Tooze SA (2010) Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation. Autophagy 6: 506522
  • 103
    Simonsen A, Birkeland HC, Gillooly DJ, Mizushima N, Kuma A, Yoshimori T, Slagsvold T, Brech A, Stenmark H (2004) Alfy, a novel FYVE-domain-containing protein associated with protein granules and autophagic membranes. J Cell Sci 117: 42394251
  • 104
    Filimonenko M, Isakson P, Finley KD, Anderson M, Jeong H, Melia TJ, Bartlett BJ, Myers KM, Birkeland HC, Lamark T et al (2010) The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Mol Cell 38: 265279
  • 105
    Clausen TH, Lamark T, Isakson P, Finley K, Larsen KB, Brech A, Øvervatn A, Stenmark H, Bjørkøy G, Simonsen A et al (2010) p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy. Autophagy 6: 330344
  • 106
    Isakson P, Lystad AH, Breen K, Koster G, Stenmark H, Simonsen A (2013) TRAF6 mediates ubiquitination of KIF23/MKLP1 and is required for midbody ring degradation by selective autophagy. Autophagy 9: 19551964
  • 107
    Filimonenko M, Stuffers S, Raiborg C, Yamamoto A, Malerød L, Fisher EM, Isaacs A, Brech A, Stenmark H, Simonsen A (2007) Functional multivesicular bodies are required for autophagic clearance of protein aggregates associated with neurodegenerative disease. J Cell Biol 179: 485500
  • 108
    Isakson P, Holland P, Simonsen A (2013) The role of ALFY in selective autophagy. Cell Death Differ 20: 1220
  • 109
    Itakura E, Kishi C, Inoue K, Mizushima N (2008) Beclin 1 forms two distinct phosphatidylinositol 3-kinase complexes with mammalian Atg14 and UVRAG. Mol Biol Cell 19: 53605372
  • 110
    Fimia GM, Stoykova A, Romagnoli A, Giunta L, Di Bartolomeo S, Nardacci R, Corazzari M, Fuoco C, Ucar A, Schwartz P et al (2007) Ambra1 regulates autophagy and development of the nervous system. Nature 447: 11211125
  • 111
    Nazio F, Strappazzon F, Antonioli M, Bielli P, Cianfanelli V, Bordi M, Gretzmeier C, Dengjel J, Piacentini M, Fimia GM et al (2013) mTOR inhibits autophagy by controlling ULK1 ubiquitylation, self-association and function through AMBRA1 and TRAF6. Nat Cell Biol 15: 406416
  • 112
    Di Bartolomeo S, Corazzari M, Nazio F, Oliverio S, Lisi G, Antonioli M, Pagliarini V, Matteoni S, Fuoco C, Giunta L et al (2010) The dynamic interaction of AMBRA1 with the dynein motor complex regulates mammalian autophagy. J Cell Biol 191: 155168
  • 113
    Xia P, Wang S, Du Y, Zhao Z, Shi L, Sun L, Huang G, Ye B, Li C, Dai Z et al (2013) WASH inhibits autophagy through suppression of Beclin 1 ubiquitination. EMBO J 32: 26852696
  • 114
    Papinski D, Schuschnig M, Reiter W, Wilhelm L, Barnes CA, Maiolica A, Hansmann I, Pfaffenwimmer T, Kijanska M, Stoffel I et al (2014) Early steps in autophagy depend on direct phosphorylation of atg9 by the atg1 kinase. Mol Cell 53: 471483
  • 115
    Bejarano E, Yuste A, Patel B, Stout RF Jr, Spray DC, Cuervo AM (2014) Connexins modulate autophagosome biogenesis. Nat Cell Biol 16: 401414
  • 116
    Kaiser SE, Mao K, Taherbhoy AM, Yu S, Olszewski JL, Duda DM, Kurinov I, Deng A, Fenn TD, Klionsky DJ et al (2012) Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures. Nat Struct Mol Biol 19: 12421249
  • 117
    Mizushima N, Noda T, Ohsumi Y (1999) Apg16p is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway. EMBO J 18: 38883896
  • 118
    Kuma A, Mizushima N, Ishihara N, Ohsumi Y (2002) Formation of the approximately 350-kDa Apg12-Apg5.Apg16 multimeric complex, mediated by Apg16 oligomerization, is essential for autophagy in yeast. J Biol Chem 277: 1861918625
  • 119
    Mizushima N, Kuma A, Kobayashi Y, Yamamoto A, Matsubae M, Takao T, Natsume T, Ohsumi Y, Yoshimori T (2003) Mouse Apg16L, a novel WD-repeat protein, targets to the autophagic isolation membrane with the Apg12-Apg5 conjugate. J Cell Sci 116: 16791688
  • 120
    Shpilka T, Weidberg H, Pietrokovski S, Elazar Z (2011) Atg8: an autophagy-related ubiquitin-like protein family. Genome Biol 12: 226
  • 121
    Dooley HC, Razi M, Polson HE, Girardin SE, Wilson MI, Tooze SA (2014) WIPI2 links LC3 conjugation with PI3P, autophagosome formation, and pathogen clearance by recruiting Atg12–5-16L1. Mol Cell, DOI 10.1016/j.molcel.2014.05.021
  • 122
    Romanov J, Walczak M, Ibiricu I, Schuchner S, Ogris E, Kraft C, Martens S (2012) Mechanism and functions of membrane binding by the Atg5-Atg12/Atg16 complex during autophagosome formation. EMBO J 31: 43044317
  • 123
    Nath S, Dancourt J, Shteyn V, Puente G, Fong WM, Nag S, Bewersdorf J, Yamamoto A, Antonny B, Melia TJ (2014) Lipidation of the LC3/GABARAP family of autophagy proteins relies on a membrane-curvature-sensing domain in Atg3. Nat Cell Biol 16: 415424
  • 124
    Kaufmann A, Beier V, Franquelim HG, Wollert T (2014) Molecular mechanism of autophagic membrane-scaffold assembly and disassembly. Cell 156: 469481
  • 125
    Knævelsrud H, Søreng K, Raiborg C, Håberg K, Rasmuson F, Brech A, Liestøl K, Rusten TE, Stenmark H, Neufeld TP et al (2013) Membrane remodeling by the PX-BAR protein SNX18 promotes autophagosome formation. J Cell Biol 202: 331349
  • 126
    Longatti A, Lamb CA, Razi M, Yoshimura S, Barr FA, Tooze SA (2012) TBC1D14 regulates autophagosome formation via Rab11- and ULK1-positive recycling endosomes. J Cell Biol 197: 659675
  • 127
    Nishimura T, Kaizuka T, Cadwell K, Sahani MH, Saitoh T, Akira S, Virgin HW, Mizushima N (2013) FIP200 regulates targeting of Atg16L1 to the isolation membrane. EMBO Rep 14: 284291
  • 128
    Yamamoto H, Kakuta S, Watanabe TM, Kitamura A, Sekito T, Kondo-Kakuta C, Ichikawa R, Kinjo M, Ohsumi Y (2012) Atg9 vesicles are an important membrane source during early steps of autophagosome formation. J Cell Biol 198: 219233
  • 129
    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: 10051022
  • 130
    Orsi A, Razi M, Dooley HC, Robinson D, Weston AE, Collinson LM, Tooze SA (2012) Dynamic and transient interactions of Atg9 with autophagosomes, but not membrane integration, are required for autophagy. Mol Biol Cell 23: 18601873
  • 131
    Shirahama-Noda K, Kira S, Yoshimori T, Noda T (2013) TRAPPIII is responsible for vesicular transport from early endosomes to Golgi, facilitating Atg9 cycling in autophagy. J Cell Sci 126: 49634973
  • 132
    Young AR, Chan EY, Hu XW, Kochl R, Crawshaw SG, High S, Hailey DW, Lippincott-Schwartz J, Tooze SA (2006) Starvation and ULK1-dependent cycling of mammalian Atg9 between the TGN and endosomes. J Cell Sci 119: 38883900
  • 133
    Yang A, Li Y, Pantoom S, Triola G, Wu YW (2013) Semisynthetic lipidated LC3 protein mediates membrane fusion. ChemBioChem 14: 12961300
  • 134
    Nakatogawa H, Ichimura Y, Ohsumi Y (2007) Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusion. Cell 130: 165178
  • 135
    Xie Z, Nair U, Klionsky DJ (2008) Atg8 controls phagophore expansion during autophagosome formation. Mol Biol Cell 19: 32903298
  • 136
    Weidberg H, Shvets E, Shpilka T, Shimron F, Shinder V, Elazar Z (2010) LC3 and GATE-16/GABARAP subfamilies are both essential yet act differently in autophagosome biogenesis. EMBO J 29: 17921802
  • 137
    Weidberg H, Shpilka T, Shvets E, Abada A, Shimron F, Elazar Z (2011) LC3 and GATE-16 N termini mediate membrane fusion processes required for autophagosome biogenesis. Dev Cell 20: 444454
  • 138
    Manil-Segalen M, Lefebvre C, Jenzer C, Trichet M, Boulogne C, Satiat-Jeunemaitre B, Legouis R (2014) The C. elegans LC3 acts downstream of GABARAP to degrade autophagosomes by interacting with the HOPS subunit VPS39. Dev Cell 28: 4355
  • 139
    Nakatogawa H, Ishii J, Asai E, Ohsumi Y (2012) Atg4 recycles inappropriately lipidated Atg8 to promote autophagosome biogenesis. Autophagy 8: 177186
  • 140
    Betin VM, Singleton BK, Parsons SF, Anstee DJ, Lane JD (2013) Autophagy facilitates organelle clearance during differentiation of human erythroblasts: evidence for a role for ATG4 paralogs during autophagosome maturation. Autophagy 9: 881893
  • 141
    Ma J, Becker C, Reyes C, Underhill DM (2014) Cutting edge: FYCO1 recruitment to dectin-1 phagosomes is accelerated by light chain 3 protein and regulates phagosome maturation and reactive oxygen production. J Immunol 192: 13561360
  • 142
    Ao X, Zou L, Wu Y (2014) Regulation of autophagy by the Rab GTPase network. Cell Death Differ 21: 348358
  • 143
    Lu Y, Zhang Z, Sun D, Sweeney ST, Gao FB (2013) Syntaxin 13, a genetic modifier of mutant CHMP2B in frontotemporal dementia, is required for autophagosome maturation. Mol Cell 52: 264271
  • 144
    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: 12561269
  • 145
    Jiang P, Nishimura T, Sakamaki Y, Itakura E, Hatta T, Natsume T, Mizushima N (2014) The HOPS complex mediates autophagosome-lysosome fusion through interaction with syntaxin 17. Mol Biol Cell 25: 13271337
  • 146
    Takáts S, Pircs K, Nagy P, Varga Á, Kárpáti M, Hegedus K, Kramer H, Kovács AL, Sass M, Juhász G (2014) Interaction of the HOPS complex with Syntaxin 17 mediates autophagosome clearance in Drosophila. Mol Biol Cell 25: 13381354
  • 147
    Chen D, Fan W, Lu Y, Ding X, Chen S, Zhong Q (2012) A mammalian autophagosome maturation mechanism mediated by TECPR1 and the Atg12-Atg5 conjugate. Mol Cell 45: 629641
  • 148
    Ogawa M, Yoshikawa Y, Kobayashi T, Mimuro H, Fukumatsu M, Kiga K, Piao Z, Ashida H, Yoshida M, Kakuta S et al (2011) A Tecpr1-dependent selective autophagy pathway targets bacterial pathogens. Cell Host Microbe 9: 376389