Atg41/Icy2 regulates autophagosome formation

References

• Shintani T, Klionsky DJ. Autophagy in health and disease: a double-edged sword. Science 2004; 306:990-5; PMID:15528435; http://dx.doi.org/10.1126/science.1099993
   PubMed Web of Science ®Google Scholar
• Mari M, Griffith J, Rieter E, Krishnappa L, Klionsky DJ, Reggiori F. An Atg9-containing compartment that functions in the early steps of autophagosome biogenesis. J Cell Biol 2010; 190:1005-22; PMID:20855505; http://dx.doi.org/10.1083/jcb.200912089
   PubMed Web of Science ®Google Scholar
• Feng Y, He D, Yao Z, Klionsky DJ. The machinery of macroautophagy. Cell Res 2014; 24:24-41; PMID:24366339; http://dx.doi.org/10.1038/cr.2013.168
   PubMed Web of Science ®Google Scholar
• Reggiori F, Shintani T, Nair U, Klionsky DJ. Atg9 cycles between mitochondria and the pre-autophagosomal structure in yeasts. Autophagy 2005; 1:101-9.; PMID:16874040; http://dx.doi.org/10.4161/auto.1.2.1840
   PubMed Web of Science ®Google Scholar
• 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; PMID:14723849; http://dx.doi.org/10.1016/S1534-5807(03)00402-7
   PubMed Web of Science ®Google Scholar
• Yen WL, Legakis JE, Nair U, Klionsky DJ. Atg27 is required for autophagy-dependent cycling of Atg9. Mol Biol Cell 2007; 18:581-93; PMID:17135291; http://dx.doi.org/10.1091/mbc.E06-07-0612
   PubMed Web of Science ®Google Scholar
• Tsukada M, Ohsumi Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett 1993; 333:169-74; PMID:8224160; http://dx.doi.org/10.1016/0014-5793(93)80398-E
   PubMed Web of Science ®Google Scholar
• Jones DL, Petty J, Hoyle DC, Hayes A, Oliver SG, Riba-Garcia I, Gaskell SJ, Stateva L. Genome-wide analysis of the effects of heat shock on a Saccharomyces cerevisiae mutant with a constitutively activated cAMP-dependent pathway. Comp Funct Genomics 2004; 5:419-31; PMID:18629174; http://dx.doi.org/10.1002/cfg.415
   PubMed Web of Science ®Google Scholar
• Kuhn KM, DeRisi JL, Brown PO, Sarnow P. Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol Cell Biol 2001; 21:916-27; PMID:11154278; http://dx.doi.org/10.1128/MCB.21.3.916-927.2001
   PubMed Web of Science ®Google Scholar
• Ubersax JA, Woodbury EL, Quang PN, Paraz M, Blethrow JD, Shah K, Shokat KM, Morgan DO. Targets of the cyclin-dependent kinase Cdk1. Nature 2003; 425:859-64; PMID:14574415; http://dx.doi.org/10.1038/nature02062
   PubMed Web of Science ®Google Scholar
• Byrne KP, Wolfe KH. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 2005; 15:1456-61; PMID:16169922; http://dx.doi.org/10.1101/gr.3672305
   PubMed Web of Science ®Google Scholar
• Kanki T, Wang K, Baba M, Bartholomew CR, Lynch-Day MA, Du Z, Geng J, Mao K, Yang Z, Yen WL, et al. A genomic screen for yeast mutants defective in selective mitochondria autophagy. Mol Biol Cell 2009; 20:4730-8; PMID:19793921; http://dx.doi.org/10.1091/mbc.E09-03-0225
   PubMed Web of Science ®Google Scholar
• Shintani T, Klionsky DJ. Cargo proteins facilitate the formation of transport vesicles in the cytoplasm to vacuole targeting pathway. J Biol Chem 2004; 279:29889-94; PMID:15138258; http://dx.doi.org/10.1074/jbc.M404399200
   PubMed Web of Science ®Google Scholar
• Klionsky DJ, Emr SD. Membrane protein sorting: biosynthesis, transport and processing of yeast vacuolar alkaline phosphatase. Embo J 1989; 8:2241-50; PMID:2676517
   PubMed Web of Science ®Google Scholar
• Noda T, Klionsky DJ. The quantitative Pho8Delta60 assay of nonspecific autophagy. Methods Enzymol 2008; 451:33-42; PMID:19185711; http://dx.doi.org/10.1016/S0076-6879(08)03203-5
   PubMed Web of Science ®Google Scholar
• Bartholomew CR, Suzuki T, Du Z, Backues SK, Jin M, Lynch-Day MA, Umekawa M, Kamath A, Zhao M, Xie Z, et al. Ume6 transcription factor is part of a signaling cascade that regulates autophagy. Proc Natl Acad Sci U S A 2012; 109:11206-10; PMID:22733735; http://dx.doi.org/10.1073/pnas.1200313109
   PubMed Web of Science ®Google Scholar
• Jin M, He D, Backues SK, Freeberg MA, Liu X, Kim JK, Klionsky DJ. Transcriptional regulation by Pho23 modulates the frequency of autophagosome formation. Curr Biol 2014; 24:1314-22; PMID:24881874; http://dx.doi.org/10.1016/j.cub.2014.04.048
   PubMed Web of Science ®Google Scholar
• Bernard A, Jin M, Gonzalez-Rodriguez P, Fullgrabe J, Delorme-Axford E, Backues SK, Joseph B, Klionsky DJ. Rph1/KDM4 Mediates Nutrient-Limitation Signaling that Leads to the Transcriptional Induction of Autophagy. Curr Biol 2015; 25(5):546-55
   PubMed Web of Science ®Google Scholar
• Lynch-Day MA, Klionsky DJ. The Cvt pathway as a model for selective autophagy. FEBS Lett 2010; 584:1359-66; PMID:20146925; http://dx.doi.org/10.1016/j.febslet.2010.02.013
   PubMed Web of Science ®Google Scholar
• Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH. Autophagy driven by a master regulator of hematopoiesis. Mol Cell Biol 2012; 32:226-39; PMID:22025678; http://dx.doi.org/10.1128/MCB.06166-11
   PubMed Web of Science ®Google Scholar
• Xie Z, Nair U, Klionsky DJ. Atg8 controls phagophore expansion during autophagosome formation. Mol Biol Cell 2008; 19:3290-8; PMID:18508918; http://dx.doi.org/10.1091/mbc.E07-12-1292
   PubMed Web of Science ®Google Scholar
• Jin M, Klionsky DJ. Transcriptional regulation of ATG9 by the Pho23-Rpd3 complex modulates the frequency of autophagosome formation. Autophagy 2014; 10:1681-2; PMID:25046109; http://dx.doi.org/10.4161/auto.29641
   PubMed Web of Science ®Google Scholar
• Backues SK, Chen D, Ruan J, Xie Z, Klionsky DJ. Estimating the size and number of autophagic bodies by electron microscopy. Autophagy 2014; 10:155-64; PMID:24270884; http://dx.doi.org/10.4161/auto.26856
   PubMed Web of Science ®Google Scholar
• Xie Z, Klionsky DJ. Autophagosome formation: core machinery and adaptations. Nat Cell Biol 2007; 9:1102-9; PMID:17909521; http://dx.doi.org/10.1038/ncb1007-1102
   PubMed Web of Science ®Google Scholar
• Sung MK, Huh WK. Bimolecular fluorescence complementation analysis system for in vivo detection of protein-protein interaction in Saccharomyces cerevisiae. Yeast 2007; 24:767-75; PMID:17534848; http://dx.doi.org/10.1002/yea.1504
   PubMed Web of Science ®Google Scholar
• Popelka H, Uversky VN, Klionsky DJ. Identification of Atg3 as an intrinsically disordered polypeptide yields insights into the molecular dynamics of autophagy-related proteins in yeast. Autophagy 2014; 10:1093-104; PMID:24879155; http://dx.doi.org/10.4161/auto.28616
   PubMed Web of Science ®Google Scholar
• Mei Y, Su M, Soni G, Salem S, Colbert CL, Sinha SC. Intrinsically disordered regions in autophagy proteins. Proteins 2014; 82:565-78; PMID:24115198; http://dx.doi.org/10.1002/prot.24424
   PubMed Web of Science ®Google Scholar
• Xue B, Dunbrack RL, Williams RW, Dunker AK, Uversky VN. PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim Biophys Acta 2010; 1804:996-1010; PMID:20100603; http://dx.doi.org/10.1016/j.bbapap.2010.01.011
   PubMed Web of Science ®Google Scholar
• Natarajan K, Meyer MR, Jackson BM, Slade D, Roberts C, Hinnebusch AG, Marton MJ. Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol Cell Biol 2001; 21:4347-68; PMID:11390663; http://dx.doi.org/10.1128/MCB.21.13.4347-4368.2001
   PubMed Web of Science ®Google Scholar
• Fedorova AV, Chan IS, Shin JA. The GCN4 bZIP can bind to noncognate gene regulatory sequences. Biochim Biophys Acta 2006; 1764:1252-9; PMID:16784907; http://dx.doi.org/10.1016/j.bbapap.2006.04.009
   PubMed Web of Science ®Google Scholar
• Yang Z, Geng J, Yen WL, Wang K, Klionsky DJ. Positive or negative roles of different cyclin-dependent kinase Pho85-cyclin complexes orchestrate induction of autophagy in Saccharomyces cerevisiae. Mol Cell 2010; 38:250-64; PMID:20417603; http://dx.doi.org/10.1016/j.molcel.2010.02.033
   PubMed Web of Science ®Google Scholar
• Hara T, Mizushima N. Role of ULK-FIP200 complex in mammalian autophagy: FIP200, a counterpart of yeast Atg17? Autophagy 2009; 5:85-7; PMID:18981720; http://dx.doi.org/10.4161/auto.5.1.7180
   PubMed Web of Science ®Google Scholar
• 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; 119:287-99; PMID:1400574; http://dx.doi.org/10.1083/jcb.119.2.287
   PubMed Web of Science ®Google Scholar
• Noda T, Kim J, Huang WP, Baba M, Tokunaga C, Ohsumi Y, Klionsky DJ. Apg9p/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways. J Cell Biol 2000; 148:465-80; PMID:10662773; http://dx.doi.org/10.1083/jcb.148.3.465
   PubMed Web of Science ®Google Scholar
• 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. EMBO J 2001; 20:5971-81; PMID:11689437; http://dx.doi.org/10.1093/emboj/20.21.5971
   PubMed Web of Science ®Google Scholar
• Govin J, Dorsey J, Gaucher J, Rousseaux S, Khochbin S, Berger SL. Systematic screen reveals new functional dynamics of histones H3 and H4 during gametogenesis. Genes Dev 2010; 24:1772-86; PMID:20713519; http://dx.doi.org/10.1101/gad.1954910
   PubMed Web of Science ®Google Scholar
• Klionsky DJ, Abdalla FC, Abeliovich H, Abraham RT, Acevedo-Arozena A, Adeli K, Agholme L, Agnello M, Agostinis P, Aguirre-Ghiso JA, et al. Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy 2012; 8:445-544; PMID:22966490; http://dx.doi.org/10.4161/auto.19496
   PubMed Web of Science ®Google Scholar
• Gueldener U, Heinisch J, Koehler GJ, Voss D, Hegemann JH. A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Res 2002; 30:e23; PMID:11884642
   PubMed Web of Science ®Google Scholar
• Longtine MS, McKenzie A, 3rd, Demarini DJ, Shah NG, Wach A, Brachat A, Philippsen P, Pringle JR. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 1998; 14:953-61; PMID:9717241; http://dx.doi.org/10.1002/(SICI)1097-0061(199807)14:10%3c953::AID-YEA293%3e3.0.CO;2-U
   PubMed Web of Science ®Google Scholar