Molecular definitions of autophagy and related processes

EMBO Journal

Volumn 36, Issue 13, 2017, Pages 1811-1836

  Galluzzi, Lorenzo ^a,b   Baehrecke, Eric H ^c   Ballabio, Andrea ^d,e,f,g   Boya, Patricia ^h   Bravo San Pedro, José Manuel ^b,i,j,k,l   Cecconi, Francesco ^m,n,o   Choi, Augustine M ^a   Chu, Charleen T ^p   Codogno, Patrice ^b,q,r   Colombo, Maria Isabel ^s,t   Cuervo, Ana Maria ^u   Debnath, Jayanta ^v   Deretic, Vojo ^w   Dikic, Ivan ^x,y   Eskelinen, Eeva Liisa ^z   Fimia, Gian Maria ^aa,ab   Fulda, Simone ^x,ac   Gewirtz, David A ^ad,ae   Green, Douglas R ^af   Hansen, Malene ^ag   Harper, J Wade ^ah   Jäättelä, Marja ⁿ   Johansen, Terje ^ai   Juhasz, Gabor ^aj,ak   Kimmelman, Alec C ^al   Kraft, Claudine ^am   Ktistakis, Nicholas T ^an   Kumar, Sharad ^ao   Levine, Beth ^ap,aq   Lopez Otin, Carlos ^ar,as   Madeo, Frank ^at,au   Martens, Sascha ^am   Martinez, Jennifer ^av   Melendez, Alicia ^aw,ax   Mizushima, Noboru ^ay   Münz, Christian ^az   Murphy, Leon O ^ba   Penninger, Josef M ^bb   Piacentini, Mauro ^m,aa   Reggiori, Fulvio ^bc   Rubinsztein, David C ^bd   Ryan, Kevin M ^be   Santambrogio, Laura ^u   Scorrano, Luca ^bf,bg   Simon, Anna Katharina ^bh,bi   Simon, Hans Uwe ^bj   Simonsen, Anne ^bk   Tavernarakis, Nektarios ^bl,bm   Tooze, Sharon A ^bn   Yoshimori, Tamotsu ^bo   Yuan, Junying ^ah   Yue, Zhenyu ^bp   Zhong, Qing ^ap   Kroemer, Guido ^{b,i,j,k,l,bq,br}   more..

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b UNIVERSITÉ PARIS DESCARTES   (France)

^c UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^d TELETHON INSTITUTE OF GENETICS AND MEDICINE TIGEM   (Italy)

^e UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^f BAYLOR COLLEGE OF MEDICINE   (United States)

^g TEXAS CHILDREN S HOSPITAL   (United States)

^h CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

ⁱ SORBONNE UNIVERSITÉ   (France)

^j CENTRE DE RECHERCHE DES CORDELIERS   (France)

^k INSERM   (France)

^l INSTITUT GUSTAVE ROUSSY   (France)

^m UNIVERSITY OF ROME TOR VERGATA   (Italy)

ⁿ DANISH CANCER SOCIETY RESEARCH CENTER   (Denmark)

^o BAMBINO GESÙ CHILDREN S HOSPITAL   (Italy)

^p UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^q INSTITUT NECKER ENFANTS MALADES   (France)

^r CNRS   (France)

^s Instituto de Histologia y Embriologia   (Argentina)

^t FACULTAD DE CIENCIAS MÉDICAS   (Argentina)

^u ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^v UNIVERSITY OF CALIFORNIA   (United States)

^w UNIVERSITY OF NEW MEXICO HEALTH SCIENCES CENTER   (United States)

^x GOETHE UNIVERSITY   (Germany)

^y UNIVERSITY OF SPLIT   (Croatia)

^z UNIVERSITY OF HELSINKI   (Finland)

^aa NATIONAL INSTITUTE FOR INFECTIOUS DISEASES L SPALLANZANI   (Italy)

^ab UNIVERSITY OF SALENTO   (Italy)

^ac GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^ad VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^ae VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^af ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^ag BURNHAM INSTITUTE   (United States)

^ah HARVARD MEDICAL SCHOOL   (United States)

^ai UNIVERSITY OF TROMSØ   (Norway)

^aj EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^ak INSTITUTE OF BIOCHEMISTRY   (Hungary)

^al NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^am UNIVERSITY OF VIENNA   (Austria)

^an BABRAHAM INSTITUTE   (United Kingdom)

^ao UNIVERSITY OF SOUTH AUSTRALIA   (Australia)

^ap UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^aq HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^ar UNIVERSIDAD DE OVIEDO   (Spain)

^as Centro de Investigación en Red de Cáncer   (Spain)

^at UNIVERSITY OF GRAZ   (Austria)

^au BIOTECHMED GRAZ   (Austria)

^av NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^aw CITY UNIVERSITY OF NEW YORK   (United States)

^ax CITY UNIVERSITY OF NEW YORK   (United States)

^ay UNIVERSITY OF TOKYO   (Japan)

^az UNIVERSITY OF ZURICH   (Switzerland)

^ba NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

^bb ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

^bc UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

^bd UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^be BEATSON INSTITUTE FOR CANCER RESEARCH   (United Kingdom)

^bf UNIVERSITY OF PADOVA   (Italy)

^bg VENETIAN INSTITUTE OF MOLECULAR MEDICINE   (Italy)

^bh UNIVERSITY OF OXFORD   (United Kingdom)

^bi UNIVERSITY OF OXFORD   (United Kingdom)

^bj UNIVERSITY OF BERN   (Switzerland)

^bk UNIVERSITY OF OSLO   (Norway)

^bl INSTITUTE OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY   (Greece)

^bm UNIVERSITY OF CRETE   (Greece)

^bn THE FRANCIS CRICK INSTITUTE   (United Kingdom)

^bo OSAKA UNIVERSITY   (Japan)

^bp MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^bq KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^br HÔPITAL EUROPÉEN GEORGES POMPIDOU   (France)

more..

Author keywords

chaperone mediated autophagy; LC3 associated phagocytosis; microautophagy; mitophagy; xenophagy

Indexed keywords

AGGREPHAGY; AMPHISOME; AUTOLYSOSOME; AUTOPHAGOSOME; AUTOPHAGY; CELL AGING, CELL DEGENERATION AND CELL SURVIVAL; CELL DEATH; CELL VACUOLE; CHAPERONE-MEDIATED AUTOPHAGY; CRINOPHAGY; CYTOPLASM; HUMAN; LC3 ASSOCIATED PHAGOCYTOSIS; LIPOPHAGOCYTOSIS; LYSOPHAGY; LYSOSOME; MACROAUTOPHAGY; MEMBRANE; MICROAUTOPHAGY; MITOPHAGY; NONHUMAN; NUCLEOPHAGOCYTOSIS; PEXOPHAGY; PHAGOCYTOSIS; PHAGOPHORE; PRIORITY JOURNAL; PROTEAPHAGY; RETICULOPHAGY; REVIEW; RIBOPHAGY; XENOPHAGY; ANIMAL; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; GENE REGULATORY NETWORK; MOUSE; NOMENCLATURE; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE;

ANIMALS; AUTOPHAGY; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; GENE REGULATORY NETWORKS; MICE; SACCHAROMYCES CEREVISIAE; TERMINOLOGY AS TOPIC;

EID: 85020297927     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.15252/embj.201796697     Document Type: Review

References (376)

1. Agarraberes FA, Terlecky SR, Dice JF (1997) An intralysosomal hsp70 is required for a selective pathway of lysosomal protein degradation. J Cell Biol 137: 825–834
2. Al Rawi S, Louvet-Vallee S, Djeddi A, Sachse M, Culetto E, Hajjar C, Boyd L, Legouis R, Galy V (2011) Postfertilization autophagy of sperm organelles prevents paternal mitochondrial DNA transmission. Science 334: 1144–1147
3. Amaravadi R, Kimmelman AC, White E (2016) Recent insights into the function of autophagy in cancer. Genes Dev 30: 1913–1930
4. Amaya C, Fader CM, Colombo MI (2015) Autophagy and proteins involved in vesicular trafficking. FEBS Lett 589: 3343–3353
5. Antonioli M, Di Rienzo M, Piacentini M, Fimia GM (2016) Emerging mechanisms in initiating and terminating autophagy. Trends Biochem Sci 42: 28–41
6. Arias E, Koga H, Diaz A, Mocholi E, Patel B, Cuervo AM (2015) Lysosomal mTORC2/PHLPP1/Akt regulate chaperone-mediated autophagy. Mol Cell 59: 270–284
7. Arndt V, Dick N, Tawo R, Dreiseidler M, Wenzel D, Hesse M, Furst DO, Saftig P, Saint R, Fleischmann BK, Hoch M, Hohfeld J (2010) Chaperone-assisted selective autophagy is essential for muscle maintenance. Curr Biol 20: 143–148
8. 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: 685–701
9. Bader CA, Shandala T, Ng YS, Johnson IR, Brooks DA (2015) Atg9 is required for intraluminal vesicles in amphisomes and autolysosomes. Biol Open 4: 1345–1355
10. Bakowski MA, Desjardins CA, Smelkinson MG, Dunbar TL, Lopez-Moyado IF, Rifkin SA, Cuomo CA, Troemel ER (2014) Ubiquitin-mediated response to microsporidia and virus infection in Caenorhabditis elegans. PLoS Pathog 10: e1004200
11. Bandyopadhyay U, Kaushik S, Varticovski L, Cuervo AM (2008) The chaperone-mediated autophagy receptor organizes in dynamic protein complexes at the lysosomal membrane. Mol Cell Biol 28: 5747–5763
12. Bandyopadhyay U, Sridhar S, Kaushik S, Kiffin R, Cuervo AM (2010) Identification of regulators of chaperone-mediated autophagy. Mol Cell 39: 535–547
13. Berry DL, Baehrecke EH (2007) Growth arrest and autophagy are required for salivary gland cell degradation in Drosophila. Cell 131: 1137–1148
14. Bertipaglia C, Schneider S, Jakobi AJ, Tarafder AK, Bykov YS, Picco A, Kukulski W, Kosinski J, Hagen WJ, Ravichandran AC, Wilmanns M, Kaksonen M, Briggs JA, Sachse C (2016) Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle. EMBO Rep 17: 1044–1060
15. Bhattacharyya S, Yu H, Mim C, Matouschek A (2014) Regulated protein turnover: snapshots of the proteasome in action. Nat Rev Mol Cell Biol 15: 122–133
16. Birgisdottir AB, Lamark T, Johansen T (2013) The LIR motif - crucial for selective autophagy. J Cell Sci 126: 3237–3247
17. Bjorkoy G, Lamark T, Brech A, Outzen H, Perander M, Overvatn A, Stenmark H, Johansen T (2005) p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death. J Cell Biol 171: 603–614
18. Boya P, Gonzalez-Polo RA, Casares N, Perfettini JL, Dessen P, Larochette N, Metivier D, Meley D, Souquere S, Yoshimori T, Pierron G, Codogno P, Kroemer G (2005) Inhibition of macroautophagy triggers apoptosis. Mol Cell Biol 25: 1025–1040
19. Boya P, Reggiori F, Codogno P (2013) Emerging regulation and functions of autophagy. Nat Cell Biol 15: 713–720
20. Buchan JR, Kolaitis RM, Taylor JP, Parker R (2013) Eukaryotic stress granules are cleared by autophagy and Cdc48/VCP function. Cell 153: 1461–1474
21. Burnett SF, Farre JC, Nazarko TY, Subramani S (2015) Peroxisomal Pex3 activates selective autophagy of peroxisomes via interaction with the pexophagy receptor Atg30. J Biol Chem 290: 8623–8631
22. Chandra P, Ghanwat S, Matta SK, Yadav SS, Mehta M, Siddiqui Z, Singh A, Kumar D (2015) Mycobacterium tuberculosis inhibits RAB7 recruitment to selectively modulate autophagy flux in macrophages. Sci Rep 5: 16320
23. Chang TK, Shravage BV, Hayes SD, Powers CM, Simin RT, Wade Harper J, Baehrecke EH (2013) Uba1 functions in Atg7- and Atg3-independent autophagy. Nat Cell Biol 15: 1067–1078
24. Chanoca A, Kovinich N, Burkel B, Stecha S, Bohorquez-Restrepo A, Ueda T, Eliceiri KW, Grotewold E, Otegui MS (2015) Anthocyanin vacuolar inclusions form by a microautophagy mechanism. Plant Cell 27: 2545–2559
25. Chauhan S, Mandell MA, Deretic V (2015) IRGM governs the core autophagy machinery to conduct antimicrobial defense. Mol Cell 58: 507–521
26. Chauhan S, Kumar S, Jain A, Ponpuak M, Mudd MH, Kimura T, Choi SW, Peters R, Mandell M, Bruun JA, Johansen T, Deretic V (2016) TRIMs and galectins globally cooperate and TRIM16 and galectin-3 co-direct autophagy in endomembrane damage homeostasis. Dev Cell 39: 13–27
27. 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: 629–641
28. Cherra SJ III, Dagda RK, Chu CT (2010a) Review: autophagy and neurodegeneration: survival at a cost? Neuropathol Appl Neurobiol 36: 125–132
29. Cherra SJ III, Kulich SM, Uechi G, Balasubramani M, Mountzouris J, Day BW, Chu CT (2010b) Regulation of the autophagy protein LC3 by phosphorylation. J Cell Biol 190: 533–539
30. Chiang HL, Terlecky SR, Plant CP, Dice JF (1989) A role for a 70-kilodalton heat shock protein in lysosomal degradation of intracellular proteins. Science 246: 382–385
31. Choi AM, Ryter SW, Levine B (2013) Autophagy in human health and disease. N Engl J Med 368: 651–662
32. Choi J, Park S, Biering SB, Selleck E, Liu CY, Zhang X, Fujita N, Saitoh T, Akira S, Yoshimori T, Sibley LD, Hwang S, Virgin HW (2014) The parasitophorous vacuole membrane of Toxoplasma gondii is targeted for disruption by ubiquitin-like conjugation systems of autophagy. Immunity 40: 924–935
33. Chourasia AH, Tracy K, Frankenberger C, Boland ML, Sharifi MN, Drake LE, Sachleben JR, Asara JM, Locasale JW, Karczmar GS, Macleod KF (2015) Mitophagy defects arising from BNip3 loss promote mammary tumor progression to metastasis. EMBO Rep 16: 1145–1163
34. Chu CT (2011) Autophagy in different flavors: dysregulated protein degradation in neurological diseases. Neurobiol Dis 43: 1–3
35. Chu CT, Ji J, Dagda RK, Jiang JF, Tyurina YY, Kapralov AA, Tyurin VA, Yanamala N, Shrivastava IH, Mohammadyani D, Qiang Wang KZ, Zhu J, Klein-Seetharaman J, Balasubramanian K, Amoscato AA, Borisenko G, Huang Z, Gusdon AM, Cheikhi A, Steer EK et al (2013) Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells. Nat Cell Biol 15: 1197–1205
36. Clark IE, Dodson MW, Jiang C, Cao JH, Huh JR, Seol JH, Yoo SJ, Hay BA, Guo M (2006) Drosophila pink1 is required for mitochondrial function and interacts genetically with parkin. Nature 441: 1162–1166
37. Codogno P, Mehrpour M, Proikas-Cezanne T (2012) Canonical and non-canonical autophagy: variations on a common theme of self-eating? Nat Rev Mol Cell Biol 13: 7–12
38. Cohen-Kaplan V, Livneh I, Avni N, Fabre B, Ziv T, Kwon YT, Ciechanover A (2016) p62- and ubiquitin-dependent stress-induced autophagy of the mammalian 26S proteasome. Proc Natl Acad Sci USA 113: E7490–E7499
39. Cooney R, Baker J, Brain O, Danis B, Pichulik T, Allan P, Ferguson DJ, Campbell BJ, Jewell D, Simmons A (2010) NOD2 stimulation induces autophagy in dendritic cells influencing bacterial handling and antigen presentation. Nat Med 16: 90–97
40. Cuervo AM, Palmer A, Rivett AJ, Knecht E (1995) Degradation of proteasomes by lysosomes in rat liver. Eur J Biochem 227: 792–800
41. Cuervo AM, Dice JF (1996) A receptor for the selective uptake and degradation of proteins by lysosomes. Science 273: 501–503
42. Cuervo AM, Dice JF (2000) Age-related decline in chaperone-mediated autophagy. J Biol Chem 275: 31505–31513
43. Cuervo AM, Wong E (2014) Chaperone-mediated autophagy: roles in disease and aging. Cell Res 24: 92–104
44. D'Eletto M, Farrace MG, Rossin F, Strappazzon F, Giacomo GD, Cecconi F, Melino G, Sepe S, Moreno S, Fimia GM, Falasca L, Nardacci R, Piacentini M (2012) Type 2 transglutaminase is involved in the autophagy-dependent clearance of ubiquitinated proteins. Cell Death Differ 19: 1228–1238
45. Demontis F, Perrimon N (2010) FOXO/4E-BP signaling in Drosophila muscles regulates organism-wide proteostasis during aging. Cell 143: 813–825
46. Denton D, Shravage B, Simin R, Mills K, Berry DL, Baehrecke EH, Kumar S (2009) Autophagy, not apoptosis, is essential for midgut cell death in Drosophila. Curr Biol 19: 1741–1746
47. Denton D, Aung-Htut MT, Lorensuhewa N, Nicolson S, Zhu W, Mills K, Cakouros D, Bergmann A, Kumar S (2013) UTX coordinates steroid hormone-mediated autophagy and cell death. Nat Commun 4: 2916
48. Denton D, Xu T, Kumar S (2015) Autophagy as a pro-death pathway. Immunol Cell Biol 93: 35–42
49. Deosaran E, Larsen KB, Hua R, Sargent G, Wang Y, Kim S, Lamark T, Jauregui M, Law K, Lippincott-Schwartz J, Brech A, Johansen T, Kim PK (2013) NBR1 acts as an autophagy receptor for peroxisomes. J Cell Sci 126: 939–952
50. Deretic V, Saitoh T, Akira S (2013) Autophagy in infection, inflammation and immunity. Nat Rev Immunol 13: 722–737
51. Diao J, Liu R, Rong Y, Zhao M, Zhang J, Lai Y, Zhou Q, Wilz LM, Li J, Vivona S, Pfuetzner RA, Brunger AT, Zhong Q (2015) ATG14 promotes membrane tethering and fusion of autophagosomes to endolysosomes. Nature 520: 563–566
52. Dice JF (1990) Peptide sequences that target cytosolic proteins for lysosomal proteolysis. Trends Biochem Sci 15: 305–309
53. 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 55: 238–252
54. Dou Z, Xu C, Donahue G, Shimi T, Pan JA, Zhu J, Ivanov A, Capell BC, Drake AM, Shah PP, Catanzaro JM, Ricketts MD, Lamark T, Adam SA, Marmorstein R, Zong WX, Johansen T, Goldman RD, Adams PD, Berger SL (2015) Autophagy mediates degradation of nuclear lamina. Nature 527: 105–109
55. Dowdle WE, Nyfeler B, Nagel J, Elling RA, Liu S, Triantafellow E, Menon S, Wang Z, Honda A, Pardee G, Cantwell J, Luu C, Cornella-Taracido I, Harrington E, Fekkes P, Lei H, Fang Q, Digan ME, Burdick D, Powers AF et al (2014) Selective VPS34 inhibitor blocks autophagy and uncovers a role for NCOA4 in ferritin degradation and iron homeostasis in vivo. Nat Cell Biol 16: 1069–1079
56. Dupont N, Jiang S, Pilli M, Ornatowski W, Bhattacharya D, Deretic V (2011) Autophagy-based unconventional secretory pathway for extracellular delivery of IL-1beta. EMBO J 30: 4701–4711
57. Egan DF, Shackelford DB, Mihaylova MM, Gelino S, Kohnz RA, Mair W, Vasquez DS, Joshi A, Gwinn DM, Taylor R, Asara JM, Fitzpatrick J, Dillin A, Viollet B, Kundu M, Hansen M, Shaw RJ (2011) Phosphorylation of ULK1 (hATG1) by AMP-activated protein kinase connects energy sensing to mitophagy. Science 331: 456–461
58. Eng CH, Wang Z, Tkach D, Toral-Barza L, Ugwonali S, Liu S, Fitzgerald SL, George E, Frias E, Cochran N, De Jesus R, McAllister G, Hoffman GR, Bray K, Lemon L, Lucas J, Fantin VR, Abraham RT, Murphy LO, Nyfeler B (2016) Macroautophagy is dispensable for growth of KRAS mutant tumors and chloroquine efficacy. Proc Natl Acad Sci USA 113: 182–187
59. Eskelinen EL, Cuervo AM, Taylor MR, Nishino I, Blum JS, Dice JF, Sandoval IV, Lippincott-Schwartz J, August JT, Saftig P (2005) Unifying nomenclature for the isoforms of the lysosomal membrane protein LAMP-2. Traffic 6: 1058–1061
60. Eskelinen EL, Reggiori F, Baba M, Kovacs AL, Seglen PO (2011) Seeing is believing: the impact of electron microscopy on autophagy research. Autophagy 7: 935–956
61. Fader CM, Sanchez DG, Mestre MB, Colombo MI (2009) TI-VAMP/VAMP7 and VAMP3/cellubrevin: two v-SNARE proteins involved in specific steps of the autophagy/multivesicular body pathways. Biochim Biophys Acta 1793: 1901–1916
62. Fader CM, Salassa BN, Grosso RA, Vergara AN, Colombo MI (2016) Hemin induces mitophagy in a leukemic erythroblast cell line. Biol Cell 108: 77–95
63. Fan W, Nassiri A, Zhong Q (2011) Autophagosome targeting and membrane curvature sensing by Barkor/Atg14(L). Proc Natl Acad Sci USA 108: 7769–7774
64. Farre JC, Subramani S (2004) Peroxisome turnover by micropexophagy: an autophagy-related process. Trends Cell Biol 14: 515–523
65. Farre JC, Manjithaya R, Mathewson RD, Subramani S (2008) PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev Cell 14: 365–376
66. Farre JC, Subramani S (2016) Mechanistic insights into selective autophagy pathways: lessons from yeast. Nat Rev Mol Cell Biol 17: 537–552
67. Filimonenko M, Isakson P, Finley KD, Anderson M, Jeong H, Melia TJ, Bartlett BJ, Myers KM, Birkeland HC, Lamark T, Krainc D, Brech A, Stenmark H, Simonsen A, Yamamoto A (2010) The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Mol Cell 38: 265–279
68. Fimia GM, Stoykova A, Romagnoli A, Giunta L, Di Bartolomeo S, Nardacci R, Corazzari M, Fuoco C, Ucar A, Schwartz P, Gruss P, Piacentini M, Chowdhury K, Cecconi F (2007) Ambra1 regulates autophagy and development of the nervous system. Nature 447: 1121–1125
69. Florey O, Kim SE, Sandoval CP, Haynes CM, Overholtzer M (2011) Autophagy machinery mediates macroendocytic processing and entotic cell death by targeting single membranes. Nat Cell Biol 13: 1335–1343
70. Folick A, Oakley HD, Yu Y, Armstrong EH, Kumari M, Sanor L, Moore DD, Ortlund EA, Zechner R, Wang MC (2015) Aging. Lysosomal signaling molecules regulate longevity in Caenorhabditis elegans. Science 347: 83–86
71. Foot N, Henshall T, Kumar S (2017) Ubiquitination and the regulation of membrane proteins. Physiol Rev 97: 253–281
72. Fracchiolla D, Sawa-Makarska J, Zens B, Ruiter A, Zaffagnini G, Brezovich A, Romanov J, Runggatscher K, Kraft C, Zagrovic B, Martens S (2016) Mechanism of cargo-directed Atg8 conjugation during selective autophagy. Elife 5: e18544
73. Fumagalli F, Noack J, Bergmann TJ, Cebollero E, Pisoni GB, Fasana E, Fregno I, Galli C, Loi M, Solda T, D'Antuono R, Raimondi A, Jung M, Melnyk A, Schorr S, Schreiber A, Simonelli L, Varani L, Wilson-Zbinden C, Zerbe O et al (2016) Translocon component Sec62 acts in endoplasmic reticulum turnover during stress recovery. Nat Cell Biol 18: 1173–1184
74. Galluzzi L, Vitale I, Abrams JM, Alnemri ES, Baehrecke EH, Blagosklonny MV, Dawson TM, Dawson VL, El-Deiry WS, Fulda S, Gottlieb E, Green DR, Hengartner MO, Kepp O, Knight RA, Kumar S, Lipton SA, Lu X, Madeo F, Malorni W et al (2012) Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012. Cell Death Differ 19: 107–120
75. Galluzzi L, Pietrocola F, Levine B, Kroemer G (2014) Metabolic control of autophagy. Cell 159: 1263–1276
76. Galluzzi L, Bravo-San Pedro JM, Vitale I, Aaronson SA, Abrams JM, Adam D, Alnemri ES, Altucci L, Andrews D, Annicchiarico-Petruzzelli M, Baehrecke EH, Bazan NG, Bertrand MJ, Bianchi K, Blagosklonny MV, Blomgren K, Borner C, Bredesen DE, Brenner C, Campanella M et al (2015a) Essential versus accessory aspects of cell death: recommendations of the NCCD 2015. Cell Death Differ 22: 58–73
77. Galluzzi L, Pietrocola F, Bravo-San Pedro JM, Amaravadi RK, Baehrecke EH, Cecconi F, Codogno P, Debnath J, Gewirtz DA, Karantza V, Kimmelman A, Kumar S, Levine B, Maiuri MC, Martin SJ, Penninger J, Piacentini M, Rubinsztein DC, Simon HU, Simonsen A et al (2015b) Autophagy in malignant transformation and cancer progression. EMBO J 34: 856–880
78. Galluzzi L, Bravo-San Pedro JM, Blomgren K, Kroemer G (2016) Autophagy in acute brain injury. Nat Rev Neurosci 17: 467–484
79. Galluzzi L, Bravo-San Pedro JM, Demaria S, Formenti SC, Kroemer G (2017a) Activating autophagy to potentiate immunogenic chemotherapy and radiation therapy. Nat Rev Clin Oncol 14: 247–258
80. Galluzzi L, Bravo-San Pedro JM, Levine B, Green DR, Kroemer G (2017b) Pharmacological modulation of autophagy: therapeutic potential and persisting obstacles. Nat Rev Drug Discov https://doi.org/10.1038/nrd.2017.22.
81. Gan B, Peng X, Nagy T, Alcaraz A, Gu H, Guan JL (2006) Role of FIP200 in cardiac and liver development and its regulation of TNFalpha and TSC-mTOR signaling pathways. J Cell Biol 175: 121–133
82. Gannage M, Dormann D, Albrecht R, Dengjel J, Torossi T, Ramer PC, Lee M, Strowig T, Arrey F, Conenello G, Pypaert M, Andersen J, Garcia-Sastre A, Munz C (2009) Matrix protein 2 of influenza A virus blocks autophagosome fusion with lysosomes. Cell Host Microbe 6: 367–380
83. Geisler S, Holmstrom KM, Skujat D, Fiesel FC, Rothfuss OC, Kahle PJ, Springer W (2010) PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1. Nat Cell Biol 12: 119–131
84. Gerstenmaier L, Pilla R, Herrmann L, Herrmann H, Prado M, Villafano GJ, Kolonko M, Reimer R, Soldati T, King JS, Hagedorn M (2015) The autophagic machinery ensures nonlytic transmission of mycobacteria. Proc Natl Acad Sci USA 112: E687–E692
85. Gomes LC, Di Benedetto G, Scorrano L (2011a) During autophagy mitochondria elongate, are spared from degradation and sustain cell viability. Nat Cell Biol 13: 589–598
86. Gomes LC, Di Benedetto G, Scorrano L (2011b) Essential amino acids and glutamine regulate induction of mitochondrial elongation during autophagy. Cell Cycle 10: 2635–2639
87. Gomez-Sanchez JA, Carty L, Iruarrizaga-Lejarreta M, Palomo-Irigoyen M, Varela-Rey M, Griffith M, Hantke J, Macias-Camara N, Azkargorta M, Aurrekoetxea I, De Juan VG, Jefferies HB, Aspichueta P, Elortza F, Aransay AM, Martinez-Chantar ML, Baas F, Mato JM, Mirsky R, Woodhoo A et al (2015) Schwann cell autophagy, myelinophagy, initiates myelin clearance from injured nerves. J Cell Biol 210: 153–168
88. Gong L, Cullinane M, Treerat P, Ramm G, Prescott M, Adler B, Boyce JD, Devenish RJ (2011) The Burkholderia pseudomallei type III secretion system and BopA are required for evasion of LC3-associated phagocytosis. PLoS ONE 6: e17852
89. Gonzalez-Polo RA, Boya P, Pauleau AL, Jalil A, Larochette N, Souquere S, Eskelinen EL, Pierron G, Saftig P, Kroemer G (2005) The apoptosis/autophagy paradox: autophagic vacuolization before apoptotic death. J Cell Sci 118: 3091–3102
90. Gordon PB, Seglen PO (1988) Prelysosomal convergence of autophagic and endocytic pathways. Biochem Biophys Res Commun 151: 40–47
91. Grasso D, Ropolo A, Lo Re A, Boggio V, Molejon MI, Iovanna JL, Gonzalez CD, Urrutia R, Vaccaro MI (2011) Zymophagy, a novel selective autophagy pathway mediated by VMP1-USP9x-p62, prevents pancreatic cell death. J Biol Chem 286: 8308–8324
92. Green DR, Levine B (2014) To be or not to be? How selective autophagy and cell death govern cell fate. Cell 157: 65–75
93. Griffiths RE, Kupzig S, Cogan N, Mankelow TJ, Betin VM, Trakarnsanga K, Massey EJ, Lane JD, Parsons SF, Anstee DJ (2012) Maturing reticulocytes internalize plasma membrane in glycophorin A-containing vesicles that fuse with autophagosomes before exocytosis. Blood 119: 6296–6306
94. Gutierrez MG, Munafo DB, Beron W, Colombo MI (2004) Rab7 is required for the normal progression of the autophagic pathway in mammalian cells. J Cell Sci 117: 2687–2697
95. Hara T, Nakamura K, Matsui M, Yamamoto A, Nakahara Y, Suzuki-Migishima R, Yokoyama M, Mishima K, Saito I, Okano H, Mizushima N (2006) Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice. Nature 441: 885–889
96. Hasegawa J, Iwamoto R, Otomo T, Nezu A, Hamasaki M, Yoshimori T (2016) Autophagosome-lysosome fusion in neurons requires INPP5E, a protein associated with Joubert syndrome. EMBO J 35: 1853–1867
97. Heath RJ, Goel G, Baxt LA, Rush JS, Mohanan V, Paulus GL, Jani V, Lassen KG, Xavier RJ (2016) RNF166 determines recruitment of adaptor proteins during antibacterial autophagy. Cell Rep 17: 2183–2194
98. Heo JM, Ordureau A, Paulo JA, Rinehart J, Harper JW (2015) The PINK1-PARKIN mitochondrial ubiquitylation pathway drives a program of OPTN/NDP52 recruitment and TBK1 activation to promote mitophagy. Mol Cell 60: 7–20
99. Hjerpe R, Bett JS, Keuss MJ, Solovyova A, McWilliams TG, Johnson C, Sahu I, Varghese J, Wood N, Wightman M, Osborne G, Bates GP, Glickman MH, Trost M, Knebel A, Marchesi F, Kurz T (2016) UBQLN2 mediates autophagy-independent protein aggregate clearance by the proteasome. Cell 166: 935–949
100. Huang J, Brumell JH (2014) Bacteria-autophagy interplay: a battle for survival. Nat Rev Microbiol 12: 101–114
101. Huang H, Kawamata T, Horie T, Tsugawa H, Nakayama Y, Ohsumi Y, Fukusaki E (2015) Bulk RNA degradation by nitrogen starvation-induced autophagy in yeast. EMBO J 34: 154–168
102. Huang K, Liu D (2016) Targeting non-canonical autophagy overcomes erlotinib resistance in tongue cancer. Tumour Biol 37: 9625–9633
103. Hung YH, Chen LM, Yang JY, Yang WY (2013) Spatiotemporally controlled induction of autophagy-mediated lysosome turnover. Nat Commun 4: 2111
104. Hwang S, Maloney NS, Bruinsma MW, Goel G, Duan E, Zhang L, Shrestha B, Diamond MS, Dani A, Sosnovtsev SV, Green KY, Lopez-Otin C, Xavier RJ, Thackray LB, Virgin HW (2012) Nondegradative role of Atg5-Atg12/Atg16L1 autophagy protein complex in antiviral activity of interferon gamma. Cell Host Microbe 11: 397–409
105. Ichimura Y, Kirisako T, Takao T, Satomi Y, Shimonishi Y, Ishihara N, Mizushima N, Tanida I, Kominami E, Ohsumi M, Noda T, Ohsumi Y (2000) A ubiquitin-like system mediates protein lipidation. Nature 408: 488–492
106. Inoki K, Li Y, Zhu T, Wu J, Guan KL (2002) TSC2 is phosphorylated and inhibited by Akt and suppresses mTOR signalling. Nat Cell Biol 4: 648–657
107. 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: 5360–5372
108. 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
109. Jager S, Bucci C, Tanida I, Ueno T, Kominami E, Saftig P, Eskelinen EL (2004) Role for Rab7 in maturation of late autophagic vacuoles. J Cell Sci 117: 4837–4848
110. Jia K, Hart AC, Levine B (2007) Autophagy genes protect against disease caused by polyglutamine expansion proteins in Caenorhabditis elegans. Autophagy 3: 21–25
111. Jia K, Thomas C, Akbar M, Sun Q, Adams-Huet B, Gilpin C, Levine B (2009) Autophagy genes protect against Salmonella typhimurium infection and mediate insulin signaling-regulated pathogen resistance. Proc Natl Acad Sci USA 106: 14564–14569
112. Joachim J, Jefferies HB, Razi M, Frith D, Snijders AP, Chakravarty P, Judith D, Tooze SA (2015) Activation of ULK kinase and autophagy by GABARAP trafficking from the centrosome is regulated by WAC and GM130. Mol Cell 60: 899–913
113. 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: 1992–2003
114. Kabeya Y, Mizushima N, Ueno T, Yamamoto A, Kirisako T, Noda T, Kominami E, Ohsumi Y, Yoshimori T (2000) LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J 19: 5720–5728
115. Kagan VE, Jiang J, Huang Z, Tyurina YY, Desbourdes C, Cottet-Rousselle C, Dar HH, Verma M, Tyurin VA, Kapralov AA, Cheikhi A, Mao G, Stolz D, St Croix CM, Watkins S, Shen Z, Li Y, Greenberg ML, Tokarska-Schlattner M, Boissan M et al (2016) NDPK-D (NM23-H4)-mediated externalization of cardiolipin enables elimination of depolarized mitochondria by mitophagy. Cell Death Differ 23: 1140–1151
116. Kaizuka T, Morishita H, Hama Y, Tsukamoto S, Matsui T, Toyota Y, Kodama A, Ishihara T, Mizushima T, Mizushima N (2016) An autophagic flux probe that releases an internal control. Mol Cell 64: 835–849
117. Kanki T, Wang K, Cao Y, Baba M, Klionsky DJ (2009) Atg32 is a mitochondrial protein that confers selectivity during mitophagy. Dev Cell 17: 98–109
118. Karanasios E, Stapleton E, Manifava M, Kaizuka T, Mizushima N, Walker SA, Ktistakis NT (2013) Dynamic association of the ULK1 complex with omegasomes during autophagy induction. J Cell Sci 126: 5224–5238
119. Karanasios E, Walker SA, Okkenhaug H, Manifava M, Hummel E, Zimmermann H, Ahmed Q, Domart MC, Collinson L, Ktistakis NT (2016) Autophagy initiation by ULK complex assembly on ER tubulovesicular regions marked by ATG9 vesicles. Nat Commun 7: 12420
120. Katayama H, Kogure T, Mizushima N, Yoshimori T, Miyawaki A (2011) A sensitive and quantitative technique for detecting autophagic events based on lysosomal delivery. Chem Biol 18: 1042–1052
121. Kaur J, Debnath J (2015) Autophagy at the crossroads of catabolism and anabolism. Nat Rev Mol Cell Biol 16: 461–472
122. Kaushik S, Massey AC, Cuervo AM (2006) Lysosome membrane lipid microdomains: novel regulators of chaperone-mediated autophagy. EMBO J 25: 3921–3933
123. Kaushik S, Cuervo AM (2012) Chaperone-mediated autophagy: a unique way to enter the lysosome world. Trends Cell Biol 22: 407–417
124. Kaushik S, Cuervo AM (2015) Degradation of lipid droplet-associated proteins by chaperone-mediated autophagy facilitates lipolysis. Nat Cell Biol 17: 759–770
125. Kaushik S, Cuervo AM (2016) AMPK-dependent phosphorylation of lipid droplet protein PLIN2 triggers its degradation by CMA. Autophagy 12: 432–438
126. Kawabata T, Yoshimori T (2016) Beyond starvation: an update on the autophagic machinery and its functions. J Mol Cell Cardiol 95: 2–10
127. Kelly SP, Bedwell DM (2015) Both the autophagy and proteasomal pathways facilitate the Ubp3p-dependent depletion of a subset of translation and RNA turnover factors during nitrogen starvation in Saccharomyces cerevisiae. RNA 21: 898–910
128. Khaminets A, Heinrich T, Mari M, Grumati P, Huebner AK, Akutsu M, Liebmann L, Stolz A, Nietzsche S, Koch N, Mauthe M, Katona I, Qualmann B, Weis J, Reggiori F, Kurth I, Hubner CA, Dikic I (2015) Regulation of endoplasmic reticulum turnover by selective autophagy. Nature 522: 354–358
129. Khaminets A, Behl C, Dikic I (2016) Ubiquitin-dependent and independent signals in selective autophagy. Trends Cell Biol 26: 6–16
130. Kihara A, Kabeya Y, Ohsumi Y, Yoshimori T (2001a) Beclin-phosphatidylinositol 3-kinase complex functions at the trans-Golgi network. EMBO Rep 2: 330–335
131. Kihara A, Noda T, Ishihara N, Ohsumi Y (2001b) Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in autophagy and carboxypeptidase Y sorting in Saccharomyces cerevisiae. J Cell Biol 152: 519–530
132. Kim J, Kundu M, Viollet B, Guan KL (2011) AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1. Nat Cell Biol 13: 132–141
133. Kim JJ, Lee HM, Shin DM, Kim W, Yuk JM, Jin HS, Lee SH, Cha GH, Kim JM, Lee ZW, Shin SJ, Yoo H, Park YK, Park JB, Chung J, Yoshimori T, Jo EK (2012) Host cell autophagy activated by antibiotics is required for their effective antimycobacterial drug action. Cell Host Microbe 11: 457–468
134. Kim BW, Hong SB, Kim JH, Kwon DH, Song HK (2013a) Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8. Nat Commun 4: 1613
135. Kim J, Kim YC, Fang C, Russell RC, Kim JH, Fan W, Liu R, Zhong Q, Guan KL (2013b) Differential regulation of distinct Vps34 complexes by AMPK in nutrient stress and autophagy. Cell 152: 290–303
136. Kim KH, Lee MS (2014) Autophagy–a key player in cellular and body metabolism. Nat Rev Endocrinol 10: 322–337
137. Kimura T, Jain A, Choi SW, Mandell MA, Schroder K, Johansen T, Deretic V (2015) TRIM-mediated precision autophagy targets cytoplasmic regulators of innate immunity. J Cell Biol 210: 973–989
138. Kimura T, Mandell M, Deretic V (2016) Precision autophagy directed by receptor regulators – emerging examples within the TRIM family. J Cell Sci 129: 881–891
139. Kimura T, Jia J, Kumar S, Choi SW, Gu Y, Mudd M, Dupont N, Jiang S, Peters R, Farzam F, Jain A, Lidke KA, Adams CM, Johansen T, Deretic V (2017) Dedicated SNAREs and specialized TRIM cargo receptors mediate secretory autophagy. EMBO J 36: 42–60
140. Kirkin V, Lamark T, Sou YS, Bjorkoy G, Nunn JL, Bruun JA, Shvets E, McEwan DG, Clausen TH, Wild P, Bilusic I, Theurillat JP, Overvatn A, Ishii T, Elazar Z, Komatsu M, Dikic I, Johansen T (2009a) A role for NBR1 in autophagosomal degradation of ubiquitinated substrates. Mol Cell 33: 505–516
141. Kirkin V, McEwan DG, Novak I, Dikic I (2009b) A role for ubiquitin in selective autophagy. Mol Cell 34: 259–269
142. Kissova I, Salin B, Schaeffer J, Bhatia S, Manon S, Camougrand N (2007) Selective and non-selective autophagic degradation of mitochondria in yeast. Autophagy 3: 329–336
143. Klionsky DJ, Eskelinen EL, Deretic V (2014) Autophagosomes, phagosomes, autolysosomes, phagolysosomes, autophagolysosomes. wait I'm confused. Autophagy 10: 549–551
144. Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, Adachi H, Adams CM, Adams PD, Adeli K, Adhihetty PJ, Adler SG, Agam G, Agarwal R, Aghi MK, Agnello M, Agostinis P, Aguilar PV, Aguirre-Ghiso J, Airoldi EM et al (2016) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy 12: 1–222
145. Knaevelsrud H, Soreng K, Raiborg C, Haberg K, Rasmuson F, Brech A, Liestol K, Rusten TE, Stenmark H, Neufeld TP, Carlsson SR, Simonsen A (2013) Membrane remodeling by the PX-BAR protein SNX18 promotes autophagosome formation. J Cell Biol 202: 331–349
146. Komatsu M, Waguri S, Ueno T, Iwata J, Murata S, Tanida I, Ezaki J, Mizushima N, Ohsumi Y, Uchiyama Y, Kominami E, Tanaka K, Chiba T (2005) Impairment of starvation-induced and constitutive autophagy in Atg7-deficient mice. J Cell Biol 169: 425–434
147. Komatsu M, Waguri S, Chiba T, Murata S, Iwata J, Tanida I, Ueno T, Koike M, Uchiyama Y, Kominami E, Tanaka K (2006) Loss of autophagy in the central nervous system causes neurodegeneration in mice. Nature 441: 880–884
148. Komatsu M, Waguri S, Koike M, Sou YS, Ueno T, Hara T, Mizushima N, Iwata J, Ezaki J, Murata S, Hamazaki J, Nishito Y, Iemura S, Natsume T, Yanagawa T, Uwayama J, Warabi E, Yoshida H, Ishii T, Kobayashi A et al (2007) Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice. Cell 131: 1149–1163
149. Kon M, Kiffin R, Koga H, Chapochnick J, Macian F, Varticovski L, Cuervo AM (2011) Chaperone-mediated autophagy is required for tumor growth. Sci Transl Med 3: 109ra117
150. Korac J, Schaeffer V, Kovacevic I, Clement AM, Jungblut B, Behl C, Terzic J, Dikic I (2013) Ubiquitin-independent function of optineurin in autophagic clearance of protein aggregates. J Cell Sci 126: 580–592
151. Kraft C, Deplazes A, Sohrmann M, Peter M (2008) Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease. Nat Cell Biol 10: 602–610
152. Krick R, Muehe Y, Prick T, Bremer S, Schlotterhose P, Eskelinen EL, Millen J, Goldfarb DS, Thumm M (2008) Piecemeal microautophagy of the nucleus requires the core macroautophagy genes. Mol Biol Cell 19: 4492–4505
153. Kroemer G, Galluzzi L, Vandenabeele P, Abrams J, Alnemri ES, Baehrecke EH, Blagosklonny MV, El-Deiry WS, Golstein P, Green DR, Hengartner M, Knight RA, Kumar S, Lipton SA, Malorni W, Nunez G, Peter ME, Tschopp J, Yuan J, Piacentini M et al (2009) Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009. Cell Death Differ 16: 3–11
154. Ktistakis NT, Tooze SA (2016) Digesting the expanding mechanisms of autophagy. Trends Cell Biol 26: 624–635
155. Kuma A, Hatano M, Matsui M, Yamamoto A, Nakaya H, Yoshimori T, Ohsumi Y, Tokuhisa T, Mizushima N (2004) The role of autophagy during the early neonatal starvation period. Nature 432: 1032–1036
156. Kuma A, Matsui M, Mizushima N (2007) LC3, an autophagosome marker, can be incorporated into protein aggregates independent of autophagy: caution in the interpretation of LC3 localization. Autophagy 3: 323–328
157. Kvam E, Goldfarb DS (2004) Nvj1p is the outer-nuclear-membrane receptor for oxysterol-binding protein homolog Osh1p in Saccharomyces cerevisiae. J Cell Sci 117: 4959–4968
158. Kvam E, Goldfarb DS (2007) Nucleus-vacuole junctions and piecemeal microautophagy of the nucleus in Saccharomyces cerevisiae. Autophagy 3: 85–92
159. Lam GY, Cemma M, Muise AM, Higgins DE, Brumell JH (2013) Host and bacterial factors that regulate LC3 recruitment to Listeria monocytogenes during the early stages of macrophage infection. Autophagy 9: 985–995
160. Lamb CA, Yoshimori T, Tooze SA (2013) The autophagosome: origins unknown, biogenesis complex. Nat Rev Mol Cell Biol 14: 759–774
161. Lapierre LR, Gelino S, Melendez A, Hansen M (2011) Autophagy and lipid metabolism coordinately modulate life span in germline-less Caenorhabditis elegans. Curr Biol 21: 1507–1514
162. Lapierre LR, Silvestrini MJ, Nunez L, Ames K, Wong S, Le TT, Hansen M, Melendez A (2013) Autophagy genes are required for normal lipid levels in Caenorhabditis elegans. Autophagy 9: 278–286
163. Lapierre LR, Kumsta C, Sandri M, Ballabio A, Hansen M (2015) Transcriptional and epigenetic regulation of autophagy in aging. Autophagy 11: 867–880
164. Lazarou M, Sliter DA, Kane LA, Sarraf SA, Wang C, Burman JL, Sideris DP, Fogel AI, Youle RJ (2015) The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy. Nature 524: 309–314
165. Lee JW, Park S, Takahashi Y, Wang HG (2010) The association of AMPK with ULK1 regulates autophagy. PLoS ONE 5: e15394
166. Lee JM, Wagner M, Xiao R, Kim KH, Feng D, Lazar MA, Moore DD (2014) Nutrient-sensing nuclear receptors coordinate autophagy. Nature 516: 112–115
167. Lee MY, Sumpter Jr R, Zou Z, Sirasanagandla S, Wei Y, Mishra P, Rosewich H, Crane DI, Levine B (2017) Peroxisomal protein PEX13 functions in selective autophagy. EMBO Rep 18: 48–60
168. Levine B, Mizushima N, Virgin HW (2011) Autophagy in immunity and inflammation. Nature 469: 323–335
169. Li WW, Li J, Bao JK (2012) Microautophagy: lesser-known self-eating. Cell Mol Life Sci 69: 1125–1136
170. Li S, Wandel MP, Li F, Liu Z, He C, Wu J, Shi Y, Randow F (2013) Sterical hindrance promotes selectivity of the autophagy cargo receptor NDP52 for the danger receptor galectin-8 in antibacterial autophagy. Sci Signal 6: ra9
171. Liang XH, Jackson S, Seaman M, Brown K, Kempkes B, Hibshoosh H, Levine B (1999) Induction of autophagy and inhibition of tumorigenesis by beclin 1. Nature 402: 672–676
172. Liang C, Lee JS, Inn KS, Gack MU, Li Q, Roberts EA, Vergne I, Deretic V, Feng P, Akazawa C, Jung JU (2008) Beclin1-binding UVRAG targets the class C Vps complex to coordinate autophagosome maturation and endocytic trafficking. Nat Cell Biol 10: 776–787
173. Lim J, Yue Z (2015) Neuronal aggregates: formation, clearance, and spreading. Dev Cell 32: 491–501
174. Lindqvist LM, Simon AK, Baehrecke EH (2015) Current questions and possible controversies in autophagy. Cell Death Discov 1: 15036
175. Lipatova Z, Shah AH, Kim JJ, Mulholland JW, Segev N (2013) Regulation of ER-phagy by a Ypt/Rab GTPase module. Mol Biol Cell 24: 3133–3144
176. Liu Y, Schiff M, Czymmek K, Talloczy Z, Levine B, Dinesh-Kumar SP (2005) Autophagy regulates programmed cell death during the plant innate immune response. Cell 121: 567–577
177. Liu L, Feng D, Chen G, Chen M, Zheng Q, Song P, Ma Q, Zhu C, Wang R, Qi W, Huang L, Xue P, Li B, Wang X, Jin H, Wang J, Yang F, Liu P, Zhu Y, Sui S et al (2012) Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells. Nat Cell Biol 14: 177–185
178. +-ATPase-regulated form of cell death triggered by autophagy-inducing peptides, starvation, and hypoxia-ischemia. Proc Natl Acad Sci USA 110: 20364–20371
179. Liu EY, Xu N, O'Prey J, Lao LY, Joshi S, Long JS, O'Prey M, Croft DR, Beaumatin F, Baudot AD, Mrschtik M, Rosenfeldt M, Zhang Y, Gillespie DA, Ryan KM (2015a) Loss of autophagy causes a synthetic lethal deficiency in DNA repair. Proc Natl Acad Sci USA 112: 773–778
180. Liu XM, Sun LL, Hu W, Ding YH, Dong MQ, Du LL (2015b) ESCRTs cooperate with a selective autophagy receptor to mediate vacuolar targeting of soluble cargos. Mol Cell 59: 1035–1042
181. Lock R, Kenific CM, Leidal AM, Salas E, Debnath J (2014) Autophagy-dependent production of secreted factors facilitates oncogenic RAS-driven invasion. Cancer Discov 4: 466–479
182. Loos B, du Toit A, Hofmeyr JH (2014) Defining and measuring autophagosome flux-concept and reality. Autophagy 10: 2087–2096
183. Lopez-Otin C, Galluzzi L, Freije JM, Madeo F, Kroemer G (2016) Metabolic control of longevity. Cell 166: 802–821
184. Lu Q, Wu F, Zhang H (2013) Aggrephagy: lessons from Caenorhabditis elegans. Biochem J 452: 381–390
185. Lu J, He L, Behrends C, Araki M, Araki K, Jun Wang Q, Catanzaro JM, Friedman SL, Zong WX, Fiel MI, Li M, Yue Z (2014a) NRBF2 regulates autophagy and prevents liver injury by modulating Atg14L-linked phosphatidylinositol-3 kinase III activity. Nat Commun 5: 3920
186. Lu K, Psakhye I, Jentsch S (2014b) Autophagic clearance of polyQ proteins mediated by ubiquitin-Atg8 adaptors of the conserved CUET protein family. Cell 158: 549–563
187. Maejima I, Takahashi A, Omori H, Kimura T, Takabatake Y, Saitoh T, Yamamoto A, Hamasaki M, Noda T, Isaka Y, Yoshimori T (2013) Autophagy sequesters damaged lysosomes to control lysosomal biogenesis and kidney injury. EMBO J 32: 2336–2347
188. Maes H, Kuchnio A, Peric A, Moens S, Nys K, De Bock K, Quaegebeur A, Schoors S, Georgiadou M, Wouters J, Vinckier S, Vankelecom H, Garmyn M, Vion AC, Radtke F, Boulanger C, Gerhardt H, Dejana E, Dewerchin M, Ghesquiere B et al (2014) Tumor vessel normalization by chloroquine independent of autophagy. Cancer Cell 26: 190–206
189. Mancias JD, Wang X, Gygi SP, Harper JW, Kimmelman AC (2014) Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy. Nature 509: 105–109
190. Mandell MA, Jain A, Arko-Mensah J, Chauhan S, Kimura T, Dinkins C, Silvestri G, Munch J, Kirchhoff F, Simonsen A, Wei Y, Levine B, Johansen T, Deretic V (2014) TRIM proteins regulate autophagy and can target autophagic substrates by direct recognition. Dev Cell 30: 394–409
191. Manjithaya R, Anjard C, Loomis WF, Subramani S (2010) Unconventional secretion of Pichia pastoris Acb1 is dependent on GRASP protein, peroxisomal functions, and autophagosome formation. J Cell Biol 188: 537–546
192. Marino G, Fernandez AF, Cabrera S, Lundberg YW, Cabanillas R, Rodriguez F, Salvador-Montoliu N, Vega JA, Germana A, Fueyo A, Freije JM, Lopez-Otin C (2010) Autophagy is essential for mouse sense of balance. J Clin Invest 120: 2331–2344
193. Marshall RS, Li F, Gemperline DC, Book AJ, Vierstra RD (2015) Autophagic degradation of the 26S proteasome is mediated by the dual ATG8/ubiquitin receptor RPN10 in Arabidopsis. Mol Cell 58: 1053–1066
194. Marshall RS, McLoughlin F, Vierstra RD (2016) Autophagic turnover of inactive 26S proteasomes in yeast is directed by the ubiquitin receptor Cue5 and the Hsp42 chaperone. Cell Rep 16: 1717–1732
195. Martinez J, Malireddi RK, Lu Q, Cunha LD, Pelletier S, Gingras S, Orchard R, Guan JL, Tan H, Peng J, Kanneganti TD, Virgin HW, Green DR (2015) Molecular characterization of LC3-associated phagocytosis reveals distinct roles for Rubicon, NOX2 and autophagy proteins. Nat Cell Biol 17: 893–906
196. Martinez J, Cunha LD, Park S, Yang M, Lu Q, Orchard R, Li QZ, Yan M, Janke L, Guy C, Linkermann A, Virgin HW, Green DR (2016) Noncanonical autophagy inhibits the autoinflammatory, lupus-like response to dying cells. Nature 533: 115–119
197. Marzella L, Ahlberg J, Glaumann H (1981) Autophagy, heterophagy, microautophagy and crinophagy as the means for intracellular degradation. Virchows Arch B Cell Pathol Incl Mol Pathol 36: 219–234
198. Masini M, Lupi R, Bugliani M, Boggi U, Filipponi F, Masiello P, Marchetti P (2009) A role for autophagy in beta-cell life and death. Islets 1: 157–159
199. Maskey D, Yousefi S, Schmid I, Zlobec I, Perren A, Friis R, Simon HU (2013) ATG5 is induced by DNA-damaging agents and promotes mitotic catastrophe independent of autophagy. Nat Commun 4: 2130
200. Massey AC, Kaushik S, Sovak G, Kiffin R, Cuervo AM (2006) Consequences of the selective blockage of chaperone-mediated autophagy. Proc Natl Acad Sci USA 103: 5805–5810
201. Matsunaga K, Saitoh T, Tabata K, Omori H, Satoh T, Kurotori N, Maejima I, Shirahama-Noda K, Ichimura T, Isobe T, Akira S, Noda T, Yoshimori T (2009) Two Beclin 1-binding proteins, Atg14L and Rubicon, reciprocally regulate autophagy at different stages. Nat Cell Biol 11: 385–396
202. Matsunaga K, Morita E, Saitoh T, Akira S, Ktistakis NT, Izumi T, Noda T, Yoshimori T (2010) Autophagy requires endoplasmic reticulum targeting of the PI3-kinase complex via Atg14L. J Cell Biol 190: 511–521
203. Maycotte P, Aryal S, Cummings CT, Thorburn J, Morgan MJ, Thorburn A (2012) Chloroquine sensitizes breast cancer cells to chemotherapy independent of autophagy. Autophagy 8: 200–212
204. McEwan DG, Popovic D, Gubas A, Terawaki S, Suzuki H, Stadel D, Coxon FP, Miranda de Stegmann D, Bhogaraju S, Maddi K, Kirchof A, Gatti E, Helfrich MH, Wakatsuki S, Behrends C, Pierre P, Dikic I (2015) PLEKHM1 regulates autophagosome-lysosome fusion through HOPS complex and LC3/GABARAP proteins. Mol Cell 57: 39–54
205. Melendez A, Talloczy Z, Seaman M, Eskelinen EL, Hall DH, Levine B (2003) Autophagy genes are essential for dauer development and life-span extension in Caenorhabditis elegans. Science 301: 1387–1391
206. Menzies FM, Fleming A, Rubinsztein DC (2015) Compromised autophagy and neurodegenerative diseases. Nat Rev Neurosci 16: 345–357
207. Mijaljica D, Prescott M, Devenish RJ (2012) A late form of nucleophagy in Saccharomyces cerevisiae. PLoS ONE 7: e40013
208. Mindell JA (2012) Lysosomal acidification mechanisms. Annu Rev Physiol 74: 69–86
209. Mizushima N, Noda T, Yoshimori T, Tanaka Y, Ishii T, George MD, Klionsky DJ, Ohsumi M, Ohsumi Y (1998) A protein conjugation system essential for autophagy. Nature 395: 395–398
210. Mochida K, Oikawa Y, Kimura Y, Kirisako H, Hirano H, Ohsumi Y, Nakatogawa H (2015) Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus. Nature 522: 359–362
211. Moore AS, Holzbaur EL (2016) Dynamic recruitment and activation of ALS-associated TBK1 with its target optineurin are required for efficient mitophagy. Proc Natl Acad Sci USA 113: E3349–E3358
212. Morozova K, Clement CC, Kaushik S, Stiller B, Arias E, Ahmad A, Rauch JN, Chatterjee V, Melis C, Scharf B, Gestwicki JE, Cuervo AM, Zuiderweg ER, Santambrogio L (2016) Structural and biological interaction of hsc-70 protein with phosphatidylserine in endosomal microautophagy. J Biol Chem 291: 18096–18106
213. Mortensen M, Ferguson DJ, Edelmann M, Kessler B, Morten KJ, Komatsu M, Simon AK (2010) Loss of autophagy in erythroid cells leads to defective removal of mitochondria and severe anemia in vivo. Proc Natl Acad Sci USA 107: 832–837
214. Moscat J, Karin M, Diaz-Meco MT (2016) p62 in cancer: signaling adaptor beyond autophagy. Cell 167: 606–609
215. Motley AM, Nuttall JM, Hettema EH (2012) Pex3-anchored Atg36 tags peroxisomes for degradation in Saccharomyces cerevisiae. EMBO J 31: 2852–2868
216. Moy RH, Gold B, Molleston JM, Schad V, Yanger K, Salzano MV, Yagi Y, Fitzgerald KA, Stanger BZ, Soldan SS, Cherry S (2014) Antiviral autophagy restricts Rift Valley fever virus infection and is conserved from flies to mammals. Immunity 40: 51–65
217. Mrschtik M, O'Prey J, Lao LY, Long JS, Beaumatin F, Strachan D, O'Prey M, Skommer J, Ryan KM (2015) DRAM-3 modulates autophagy and promotes cell survival in the absence of glucose. Cell Death Differ 22: 1714–1726
218. von Muhlinen N, Akutsu M, Ravenhill BJ, Foeglein A, Bloor S, Rutherford TJ, Freund SM, Komander D, Randow F (2012) LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy. Mol Cell 48: 329–342
219. Mukherjee A, Patel B, Koga H, Cuervo AM, Jenny A (2016) Selective endosomal microautophagy is starvation-inducible in Drosophila. Autophagy 12: 1984–1999
220. Munz C (2017) The macroautophagy machinery in endo- and exocytosis. J Mol Biol 429: 473–485
221. Murakawa T, Yamaguchi O, Hashimoto A, Hikoso S, Takeda T, Oka T, Yasui H, Ueda H, Akazawa Y, Nakayama H, Taneike M, Misaka T, Omiya S, Shah AM, Yamamoto A, Nishida K, Ohsumi Y, Okamoto K, Sakata Y, Otsu K (2015) Bcl-2-like protein 13 is a mammalian Atg32 homologue that mediates mitophagy and mitochondrial fragmentation. Nat Commun 6: 7527
222. Nair U, Jotwani A, Geng J, Gammoh N, Richerson D, Yen WL, Griffith J, Nag S, Wang K, Moss T, Baba M, McNew JA, Jiang X, Reggiori F, Melia TJ, Klionsky DJ (2011) SNARE proteins are required for macroautophagy. Cell 146: 290–302
223. Nakahira K, Pabon Porras MA, Choi AM (2016) Autophagy in pulmonary diseases. Am J Respir Crit Care Med 194: 1196–1207
224. Nakamoto M, Moy RH, Xu J, Bambina S, Yasunaga A, Shelly SS, Gold B, Cherry S (2012) Virus recognition by Toll-7 activates antiviral autophagy in Drosophila. Immunity 36: 658–667
225. Nardacci R, Amendola A, Ciccosanti F, Corazzari M, Esposito V, Vlassi C, Taibi C, Fimia GM, Del Nonno F, Ippolito G, D'Offizi G, Piacentini M (2014) Autophagy plays an important role in the containment of HIV-1 in nonprogressor-infected patients. Autophagy 10: 1167–1178
226. Narendra D, Kane LA, Hauser DN, Fearnley IM, Youle RJ (2010) p62/SQSTM1 is required for Parkin-induced mitochondrial clustering but not mitophagy; VDAC1 is dispensable for both. Autophagy 6: 1090–1106
227. Nazarko TY, Ozeki K, Till A, Ramakrishnan G, Lotfi P, Yan M, Subramani S (2014) Peroxisomal Atg37 binds Atg30 or palmitoyl-CoA to regulate phagophore formation during pexophagy. J Cell Biol 204: 541–557
228. Nazio F, Strappazzon F, Antonioli M, Bielli P, Cianfanelli V, Bordi M, Gretzmeier C, Dengjel J, Piacentini M, Fimia GM, Cecconi F (2013) mTOR inhibits autophagy by controlling ULK1 ubiquitylation, self-association and function through AMBRA1 and TRAF6. Nat Cell Biol 15: 406–416
229. Neefjes J, Jongsma ML, Paul P, Bakke O (2011) Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nat Rev Immunol 11: 823–836
230. Nguyen TN, Padman BS, Usher J, Oorschot V, Ramm G, Lazarou M (2016) Atg8 family LC3/GABARAP proteins are crucial for autophagosome-lysosome fusion but not autophagosome formation during PINK1/Parkin mitophagy and starvation. J Cell Biol 215: 857–874
231. Nicklin P, Bergman P, Zhang B, Triantafellow E, Wang H, Nyfeler B, Yang H, Hild M, Kung C, Wilson C, Myer VE, MacKeigan JP, Porter JA, Wang YK, Cantley LC, Finan PM, Murphy LO (2009) Bidirectional transport of amino acids regulates mTOR and autophagy. Cell 136: 521–534
232. Niki T, Saito S, Gladish DK (2014) Granular bodies in root primary meristem cells of Zea mays L. var. Cuscoensis K. (Poaceae) that enter young vacuoles by invagination: a novel ribophagy mechanism. Protoplasma 251: 1141–1149
233. Nishida Y, Arakawa S, Fujitani K, Yamaguchi H, Mizuta T, Kanaseki T, Komatsu M, Otsu K, Tsujimoto Y, Shimizu S (2009) Discovery of Atg5/Atg7-independent alternative macroautophagy. Nature 461: 654–658
234. Niso-Santano M, Malik SA, Pietrocola F, Bravo-San Pedro JM, Marino G, Cianfanelli V, Ben-Younes A, Troncoso R, Markaki M, Sica V, Izzo V, Chaba K, Bauvy C, Dupont N, Kepp O, Rockenfeller P, Wolinski H, Madeo F, Lavandero S, Codogno P et al (2015) Unsaturated fatty acids induce non-canonical autophagy. EMBO J 34: 1025–1041
235. Noda NN, Inagaki F (2015) Mechanisms of autophagy. Annu Rev Biophys 44: 101–122
236. Novak I, Kirkin V, McEwan DG, Zhang J, Wild P, Rozenknop A, Rogov V, Lohr F, Popovic D, Occhipinti A, Reichert AS, Terzic J, Dotsch V, Ney PA, Dikic I (2010) Nix is a selective autophagy receptor for mitochondrial clearance. EMBO Rep 11: 45–51
237. Ogawa M, Yoshikawa Y, Kobayashi T, Mimuro H, Fukumatsu M, Kiga K, Piao Z, Ashida H, Yoshida M, Kakuta S, Koyama T, Goto Y, Nagatake T, Nagai S, Kiyono H, Kawalec M, Reichhart JM, Sasakawa C (2011) A Tecpr1-dependent selective autophagy pathway targets bacterial pathogens. Cell Host Microbe 9: 376–389
238. Okamoto K, Kondo-Okamoto N, Ohsumi Y (2009) Mitochondria-anchored receptor Atg32 mediates degradation of mitochondria via selective autophagy. Dev Cell 17: 87–97
239. Olsvik HL, Lamark T, Takagi K, Larsen KB, Evjen G, Overvatn A, Mizushima T, Johansen T (2015) FYCO1 contains a C-terminally extended, LC3A/B-preferring LC3-interacting region (LIR) motif required for efficient maturation of autophagosomes during basal autophagy. J Biol Chem 290: 29361–29374
240. Orenstein SJ, Kuo SH, Tasset I, Arias E, Koga H, Fernandez-Carasa I, Cortes E, Honig LS, Dauer W, Consiglio A, Raya A, Sulzer D, Cuervo AM (2013) Interplay of LRRK2 with chaperone-mediated autophagy. Nat Neurosci 16: 394–406
241. O'Rourke EJ, Ruvkun G (2013) MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability. Nat Cell Biol 15: 668–676
242. 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: 1860–1873
243. Orvedahl A, Alexander D, Talloczy Z, Sun Q, Wei Y, Zhang W, Burns D, Leib DA, Levine B (2007) HSV-1 ICP34.5 confers neurovirulence by targeting the Beclin 1 autophagy protein. Cell Host Microbe 1: 23–35
244. Orvedahl A, MacPherson S, Sumpter R Jr, Talloczy Z, Zou Z, Levine B (2010) Autophagy protects against Sindbis virus infection of the central nervous system. Cell Host Microbe 7: 115–127
245. Orvedahl A, Sumpter R Jr, Xiao G, Ng A, Zou Z, Tang Y, Narimatsu M, Gilpin C, Sun Q, Roth M, Forst CV, Wrana JL, Zhang YE, Luby-Phelps K, Xavier RJ, Xie Y, Levine B (2011) Image-based genome-wide siRNA screen identifies selective autophagy factors. Nature 480: 113–117
246. Ossareh-Nazari B, Bonizec M, Cohen M, Dokudovskaya S, Delalande F, Schaeffer C, Van Dorsselaer A, Dargemont C (2010) Cdc48 and Ufd3, new partners of the ubiquitin protease Ubp3, are required for ribophagy. EMBO Rep 11: 548–554
247. Ossareh-Nazari B, Nino CA, Bengtson MH, Lee JW, Joazeiro CA, Dargemont C (2014) Ubiquitylation by the Ltn1 E3 ligase protects 60S ribosomes from starvation-induced selective autophagy. J Cell Biol 204: 909–917
248. Palikaras K, Tavernarakis N (2014) Mitochondrial homeostasis: the interplay between mitophagy and mitochondrial biogenesis. Exp Gerontol 56: 182–188
249. Palikaras K, Lionaki E, Tavernarakis N (2015) Coordination of mitophagy and mitochondrial biogenesis during ageing in Caenorhabditis elegans. Nature 521: 525–528
250. Pankiv S, Clausen TH, Lamark T, Brech A, Bruun JA, Outzen H, Overvatn A, Bjorkoy G, Johansen T (2007) p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J Biol Chem 282: 24131–24145
251. Papinski D, Schuschnig M, Reiter W, Wilhelm L, Barnes CA, Maiolica A, Hansmann I, Pfaffenwimmer T, Kijanska M, Stoffel I, Lee SS, Brezovich A, Lou JH, Turk BE, Aebersold R, Ammerer G, Peter M, Kraft C (2014) Early steps in autophagy depend on direct phosphorylation of Atg9 by the Atg1 kinase. Mol Cell 53: 471–483
252. Park J, Lee SB, Lee S, Kim Y, Song S, Kim S, Bae E, Kim J, Shong M, Kim JM, Chung J (2006) Mitochondrial dysfunction in Drosophila PINK1 mutants is complemented by parkin. Nature 441: 1157–1161
253. Park YE, Hayashi YK, Bonne G, Arimura T, Noguchi S, Nonaka I, Nishino I (2009) Autophagic degradation of nuclear components in mammalian cells. Autophagy 5: 795–804
254. Park C, Suh Y, Cuervo AM (2015) Regulated degradation of Chk1 by chaperone-mediated autophagy in response to DNA damage. Nat Commun 6: 6823
255. Park JM, Jung CH, Seo M, Otto NM, Grunwald D, Kim KH, Moriarity B, Kim YM, Starker C, Nho RS, Voytas D, Kim DH (2016) The ULK1 complex mediates MTORC1 signaling to the autophagy initiation machinery via binding and phosphorylating ATG14. Autophagy 12: 547–564
256. 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: 927–939
257. Paul P, Munz C (2016) Autophagy and mammalian viruses: roles in immune response, viral replication, and beyond. Adv Virus Res 95: 149–195
258. Poklepovic A, Gewirtz DA (2014) Outcome of early clinical trials of the combination of hydroxychloroquine with chemotherapy in cancer. Autophagy 10: 1478–1480
259. Politi Y, Gal L, Kalifa Y, Ravid L, Elazar Z, Arama E (2014) Paternal mitochondrial destruction after fertilization is mediated by a common endocytic and autophagic pathway in Drosophila. Dev Cell 29: 305–320
260. 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: 506–522
261. Ponpuak M, Mandell MA, Kimura T, Chauhan S, Cleyrat C, Deretic V (2015) Secretory autophagy. Curr Opin Cell Biol 35: 106–116
262. Proikas-Cezanne T, Takacs Z, Donnes P, Kohlbacher O (2015) WIPI proteins: essential PtdIns3P effectors at the nascent autophagosome. J Cell Sci 128: 207–217
263. Puri C, Renna M, Bento CF, Moreau K, Rubinsztein DC (2013) Diverse autophagosome membrane sources coalesce in recycling endosomes. Cell 154: 1285–1299
264. Qu X, Yu J, Bhagat G, Furuya N, Hibshoosh H, Troxel A, Rosen J, Eskelinen EL, Mizushima N, Ohsumi Y, Cattoretti G, Levine B (2003) Promotion of tumorigenesis by heterozygous disruption of the beclin 1 autophagy gene. J Clin Invest 112: 1809–1820
265. 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
266. Record M, Carayon K, Poirot M, Silvente-Poirot S (2014) Exosomes as new vesicular lipid transporters involved in cell-cell communication and various pathophysiologies. Biochim Biophys Acta 1841: 108–120
267. Reggiori F, Monastyrska I, Shintani T, Klionsky DJ (2005) The actin cytoskeleton is required for selective types of autophagy, but not nonspecific autophagy, in the yeast Saccharomyces cerevisiae. Mol Biol Cell 16: 5843–5856
268. Rello-Varona S, Lissa D, Shen S, Niso-Santano M, Senovilla L, Marino G, Vitale I, Jemaa M, Harper F, Pierron G, Castedo M, Kroemer G (2012) Autophagic removal of micronuclei. Cell Cycle 11: 170–176
269. Roberts P, Moshitch-Moshkovitz S, Kvam E, O'Toole E, Winey M, Goldfarb DS (2003) Piecemeal microautophagy of nucleus in Saccharomyces cerevisiae. Mol Biol Cell 14: 129–141
270. Rockel JS, Kapoor M (2016) Autophagy: controlling cell fate in rheumatic diseases. Nat Rev Rheumatol 12: 517–531
271. Rockenfeller P, Koska M, Pietrocola F, Minois N, Knittelfelder O, Sica V, Franz J, Carmona-Gutierrez D, Kroemer G, Madeo F (2015) Phosphatidylethanolamine positively regulates autophagy and longevity. Cell Death Differ 22: 499–508
272. Rodriguez-Muela N, Koga H, Garcia-Ledo L, de la Villa P, de la Rosa EJ, Cuervo AM, Boya P (2013) Balance between autophagic pathways preserves retinal homeostasis. Aging Cell 12: 478–488
273. Rogov V, Dotsch V, Johansen T, Kirkin V (2014) Interactions between autophagy receptors and ubiquitin-like proteins form the molecular basis for selective autophagy. Mol Cell 53: 167–178
274. Rojansky R, Cha MY, Chan DC (2016) Elimination of paternal mitochondria in mouse embryos occurs through autophagic degradation dependent on PARKIN and MUL1. Elife 5: e17896
275. Rosenfeld MR, Ye X, Supko JG, Desideri S, Grossman SA, Brem S, Mikkelson T, Wang D, Chang YC, Hu J, McAfee Q, Fisher J, Troxel AB, Piao S, Heitjan DF, Tan KS, Pontiggia L, O'Dwyer PJ, Davis LE, Amaravadi RK (2014) A phase I/II trial of hydroxychloroquine in conjunction with radiation therapy and concurrent and adjuvant temozolomide in patients with newly diagnosed glioblastoma multiforme. Autophagy 10: 1359–1368
276. Rossin F, D'Eletto M, Falasca L, Sepe S, Cocco S, Fimia GM, Campanella M, Mastroberardino PG, Farrace MG, Piacentini M (2015) Transglutaminase 2 ablation leads to mitophagy impairment associated with a metabolic shift towards aerobic glycolysis. Cell Death Differ 22: 408–418
277. Rubinstein AD, Eisenstein M, Ber Y, Bialik S, Kimchi A (2011) The autophagy protein Atg12 associates with antiapoptotic Bcl-2 family members to promote mitochondrial apoptosis. Mol Cell 44: 698–709
278. Russell RC, Tian Y, Yuan H, Park HW, Chang YY, Kim J, Kim H, Neufeld TP, Dillin A, Guan KL (2013) ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase. Nat Cell Biol 15: 741–750
279. Sahu R, Kaushik S, Clement CC, Cannizzo ES, Scharf B, Follenzi A, Potolicchio I, Nieves E, Cuervo AM, Santambrogio L (2011) Microautophagy of cytosolic proteins by late endosomes. Dev Cell 20: 131–139
280. Saitoh T, Fujita N, Jang MH, Uematsu S, Yang BG, Satoh T, Omori H, Noda T, Yamamoto N, Komatsu M, Tanaka K, Kawai T, Tsujimura T, Takeuchi O, Yoshimori T, Akira S (2008) Loss of the autophagy protein Atg16L1 enhances endotoxin-induced IL-1beta production. Nature 456: 264–268
281. Saitoh T, Fujita N, Hayashi T, Takahara K, Satoh T, Lee H, Matsunaga K, Kageyama S, Omori H, Noda T, Yamamoto N, Kawai T, Ishii K, Takeuchi O, Yoshimori T, Akira S (2009) Atg9a controls dsDNA-driven dynamic translocation of STING and the innate immune response. Proc Natl Acad Sci USA 106: 20842–20846
282. Saleh T, Cuttino L, Gewirtz DA (2016) Autophagy is not uniformly cytoprotective: a personalized medicine approach for autophagy inhibition as a therapeutic strategy in non-small cell lung cancer. Biochim Biophys Acta 1860: 2130–2136
283. Salvador N, Aguado C, Horst M, Knecht E (2000) Import of a cytosolic protein into lysosomes by chaperone-mediated autophagy depends on its folding state. J Biol Chem 275: 27447–27456
284. Sandoval H, Thiagarajan P, Dasgupta SK, Schumacher A, Prchal JT, Chen M, Wang J (2008) Essential role for Nix in autophagic maturation of erythroid cells. Nature 454: 232–235
285. Sanjuan MA, Dillon CP, Tait SW, Moshiach S, Dorsey F, Connell S, Komatsu M, Tanaka K, Cleveland JL, Withoff S, Green DR (2007) Toll-like receptor signalling in macrophages links the autophagy pathway to phagocytosis. Nature 450: 1253–1257
286. Sargent G, van Zutphen T, Shatseva T, Zhang L, Di Giovanni V, Bandsma R, Kim PK (2016) PEX2 is the E3 ubiquitin ligase required for pexophagy during starvation. J Cell Biol 214: 677–690
287. Sato M, Sato K (2011) Degradation of paternal mitochondria by fertilization-triggered autophagy in Caenorhabditis elegans embryos. Science 334: 1141–1144
288. Schlegel A, Giddings TH Jr, Ladinsky MS, Kirkegaard K (1996) Cellular origin and ultrastructure of membranes induced during poliovirus infection. J Virol 70: 6576–6588
289. Schneider JL, Suh Y, Cuervo AM (2014) Deficient chaperone-mediated autophagy in liver leads to metabolic dysregulation. Cell Metab 20: 417–432
290. Schneider JL, Villarroya J, Diaz-Carretero A, Patel B, Urbanska AM, Thi MM, Villarroya F, Santambrogio L, Cuervo AM (2015) Loss of hepatic chaperone-mediated autophagy accelerates proteostasis failure in aging. Aging Cell 14: 249–264
291. Schuck S, Gallagher CM, Walter P (2014) ER-phagy mediates selective degradation of endoplasmic reticulum independently of the core autophagy machinery. J Cell Sci 127: 4078–4088
292. Schweichel JU, Merker HJ (1973) The morphology of various types of cell death in prenatal tissues. Teratology 7: 253–266
293. Scott SV, Hefner-Gravink A, Morano KA, Noda T, Ohsumi Y, Klionsky DJ (1996) Cytoplasm-to-vacuole targeting and autophagy employ the same machinery to deliver proteins to the yeast vacuole. Proc Natl Acad Sci USA 93: 12304–12308
294. Scott SV, Nice DC III, Nau JJ, Weisman LS, Kamada Y, Keizer-Gunnink I, Funakoshi T, Veenhuis M, Ohsumi Y, Klionsky DJ (2000) Apg13p and Vac8p are part of a complex of phosphoproteins that are required for cytoplasm to vacuole targeting. J Biol Chem 275: 25840–25849
295. Scott SV, Guan J, Hutchins MU, Kim J, Klionsky DJ (2001) Cvt19 is a receptor for the cytoplasm-to-vacuole targeting pathway. Mol Cell 7: 1131–1141
296. Seay MD, Dinesh-Kumar SP (2005) Life after death: are autophagy genes involved in cell death and survival during plant innate immune responses? Autophagy 1: 185–186
297. Selleck EM, Orchard RC, Lassen KG, Beatty WL, Xavier RJ, Levine B, Virgin HW, Sibley LD (2015) A noncanonical autophagy pathway restricts Toxoplasma gondii growth in a strain-specific manner in IFN-gamma-activated human cells. MBio 6: e01157-15
298. Seok S, Fu T, Choi SE, Li Y, Zhu R, Kumar S, Sun X, Yoon G, Kang Y, Zhong W, Ma J, Kemper B, Kemper JK (2014) Transcriptional regulation of autophagy by an FXR-CREB axis. Nature 516: 108–111
299. Settembre C, Di Malta C, Polito VA, Garcia Arencibia M, Vetrini F, Erdin S, Erdin SU, Huynh T, Medina D, Colella P, Sardiello M, Rubinsztein DC, Ballabio A (2011) TFEB links autophagy to lysosomal biogenesis. Science 332: 1429–1433
300. Settembre C, Zoncu R, Medina DL, Vetrini F, Erdin S, Erdin S, Huynh T, Ferron M, Karsenty G, Vellard MC, Facchinetti V, Sabatini DM, Ballabio A (2012) A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB. EMBO J 31: 1095–1108
301. Settembre C, Fraldi A, Medina DL, Ballabio A (2013) Signals from the lysosome: a control centre for cellular clearance and energy metabolism. Nat Rev Mol Cell Biol 14: 283–296
302. Sharma K, Le N, Alotaibi M, Gewirtz DA (2014) Cytotoxic autophagy in cancer therapy. Int J Mol Sci 15: 10034–10051
303. Shcherbik N, Pestov DG (2011) The ubiquitin ligase Rsp5 is required for ribosome stability in Saccharomyces cerevisiae. RNA 17: 1422–1428
304. Shibutani ST, Yoshimori T (2014) A current perspective of autophagosome biogenesis. Cell Res 24: 58–68
305. Shirakabe A, Ikeda Y, Sciarretta S, Zablocki DK, Sadoshima J (2016) Aging and autophagy in the heart. Circ Res 118: 1563–1576
306. Shpilka T, Weidberg H, Pietrokovski S, Elazar Z (2011) Atg8: an autophagy-related ubiquitin-like protein family. Genome Biol 12: 226
307. Shravage BV, Hill JH, Powers CM, Wu L, Baehrecke EH (2013) Atg6 is required for multiple vesicle trafficking pathways and hematopoiesis in Drosophila. Development 140: 1321–1329
308. Shvets E, Elazar Z (2008) Autophagy-independent incorporation of GFP-LC3 into protein aggregates is dependent on its interaction with p62/SQSTM1. Autophagy 4: 1054–1056
309. Sica V, Galluzzi L, Bravo-San Pedro JM, Izzo V, Maiuri MC, Kroemer G (2015) Organelle-specific initiation of autophagy. Mol Cell 59: 522–539
310. 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: 4239–4251
311. Simonsen A, Cumming RC, Brech A, Isakson P, Schubert DR, Finley KD (2008) Promoting basal levels of autophagy in the nervous system enhances longevity and oxidant resistance in adult Drosophila. Autophagy 4: 176–184
312. Singh R, Kaushik S, Wang Y, Xiang Y, Novak I, Komatsu M, Tanaka K, Cuervo AM, Czaja MJ (2009) Autophagy regulates lipid metabolism. Nature 458: 1131–1135
313. Sou YS, Waguri S, Iwata J, Ueno T, Fujimura T, Hara T, Sawada N, Yamada A, Mizushima N, Uchiyama Y, Kominami E, Tanaka K, Komatsu M (2008) The Atg8 conjugation system is indispensable for proper development of autophagic isolation membranes in mice. Mol Biol Cell 19: 4762–4775
314. Spinnenhirn V, Farhan H, Basler M, Aichem A, Canaan A, Groettrup M (2014) The ubiquitin-like modifier FAT10 decorates autophagy-targeted Salmonella and contributes to Salmonella resistance in mice. J Cell Sci 127: 4883–4893
315. Sriram SM, Kim BY, Kwon YT (2011) The N-end rule pathway: emerging functions and molecular principles of substrate recognition. Nat Rev Mol Cell Biol 12: 735–747
316. Stanley RE, Ragusa MJ, Hurley JH (2014) The beginning of the end: how scaffolds nucleate autophagosome biogenesis. Trends Cell Biol 24: 73–81
317. Stolz A, Ernst A, Dikic I (2014) Cargo recognition and trafficking in selective autophagy. Nat Cell Biol 16: 495–501
318. Sumpter R Jr, Sirasanagandla S, Fernandez AF, Wei Y, Dong X, Franco L, Zou Z, Marchal C, Lee MY, Clapp DW, Hanenberg H, Levine B (2016) Fanconi anemia proteins function in mitophagy and immunity. Cell 165: 867–881
319. Sun Q, Fan W, Chen K, Ding X, Chen S, Zhong Q (2008) Identification of Barkor as a mammalian autophagy-specific factor for Beclin 1 and class III phosphatidylinositol 3-kinase. Proc Natl Acad Sci USA 105: 19211–19216
320. Talloczy Z, Jiang W, Virgin H, Leib DA, Scheuner D, Kaufman RJ, Eskelinen EL, Levine B (2002) Regulation of starvation- and virus-induced autophagy by the eIF2alpha kinase signaling pathway. Proc Natl Acad Sci USA 99: 190–195
321. Tanaka C, Tan LJ, Mochida K, Kirisako H, Koizumi M, Asai E, Sakoh-Nakatogawa M, Ohsumi Y, Nakatogawa H (2014) Hrr25 triggers selective autophagy-related pathways by phosphorylating receptor proteins. J Cell Biol 207: 91–105
322. Tang Z, Lin MG, Stowe TR, Chen S, Zhu M, Stearns T, Franco B, Zhong Q (2013) Autophagy promotes primary ciliogenesis by removing OFD1 from centriolar satellites. Nature 502: 254–257
323. Tasset I, Cuervo AM (2016) Role of chaperone-mediated autophagy in metabolism. FEBS J 283: 2403–2413
324. Thurston TL, Ryzhakov G, Bloor S, von Muhlinen N, Randow F (2009) The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria. Nat Immunol 10: 1215–1221
325. Thurston TL, Wandel MP, von Muhlinen N, Foeglein A, Randow F (2012) Galectin 8 targets damaged vesicles for autophagy to defend cells against bacterial invasion. Nature 482: 414–418
326. Thurston TL, Boyle KB, Allen M, Ravenhill BJ, Karpiyevich M, Bloor S, Kaul A, Noad J, Foeglein A, Matthews SA, Komander D, Bycroft M, Randow F (2016) Recruitment of TBK1 to cytosol-invading Salmonella induces WIPI2-dependent antibacterial autophagy. EMBO J 35: 1779–1792
327. Tian Y, Li Z, Hu W, Ren H, Tian E, Zhao Y, Lu Q, Huang X, Yang P, Li X, Wang X, Kovacs AL, Yu L, Zhang H (2010) Caenorhabditis elegans screen identifies autophagy genes specific to multicellular organisms. Cell 141: 1042–1055
328. Tooze SA, Abada A, Elazar Z (2014) Endocytosis and autophagy: exploitation or cooperation? Cold Spring Harb Perspect Biol 6: a018358
329. Torggler R, Papinski D, Brach T, Bas L, Schuschnig M, Pfaffenwimmer T, Rohringer S, Matzhold T, Schweida D, Brezovich A, Kraft C (2016) Two independent pathways within selective autophagy converge to activate Atg1 kinase at the vacuole. Mol Cell 64: 221–235
330. Toyooka K, Moriyasu Y, Goto Y, Takeuchi M, Fukuda H, Matsuoka K (2006) Protein aggregates are transported to vacuoles by a macroautophagic mechanism in nutrient-starved plant cells. Autophagy 2: 96–106
331. Travassos LH, Carneiro LA, Ramjeet M, Hussey S, Kim YG, Magalhaes JG, Yuan L, Soares F, Chea E, Le Bourhis L, Boneca IG, Allaoui A, Jones NL, Nunez G, Girardin SE, Philpott DJ (2010) Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry. Nat Immunol 11: 55–62
332. Tsuboyama K, Koyama-Honda I, Sakamaki Y, Koike M, Morishita H, Mizushima N (2016) The ATG conjugation systems are important for degradation of the inner autophagosomal membrane. Science 354: 1036–1041
333. Tsukada M, Ohsumi Y (1993) Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett 333: 169–174
334. Tumbarello DA, Manna PT, Allen M, Bycroft M, Arden SD, Kendrick-Jones J, Buss F (2015) The autophagy receptor TAX1BP1 and the molecular motor myosin VI are required for clearance of Salmonella Typhimurium by autophagy. PLoS Pathog 11: e1005174
335. Umekawa M, Klionsky DJ (2012) The cytoplasm-to-vacuole targeting pathway: a historical perspective. Int J Cell Biol 2012: 142634
336. Uttenweiler A, Mayer A (2008) Microautophagy in the yeast Saccharomyces cerevisiae. Methods Mol Biol 445: 245–259
337. Uytterhoeven V, Lauwers E, Maes I, Miskiewicz K, Melo MN, Swerts J, Kuenen S, Wittocx R, Corthout N, Marrink SJ, Munck S, Verstreken P (2015) Hsc70-4 deforms membranes to promote synaptic protein turnover by endosomal microautophagy. Neuron 88: 735–748
338. Vakifahmetoglu-Norberg H, Xia HG, Yuan J (2015) Pharmacologic agents targeting autophagy. J Clin Invest 125: 5–13
339. Valdor R, Mocholi E, Botbol Y, Guerrero-Ros I, Chandra D, Koga H, Gravekamp C, Cuervo AM, Macian F (2014) Chaperone-mediated autophagy regulates T cell responses through targeted degradation of negative regulators of T cell activation. Nat Immunol 15: 1046–1054
340. Verlhac P, Gregoire IP, Azocar O, Petkova DS, Baguet J, Viret C, Faure M (2015) Autophagy receptor NDP52 regulates pathogen-containing autophagosome maturation. Cell Host Microbe 17: 515–525
341. Vevea JD, Garcia EJ, Chan RB, Zhou B, Schultz M, Di Paolo G, McCaffery JM, Pon LA (2015) Role for lipid droplet biogenesis and microlipophagy in adaptation to lipid imbalance in yeast. Dev Cell 35: 584–599
342. Vicinanza M, Korolchuk VI, Ashkenazi A, Puri C, Menzies FM, Clarke JH, Rubinsztein DC (2015) PI(5)P regulates autophagosome biogenesis. Mol Cell 57: 219–234
343. Waite KA, De-La Mota-Peynado A, Vontz G, Roelofs J (2016) Starvation induces proteasome autophagy with different pathways for core and regulatory particles. J Biol Chem 291: 3239–3253
344. Waliullah TM, Yeasmin AM, Kaneko A, Koike N, Terasawa M, Totsuka T, Ushimaru T (2017) Rim15 and Sch9 kinases are involved in induction of autophagic degradation of ribosomes in budding yeast. Biosci Biotechnol Biochem 81: 307–310
345. Walter KM, Schonenberger MJ, Trotzmuller M, Horn M, Elsasser HP, Moser AB, Lucas MS, Schwarz T, Gerber PA, Faust PL, Moch H, Kofeler HC, Krek W, Kovacs WJ (2014) Hif-2alpha promotes degradation of mammalian peroxisomes by selective autophagy. Cell Metab 20: 882–897
346. Wang CW, Miao YH, Chang YS (2014) A sterol-enriched vacuolar microdomain mediates stationary phase lipophagy in budding yeast. J Cell Biol 206: 357–366
347. Wang Y, Zhang Y, Chen L, Liang Q, Yin XM, Miao L, Kang BH, Xue D (2016) Kinetics and specificity of paternal mitochondrial elimination in Caenorhabditis elegans. Nat Commun 7: 12569
348. Weckman A, Di Ieva A, Rotondo F, Syro LV, Ortiz LD, Kovacs K, Cusimano MD (2014) Autophagy in the endocrine glands. J Mol Endocrinol 52: R151–R163
349. Wei Y, Chiang WC, Sumpter R Jr, Mishra P, Levine B (2017) Prohibitin 2 is an inner mitochondrial membrane mitophagy receptor. Cell 168: 224–238
350. Wild P, Farhan H, McEwan DG, Wagner S, Rogov VV, Brady NR, Richter B, Korac J, Waidmann O, Choudhary C, Dotsch V, Bumann D, Dikic I (2011) Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth. Science 333: 228–233
351. Wild P, McEwan DG, Dikic I (2014) The LC3 interactome at a glance. J Cell Sci 127: 3–9
352. Wilkinson DS, Jariwala JS, Anderson E, Mitra K, Meisenhelder J, Chang JT, Ideker T, Hunter T, Nizet V, Dillin A, Hansen M (2015) Phosphorylation of LC3 by the Hippo kinases STK3/STK4 is essential for autophagy. Mol Cell 57: 55–68
353. Wing SS, Chiang HL, Goldberg AL, Dice JF (1991) Proteins containing peptide sequences related to Lys-Phe-Glu-Arg-Gln are selectively depleted in liver and heart, but not skeletal muscle, of fasted rats. Biochem J 275(Pt 1): 165–169
354. Wold MS, Lim J, Lachance V, Deng Z, Yue Z (2016) ULK1-mediated phosphorylation of ATG14 promotes autophagy and is impaired in Huntington's disease models. Mol Neurodegener 11: 76
355. Wong YC, Holzbaur EL (2014) Optineurin is an autophagy receptor for damaged mitochondria in parkin-mediated mitophagy that is disrupted by an ALS-linked mutation. Proc Natl Acad Sci USA 111: E4439–E4448
356. Wu J, Randle KE, Wu LP (2007) ird1 is a Vps15 homologue important for antibacterial immune responses in Drosophila. Cell Microbiol 9: 1073–1085
357. Xie C, Ginet V, Sun Y, Koike M, Zhou K, Li T, Li H, Li Q, Wang X, Uchiyama Y, Truttmann AC, Kroemer G, Puyal J, Blomgren K, Zhu C (2016) Neuroprotection by selective neuronal deletion of Atg7 in neonatal brain injury. Autophagy 12: 410–423
358. Xu T, Nicolson S, Denton D, Kumar S (2015) Distinct requirements of Autophagy-related genes in programmed cell death. Cell Death Differ 22: 1792–1802
359. 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: 219–233
360. Yamashita S, Abe K, Tatemichi Y, Fujiki Y (2014) The membrane peroxin PEX3 induces peroxisome-ubiquitination-linked pexophagy. Autophagy 10: 1549–1564
361. Yang Z, Klionsky DJ (2010) Eaten alive: a history of macroautophagy. Nat Cell Biol 12: 814–822
362. Yano T, Mita S, Ohmori H, Oshima Y, Fujimoto Y, Ueda R, Takada H, Goldman WE, Fukase K, Silverman N, Yoshimori T, Kurata S (2008) Autophagic control of listeria through intracellular innate immune recognition in Drosophila. Nat Immunol 9: 908–916
363. Yousefi S, Perozzo R, Schmid I, Ziemiecki A, Schaffner T, Scapozza L, Brunner T, Simon HU (2006) Calpain-mediated cleavage of Atg5 switches autophagy to apoptosis. Nat Cell Biol 8: 1124–1132
364. Yu L, McPhee CK, Zheng L, Mardones GA, Rong Y, Peng J, Mi N, Zhao Y, Liu Z, Wan F, Hailey DW, Oorschot V, Klumperman J, Baehrecke EH, Lenardo MJ (2010) Termination of autophagy and reformation of lysosomes regulated by mTOR. Nature 465: 942–946
365. Yue Z, Jin S, Yang C, Levine AJ, Heintz N (2003) Beclin 1, an autophagy gene essential for early embryonic development, is a haploinsufficient tumor suppressor. Proc Natl Acad Sci USA 100: 15077–15082
366. Zaffagnini G, Martens S (2016) Mechanisms of selective autophagy. J Mol Biol 428: 1714–1724
367. Zalckvar E, Berissi H, Mizrachy L, Idelchuk Y, Koren I, Eisenstein M, Sabanay H, Pinkas-Kramarski R, Kimchi A (2009) DAP-kinase-mediated phosphorylation on the BH3 domain of beclin 1 promotes dissociation of beclin 1 from Bcl-XL and induction of autophagy. EMBO Rep 10: 285–292
368. Zhang J, Tripathi DN, Jing J, Alexander A, Kim J, Powell RT, Dere R, Tait-Mulder J, Lee JH, Paull TT, Pandita RK, Charaka VK, Pandita TK, Kastan MB, Walker CL (2015) ATM functions at the peroxisome to induce pexophagy in response to ROS. Nat Cell Biol 17: 1259–1269
369. Zhao Z, Fux B, Goodwin M, Dunay IR, Strong D, Miller BC, Cadwell K, Delgado MA, Ponpuak M, Green KG, Schmidt RE, Mizushima N, Deretic V, Sibley LD, Virgin HW (2008) Autophagosome-independent essential function for the autophagy protein Atg5 in cellular immunity to intracellular pathogens. Cell Host Microbe 4: 458–469
370. Zhong Y, Wang QJ, Li X, Yan Y, Backer JM, Chait BT, Heintz N, Yue Z (2009) Distinct regulation of autophagic activity by Atg14L and Rubicon associated with Beclin 1-phosphatidylinositol-3-kinase complex. Nat Cell Biol 11: 468–476
371. Zhong Z, Sanchez-Lopez E, Karin M (2016) Autophagy, inflammation, and immunity: a troika governing cancer and its treatment. Cell 166: 288–298
372. Zhou Q, Li H, Li H, Nakagawa A, Lin JL, Lee ES, Harry BL, Skeen-Gaar RR, Suehiro Y, William D, Mitani S, Yuan HS, Kang BH, Xue D (2016) Mitochondrial endonuclease G mediates breakdown of paternal mitochondria upon fertilization. Science 353: 394–399
373. Zhu JH, Horbinski C, Guo F, Watkins S, Uchiyama Y, Chu CT (2007) Regulation of autophagy by extracellular signal-regulated protein kinases during 1-methyl-4-phenylpyridinium-induced cell death. Am J Pathol 170: 75–86
374. Zhu J, Wang KZ, Chu CT (2013) After the banquet: mitochondrial biogenesis, mitophagy, and cell survival. Autophagy 9: 1663–1676
375. Zou CG, Ma YC, Dai LL, Zhang KQ (2014) Autophagy protects Caenorhabditis elegans against necrosis during Pseudomonas aeruginosa infection. Proc Natl Acad Sci USA 111: 12480–12485
376. Zutphen T, Veenhuis M, van der Klei IJ (2008) Pex14 is the sole component of the peroxisomal translocon that is required for pexophagy. Autophagy 4: 63–66