Autophagy in cell life and cell death

Current Topics in Developmental Biology

Volumn 114, Issue , 2015, Pages 67-91

  Anding, Allyson L ^a   Baehrecke, Eric H ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

Apoptosis; Atg genes; Autophagy; Caspase; Necrosis; Programmed cell death

Indexed keywords

ANIMAL; APOPTOSIS; AUTOPHAGY; CAENORHABDITIS ELEGANS; CELL DEATH; CELL SURVIVAL; CYTOLOGY; DICTYOSTELIUM; DROSOPHILA MELANOGASTER; PHYSIOLOGY; STARVATION; VERTEBRATE;

ANIMALS; APOPTOSIS; AUTOPHAGY; CAENORHABDITIS ELEGANS; CELL DEATH; CELL SURVIVAL; DICTYOSTELIUM; DROSOPHILA MELANOGASTER; STARVATION; VERTEBRATES;

EID: 84954025740     PISSN: 00702153     EISSN: None     Source Type: Book Series    
DOI: 10.1016/bs.ctdb.2015.07.012     Document Type: Chapter

References (124)

1. Anding A.L., Baehrecke E.H. Vps15 is required for stress induced and developmentally triggered autophagy and salivary gland protein secretion in Drosophila. Cell Death and Differentiation 2015, 22(3):457-464. 10.1038/cdd.2014.174.
2. Barth J.M.I., Szabad J., Hafen E., Köhler K. Autophagy in Drosophila ovaries is induced by starvation and is required for oogenesis. Cell Death and Differentiation 2011, 18(6):915-924. 10.1038/cdd.2010.157.
3. Basit F., Cristofanon S., Fulda S. Obatoclax (GX15-070) triggers necroptosis by promoting the assembly of the necrosome on autophagosomal membranes. Cell Death and Differentiation 2013, 20(9):1161-1173. 10.1038/cdd.2013.45.
4. Berry D.L., Baehrecke E.H. Growth arrest and autophagy are required for salivary gland cell degradation in Drosophila. Cell 2007, 131(6):1137-1148. 10.1016/j.cell.2007.10.048.
5. Birgisdottir Å.B., Lamark T., Johansen T. The LIR motif-Crucial for selective autophagy. Journal of Cell Science 2013, 126(Pt. 15):3237-3247. 10.1242/jcs.126128.
6. Bjørkøy G., Lamark T., Brech A., Outzen H., Perander M., Overvatn A., et al. p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death. The Journal of Cell Biology 2005, 171(4):603-614. 10.1083/jcb.200507002.
7. Bray K., Mathew R., Lau A., Kamphorst J.J., Fan J., Chen J., et al. Autophagy suppresses RIP kinase-dependent necrosis enabling survival to mTOR inhibition. PLoS One 2012, 7(7):e41831. 10.1371/journal.pone.0041831.
8. Cecconi F., Levine B. The role of autophagy in mammalian development: Cell makeover rather than cell death. Developmental Cell 2008, 15(3):344-357. 10.1016/j.devcel.2008.08.012.
9. Chang T.-K., Shravage B.V., Hayes S.D., Powers C.M., Simin R.T., Wade Harper J., et al. Uba1 functions in Atg7- and Atg3-independent autophagy. Nature Cell Biology 2013, 15(9):1067-1078. 10.1038/ncb2804.
10. Choi J., Jo M., Lee E., Choi D. The role of autophagy in corpus luteum regression in the rat. Biology of Reproduction 2011, 85(3):465-472. 10.1095/biolreprod.111.091314.
11. Clausen T.H., Lamark T., Isakson P., Finley K., Larsen K.B., Brech A., et al. p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy. Autophagy 2010, 6(3):330-344.
12. Cornillon S., Foa C., Davoust J., Buonavista N., Gross J.D., Golstein P. Programmed cell death in Dictyostelium. Journal of Cell Science 1994, 107(Pt. 10):2691-2704.
13. de Chastellier C., Ryter A. Changes of the cell surface and of the digestive apparatus of Dictyostelium discoideum during the starvation period triggering aggregation. The Journal of Cell Biology 1977, 75(1):218-236.
14. Denton D., Shravage B., Simin R., Mills K., Berry D.L., Baehrecke E.H., et al. Autophagy, not apoptosis, is essential for midgut cell death in Drosophila. Current Biology: CB 2009, 19(20):1741-1746. 10.1016/j.cub.2009.08.042.
15. Denton D., Xu T., Kumar S. Autophagy as a pro-death pathway. Immunology and Cell Biology 2015, 93(1):35-42. 10.1038/icb.2014.85.
16. Deosaran E., Larsen K.B., Hua R., Sargent G., Wang Y., Kim S., et al. NBR1 acts as an autophagy receptor for peroxisomes. Journal of Cell Science 2013, 126(Pt. 4):939-952. 10.1242/jcs.114819.
17. Elgendy M., Sheridan C., Brumatti G., Martin S.J. Oncogenic Ras-induced expression of Noxa and Beclin-1 promotes autophagic cell death and limits clonogenic survival. Molecular Cell 2011, 42(1):23-35. 10.1016/j.molcel.2011.02.009.
18. Filimonenko M., Isakson P., Finley K.D., Anderson M., Jeong H., Melia T.J., et al. The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. Molecular Cell 2010, 38(2):265-279. 10.1016/j.molcel.2010.04.007.
19. Fimia G.M., Stoykova A., Romagnoli A., Giunta L., Di Bartolomeo S., Nardacci R., et al. Ambra1 regulates autophagy and development of the nervous system. Nature 2007, 447(7148):1121-1125. 10.1038/nature05925.
20. Fraser H.M., Lunn S.F., Harrison D.J., Kerr J.B. Luteal regression in the primate: Different forms of cell death during naturaland gonadotropin-releasing hormone antagonist or prostaglandin analogue-induced luteolysis. Biology of Reproduction 1999, 61(6):1468-1479.
21. Gajewska M., Sobolewska A., Kozlowski M., Motyl T. Role of autophagy in mammary gland development. Journal of Physiology and Pharmacology: An Official Journal of the Polish Physiological Society 2008, 59(Suppl. 9):237-249.
22. Galluzzi L., Vitale I., Abrams J.M., Alnemri E.S., Baehrecke E.H., Blagosklonny M.V., et al. Molecular definitions of cell death subroutines: Recommendations of the Nomenclature Committee on Cell Death 2012. Cell Death and Differentiation 2012, 19(1):107-120. 10.1038/cdd.2011.96.
23. Gan B., Peng X., Nagy T., Alcaraz A., Gu H., Guan J.-L. Role of FIP200 in cardiac and liver development and its regulation of TNFalpha and TSC-mTOR signaling pathways. The Journal of Cell Biology 2006, 175(1):121-133. 10.1083/jcb.200604129.
24. Geisler S., Holmström K.M., Skujat D., Fiesel F.C., Rothfuss O.C., Kahle P.J., et al. PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1. Nature Cell Biology 2010, 12(2):119-131. 10.1038/ncb2012.
25. Gewirtz D.A. When cytoprotective autophagy isn't. and even when it is. Autophagy 2014, 10(3):391-392. 10.4161/auto.27719.
26. Gwinn D.M., Shackelford D.B., Egan D.F., Mihaylova M.M., Mery A., Vasquez D.S., et al. AMPK phosphorylation of raptor mediates a metabolic checkpoint. Molecular Cell 2008, 30(2):214-226. 10.1016/j.molcel.2008.03.003.
27. Hanada T., Noda N.N., Satomi Y., Ichimura Y., Fujioka Y., Takao T., et al. The Atg12-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy. The Journal of Biological Chemistry 2007, 282(52):37298-37302. 10.1074/jbc.C700195200.
28. Hanna R.A., Quinsay M.N., Orogo A.M., Giang K., Rikka S., Gustafsson Å.B. Microtubule-associated protein 1 light chain 3 (LC3) interacts with Bnip3 protein to selectively remove endoplasmic reticulum and mitochondria via autophagy. The Journal of Biological Chemistry 2012, 287(23):19094-19104. 10.1074/jbc.M111.322933.
29. Hara T., Nakamura K., Matsui M., Yamamoto A., Nakahara Y., Suzuki-Migishima R., et al. Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice. Nature 2006, 441(7095):885-889. 10.1038/nature04724.
30. He M.-X., He Y.-W. A role for c-FLIP(L) in the regulation of apoptosis, autophagy, and necroptosis in T lymphocytes. Cell Death and Differentiation 2013, 20(2):188-197. 10.1038/cdd.2012.148.
31. Hengartner M.O., Horvitz H.R. Programmed cell death in Caenorhabditis elegans. Current Opinion in Genetics & Development 1994, 4(4):581-586.
32. Irvine G.B., El-Agnaf O.M., Shankar G.M., Walsh D.M. Protein aggregation in the brain: The molecular basis for Alzheimer's and Parkinson's diseases. Molecular Medicine 2008, 14(7-8):451-464. 10.2119/2007-00100.Irvine.
33. Itakura E., Mizushima N. p62 Targeting to the autophagosome formation site requires self-oligomerization but not LC3 binding. The Journal of Cell Biology 2011, 192(1):17-27. 10.1083/jcb.201009067.
34. Juhász G., Hill J.H., Yan Y., Sass M., Baehrecke E.H., Backer J.M., et al. The class III PI(3)K Vps34 promotes autophagy and endocytosis but not TOR signaling in Drosophila. The Journal of Cell Biology 2008, 181(4):655-666. 10.1083/jcb.200712051.
35. Kamada Y., Funakoshi T., Shintani T., Nagano K., Ohsumi M., Ohsumi Y. Tor-mediated induction of autophagy via an Apg1 protein kinase complex. The Journal of Cell Biology 2000, 150(6):1507-1513.
36. Kanki T., Wang K., Baba M., Bartholomew C.R., Lynch-Day M.A., Du Z., et al. A genomic screen for yeast mutants defective in selective mitochondria autophagy. Molecular Biology of the Cell 2009, 20(22):4730-4738. 10.1091/mbc.E09-03-0225.
37. Kanki T., Wang K., Cao Y., Baba M., Klionsky D.J. Atg32 is a mitochondrial protein that confers selectivity during mitophagy. Developmental Cell 2009, 17(1):98-109. 10.1016/j.devcel.2009.06.014.
38. Kawaguchi Y., Kovacs J.J., McLaurin A., Vance J.M., Ito A., Yao T.P. The deacetylase HDAC6 regulates aggresome formation and cell viability in response to misfolded protein stress. Cell 2003, 115(6):727-738.
39. Kessin R.H. Dictyostelium: Evolution, cell biology and the development of multicellularity 2001, Cambridge University Press, Cambridge, UK.
40. Kim P.K., Hailey D.W., Mullen R.T., Lippincott-Schwartz J. Ubiquitin signals autophagic degradation of cytosolic proteins and peroxisomes. Proceedings of the National Academy of Sciences of the United States of America 2008, 105(52):20567-20574. 10.1073/pnas.0810611105.
41. Kim J., Kundu M., Viollet B., Guan K.-L. AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1. Nature Cell Biology 2011, 13(2):132-141. 10.1038/ncb2152.
42. Kirkin V., Lamark T., Johansen T., Dikic I. NBR1 cooperates with p62 in selective autophagy of ubiquitinated targets. Autophagy 2009, 5(5):732-733.
43. Kitada T., Asakawa S., Hattori N., Matsumine H., Yamamura Y., Minoshima S., et al. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Nature 1998, 392(6676):605-608. 10.1038/33416.
44. Kitanaka C., Kato K., Ijiri R., Sakurada K., Tomiyama A., Noguchi K., et al. Increased Ras expression and caspase-independent neuroblastoma cell death: Possible mechanism of spontaneous neuroblastoma regression. Journal of the National Cancer Institute 2002, 94(5):358-368.
45. Komatsu M., Waguri S., Ueno T., Iwata J., Murata S., Tanida I., et al. Impairment of starvation-induced and constitutive autophagy in Atg7-deficient mice. The Journal of Cell Biology 2005, 169(3):425-434. 10.1083/jcb.200412022.
46. Kondo Y., Kanzawa T., Sawaya R., Kondo S. The role of autophagy in cancer development and response to therapy. Nature Reviews. Cancer 2005, 5(9):726-734. 10.1038/nrc1692.
47. Korac J., Schaeffer V., Kovacevic I., Clement A.M., Jungblut B., Behl C., et al. Ubiquitin-independent function of optineurin in autophagic clearance of protein aggregates. Journal of Cell Science 2013, 126(Pt. 2):580-592. 10.1242/jcs.114926.
48. Kosta A., Roisin-Bouffay C., Luciani M.-F., Otto G.P., Kessin R.H., Golstein P. Autophagy gene disruption reveals a non-vacuolar cell death pathway in Dictyostelium. The Journal of Biological Chemistry 2004, 279(46):48404-48409. 10.1074/jbc.M408924200.
49. Kuma A., Hatano M., Matsui M., Yamamoto A., Nakaya H., Yoshimori T., et al. The role of autophagy during the early neonatal starvation period. Nature 2004, 432(7020):1032-1036. 10.1038/nature03029.
50. Lalaoui N., Lindqvist L.M., Sandow J.J., Ekert P.G. The molecular relationships between apoptosis, autophagy and necroptosis. Seminars in Cell & Developmental Biology 2015, 39:63-69. 10.1016/j.semcdb.2015.02.003.
51. Lamark T., Johansen T. Aggrephagy: Selective disposal of protein aggregates by macroautophagy. International Journal of Cell Biology 2012, 2012(12):736905-736921. 10.1155/2012/736905.
52. Lamark T., Kirkin V., Dikic I., Johansen T. NBR1 and p62 as cargo receptors for selective autophagy of ubiquitinated targets. Cell Cycle 2009, 8(13):1986-1990.
53. Lee C.Y., Baehrecke E.H. Steroid regulation of autophagic programmed cell death during development. Development (Cambridge, England) 2001, 128(8):1443-1455.
54. Lee C.-Y., Cooksey B.A.K., Baehrecke E.H. Steroid regulation of midgut cell death during Drosophila development. Developmental Biology 2002, 250(1):101-111.
55. Lee J.-Y., Koga H., Kawaguchi Y., Tang W., Wong E., Gao Y.-S., et al. HDAC6 controls autophagosome maturation essential for ubiquitin-selective quality-control autophagy. The EMBO Journal 2010, 29(5):969-980. 10.1038/emboj.2009.405.
56. Levraud J.-P., Adam M., Luciani M.-F., de Chastellier C., Blanton R.L., Golstein P. Dictyostelium cell death: Early emergence and demise of highly polarized paddle cells. The Journal of Cell Biology 2003, 160(7):1105-1114. 10.1083/jcb.200212104.
57. Liu L., Feng D., Chen G., Chen M., Zheng Q., Song P., et al. Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells. Nature Cell Biology 2012, 14(2):177-185. 10.1038/ncb2422.
58. Liu Y., Shoji-Kawata S., Sumpter R.M., Wei Y., Ginet V., Zhang L., et al. Autosis is a Na+, K+-ATPase-regulated form of cell death triggered by autophagy-inducing peptides, starvation, and hypoxia-ischemia. Proceedings of the National Academy of Sciences of the United States of America 2013, 110(51):20364-20371. 10.1073/pnas.1319661110.
59. Martin D.N., Baehrecke E.H. Caspases function in autophagic programmed cell death in Drosophila. Development (Cambridge, England) 2004, 131(2):275-284. 10.1242/dev.00933.
60. Matsuura A., Tsukada M., Wada Y., Ohsumi Y. Apg1p, a novel protein kinase required for the autophagic process in Saccharomyces cerevisiae. Gene 1997, 192(2):245-250.
61. McPhee C.K., Baehrecke E.H. The engulfment receptor Draper is required for autophagy during cell death. Autophagy 2010, 6(8):1192-1193. 10.4161/auto.6.8.13474.
62. Meléndez A., Tallóczy Z., Seaman M., Eskelinen E.-L., Hall D.H., Levine B. Autophagy genes are essential for dauer development and life-span extension in C. elegans. Science (New York, N.Y.) 2003, 301(5638):1387-1391. 10.1126/science.1087782.
63. Miller B.C., Zhao Z., Stephenson L.M., Cadwell K., Pua H.H., Lee H.K., et al. The autophagy gene ATG5 plays an essential role in B lymphocyte development. Autophagy 2008, 4(3):309-314.
64. Mizushima N., Levine B. Autophagy in mammalian development and differentiation. Nature Cell Biology 2010, 12(9):823-830. 10.1038/ncb0910-823.
65. Monks J., Henson P.M. Differentiation of the mammary epithelial cell during involution: Implications for breast cancer. Journal of Mammary Gland Biology and Neoplasia 2009, 14(2):159-170. 10.1007/s10911-009-9121-0.
66. Moretti L., Yang E.S., Kim K.W., Lu B. Autophagy signaling in cancer and its potential as novel target to improve anticancer therapy. Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy 2007, 10(4-5):135-143. 10.1016/j.drup.2007.05.001.
67. Mortensen M., Simon A.K. Nonredundant role of Atg7 in mitochondrial clearance during erythroid development. Autophagy 2010, 6(3):423-425.
68. Motley A.M., Nuttall J.M., Hettema E.H. Pex3-anchored Atg36 tags peroxisomes for degradation in Saccharomyces cerevisiae. The EMBO Journal 2012, 31(13):2852-2868. 10.1038/emboj.2012.151.
69. Motyl T., Gajewska M., Zarzynska J., Sobolewska A., Gajkowska B. Regulation of autophagy in bovine mammary epithelial cells. Autophagy 2007, 3(5):484-486.
70. Nakatogawa H., Ichimura Y., Ohsumi Y. Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusion. Cell 2007, 130(1):165-178. 10.1016/j.cell.2007.05.021.
71. Narendra D., Kane L.A., Hauser D.N., Fearnley I.M., Youle R.J. p62/SQSTM1 is required for Parkin-induced mitochondrial clustering but not mitophagy; VDAC1 is dispensable for both. Autophagy 2010, 6(8):1090-1106.
72. Nelson C., Ambros V., Baehrecke E.H. miR-14 regulates autophagy during developmental cell death by targeting ip3-kinase 2. Molecular Cell 2014, 56(3):376-388. 10.1016/j.molcel.2014.09.011.
73. Noda T., Ohsumi Y. Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast. The Journal of Biological Chemistry 1998, 273(7):3963-3966.
74. Novak I., Dikic I. Autophagy receptors in developmental clearance of mitochondria. Autophagy 2011, 7(3):301-303.
75. Novak I., Kirkin V., McEwan D.G., Zhang J., Wild P., Rozenknop A., et al. Nix is a selective autophagy receptor for mitochondrial clearance. EMBO Reports 2010, 11(1):45-51. 10.1038/embor.2009.256.
76. Okamoto K. Organellophagy: Eliminating cellular building blocks via selective autophagy. The Journal of Cell Biology 2014, 205(4):435-445. 10.1083/jcb.201402054.
77. Okamoto K., Kondo-Okamoto N., Ohsumi Y. A landmark protein essential for mitophagy: Atg32 recruits the autophagic machinery to mitochondria. Autophagy 2009, 5(8):1203-1205.
78. Okatsu K., Saisho K., Shimanuki M., Nakada K., Shitara H., Sou Y.-S., et al. p62/SQSTM1 cooperates with Parkin for perinuclear clustering of depolarized mitochondria. Genes to Cells: Devoted to Molecular & Cellular Mechanisms 2010, 15(8):887-900. 10.1111/j.1365-2443.2010.01426.x.
79. Oku M., Sakai Y. Peroxisomes as dynamic organelles: Autophagic degradation. The FEBS Journal 2010, 277(16):3289-3294. 10.1111/j.1742-4658.2010.07741.x.
80. Otto G.P., Wu M.Y., Kazgan N., Anderson O.R., Kessin R.H. Macroautophagy is required for multicellular development of the social amoeba Dictyostelium discoideum. The Journal of Biological Chemistry 2003, 278(20):17636-17645. 10.1074/jbc.M212467200.
81. Pankiv S., Clausen T.H., Lamark T., Brech A., Bruun J.-A., Outzen H., et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. The Journal of Biological Chemistry 2007, 282(33):24131-24145. 10.1074/jbc.M702824200.
82. Papinski D., Schuschnig M., Reiter W., Wilhelm L., Barnes C.A., Maiolica A., et al. Early steps in autophagy depend on direct phosphorylation of Atg9 by the Atg1 kinase. Molecular Cell 2014, 53(3):471-483. 10.1016/j.molcel.2013.12.011.
83. Pua H.H., Dzhagalov I., Chuck M., Mizushima N., He Y.-W. A critical role for the autophagy gene Atg5 in T cell survival and proliferation. The Journal of Experimental Medicine 2007, 204(1):25-31. 10.1084/jem.20061303.
84. Qu X., Zou Z., Sun Q., Luby-Phelps K., Cheng P., Hogan R.N., et al. Autophagy gene-dependent clearance of apoptotic cells during embryonic development. Cell 2007, 128(5):931-946. 10.1016/j.cell.2006.12.044.
85. Reef S., Zalckvar E., Shifman O., Bialik S., Sabanay H., Oren M., et al. A short mitochondrial form of p19ARF induces autophagy and caspase-independent cell death. Molecular Cell 2006, 22(4):463-475. 10.1016/j.molcel.2006.04.014.
86. Riddle D.L., Blumenthal T., Meyer B.J., Priess J.R., Albert P.S. Genetic and environmental regulation of dauer larva development 1997, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. 2nd ed.
87. Roggo L., Bernard V., Kovács A.L., Rose A.M., Savoy F., Zetka M., et al. Membrane transport in Caenorhabditis elegans: An essential role for VPS34 at the nuclear membrane. The EMBO Journal 2002, 21(7):1673-1683. 10.1093/emboj/21.7.1673.
88. Ruck A., Attonito J., Garces K.T., Núnez L., Palmisano N.J., Rubel Z., et al. The Atg6/Vps30/Beclin 1 ortholog BEC-1 mediates endocytic retrograde transport in addition to autophagy in C. elegans. Autophagy 2011, 7(4):386-400.
89. Rusten T.E., Lindmo K., Juhász G., Sass M., Seglen P.O., Brech A., et al. Programmed autophagy in the Drosophila fat body is induced by ecdysone through regulation of the PI3K pathway. Developmental Cell 2004, 7(2):179-192. 10.1016/j.devcel.2004.07.005.
90. Saitoh T., Fujita N., Hayashi T., Takahara K., Satoh T., Lee H., et al. Atg9a controls dsDNA-driven dynamic translocation of STING and the innate immune response. Proceedings of the National Academy of Sciences of the United States of America 2009, 106(49):20842-20846. 10.1073/pnas.0911267106.
91. Saitoh T., Fujita N., Jang M.H., Uematsu S., Yang B.-G., Satoh T., et al. Loss of the autophagy protein Atg16L1 enhances endotoxin-induced IL-1beta production. Nature 2008, 456(7219):264-268. 10.1038/nature07383.
92. Sandoval H., Thiagarajan P., Dasgupta S.K., Schumacher A., Prchal J.T., Chen M., et al. Essential role for Nix in autophagic maturation of erythroid cells. Nature 2008, 454(7201):232-235. 10.1038/nature07006.
93. Sarraf S.A., Raman M., Guarani-Pereira V., Sowa M.E., Huttlin E.L., Gygi S.P., et al. Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization. Nature 2013, 496(7445):372-376. 10.1038/nature12043.
94. Schweers R.L., Zhang J., Randall M.S., Loyd M.R., Li W., Dorsey F.C., et al. NIX is required for programmed mitochondrial clearance during reticulocyte maturation. Proceedings of the National Academy of Sciences of the United States of America 2007, 104(49):19500-19505. 10.1073/pnas.0708818104.
95. Scott R.C., Juhász G., Neufeld T.P. Direct induction of autophagy by Atg1 inhibits cell growth and induces apoptotic cell death. Current Biology: CB 2007, 17(1):1-11. 10.1016/j.cub.2006.10.053.
96. Scott R.C., Schuldiner O., Neufeld T.P. Role and regulation of starvation-induced autophagy in the Drosophila fat body. Developmental Cell 2004, 7(2):167-178. 10.1016/j.devcel.2004.07.009.
97. Sharma K., Le N., Alotaibi M., Gewirtz D.A. Cytotoxic autophagy in cancer therapy. International Journal of Molecular Sciences 2014, 15(6):10034-10051. 10.3390/ijms150610034.
98. Shimizu S., Kanaseki T., Mizushima N., Mizuta T., Arakawa-Kobayashi S., Thompson C.B., et al. Role of Bcl-2 family proteins in a non-apoptotic programmed cell death dependent on autophagy genes. Nature Cell Biology 2004, 6(12):1221-1228. 10.1038/ncb1192.
99. Simonsen A., Birkeland H.C.G., Gillooly D.J., Mizushima N., Kuma A., Yoshimori T., et al. Alfy, a novel FYVE-domain-containing protein associated with protein granules and autophagic membranes. Journal of Cell Science 2004, 117(Pt. 18):4239-4251. 10.1242/jcs.01287.
100. Sou Y.-S., Waguri S., Iwata J.-I., Ueno T., Fujimura T., Hara T., et al. The Atg8 conjugation system is indispensable for proper development of autophagic isolation membranes in mice. Molecular Biology of the Cell 2008, 19(11):4762-4775. 10.1091/mbc.E08-03-0309.
101. Stocco C., Telleria C., Gibori G. The molecular control of corpus luteum formation, function, and regression. Endocrine Reviews 2007, 28(1):117-149. 10.1210/er.2006-0022.
102. Strappazzon F., Nazio F., Corrado M., Cianfanelli V., Romagnoli A., Fimia G.M., et al. AMBRA1 is able to induce mitophagy via LC3 binding, regardless of PARKIN and p62/SQSTM1. Cell Death and Differentiation 2015, 22(3):419-432. 10.1038/cdd.2014.139.
103. Su L., Quade B., Wang H., Sun L., Wang X., Rizo J. A plug release mechanism for membrane permeation by MLKL. Structure 2014, 22(10):1489-1500. 10.1016/j.str.2014.07.014.
104. Suzuki K., Kirisako T., Kamada Y., Mizushima N., Noda T., Ohsumi Y. The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. The EMBO Journal 2001, 20(21):5971-5981. 10.1093/emboj/20.21.5971.
105. Takács-Vellai K., Vellai T., Puoti A., Passannante M., Wicky C., Streit A., et al. Inactivation of the autophagy gene bec-1 triggers apoptotic cell death in C. elegans. Current Biology: CB 2005, 15(16):1513-1517. 10.1016/j.cub.2005.07.035.
106. Tanaka A., Cleland M.M., Xu S., Narendra D.P., Suen D.-F., Karbowski M., et al. Proteasome and p97 mediate mitophagy and degradation of mitofusins induced by Parkin. The Journal of Cell Biology 2010, 191(7):1367-1380. 10.1083/jcb.201007013.
107. Tanaka C., Tan L.-J., Mochida K., Kirisako H., Koizumi M., Asai E., et al. Hrr25 triggers selective autophagy-related pathways by phosphorylating receptor proteins. The Journal of Cell Biology 2014, 207(1):91-105. 10.1083/jcb.201402128.
108. Tanida I., Mizushima N., Kiyooka M., Ohsumi M., Ueno T., Ohsumi Y., et al. Apg7p/Cvt2p: A novel protein-activating enzyme essential for autophagy. Molecular Biology of the Cell 1999, 10(5):1367-1379.
109. Teplova I., Lozy F., Price S., Singh S., Barnard N., Cardiff R.D., et al. ATG proteins mediate efferocytosis and suppress inflammation in mammary involution. Autophagy 2013, 9(4):459-475. 10.4161/auto.23164.
110. Tomoda T., Bhatt R.S., Kuroyanagi H., Shirasawa T., Hatten M.E. A mouse serine/threonine kinase homologous to C. elegans UNC51 functions in parallel fiber formation of cerebellar granule neurons. Neuron 1999, 24(4):833-846.
111. Town C.D., Gross J.D., Kay R.R. Cell differentiation without morphogenesis in Dictyostelium discoideum. Nature 1976, 262(5570):717-719.
112. Tsukada M., Ohsumi Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Letters 1993, 333(1-2):169-174.
113. Tsukamoto S., Kuma A., Murakami M., Kishi C., Yamamoto A., Mizushima N. Autophagy is essential for preimplantation development of mouse embryos. Science (New York, N.Y.) 2008, 321(5885):117-120. 10.1126/science.1154822.
114. Valente E.M., Abou-Sleiman P.M., Caputo V., Muqit M.M.K., Harvey K., Gispert S., et al. Hereditary early-onset Parkinson's disease caused by mutations in PINK1. Science (New York, N.Y.) 2004, 304(5674):1158-1160. 10.1126/science.1096284.
115. Van Humbeeck C., Cornelissen T., Hofkens H., Mandemakers W., Gevaert K., De Strooper B., et al. Parkin interacts with Ambra1 to induce mitophagy. The Journal of Neuroscience: The Official Journal of the Society for Neuroscience 2011, 31(28):10249-10261. 10.1523/JNEUROSCI.1917-11.2011.
116. Wang H., Lu Q., Cheng S., Wang X., Zhang H. Autophagy activity contributes to programmed cell death in Caenorhabditis elegans. Autophagy 2013, 9(12):1975-1982.
117. Wang H., Sun L., Su L., Rizo J., Liu L., Wang L.-F., et al. Mixed lineage kinase domain-like protein MLKL causes necrotic membrane disruption upon phosphorylation by RIP3. Molecular Cell 2014, 54(1):133-146. 10.1016/j.molcel.2014.03.003.
118. Watanabe Y., Tanaka M. p62/SQSTM1 in autophagic clearance of a non-ubiquitylated substrate. Journal of Cell Science 2011, 124(Pt. 16):2692-2701. 10.1242/jcs.081232.
119. Weidberg H., Shvets E., Shpilka T., Shimron F., Shinder V., Elazar Z. LC3 and GATE-16/GABARAP subfamilies are both essential yet act differently in autophagosome biogenesis. The EMBO Journal 2010, 29(11):1792-1802. 10.1038/emboj.2010.74.
120. Whittingham W.F., Raper K.B. Non-viability of stalk cells in Dictyostelium. Proceedings of the National Academy of Sciences of the United States of America 1960, 46(5):642-649.
121. Wong Y.C., Holzbaur E.L.F. Optineurin is an autophagy receptor for damaged mitochondria in parkin-mediated mitophagy that is disrupted by an ALS-linked mutation. Proceedings of the National Academy of Sciences of the United States of America 2014, 111(42):E4439-E4448. 10.1073/pnas.1405752111.
122. Yu L., Alva A., Su H., Dutt P., Freundt E., Welsh S., et al. Regulation of an ATG7-beclin 1 program of autophagic cell death by caspase-8. Science (New York, N.Y.) 2004, 304(5676):1500-1502. 10.1126/science.1096645.
123. Yue Z., Jin S., Yang C., Levine A.J., Heintz N. Beclin 1, an autophagy gene essential for early embryonic development, is a haploinsufficient tumor suppressor. Proceedings of the National Academy of Sciences of the United States of America 2003, 100(25):15077-15082. 10.1073/pnas.2436255100.
124. Zarzyńska J., Gajkowska B., Wojewódzka U., Dymnicki E., Motyl T. Apoptosis and autophagy in involuting bovine mammary gland is accompanied by up-regulation of TGF-beta1 and suppression of somatotropic pathway. Polish Journal of Veterinary Sciences 2007, 10(1):1-9.