The machinery of macroautophagy
Tóm tắt
Từ khóa
Tài liệu tham khảo
Klionsky DJ, Baehrecke EH, Brumell JH, et al. A comprehensive glossary of autophagy-related molecules and processes (2nd edition). Autophagy 2011; 7:1273–1294.
Klionsky DJ . The molecular machinery of autophagy: unanswered questions. J Cell Sci 2005; 118:7–18.
Yorimitsu T, Klionsky DJ . Autophagy: molecular machinery for self-eating. Cell Death Differ 2005; 12:1542–1552.
Baba M, Osumi M, Ohsumi Y . Analysis of the membrane structures involved in autophagy in yeast by freeze-replica method. Cell Struct Funct 1995; 20:465–471.
Fimia GM, Stoykova A, Romagnoli A, et al. Ambra1 regulates autophagy and development of the nervous system. Nature 2007; 447:1121–1125.
Dunn WA Jr . Studies on the mechanisms of autophagy: maturation of the autophagic vacuole. J Cell Biol 1990; 110:1935–1945.
Suzuki K, Kirisako T, Kamada Y, et al. The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. EMBO J 2001; 20:5971–5981.
Kim J, Huang WP, Stromhaug PE, Klionsky DJ . Convergence of multiple autophagy and cytoplasm to vacuole targeting components to a perivacuolar membrane compartment prior to de novo vesicle formation. J Biol Chem 2002; 277:763–773.
Seglen PO, Gordon PB, Holen I . Non-selective autophagy. Semin Cell Biol 1990; 1:441–448.
de Duve C, Pressman BC, Gianetto R, Wattiaux R, Appelmans F . Tissue fractionation studies. 6. Intracellular distribution patterns of enzymes in rat-liver tissue. Biochem J 1955; 60:604–617.
Ashford TP, Porter KR . Cytoplasmic components in hepatic cell lysosomes. J Cell Biol 1962; 12:198–202.
Clark SL Jr . Cellular differentiation in the kidneys of newborn mice studied with the electron microscope. J Biophys Biochem Cytol 1957; 3:349–362.
Novikoff AB . The proximal tubule cell in experimental hydronephrosis. J Biophys Biochem Cytol 1959; 6:136–138.
Deter RL, Baudhuin P, de Duve C . Participation of lysosomes in cellular autophagy induced in rat liver by glucagon. J Cell Biol 1967; 35:C11–C16.
Seglen PO, Gordon PB . 3-Methyladenine: specific inhibitor of autophagic/lysosomal protein degradation in isolated rat hepatocytes. Proc Natl Acad Sci USA 1982; 79:1889–1892.
Bolender RP, Weibel ER . A morphometric study of the removal of phenobarbital-induced membranes from hepatocytes after cessation of threatment. J Cell Biol 1973; 56:746–761.
Beaulaton J, Lockshin RA . Ultrastructural study of the normal degeneration of the intersegmental muscles of Anthereae polyphemus and Manduca sexta (Insecta, Lepidoptera) with particular reference of cellular autophagy. J Morphol 1977; 154:39–57.
Veenhuis M, Douma A, Harder W, Osumi M . Degradation and turnover of peroxisomes in the yeast Hansenula polymorpha induced by selective inactivation of peroxisomal enzymes. Arch Microbiol 1983; 134:193–203.
Thumm M, Egner R, Koch B, et al. Isolation of autophagocytosis mutants of Saccharomyces cerevisiae. FEBS Lett 1994; 349:275–280.
Tsukada M, Ohsumi Y . Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett 1993; 333:169–174.
Klionsky DJ, Cregg JM, Dunn WA Jr, et al. A unified nomenclature for yeast autophagy-related genes. Dev Cell 2003; 5:539–545.
Matsuura A, Tsukada M, Wada Y, Ohsumi Y . Apg1p, a novel protein kinase required for the autophagic process in Saccharomyces cerevisiae. Gene 1997; 192:245–250.
Liang XH, Jackson S, Seaman M, et al. Induction of autophagy and inhibition of tumorigenesis by beclin 1. Nature 1999; 402:672–676.
Rikihisa Y . Glycogen autophagosomes in polymorphonuclear leukocytes induced by rickettsiae. Anat Rec 1984; 208:319–327.
Liang XH, Kleeman LK, Jiang HH, et al. Protection against fatal Sindbis virus encephalitis by beclin, a novel Bcl-2-interacting protein. J Virol 1998; 72:8586–8596.
Orvedahl A, Alexander D, Tallóczy Z, et al. HSV-1 ICP34.5 confers neurovirulence by targeting the Beclin 1 autophagy protein. Cell Host Microbe 2007; 1:23–35.
Tallóczy Z, Virgin HW IV, Levine B . PKR-dependent autophagic degradation of herpes simplex virus type 1. Autophagy 2006; 2:24–29.
Rubinsztein DC, DiFiglia M, Heintz N, et al. Autophagy and its possible roles in nervous system diseases, damage and repair. Autophagy 2005; 1:11–22.
Boya P, Gonzalez-Polo RA, Casares N, et al. Inhibition of macroautophagy triggers apoptosis. Mol Cell Biol 2005; 25:1025–1040.
Yu L, Alva A, Su H, et al. Regulation of an ATG7-beclin 1 program of autophagic cell death by caspase-8. Science 2004; 304:1500–1502.
Shintani T, Klionsky DJ . Autophagy in health and disease: a double-edged sword. Science 2004; 306:990–995.
Kunz JB, Schwarz H, Mayer A . Determination of four sequential stages during microautophagy in vitro. J Biol Chem 2004; 279:9987–9996.
Deffieu M, Bhatia-Kissova I, Salin B, et al. Glutathione participates in the regulation of mitophagy in yeast. J Biol Chem 2009; 284:14828–14837.
Dunn WA Jr, Cregg JM, Kiel JAKW, et al. Pexophagy: the selective autophagy of peroxisomes. Autophagy 2005; 1:75–83.
Huang W-P, Scott SV, Kim J, Klionsky DJ . The itinerary of a vesicle component, Aut7p/Cvt5p, terminates in the yeast vacuole via the autophagy/Cvt pathways. J Biol Chem 2000; 275:5845–5851.
Kirisako T, Baba M, Ishihara N, et al. Formation process of autophagosome is traced with Apg8/Aut7p in yeast. J Cell Biol 1999; 147:435–446.
Suzuki K, Kubota Y, Sekito T, Ohsumi Y . Hierarchy of Atg proteins in pre-autophagosomal structure organization. Genes Cells 2007; 12:209–218.
Cheong H, Klionsky DJ . Dual role of Atg1 in regulation of autophagy-specific PAS assembly in Saccharomyces cerevisiae. Autophagy 2008; 4:724–726.
Mao K, Chew LH, Inoue-Aono Y, et al. Atg29 phosphorylation regulates coordination of the Atg17-Atg31-Atg29 complex with the Atg11 scaffold during autophagy initiation. Proc Natl Acad Sci USA 2013; 110:E2875–E2884.
Mizushima N, Yamamoto A, Hatano M, et al. Dissection of autophagosome formation using Apg5-deficient mouse embryonic stem cells. J Cell Biol 2001; 152:657–668.
Yamada T, Carson AR, Caniggia I, et al. Endothelial nitric-oxide synthase antisense (NOS3AS) gene encodes an autophagy-related protein (APG9-like2) highly expressed in trophoblast. J Biol Chem 2005; 280:18283–18290.
Young ARJ, Chan EYW, Hu XW, et al. Starvation and ULK1-dependent cycling of mammalian Atg9 between the TGN and endosomes. J Cell Sci 2006; 119:3888–3900.
Noda T, Suzuki K, Ohsumi Y . Yeast autophagosomes: de novo formation of a membrane structure. Trends Cell Biol 2002; 12:231–235.
Kovács AL, Palfia Z, Rez G, Vellai T, Kovács J . Sequestration revisited: integrating traditional electron microscopy, de novo assembly and new results. Autophagy 2007; 3:655–662.
Gordon PB, Seglen PO . Prelysosomal convergence of autophagic and endocytic pathways. Biochem Biophys Res Commun 1988; 151:40–47.
Geng J, Klionsky DJ . The Atg8 and Atg12 ubiquitin-like conjugation systems in macroautophagy. EMBO Rep 2008; 9:859–864.
Mari M, Griffith J, Rieter E, et al. An Atg9-containing compartment that functions in the early steps of autophagosome biogenesis. J Cell Biol 2010; 190:1005–1022.
van der Vaart A, Griffith J, Reggiori F . Exit from the Golgi is required for the expansion of the autophagosomal phagophore in yeast Saccharomyces cerevisiae. Mol Biol Cell 2010; 21:2270–2284.
Yen W-L, Shintani T, Nair U, et al. The conserved oligomeric Golgi complex is involved in double-membrane vesicle formation during autophagy. J Cell Biol 2010; 188:101–114.
Taylor R Jr, Chen PH, Chou CC, Patel J, Jin SV . KCS1 deletion in Saccharomyces cerevisiae leads to a defect in translocation of autophagic proteins and reduces autophagosome formation. Autophagy 2012; 8:1300–1311.
Axe EL, Walker SA, Manifava M, et al. Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J Cell Biol 2008; 182:685–701.
Harding TM, Morano KA, Scott SV, Klionsky DJ . Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway. J Cell Biol 1995; 131:591–602.
Mizushima N, Yoshimori T, Ohsumi Y . The role of Atg proteins in autophagosome formation. Annu Rev Cell Dev Biol 2011; 27:107–132.
Xie Z, Klionsky DJ . Autophagosome formation: core machinery and adaptations. Nat Cell Biol 2007; 9:1102–1109.
Cheong H, Yorimitsu T, Reggiori F, et al. Atg17 regulates the magnitude of the autophagic response. Mol Biol Cell 2005; 16:3438–3453.
Kabeya Y, Kamada Y, Baba M, et al. Atg17 functions in cooperation with Atg1 and Atg13 in yeast autophagy. Mol Biol Cell 2005; 16:2544–2553.
Kabeya Y, Kawamata T, Suzuki K, Ohsumi Y . Cis1/Atg31 is required for autophagosome formation in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2007; 356:405–410.
Kamada Y, Funakoshi T, Shintani T, et al. Tor-mediated induction of autophagy via an Apg1 protein kinase complex. J Cell Biol 2000; 150:1507–1513.
Kawamata T, Kamada Y, Suzuki K, et al. Characterization of a novel autophagy-specific gene, ATG29. Biochem Biophys Res Commun 2005; 338:1884–1889.
Reggiori F, Tucker KA, Stromhaug PE, Klionsky DJ . The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure. Dev Cell 2004; 6:79–90.
Abeliovich H, Zhang C, Dunn WA Jr, Shokat KM, Klionsky DJ . Chemical genetic analysis of Apg1 reveals a non-kinase role in the induction of autophagy. Mol Biol Cell 2003; 14:477–490.
Nair U, Klionsky DJ . Molecular mechanisms and regulation of specific and nonspecific autophagy pathways in yeast. J Biol Chem 2005; 280:41785–41788.
Stephan JS, Yeh YY, Ramachandran V, Deminoff SJ, Herman PK . The Tor and PKA signaling pathways independently target the Atg1/Atg13 protein kinase complex to control autophagy. Proc Natl Acad Sci USA 2009; 106:17049–17054.
Yeh YY, Wrasman K, Herman PK . Autophosphorylation within the Atg1 activation loop is required for both kinase activity and the induction of autophagy in Saccharomyces cerevisiae. Genetics 2010; 185:871–882.
Kijanska M, Dohnal I, Reiter W, et al. Activation of Atg1 kinase in autophagy by regulated phosphorylation. Autophagy 2010; 6:1168–1178.
Kamada Y, Yoshino K, Kondo C, et al. Tor directly controls the Atg1 kinase complex to regulate autophagy. Mol Cell Biol 2010; 30:1049–1058.
Budovskaya YV, Stephan JS, Deminoff SJ, Herman PK . An evolutionary proteomics approach identifies substrates of the cAMP-dependent protein kinase. Proc Natl Acad Sci USA 2005; 102:13933–13938.
Scott SV, Nice DC, III, Nau JJ, et al. Apg13p and Vac8p are part of a complex of phosphoproteins that are required for cytoplasm to vacuole targeting. J Biol Chem 2000; 275:25840–25849.
Kraft C, Kijanska M, Kalie E, et al. Binding of the Atg1/ULK1 kinase to the ubiquitin-like protein Atg8 regulates autophagy. EMBO J 2012; 31:3691–3703.
Cao Y, Nair U, Yasumura-Yorimitsu K, Klionsky DJ . A multiple ATG gene knockout strain for yeast two-hybrid analysis. Autophagy 2009; 5:699–705.
Kabeya Y, Noda NN, Fujioka Y, et al. Characterization of the Atg17-Atg29-Atg31 complex specifically required for starvation-induced autophagy in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2009; 389:612–615.
Ragusa MJ, Stanley RE, Hurley JH . Architecture of the Atg17 complex as a scaffold for autophagosome biogenesis. Cell 2012; 151:1501–1512.
Hosokawa N, Hara T, Kaizuka T, et al. Nutrient-dependent mTORC1 association with the ULK1-Atg13-FIP200 complex required for autophagy. Mol Biol Cell 2009; 20:1981–1991.
Mizushima N . The role of the Atg1/ULK1 complex in autophagy regulation. Curr Opin Cell Biol 2010; 22:132–139.
Hosokawa N, Sasaki T, Iemura S, et al. Atg101, a novel mammalian autophagy protein interacting with Atg13. Autophagy 2009; 5:973–979.
Mercer CA, Kaliappan A, Dennis PB . A novel, human Atg13 binding protein, Atg101, interacts with ULK1 and is essential for macroautophagy. Autophagy 2009; 5:649–662.
Hara T, Takamura A, Kishi C, et al. FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells. J Cell Biol 2008; 181:497–510.
Jung CH, Jun CB, Ro SH, et al. ULK-Atg13-FIP200 complexes mediate mTOR signaling to the autophagy machinery. Mol Biol Cell 2009; 20:1992–2003.
Kim J, Kundu M, Viollet B, Guan KL . AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1. Nat Cell Biol 2011; 13:132–141.
Di Bartolomeo S, Corazzari M, Nazio F, et al. The dynamic interaction of AMBRA1 with the dynein motor complex regulates mammalian autophagy. J Cell Biol 2010; 191:155–168.
Russell RC, Tian Y, Yuan H, et al. ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase. Nat Cell Biol 2013; 15:741–750.
Reggiori F, Shintani T, Nair U, Klionsky DJ . Atg9 cycles between mitochondria and the pre-autophagosomal structure in yeasts. Autophagy 2005; 1:101–109.
He C, Baba M, Cao Y, Klionsky DJ . Self-interaction is critical for Atg9 transport and function at the phagophore assembly site during autophagy. Mol Biol Cell 2008; 19:5506–5516.
He C, Song H, Yorimitsu T, et al. Recruitment of Atg9 to the preautophagosomal structure by Atg11 is essential for selective autophagy in budding yeast. J Cell Biol 2006; 175:925–935.
Legakis JE, Yen W-L, Klionsky DJ . A cycling protein complex required for selective autophagy. Autophagy 2007; 3:422–432.
Yen WL, Legakis JE, Nair U, Klionsky DJ . Atg27 is required for autophagy-dependent cycling of Atg9. Mol Biol Cell 2007; 18:581–593.
Orsi A, Razi M, Dooley HC, et al. Dynamic and transient interactions of Atg9 with autophagosomes, but not membrane integration, are required for autophagy. Mol Biol Cell 2012; 23:1860–1873.
Puri C, Renna M, Bento CF, Moreau K, Rubinsztein DC . Diverse autophagosome membrane sources coalesce in recycling endosomes. Cell 2013; 154:1285–1299.
Obara K, Sekito T, Ohsumi Y . Assortment of phosphatidy-linositol 3-kinase complexes–Atg14p directs association of complex I to the pre-autophagosomal structure in Saccharomyces cerevisiae. Mol Biol Cell 2006; 17:1527–1539.
Kihara A, Noda T, Ishihara N, Ohsumi Y . Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in autophagy and carboxypeptidase Y sorting in Saccharomyces cerevisiae. J Cell Biol 2001; 152:519–530.
Araki Y, Ku WC, Akioka M, et al. Atg38 is required for autophagy-specific phosphatidylinositol 3-kinase complex integrity. J Cell Biol 2013; 203:299–313.
Itakura E, Kishi C, Inoue K, Mizushima N . Beclin 1 forms two distinct phosphatidylinositol 3-kinase complexes with mammalian Atg14 and UVRAG. Mol Biol Cell 2008; 19:5360–5372.
Yang Z, Klionsky DJ . Mammalian autophagy: core molecular machinery and signaling regulation. Curr Opin Cell Biol 2010; 22:124–131.
Parzych KR, Klionsky DJ . An overview of autophagy: Morphology, mechanism, and regulation. Antioxid Redox Signal 2013 Aug 2. doi:10.1089/ars.2013.5371
Xie Z, Nair U, Klionsky DJ . Atg8 controls phagophore expansion during autophagosome formation. Mol Biol Cell 2008; 19:3290–3298.
Shintani T, Huang W-P, Stromhaug PE, Klionsky DJ . Mechanism of cargo selection in the cytoplasm to vacuole targeting pathway. Dev Cell 2002; 3:825–837.
Kim J, Dalton VM, Eggerton KP, Scott SV, Klionsky DJ . Apg7p/Cvt2p is required for the cytoplasm-to-vacuole targeting, macroautophagy, and peroxisome degradation pathways. Mol Biol Cell 1999; 10:1337–1351.
Kirisako T, Ichimura Y, Okada H, et al. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway. J Cell Biol 2000; 151:263–276.
Ichimura Y, Kirisako T, Takao T, et al. A ubiquitin-like system mediates protein lipidation. Nature 2000; 408:488–492.
Mizushima N, Noda T, Yoshimori T, et al. A protein conjugation system essential for autophagy. Nature 1998; 395:395–398.
Tanida I, Mizushima N, Kiyooka M, et al. Apg7p/Cvt2p: A novel protein-activating enzyme essential for autophagy. Mol Biol Cell 1999; 10:1367–1379.
Shintani T, Mizushima N, Ogawa Y, et al. Apg10p, a novel protein-conjugating enzyme essential for autophagy in yeast. EMBO J 1999; 18:5234–5241.
Mizushima N, Sugita H, Yoshimori T, Ohsumi Y . A new protein conjugation system in human. The counterpart of the yeast Apg12p conjugation system essential for autophagy. J Biol Chem 1998; 273:33889–33892.
Tanida I, Tanida-Miyake E, Ueno T, Kominami E . The human homolog of Saccharomyces cerevisiae Apg7p is a protein-activating enzyme for multiple substrates including human Apg12p, GATE-16, GABARAP, and MAP-LC3. J Biol Chem 2001; 276:1701–1706.
Mizushima N, Yoshimori T, Ohsumi Y . Mouse Apg10 as an Apg12-conjugating enzyme: analysis by the conjugation-mediated yeast two-hybrid method. FEBS Lett 2002; 532:450–454.
Mizushima N, Kuma A, Kobayashi Y, et al. Mouse Apg16L, a novel WD-repeat protein, targets to the autophagic isolation membrane with the Apg12-Apg5 conjugate. J Cell Sci 2003; 116:1679–1688.
Weidberg H, Shvets E, Shpilka T, et al. LC3 and GATE-16/GABARAP subfamilies are both essential yet act differently in autophagosome biogenesis. EMBO J 2010; 29:1792–1802.
Li M, Hou Y, Wang J, et al. Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8 substrates. J Biol Chem 2011; 286:7327–7338.
Kabeya Y, Mizushima N, Yamamoto A, et al. LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation. J Cell Sci 2004; 117:2805–2812.
Scott SV, Guan J, Hutchins MU, Kim J, Klionsky DJ . Cvt19 is a receptor for the cytoplasm-to-vacuole targeting pathway. Mol Cell 2001; 7:1131–1141.
Watanabe Y, Noda NN, Kumeta H, et al. Selective transport of α-mannosidase by autophagic pathways: structural basis for cargo recognition by Atg19 and Atg34. J Biol Chem 2010; 285:30026–30033.
Kanki T, Klionsky DJ . Mitophagy in yeast occurs through a selective mechanism. J Biol Chem 2008; 283:32386–32393.
Okamoto K, Kondo-Okamoto N, Ohsumi Y . Mitochondria-anchored receptor Atg32 mediates degradation of mitochondria via selective autophagy. Dev Cell 2009; 17:87–97.
Motley AM, Nuttall JM, Hettema EH . Pex3-anchored Atg36 tags peroxisomes for degradation in Saccharomyces cerevisiae. EMBO J 2012; 31:2852–2868.
Mijaljica D, Nazarko TY, Brumell JH, et al. Receptor protein complexes are in control of autophagy. Autophagy 2012; 8:1701–1705.
Lynch-Day MA, Klionsky DJ . The Cvt pathway as a model for selective autophagy. FEBS Lett 2010; 584:1359–1366.
Klionsky DJ, Cueva R, Yaver DS . Aminopeptidase I of Saccharomyces cerevisiae is localized to the vacuole independent of the secretory pathway. J Cell Biol 1992; 119:287–299.
Oda MN, Scott SV, Hefner-Gravink A, Caffarelli AD, Klionsky DJ . Identification of a cytoplasm to vacuole targeting determinant in aminopeptidase I. J Cell Biol 1996; 132:999–1010.
Scott SV, Hefner-Gravink A, Morano KA, et al. Cytoplasm-to-vacuole targeting and autophagy employ the same machinery to deliver proteins to the yeast vacuole. Proc Natl Acad Sci USA 1996; 93:12304–12308.
Baba M, Osumi M, Scott SV, Klionsky DJ, Ohsumi Y . Two distinct pathways for targeting proteins from the cytoplasm to the vacuole/lysosome. J Cell Biol 1997; 139:1687–1695.
Scott SV, Baba M, Ohsumi Y, Klionsky DJ . Aminopeptidase I is targeted to the vacuole by a nonclassical vesicular mechanism. J Cell Biol 1997; 138:37–44.
Kim J, Scott SV, Oda MN, Klionsky DJ . Transport of a large oligomeric protein by the cytoplasm to vacuole protein targeting pathway. J Cell Biol 1997; 137:609–618.
Kim J, Kamada Y, Stromhaug PE, et al. Cvt9/Gsa9 functions in sequestering selective cytosolic cargo destined for the vacuole. J Cell Biol 2001; 153:381–396.
Geng J, Klionsky DJ . Quantitative regulation of vesicle formation in yeast nonspecific autophagy. Autophagy 2008; 4:955–957.
Kanki T, Wang K, Cao Y, Baba M, Klionsky DJ . Atg32 is a mitochondrial protein that confers selectivity during mitophagy. Dev Cell 2009; 17:98–109.
Kanki T, Wang K, Baba M, et al. A genomic screen for yeast mutants defective in selective mitochondria autophagy. Mol Biol Cell 2009; 20:4730–4738.
Mao K, Wang K, Zhao M, Xu T, Klionsky DJ . Two MAPK-signaling pathways are required for mitophagy in Saccharomyces cerevisiae. J Cell Biol 2011; 193:755–767.
Kissova I, Deffieu M, Manon S, Camougrand N . Uth1p is involved in the autophagic degradation of mitochondria. J Biol Chem 2004; 279:39068–39074.
Tal R, Winter G, Ecker N, Klionsky DJ, Abeliovich H . Aup1p, a yeast mitochondrial protein phosphatase homolog, is required for efficient stationary phase mitophagy and cell survival. J Biol Chem 2007; 282:5617–5624.
Journo D, Mor A, Abeliovich H . Aup1-mediated regulation of Rtg3 during mitophagy. J Biol Chem 2009; 284:35885–35895.
Kim I, Rodriguez-Enriquez S, Lemasters JJ . Selective degradation of mitochondria by mitophagy. Arch Biochem Biophys 2007; 462:245–253.
Mortensen M, Ferguson DJ, Simon AK . Mitochondrial clearance by autophagy in developing erythrocytes: clearly important, but just how much so? Cell Cycle 2010; 9:1901–1906.
Novak I, Kirkin V, McEwan DG, et al. Nix is a selective autophagy receptor for mitochondrial clearance. EMBO Rep 2010; 11:45–51.
Novak I, Dikic I . Autophagy receptors in developmental clearance of mitochondria. Autophagy 2011; 7:301–303.
Kitada T, Asakawa S, Hattori N, et al. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Nature 1998; 392:605–608.
Valente EM, Abou-Sleiman PM, Caputo V, et al. Hereditary early-onset Parkinson's disease caused by mutations in PINK1. Science 2004; 304:1158–1160.
Osellame LD, Duchen MR . Defective quality control mechanisms and accumulation of damaged mitochondria link Gaucher and Parkinson diseases. Autophagy 2013; 9:1633–1635.
Hutchins MU, Veenhuis M, Klionsky DJ . Peroxisome degradation in Saccharomyces cerevisiae is dependent on machinery of macroautophagy and the Cvt pathway. J Cell Sci 1999; 112:4079–4087.
Farré JC, Manjithaya R, Mathewson RD, Subramani S . PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev Cell 2008; 14:365–376.
Nazarko TY, Farre JC, Subramani S . Peroxisome size provides insights into the function of autophagy-related proteins. Mol Biol Cell 2009; 20:3828–3839.
Hara-Kuge S, Fujiki Y . The peroxin Pex14p is involved in LC3-dependent degradation of mammalian peroxisomes. Exp Cell Res 2008; 314:3531–3541.
Kim PK, Hailey DW, Mullen RT, Lippincott-Schwartz J . Ubiquitin signals autophagic degradation of cytosolic proteins and peroxisomes. Proc Natl Acad Sci USA 2008; 105:20567–20574.
Jao CC, Ragusa MJ, Stanley RE, Hurley JH . A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy. Proc Natl Acad Sci USA 2013; 110:5486–5491.
Chew LH, Setiaputra D, Klionsky DJ, Yip CK . Structural characterization of the Saccharomyces cerevisiae autophagy regulatory complex Atg17-Atg31-Atg29. Autophagy 2013; 9:1467–1474.
Yeh YY, Shah KH, Herman PK . An Atg13 protein-mediated self-association of the Atg1 protein kinase is important for the induction of autophagy. J Biol Chem 2011; 286:28931–28939.
Krick R, Busse RA, Scacioc A, et al. Structural and functional characterization of the two phosphoinositide binding sites of PROPPINs, a β-propeller protein family. Proc Natl Acad Sci USA 2012; 109:E2042–E2049.
Watanabe Y, Kobayashi T, Yamamoto H, et al. Structure-based analyses reveal distinct binding sites for Atg2 and phosphoinositides in Atg18. J Biol Chem 2012; 287:31681–31690.
Baskaran S, Ragusa MJ, Boura E, Hurley JH . Two-site recognition of phosphatidylinositol 3-phosphate by PROPPINs in autophagy. Mol Cell 2012; 47:339–348.
Dove SK, Piper RC, McEwen RK, et al. Svp1p defines a family of phosphatidylinositol 3,5-bisphosphate effectors. EMBO J 2004; 23:1922–1933.
Rieter E, Vinke F, Bakula D, et al. Atg18 function in autophagy is regulated by specific sites within its b-propeller. J Cell Sci 2013; 126:593–604.
Sugawara K, Suzuki NN, Fujioka Y, et al. The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8. Genes Cells 2004; 9:611–618.
Sugawara K, Suzuki NN, Fujioka Y, et al. Structural basis for the specificity and catalysis of human Atg4B responsible for mammalian autophagy. J Biol Chem 2005; 280:40058–40065.
Satoo K, Noda NN, Kumeta H, et al. The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy. EMBO J 2009; 28:1341–1350.
Noda NN, Satoo K, Fujioka Y, et al. Structural basis of Atg8 activation by a homodimeric E1, Atg7. Mol Cell 2011; 44:462–475.
Hong SB, Kim BW, Lee KE, et al. Insights into noncanonical E1 enzyme activation from the structure of autophagic E1 Atg7 with Atg8. Nat Struct Mol Biol 2011; 18:1323–1330.
Taherbhoy AM, Tait SW, Kaiser SE, et al. Atg8 transfer from Atg7 to Atg3: a distinctive E1-E2 architecture and mechanism in the autophagy pathway. Mol Cell 2011; 44:451–461.
Yamada Y, Suzuki NN, Hanada T, et al. The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation. J Biol Chem 2007; 282:8036–8043.
Fujita N, Itoh T, Omori H, et al. The Atg16L complex specifies the site of LC3 lipidation for membrane biogenesis in autophagy. Mol Biol Cell 2008; 19:2092–2100.
Sakoh-Nakatogawa M, Matoba K, Asai E, et al. Atg12-Atg5 conjugate enhances E2 activity of Atg3 by rearranging its catalytic site. Nat Struct Mol Biol 2013; 20:433–439.
Suzuki NN, Yoshimoto K, Fujioka Y, Ohsumi Y, Inagaki F . The crystal structure of plant ATG12 and its biological implication in autophagy. Autophagy 2005; 1:119–126.
Yamaguchi M, Noda NN, Yamamoto H, et al. Structural insights into Atg10-mediated formation of the autophagy-essential Atg12-Atg5 conjugate. Structure 2012; 20:1244–1254.
Kaiser SE, Mao K, Taherbhoy AM, et al. Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures. Nat Struct Mol Biol 2012; 19:1242–1249.
Matsushita M, Suzuki NN, Obara K, et al. Structure of Atg5·Atg16, a complex essential for autophagy. J Biol Chem 2007; 282:6763–6772.
Noda NN, Fujioka Y, Hanada T, Ohsumi Y, Inagaki F . Structure of the Atg12-Atg5 conjugate reveals a platform for stimulating Atg8-PE conjugation. EMBO Rep 2013; 14:206–211.
Fujioka Y, Noda NN, Nakatogawa H, Ohsumi Y, Inagaki F . Dimeric coiled-coil structure of Saccharomyces cerevisiae Atg16 and its functional significance in autophagy. J Biol Chem 2010; 285:1508–1515.
Otomo C, Metlagel Z, Takaesu G, Otomo T . Structure of the human ATG12∼ATG5 conjugate required for LC3 lipidation in autophagy. Nat Struct Mol Biol 2013; 20:59–66.
Reggiori F, Klionsky DJ . Autophagic processes in yeast: mechanism, machinery and regulation. Genetics 2013; 194:341–361.
Miller S, Tavshanjian B, Oleksy A, et al. Shaping development of autophagy inhibitors with the structure of the lipid kinase Vps34. Science 2010; 327:1638–1642.
Huang W, Choi W, Hu W, et al. Crystal structure and biochemical analyses reveal Beclin 1 as a novel membrane binding protein. Cell Res 2012; 22:473–489.
Oberstein A, Jeffrey PD, Shi Y . Crystal structure of the Bcl-XL-Beclin 1 peptide complex: Beclin 1 is a novel BH3-only protein. J Biol Chem 2007; 282:13123–13132.
Li X, He L, Che KH, et al. Imperfect interface of Beclin1 coiled-coil domain regulates homodimer and heterodimer formation with Atg14L and UVRAG. Nat Commun 2012; 3:662.
Heenan EJ, Vanhooke JL, Temple BR, et al. Structure and function of Vps15 in the endosomal G protein signaling pathway. Biochemistry 2009; 48:6390–6401.
Itakura E, Kishi-Itakura C, Mizushima N . The hairpin-type tail-anchored SNARE syntaxin 17 targets to autophagosomes for fusion with endosomes/lysosomes. Cell 2012; 151:1256–1269.
Miller S, Oleksy A, Perisic O, Williams RL . Finding a fitting shoe for Cinderella: searching for an autophagy inhibitor. Autophagy 2010; 6:805–807.