Autophagy basics

Microbiology and Immunology

Volumn 55, Issue 1, 2011, Pages 1-11

  Tanida, Isei ^a  

^a NATIONAL INSTITUTE OF INFECTIOUS DISEASES   (Japan)

Author keywords

Autophagosome; Infection; Lysosome; Omegasome

Indexed keywords

AUTOPHAGY PROTEIN 12; AUTOPHAGY PROTEIN 5; AUTOPHAGY PROTEIN 9; BECLIN 1; BINDING PROTEIN; GREEN FLUORESCENT PROTEIN; MEMBRANE PROTEIN; MICROTUBULE ASSOCIATED PROTEIN; PHOSPHATIDYLINOSITOL 3 KINASE; PHOSPHATIDYLINOSITOL 3 PHOSPHATE; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; RAB PROTEIN; ULK1 PROTEIN KINASE; UNCLASSIFIED DRUG; VIRULENCE FACTOR;

ADAPTIVE IMMUNITY; ANTIBACTERIAL ACTIVITY; ANTIVIRAL ACTIVITY; AUTOPHAGY; BACTERIAL INFECTION; CELL BUDDING; CONJUGATION; CYTOSOL; DEGRADATION KINETICS; HUMAN; INNATE IMMUNITY; MEMBRANE FORMATION; MEMBRANE FUSION; NONHUMAN; REVIEW; VIROGENESIS; VIRUS INFECTION;

ANIMALS; AUTOPHAGY; HUMANS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; LYSOSOMES; MEMBRANE PROTEINS; MICROTUBULE-ASSOCIATED PROTEINS; PHAGOSOMES; PHOSPHATIDYLINOSITOL 3-KINASES; PHOSPHOLIPIDS; PROTEIN-SERINE-THREONINE KINASES; UBIQUITINATION;

BACTERIA (MICROORGANISMS); MAMMALIA;

EID: 78650328444     PISSN: 03855600     EISSN: 13480421     Source Type: Journal    
DOI: 10.1111/j.1348-0421.2010.00271.x     Document Type: Review

References (105)

1. Levine B., Kroemer G. (2008) Autophagy in the pathogenesis of disease. Cell 132: 27-42.
2. Eskelinen E.L., Saftig P. (2009) Autophagy: a lysosomal degradation pathway with a central role in health and disease. Biochim Biophys Acta 1793: 664-73.
3. Virgin H.W., Levine B. (2009) Autophagy genes in immunity. Nat Immunol 10: 461-70.
4. Tanida I., Ueno T., Kominami E. (2004) LC3 conjugation system in mammalian autophagy. Int J Biochem Cell Biol 36: 2503-18.
5. Nakatogawa H., Suzuki K., Kamada Y., Ohsumi Y. (2009) Dynamics and diversity in autophagy mechanisms: lessons from yeast. Nat Rev Mol Cell Biol 10: 458-67.
6. Yang Z., Klionsky D.J. (2009) An overview of the molecular mechanism of autophagy. Curr Top Microbiol Immunol 335: 1-32.
7. Kudchodkar S.B., Levine B. (2009) Viruses and autophagy. Rev Med Virol 19: 359-78.
8. Deretic V. (2010) Autophagy in infection. Curr Opin Cell Biol 22: 252-62.
9. Dreux M., Chisari F.V. (2010) Viruses and the autophagy machinery. Cell Cycle 9: 1295-307.
10. Lin L.T., Dawson P.W.H., Richardson C.D. (2010) Viral interactions with macroautophagy: a double-edged sword. Virology 402: 1-10.
11. Sir D., Ou J.H. (2010) Autophagy in viral replication and pathogenesis. Mol Cells 29: 1-7.
12. Saitoh T., Akira S. (2010) Regulation of innate immune responses by autophagy-related proteins. J Cell Biol 189: 925-35.
13. Tsukada M., Ohsumi Y. (1993) Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett 333: 169-74.
14. Klionsky D.J., Cregg J.M., Dunn W.A., Jr., Emr S.D., Sakai Y., Sandoval I.V., Sibirny A., Subramani S., Thumm M., Veenhuis M., Ohsumi Y. (2003) A unified nomenclature for yeast autophagy-related genes. Dev Cell 5: 539-45.
15. Glick D., Barth S., Macleod K.F. (2010) Autophagy: cellular and molecular mechanisms. J Pathol 221: 3-12.
16. Mizushima N. (2010) The role of the Atg1/U.K. complex in autophagy regulation. Curr Opin Cell Biol 22: 132-9.
17. Liang X.H., 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: 672-76.
18. Young A.R., Chan E.Y., Hu X.W., Kochl R., Crawshaw S.G., High S., Hailey D.W., Lippincott-Schwartz J., Tooze S.A. (2006) Starvation and U.K.-dependent cycling of mammalian Atg9 between the TGN and endosomes. J Cell Sci 119: 3888-900.
19. Webber J.L., Young A.R., Tooze S.A. (2007) Atg9 trafficking in mammalian cells. Autophagy 3: 54-6.
20. Proikas-Cezanne T., Ruckerbauer S., Stierhof Y.D., Berg C., Nordheim A. (2007) Human WIPI-1 puncta-formation: a novel assay to assess mammalian autophagy. FEBS Lett 581: 3396-404.
21. Mizushima N., Noda T., Yoshimori T., Tanaka Y., Ishii T., George M.D., Klionsky D.J., Ohsumi M., Ohsumi Y. (1998) A protein conjugation system essential for autophagy. Nature 395: 395-98.
22. Mizushima N., Sugita H., Yoshimori T., Ohsumi Y. (1998) A new protein conjugation system in human. The counterpart of the yeast Apg12p conjugation system essential for autophagy. J Biol Chem 273: 33, 889-92.
23. 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: 5720-28.
24. 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: 488-92.
25. Petiot A., Ogier-Denis E., Blommaart E.F., Meijer A.J., Codogno P. (2000) Distinct classes of phosphatidylinositol 3'-kinases are involved in signaling pathways that control macroautophagy in HT-29 cells. J Biol Chem 275: 992-8.
26. Liang C., Feng P., Ku B., Dotan I., Canaani D., Oh B.H., Jung J.U. (2006) Autophagic and tumour suppressor activity of a novel Beclin1-binding protein UVRAG. Nat Cell Biol 8: 688-99.
27. 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: 5360-72.
28. 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: 385-96.
29. Zhong Y., Wang Q.J., Li X., Yan Y., Backer J.M., Chait B.T., 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: 468-76.
30. Proikas-Cezanne T., Waddell S., Gaugel A., Frickey T., Lupas A., Nordheim A. (2004) WIPI-1alpha (WIPI49), a member of the novel 7-bladed WIPI protein family, is aberrantly expressed in human cancer and is linked to starvation-induced autophagy. Oncogene 23: 9314-25.
31. Hara T., Takamura A., Kishi C., Iemura S., Natsume T., Guan J.L., Mizushima N. (2008) FIP200, a U.K.interacting protein, is required for autophagosome formation in mammalian cells. J Cell Biol 181: 497-510.
32. Jung C.H., Jun C.B., Ro S.H., Kim Y.M., Otto N.M., Cao J., Kundu M., Kim D.H. (2009) U.K.Atg13-FIP200 complexes mediate mTOR signaling to the autophagy machinery. Mol Biol Cell 20: 1992-2003.
33. Hosokawa N., Hara T., Kaizuka T., Kishi C., Takamura A., Miura Y., Iemura S., Natsume T., Takehana K., Yamada N., Guan J.L., Oshiro N., Mizushima N. (2009) Nutrient-dependent mTORC1 association with the U.K.-Atg13-FIP200 complex required for autophagy. Mol Biol Cell 20: 1981-91.
34. Hosokawa N., Sasaki T., Iemura S., Natsume T., Hara T., Mizushima N. (2009) Atg101, a novel mammalian autophagy protein interacting with Atg13. Autophagy 5: 973-9.
35. Mercer C.A., Kaliappan A., Dennis P.B. (2009) A novel, human Atg13 binding protein, Atg101, interacts with U.K. and is essential for macroautophagy. Autophagy 5: 649-62.
36. Obara K., Sekito T., Ohsumi Y. (2006) Assortment of phosphatidylinositol 3-kinase complexes-atg14p directs association of complex I to the pre-autophagosomal structure in Saccharomyces cerevisiae. Mol Biol Cell 17: 1527-39.
37. Simonsen A., Tooze S.A. (2009) Coordination of membrane events during autophagy by multiple class III PI3-kinase complexes. J Cell Biol 186: 773-82.
38. Takahashi Y., Coppola D., Matsushita N., Cualing H.D., Sun M., Sato Y., Liang C., Jung J.U., Cheng J.Q., Mule J.J., Pledger W.J., Wang H.G. (2007) Bif-1 interacts with Beclin 1 through UVRAG and regulates autophagy and tumorigenesis. Nat Cell Biol 9: 1142-51.
39. Liang C., Lee J.S., Inn K.S., Gack M.U., Li Q., Roberts E.A., Vergne I., Deretic V., Feng P., Akazawa C., Jung J.U. (2008) Beclin1-binding UVRAG targets the class C Vps complex to coordinate autophagosome maturation and endocytic trafficking. Nat Cell Biol 10: 776-87.
40. Fimia G.M., 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: 1121-5.
41. Zhou X., Wang L., Hasegawa H., Amin P., Han B., Kaneko S., He Y., Wang F. (2010) Deletion of PIK3C3/Vps34 in sensory neurons causes rapid neurodegeneration by disrupting the endosomal but not the autophagic pathway. Proc Natl Acad Sci USA 107: 9424-9.
42. Noda T., Kim J., Huang W.P., Baba M., Tokunaga C., Ohsumi Y., Klionsky D.J. (2000) Apg9p/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways. J Cell Biol 148: 465-80.
43. Suzuki K., Kirisako T., Kamada Y., Mizushima N., Noda T., Ohsumi Y. (2001) The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. EMBO J 20: 5971-81.
44. Obara K., Sekito T., Niimi K., Ohsumi Y. (2008) The Atg18-Atg2 complex is recruited to autophagic membranes via phosphatidylinositol 3-phosphate and exerts an essential function. J Biol Chem 283: 23, 972-80.
45. Shintani T., Suzuki K., Kamada Y., Noda T., Ohsumi Y. (2001) Apg2p functions in autophagosome formation on the perivacuolar structure. J Biol Chem 276: 30, 452-60.
46. Yen W.L., Legakis J.E., Nair U., Klionsky D.J. (2007) Atg27 is required for autophagy-dependent cycling of Atg9. Mol Biol Cell 18: 581-93.
47. Mizushima N., Yamamoto A., Hatano M., Kobayashi Y., Kabeya Y., Suzuki K., Tokuhisa T., Ohsumi Y., Yoshimori T. (2001) Dissection of autophagosome formation using Apg5-deficient mouse embryonic stem cells. J Cell Biol 152: 657-68.
48. Tanida I., Mizushima N., Kiyooka M., Ohsumi M., Ueno T., Ohsumi Y., Kominami E. (1999) Apg7p/Cvt2p: A novel protein-activating enzyme essential for autophagy. Mol Biol Cell 10: 1367-79.
49. Shintani T., Mizushima N., Ogawa Y., Matsuura A., Noda T., Ohsumi Y. (1999) Apg10p, a novel protein-conjugating enzyme essential for autophagy in yeast. EMBO J 18: 5234-41.
50. Kim J., Dalton V.M., Eggerton K.P., Scott S.V., Klionsky D.J. (1999) Apg7p/Cvt2p is required for the cytoplasm-to-vacuole targeting, macroautophagy, and peroxisome degradation pathways. Mol Biol Cell 10: 1337-51.
51. Tanida I., Tanida-Miyake E., Ueno T., Kominami E. (2001) 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 276: 1701-06.
52. Mizushima N., Yoshimori T., Ohsumi Y. (2002) Mouse Apg10 as an Apg12-conjugating enzyme: analysis by the conjugation-mediated yeast two-hybrid method. FEBS Lett 532: 450-4.
53. Nemoto T., Tanida I., Tanida-Miyake E., Minematsu-Ikeguchi N., Yokota M., Ohsumi M., Ueno T., Kominami E. (2003) The mouse APG10 homologue, an E2-like enzyme for Apg12p conjugation, facilitates MAP-LC3 modification. J Biol Chem 278: 39, 517-26.
54. Mizushima N., Kuma A., Kobayashi Y., Yamamoto A., Matsubae M., Takao T., Natsume T., Ohsumi Y., Yoshimori T. (2003) Mouse Apg16L, a novel WD-repeat protein, targets to the autophagic isolation membrane with the Apg12-Apg5 conjugate. J Cell Sci 116: 1679-88.
55. Kuma A., Mizushima N., Ishihara N., Ohsumi Y. (2002) Formation of the approximately 350-kDa Apg12-Apg5.Apg16 multimeric complex, mediated by Apg16 oligomerization, is essential for autophagy in yeast. J Biol Chem 277: 18, 619-25.
56. Mizushima N., Noda T., Ohsumi Y. (1999) Apg16p is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway. EMBO J 18: 3888-96.
57. Tanida I., Sou Y.S., Minematsu-Ikeguchi N., Ueno T., Kominami E. (2006) Atg8L/Apg8L is the fourth mammalian modifier of mammalian Atg8 conjugation mediated by human Atg4B, Atg7 and Atg3. FEBS J 273: 2553-62.
58. Tanida I., Tanida-Miyake E., Komatsu M., Ueno T., Kominami E. (2002) Human Apg3p/Aut1p homologue is an authentic E2 enzyme for multiple substrates, GATE-16, GABARAP, and MAP-LC3, and facilitates the conjugation of hApg12p to hApg5p. J Biol Chem 277: 13, 739-44.
59. Sou Y.S., Tanida I., Komatsu M., Ueno T., Kominami E. (2006) Phosphatidylserine in addition to phosphatidylethanolamine is an in vitro target of the mammalian Atg8 modifiers, LC3, GABARAP, and GATE-16. J Biol Chem 281: 3017-24.
60. Tanida I., Ueno T., Kominami E. (2004) Human light chain 3/MAP1LC3B is cleaved at its carboxyl-terminal Met121 to expose Gly120 for lipidation and targeting to autophagosomal membranes. J Biol Chem 279: 47, 704-10.
61. Mizushima N., Yoshimori T., Ohsumi Y. (2003) Role of the Apg12 conjugation system in mammalian autophagy. Int J Biochem Cell Biol 35: 553-61.
62. Hanada T., Noda N.N., Satomi Y., Ichimura Y., Fujioka Y., Takao T., Inagaki F., Ohsumi Y. (2007) The Atg12-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy. J Biol Chem 282: 37, 298-302.
63. Fujita N., Itoh T., Omori H., Fukuda M., Noda T., Yoshimori T. (2008) The Atg16L complex specifies the site of LC3 lipidation for membrane biogenesis in autophagy. Mol Biol Cell 19: 2092-100.
64. Sou Y.S., 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: 4762-75.
65. Itakura E., Mizushima N. (2010) Characterization of autophagosome formation site by a hierarchical analysis of mammalian Atg proteins. Autophagy 6: 764-76.
66. Vergne I., Roberts E., Elmaoued R.A., Tosch V., Delgado M.A., Proikas-Cezanne T., Laporte J., Deretic V. (2009) Control of autophagy initiation by phosphoinositide 3-phosphatase Jumpy. EMBO J 28: 2244-58.
67. Taguchi-Atarashi N., Hamasaki M., Matsunaga K., Omori H., Ktistakis N.T., Yoshimori T., Noda T. (2010) Modulation of local PtdIns3P levels by the PI phosphatase MTMR3 regulates constitutive autophagy. Traffic 11: 468-78.
68. Itoh T., Fujita N., Kanno E., Yamamoto A., Yoshimori T., Fukuda M. (2008) Golgi-resident small GTPase Rab33B interacts with Atg16L and modulates autophagosome formation. Mol Biol Cell 19: 2916-25.
69. Hirota Y., Tanaka Y. (2009) A small GTPase, human Rab32, is required for the formation of autophagic vacuoles under basal conditions. Cell Mol Life Sci 66: 2913-32.
70. Simonsen A., Birkeland H.C., Gillooly D.J., 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: 4239-51.
71. Filimonenko M., Stuffers S., Raiborg C., Yamamoto A., Malerod L., Fisher E.M., Isaacs A., Brech A., Stenmark H., Simonsen A. (2007) Functional multivesicular bodies are required for autophagic clearance of protein aggregates associated with neurodegenerative disease. J Cell Biol 179: 485-500.
72. Jager S., Bucci C., Tanida I., Ueno T., Kominami E., Saftig P., Eskelinen E.L. (2004) Role for Rab7 in maturation of late autophagic vacuoles. J Cell Sci 117: 4837-48.
73. Gutierrez M.G., Munafo D.B., Beron W., Colombo M.I. (2004) Rab7 is required for the normal progression of the autophagic pathway in mammalian cells. J Cell Sci 117: 2687-97.
74. Pankiv S., Alemu E.A., Brech A., Bruun J.A., Lamark T., Overvatn A., Bjorkoy G., Johansen T. (2010) FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport. J Cell Biol 188: 253-69.
75. Tanida I., Wakabayashi M., Kanematsu T., Minematsu-Ikeguchi N., Sou Y.S., Hirata M., Ueno T., Kominami E. (2006) Lysosomal turnover of GABARAP-phospholipid conjugate is activated during differentiation of C2C12 cells to myotubes without inactivation of the mTor kinase-signaling pathway. Autophagy 2: 264-71.
76. Tanida I., Ueno T., Kominami E. (2008) LC3 and Autophagy. Methods Mol Biol 445: 77-88.
77. Teter S.A., Eggerton K.P., Scott S.V., Kim J., Fischer A.M., Klionsky D.J. (2001) Degradation of lipid vesicles in the yeast vacuole requires function of Cvt17, a putative lipase. J Biol Chem 276: 2083-7.
78. Epple U.D., Suriapranata I., Eskelinen E.L., Thumm M. (2001) Aut5/Cvt17p, a putative lipase essential for disintegration of autophagic bodies inside the vacuole. J Bacteriol 183: 5942-55.
79. Yang Z., Huang J., Geng J., Nair U., Klionsky D.J. (2006) Atg22 recycles amino acids to link the degradative and recycling functions of autophagy. Mol Biol Cell 17: 5094-104.
80. Yu L., Mcphee C.K.L.Z., Mardones G.A., Rong Y., Peng J., Mi N., Zhao Y., Liu Z., Wan F., Hailey D.W., Oorschot V., Klumperman J., Baehrecke E.H., Lenardo M.J. (2010) Termination of autophagy and reformation of lysosomes regulated by mTOR. Nature 465: 942-6.
81. Mizushima N., Yoshimori T. (2007) How to Interpret LC3 Immunoblotting. Autophagy 3: 6.
82. Klionsky D.J., Abeliovich H., Agostinis P., Agrawal D.K., Aliev G., Askew D.S., Baba M., Baehrecke E.H., Bahr B.A., Ballabio A., Bamber B.A., Bassham D.C., Bergamini E., Bi X., Biard-Piechaczyk M., Blum J.S., Bredesen D.E., Brodsky J.L., Brumell J.H., Brunk U.T., Bursch W., Camougrand N., Cebollero E., Cecconi F., Chen Y., Chin L.S., Choi A., Chu C.T., Chung J., Clarke P.G., Clark R.S., Clarke S.G., Clave C., Cleveland J.L., Codogno P., Colombo M.I., Coto-Montes A., Cregg J.M., Cuervo A.M., Debnath J., Demarchi F., Dennis P.B., Dennis P.A., Deretic V., Devenish R.J., Di Sano F., Dice J.F., Difiglia M., Dinesh-Kumar S., Distelhorst C.W., Djavaheri-Mergny M., Dorsey F.C., Droge W., Dron M., Dunn W.A., Jr., Duszenko M., Eissa N.T., Elazar Z., Esclatine A., Eskelinen E.L., Fesus L., Finley K.D., Fuentes J.M., Fueyo J., Fujisaki K., Galliot B., Gao F.B., Gewirtz D.A., Gibson S.B., Gohla A., Goldberg A.L., Gonzalez R., Gonzalez-Estevez C., Gorski S., Gottlieb R.A., Haussinger D., He Y.W., Heidenreich K., Hill J.A., Hoyer-Hansen M., Hu X., Huang W.P., Iwasaki A., Jaattela M., Jackson W.T., Jiang X., Jin S., Johansen T., Jung J.U., Kadowaki M., Kang C., Kelekar A., Kessel D.H., Kiel J.A., Kim H.P., Kimchi A., Kinsella T.J., Kiselyov K., Kitamoto K., Knecht E., et al (2008) Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy 4: 151-75.
83. Mizushima N., Yoshimori T., Levine B. (2010) Methods in mammalian autophagy research. Cell 140: 313-26.
84. Mizushima N., Yamamoto A., Matsui M., Yoshimori T., Ohsumi Y. (2004) In vivo analysis of autophagy in response to nutrient starvation using transgenic mice expressing a fluorescent autophagosome marker. Mol Biol Cell 15: 1101-11.
85. Mizushima N., Kuma A. (2008) Autophagosomes in GFP-LC3 transgenic mice. Methods Mol Biol 445: 119-24.
86. Ciechomska I.A., Tolkovsky A.M. (2007) Non-autophagic GFP-LC3 puncta induced by saponin and other detergents. Autophagy 3: 586-90.
87. Katayama H., Yamamoto A., Mizushima N., Yoshimori T., Miyawaki A. (2008) GFP-like proteins stably accumulate in lysosomes. Cell Struct Funct 33: 1-12.
88. Mizushima N. (2004) Methods for monitoring autophagy. Int J Biochem Cell Biol 36: 2491-502.
89. Kimura S., Noda T., Yoshimori T. (2007) Dissection of the autophagosome maturation process by a novel reporter protein, tandem fluorescent-tagged LC3. Autophagy 3: 452-60.
90. Kimura S., Fujita N., Noda T., Yoshimori T. (2009) Monitoring autophagy in mammalian cultured cells through the dynamics of LC3. Methods Enzymol 452: 1-12.
91. Tanida I., Minematsu-Ikeguchi N., Ueno T., Kominami E. (2005) Lysosomal turnover, but not a cellular level, of endogenous LC3 is a marker for autophagy. Autophagy 1: 84-91.
92. Klionsky D.J., Elazar Z., Seglen P.O., Rubinsztein D.C. (2008) Does bafilomycin A1 block the fusion of autophagosomes with lysosomes Autophagy 4: 849-950.
93. Sobota J.A., Back N., Eipper B.A., Mains R.E. (2009) Inhibitors of the V0 subunit of the vacuolar H+-ATPase prevent segregation of lysosomal- and secretory-pathway proteins. J Cell Sci 122: 3542-53.
94. Komatsu M., Waguri S., Koike M., Sou Y.S., 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., Yamamoto M., Yue Z., Uchiyama Y., Kominami E., Tanaka K. (2007) Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice. Cell 131: 1149-63.
95. Pankiv S., Clausen T.H., Lamark T., Brech A., Bruun J.A., 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: 24, 131-45.
96. 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: 603-14.
97. Ichimura Y., Kominami E., Tanaka K., Komatsu M. (2008) Selective turnover of p62/A170/SQSTM1 by autophagy. Autophagy 4: 8.
98. Tanida I., Sou Y.S., Ezaki J., Minematsu-Ikeguchi N., Ueno T., Kominami E. (2004) HsAtg4B/HsApg4B/autophagin-1 cleaves the carboxyl termini of three human Atg8 homologues and delipidates microtubule-associated protein light chain 3- and GABAA receptor-associated protein-phospholipid conjugates. J Biol Chem 279: 36, 268-76.
99. Fujita N., Hayashi-Nishino M., Fukumoto H., Omori H., Yamamoto A., Noda T., Yoshimori T. (2008) An Atg4B mutant hampers the lipidation of LC3 paralogues and causes defects in autophagosome closure. Mol Biol Cell 19: 4651-9.
100. C74A hampers autophagosome closure: a useful protein for inhibiting autophagy. Autophagy 5: 88-9.
101. Kihara A., Noda T., Ishihara N., Ohsumi Y. (2001) Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in autophagy and carboxypeptidase Y sorting in Saccharomyces cerevisiae. J Cell Biol 152: 519-30.
102. Kametaka S., Okano T., Ohsumi M., Ohsumi Y. (1998) Apg14p and Apg6/Vps30p form a protein complex essential for autophagy in the yeast, Saccharomyces cerevisiae. J Biol Chem 273: 22, 284-91.
103. A receptors and the cytoskeleton. Nature 397: 69-72.
104. Sagiv Y., Legesse-Miller A., Porat A., Elazar Z. (2000) GATE-16, a membrane transport modulator, interacts with NSF and the Golgi v-SNARE GOS-28. EMBO J 19: 1494-504.
105. Axe E.L., Walker S.A., Manifava M., Chandra P., Roderick H.L., Habermann A., Griffiths G., Ktistakis N.T. (2008) Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J Cell Biol 182: 685-701.