A unified nomenclature for yeast autophagy-related genes

Developmental Cell

Volumn 5, Issue 4, 2003, Pages 539-545

  Klionsky, Daniel J ^a   Cregg, James M ^b   Dunn Jr , William A ^c   Emr, Scott D ^d   Sakai, Yasuyoshi ^e   Sandoval, Ignacio V ^f   Sibirny, Andrei ^g   Subramani, Suresh ^h   Thumm, Michael ⁱ   Veenhuis, Marten ^j   Ohsumi, Yoshinori ^k  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b KECK GRADUATE INSTITUTE   (United States)

^c UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e KYOTO UNIVERSITY   (Japan)

^f CSIC   (Spain)

^g INSTITUTE OF CELL BIOLOGY   (Ukraine)

^h SECTION OF MOLECULAR BIOLOGY   (United States)

ⁱ UNIVERSITY OF GÖTTINGEN   (Germany)

^j UNIVERSITY OF GRONINGEN   (Netherlands)

^k NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

AUTOPHAGY; GENE DUPLICATION; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC SCREENING; LETTER; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; YEAST;

AUTOPHAGY; SACCHAROMYCES CEREVISIAE; TERMINOLOGY;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 10744225487     PISSN: 15345807     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1534-5807(03)00296-X     Document Type: Letter

References (94)

1. Abeliovich H. Darsow T. Emr S.D. Cytoplasm to vacuole trafficking of aminopeptidase I requires a t-SNARE-Sec1p complex composed of Tlg2p and Vps45p EMBO J. 18 1999 6005-6016
2. Barth H. Thumm M. A genomic screen identifies AUT8 as a novel gene essential for autophagy in the yeast Saccharomyces cerevisiae Gene 274 2001 151-156
3. Barth H. Meiling-Wesse K. Epple U.D. Thumm M. Autophagy and the cytoplasm to vacuole targeting pathway both require Aut10p FEBS Lett. 508 2001 23-28
4. Barth H. Meiling-Wesse K. Epple U.D. Thumm M. Mai1p is essential for maturation of proaminopeptidase I but not for autophagy FEBS Lett. 512 2002 173-179
5. Bellu A.R. Komori M. van der Klei I.J. Kiel J.A.K.W. Veenhuis M. Peroxisome biogenesis and selective degradation converge at Pex14p J. Biol. Chem. 276 2001a 44570-44574
6. Bellu A.R. Kram A.M. Kiel J.A. Veenhuis M. van der Klei I.J. Glucose-induced and nitrogen-starvation-induced peroxisome degradation are distinct processes in Hansenula polymorpha that involve both common and unique genes FEMS Yeast Res. 1 2001b 23-31
7. Bellu A.R. Salomons F.A. Kiel J.A.K.W. Veenhuis M. van der Klei I.J. Removal of Pex3p is an important initial stage in selective peroxisome degradation in Hansenula polymorpha J. Biol. Chem. 277 2002 42875-42880
8. Darsow T. Rieder S.E. Emr S.D. A multispecificity syntaxin homologue, Vam3p, essential for autophagic and biosynthetic protein transport to the vacuole J. Cell Biol. 138 1997 517-529
9. Doelling J.H. Walker J.M. Friedman E.M. Thompson A.R. Vierstra R.D. The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana J. Biol. Chem. 277 2002 33105-33114
10. Epple U.D. Suriapranata I. Eskelinen E.-L. Thumm M. Aut5/Cvt17p, a putative lipase essential for disintegration of autophagic bodies inside the vacuole J. Bacteriol. 183 2001 5942-5955
11. Fischer von Mollard G. Stevens T.H. The Saccharomyces cerevisiae v-SNARE Vti1p is required for multiple membrane transport pathways to the vacuole Mol. Biol. Cell 10 1999 1719-1732
12. Funakoshi T. Matsuura A. Noda T. Ohsumi Y. Analyses of APG13 gene involved in autophagy in yeast, Saccharomyces cerevisiae Gene 192 1997 207-213
13. Guan J. Stromhaug P.E. George M.D. Habibzadegah-Tari P. Bevan A. Dunn Jr. W.A. Klionsky D.J. Cvt18/Gsa12 is required for cytoplasm-to-vacuole transport, pexophagy, and autophagy in Saccharomyces cerevisiae and Pichia pastoris Mol. Biol. Cell 12 2001 3821-3838
14. Habibzadegah-Tari P. Dunn Jr. W.A. Glucose-induced pexophagy in Pichia pastoris Klionsky D.J. Autophagy 2003 Landes Biosciences Georgetown, TX in press
15. Hamasaki M. Noda T. Ohsumi Y. The early secretory pathway contributes to autophagy in yeast Cell Struct. Funct. 28 2003 49-54
16. Hanaoka H. Noda T. Shirano Y. Kato T. Hayashi H. Shibata D. Tabata S. Ohsumi Y. Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene Plant Physiol. 129 2002 1181-1193
17. Harding T.M. Morano K.A. Scott S.V. Klionsky D.J. Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway J. Cell Biol. 131 1995 591-602
18. Harding T.M. Hefner-Gravink A. Thumm M. Klionsky D.J. Genetic and phenotypic overlap between autophagy and the cytoplasm to vacuole protein targeting pathway J. Biol. Chem. 271 1996 17621-17624
19. He H. Dang Y. Dai F. Guo Z. Wu J. She X. Pei Y. Chen Y. Ling W. Wu C. et al. Post-translational modifications of three members of the human MAP1LC3 family and identification of a novel type of modification for MAP1LC3B J. Biol. Chem. 278 2003 29278-29287
20. Ichimura Y. Kirisako T. Takao T. Satomi Y. Shimonishi Y. Ishihara N. Mizushima N. Tanida I. Kominami E. Ohsumi M. et al. A ubiquitin-like system mediates protein lipidation Nature 408 2000 488-492
21. Juhasz G. Csikos G. Sinka R. Erdelyi M. Sass M. The Drosophila homolog of Aut1 is essential for autophagy and development FEBS Lett. 543 2003 154-158
22. Kamada Y. Funakoshi T. Shintani T. Nagano K. Ohsumi M. Ohsumi Y. Tor-mediated induction of autophagy via an Apg1 protein kinase complex J. Cell Biol. 150 2000 1507-1513
23. Kametaka S. Matsuura A. Wada Y. Ohsumi Y. Structural and functional analyses of APG5, a gene involved in autophagy in yeast Gene 178 1996 139-143
24. Kametaka S. Okano T. Ohsumi M. Ohsumi Y. Apg14p and Apg6/Vps30p form a protein complex essential for autophagy in the yeast, Saccharomyces cerevisiae J. Biol. Chem. 273 1998 22284-22291-
25. Kiel J.A.K.W. Rechinger K.B. van der Klei I.J. Salomons F.A. Titorenko V.I. Veenhuis M. The Hansenula polymorpha PDD1 gene product, essential for the selective degradation of peroxisomes, is a homologue of Saccharomyces cerevisiae Vps34p Yeast 15 1999 741-754
26. 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. 152 2001 519-530
27. Kim J. Dalton V.M. Eggerton K.P. Scott S.V. Klionsky D.J. Apg7p/Cvt2p is required for the cytoplasm-to-vacuole targeting, macroautophagy, and peroxisome degradation pathways Mol. Biol. Cell 10 1999 1337-1351
28. Kim J. Kamada Y. Stromhaug P.E. Guan J. Hefner-Gravink A. Baba M. Scott S.V. Ohsumi Y. Dunn Jr. W.A. Klionsky D.J. Cvt9/Gsa9 functions in sequestering selective cytosolic cargo destined for the vacuole J. Cell Biol. 153 2001 381-396
29. Kirisako T. Ichimura Y. Okada H. Kabeya Y. Mizushima N. Yoshimori T. Ohsumi M. Takao T. Noda T. Ohsumi Y. The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway J. Cell Biol. 151 2000 263-276
30. Klionsky, D.J., ed. (2003). Autophagy (Georgetown, TX: Landes Biosciences), in press
31. Komduur J.A. Veenhuis M. Kiel J.A.K.W. The Hansenula polymorpha PDD7 gene is essential for macropexophagy and microautophagy FEM. Yeast Res. 3 2003 27-34
32. Kucharczyk R. Kierzek A.M. Slonimski P.P. Rytka J. The Ccz1 protein interacts with Ypt7 GTPase during fusion of multiple transport intermediates with the vacuole in S. cerevisiae J. Cell Sci. 114 2001 3137-3145
33. Kulachkovsky A.R. Moroz O.M. Sibirny A.A. Impairment of peroxisome degradation in Pichia methanolica mutants defective in acetyl-CoA synthetase or isocitrate lyase Yeast 13 1997 1043-1052
34. Kweon Y. Rothe A. Conibear E. Stevens T.H. Ykt6p is a multifunctional yeast R-SNARE that is required for multiple membrane transport pathways to the vacuole Mol. Biol. Cell 14 2003 1868-1881
35. Lang T. Schaeffeler E. Bernreuther D. Bredschneider M. Wolf D.H. Thumm M. Aut2p and Aut7p, two novel microtubule-associated proteins are essential for delivery of autophagic vesicles to the vacuole EMBO J. 17 1998 3597-3607
36. Lang T. Reiche S. Straub M. Bredschneider M. Thumm M. Autophagy and the cvt pathway both depend on AUT9 J. Bacteriol. 182 2000 2125-2133
37. Leber R. Silles E. Sandoval I.V. Mazon M.J. Yol082p, a novel CVT protein involved in the selective targeting of aminopeptidase I to the yeast vacuole J. Biol. Chem. 276 2001 29210-29217
38. Liang X.H. Jackson S. Seaman M. Brown K. Kempkes B. Hibshoosh H. Levine B. Induction of autophagy and inhibition of tumorigenesis by beclin 1 Nature 402 1999 672-676
39. Matsuura A. Tsukada M. Wada Y. Ohsumi Y. Apg1p, a novel protein kinase required for the autophagic process in Saccharomyces cerevisiae Gene 192 1997 245-250
40. Meiling-Wesse K. Barth H. Thumm M. Ccz1p/Aut11p/Cvt16p is essential for autophagy and the cvt pathway FEBS Lett. 526 2002a 71-76
41. Meiling-Wesse K. Barth H. Voss C. Barmark G. Muren E. Ronne H. Thumm M. Yeast Mon1p/Aut12p functions in vacuolar fusion of autophagosomes and cvt-vesicles FEBS Lett. 530 2002b 174-180
42. Meléndez A. Tallóczy Z. Seaman M. Eskelinen E.-L. Hall D.H. Levine B. Autophagy genes are essential for dauer development and lifespan extension in C. elegans Science 301 2003 1387-1391
43. Mizushima N. Noda T. Yoshimori T. Tanaka Y. Ishii T. George M.D. Klionsky D.J. Ohsumi M. Ohsumi Y. A protein conjugation system essential for autophagy Nature 395 1998 395-398
44. 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. 273 1998 33889-33892
45. Mizushima N. Noda T. Ohsumi Y. Apg16p is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway EMBO J. 18 1999 3888-3896
46. Mizushima N. Yamamoto A. Hatano M. Kobayashi Y. Kabeya Y. Suzuki K. Tokuhisa T. Ohsumi Y. Yoshimori T. Dissection of autophagosome formation using Apg5-deficient mouse embryonic stem cells J. Cell Biol. 152 2001 657-668
47. Mizushima N. Yoshimori T. Ohsumi Y. Mouse Apg10 as an Apg12-conjugating enzyme: analysis by the conjugation-mediated yeast two-hybrid method FEBS Lett. 532 2002 450-454
48. Mizushima N. Kuma A. Kobayashi Y. Yamamoto A. Matsubae M. Takao T. Natsume T. Ohsumi Y. Yoshimori T. Mouse Apg16L, a novel WD-repeat protein, targets to the autophagic isolation membrane with the Apg12-Apg5 conjugate J. Cell Sci. 116 2003 1679-1688
49. Mukaiyama H. Oku M. Baba M. Samizo T. Hammond A.T. Glick B.S. Kato N. Sakai Y. Paz2 and 13 other PAZ gene products regulate vacuolar engulfment of peroxisomes during micropexophagy Genes Cells 7 2002 75-90
50. Mukaiyama, H., Baba, M., Osumi, M., Aoyagi, S., Kato, N., Ohsumi, Y., and Sakai, Y. (2004). Modification of a ubiquitin-like protein Paz2 conducted micropexophagy through formation of a novel membrane structure. Mol. Biol. Cell, in press. Published online September 17, 2003. 10.1091/mbc.E03-05-0340
51. Nice D.C. Sato T.K. Stromhaug P.E. Emr S.D. Klionsky D.J. Cooperative binding of the cytoplasm to vacuole targeting pathway proteins, Cvt13 and Cvt20, to phosphatidylinositol 3-phosphate at the pre-autophagosomal structure is required for selective autophagy J. Biol. Chem. 277 2002 30198-30207
52. Noda T. Ohsumi Y. Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast J. Biol. Chem. 273 1998 3963-3966
53. Noda T. Kim J. Huang W.-P. Baba M. Tokunaga C. Ohsumi Y. Klionsky D.J. Apg9p/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways J. Cell Biol. 148 2000 465-480
54. Oku M. Warnecke D. Noda T. Muller F. Heinz E. Mukaiyama H. Kato N. Sakai Y. Peroxisome degradation requires catalytically active sterol glucosyltransferase with a GRAM domain EMBO J. 22 2003 3231-3241
55. 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 J. Biol. Chem. 278 2003 17636-17645
56. Price A. Wickner W. Ungermann C. Proteins needed for vesicle budding from the Golgi complex are also required for the docking step of homotypic vacuole fusion J. Cell Biol. 148 2000 1223-1229
57. Reggiori F. Klionsky D.J. Autophagy in the eukaryotic cell Eukaryot. Cell 1 2002 11-21
58. Reggiori F. Wang C.-W. Stromhaug P.E. Shintani T. Klionsky D.J. Vps51 is part of the yeast Vps fifty-three tethering complex essential for retrograde traffic from the early endosome and Cvt vesicle completion J. Biol. Chem. 278 2003 5009-5020
59. Roberts P. Moshitch-Moshkovitz S. Kvam E. O'Toole E. Winey M. Goldfarb D.S. Piecemeal microautophagy of nucleus in Saccharomyces cerevisiae Mol. Biol. Cell 14 2003 129-141
60. Sakai Y. Koller A. Rangell L.K. Keller G.A. Subramani S. Peroxisome degradation by microautophagy in Pichia pastoris: identification of specific steps and morphological intermediates J. Cell Biol. 141 1998 625-636
61. Sato T.K. Darsow T. Emr S.D. Vam7p, a SNAP-25-like molecule, and Vam3p, a syntaxin homolog, function together in yeast vacuolar protein trafficking Mol. Cell. Biol. 18 1998 5308-5319
62. Sato T.K. Rehling P. Peterson M.R. Emr S.D. Class C Vps protein complex regulates vacuolar SNARE pairing and is required for vesicle docking/fusion Mol. Cell 6 2000 661-671
63. Schlumpberger M. Schaeffeler E. Straub M. Bredschneider M. Wolf D.H. Thumm M. AUT1, a gene essential for autophagocytosis in the yeast Saccharomyces cerevisiae J. Bacteriol. 179 1997 1068-1076
64. Scott S.V. Nice III D.C. Nau J.J. Weisman L.S. Kamada Y. Keizer-Gunnink I. Funakoshi T. Veenhuis M. Ohsumi Y. Klionsky D.J. Apg13p and Vac8p are part of a complex of phosphoproteins that are required for cytoplasm to vacuole targeting J. Biol. Chem. 275 2000 25840-25849
65. Scott S.V. Guan J. Hutchins M.U. Kim J. Klionsky D.J. Cvt19 is a receptor for the cytoplasm-to-vacuole targeting pathway Mol. Cell 7 2001 1131-1141
66. Shintani T. Mizushima N. Ogawa Y. Matsuura A. Noda T. Ohsumi Y. Apg10p, a novel protein-conjugating enzyme essential for autophagy in yeast EMBO J. 18 1999 5234-5241
67. Shintani T. Suzuki K. Kamada Y. Noda T. Ohsumi Y. Apg2p functions in autophagosome formation on the perivacuolar structure J. Biol. Chem. 276 2001 30452-30460
68. Stasyk O.V. van der Klei I.J. Bellu A.R. Shen S. Kiel J.A.K.W. Cregg J.M. Veenhuis M. A Pichia pastoris VPS15 homologue is required in selective peroxisome autophagy Curr. Genet. 36 1999 262-269
69. Stasyk, O.V., Nazarko, T.Y., Stasyk, O.G., Krasovska, O.S., Warnecke, D., Nicaud, J.-M., Cregg, J.M., and Sibirny, A.A. (2003). Sterol glucosyltransferases have different functional roles in Pichia pastoris and Yarrowia lipolytica. Cell Biol. Int. 27, in press.
70. Straub M. Bredschneider M. Thumm M. AUT3, a serine/threonine kinase gene, is essential for autophagocytosis in Saccharomyces cerevisiae J. Bacteriol. 179 1997 3875-3883
71. Stromhaug P.E. Bevan A. Dunn Jr. W.A. GSA11 encodes a unique 208-kDa protein required for pexophagy and autophagy in Pichia pastoris J. Biol. Chem. 276 2001 42422-42435
72. Suriapranata I. Epple U.D. Bernreuther D. Bredschneider M. Sovarasteanu K. Thumm M. The breakdown of autophagic vesicles inside the vacuole depends on Aut4p J. Cell Sci. 113 2000 4025-4033
73. Takeshige K. Baba M. Tsuboi S. Noda T. Ohsumi Y. Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction J. Cell Biol. 119 1992 301-311
74. Tanida I. Mizushima N. Kiyooka M. Ohsumi M. Ueno T. Ohsumi Y. Kominami E. Apg7p/Cvt2p: a novel protein-activating enzyme essential for autophagy Mol. Biol. Cell 10 1999 1367-1379
75. 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. 276 2001 1701-1706
76. Tanida I. Nishitani T. Nemoto T. Ueno T. Kominami E. Mammalian Apg12p, but not the Apg12p·Apg5p conjugate, facilitates LC3 processing Biochem. Biophys. Res. Commun. 296 2002a 1164-1170
77. Tanida I. Tanida-Miyake E. Komatsu M. Ueno T. Kominami E. 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 2002b 13739-13744
78. Tanida I. Tanida-Miyake E. Nishitani T. Komatsu M. Yamazaki H. Ueno T. Kominami E. Murine Apg12p has a substrate preference for murine Apg7p over three Apg8p homologs Biochem. Biophys. Res. Commun. 292 2002c 256-262
79. Teter S.A. Eggerton K.P. Scott S.V. Kim J. Fischer A.M. Klionsky D.J. Degradation of lipid vesicles in the yeast vacuole requires function of Cvt17, a putative lipase J. Biol. Chem. 276 2001 2083-2087
80. Thumm M. Kadowaki T. The loss of Drosophila APG4/AUT2 function modifies the phenotypes of cut and Notch signaling pathway mutants Mol. Genet. Genomics 266 2001 657-663
81. Thumm M. Egner R. Koch M. Schlumpberger M. Straub M. Veenhuis M. Wolf D.H. Isolation of autophagocytosis mutants of Saccharoymces cerevisiae FEBS Lett. 349 1994 275-280
82. Titorenko V.I. Keizer I. Harder W. Veenhuis M. Isolation and characterization of mutants impaired in the selective degradation of peroxisomes in the yeast Hansenula polymorpha J. Bacteriol. 177 1995 357-363
83. Tsukada M. Ohsumi Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae FEBS Lett. 333 1993 169-174
84. Tucker K.A. Reggiori F. Dunn Jr. W.A. Klionsky D.J. Atg23 is essential for the Cvt pathway and efficient autophagy but not pexophagy J. Biol. Chem. in press 2003
85. Wada Y. Ohsumi Y. Anraku Y. Genes for directing vacuolar morphogenesis in Saccharomyces cerevisiae. I. Isolation and characterization of two classes of vam mutants J. Biol. Chem. 267 1992 18665-18670
86. Wang Y.X. Catlett N.L. Weisman L.S. Vac8p, a vacuolar protein with armadillo repeats, functions in both vacuole inheritance and protein targeting from the cytoplasm to vacuole J. Cell Biol. 140 1998 1063-1074
87. Wang C.-W. Kim J. Huang W.-P. Abeliovich H. Stromhaug P.E. Dunn Jr. W.A. Klionsky D.J. Apg2 is a novel protein required for the cytoplasm to vacuole targeting, autophagy, and pexophagy pathways J. Biol. Chem. 276 2001 30442-30451
88. Wang Z. Wilson W.A. Fujino M.A. Roach P.J. Antagonistic controls of autophagy and glycogen accumulation by Snf1p, the yeast homolog of AMP-activated protein kinase, and the cyclin-dependent kinase Pho85p Mol. Cell. Biol. 21 2001 5742-5752
89. Wang C.-W. Stromhaug P.E. Shima J. Klionsky D.J. The Ccz1-Mon1 protein complex is required for the late step of multiple vacuole delivery pathways J. Biol. Chem. 277 2002 47917-47927
90. Wichmann H. Hengst L. Gallwitz D. Endocytosis in yeast: evidence for the involvement of a small GTP-binding protein (Ypt7p) Cell 71 1992 1131-1142
91. Wurmser A.E. Emr S.D. Novel PtdIns(3)P-binding protein Etf1 functions as an effector of the Vps34 PtdIns 3-kinase in autophagy J. Cell Biol. 158 2002 761-772
92. Wurmser A.E. Sato T.K. Emr S.D. New component of the vacuolar class C-Vps complex couples nucleotide exchange on the Ypt7 GTPase to SNARE-dependent docking and fusion J. Cell Biol. 151 2000 551-562
93. Yuan W. Tuttle D.L. Shi Y.J. Ralph G.S. Dunn Jr. W.A. Glucose-induced microautophagy in Pichia pastoris requires the α-subunit of phosphofructokinase J. Cell Sci. 110 1997 1935-1945
94. Yuan W. Stromhaug P.E. Dunn Jr. W.A. Glucose-induced autophagy of peroxisomes in Pichia pastoris requires a unique E1-like protein Mol. Biol. Cell 10 1999 1353-1366