The yeast autophagy protease Atg4 is regulated by thioredoxin

References

• He C, Klionsky DJ. Regulation mechanisms and signaling pathways of autophagy. Annu Rev Genet 2009; 43:67-93; PMID:19653858; http://dx.doi.org/10.1146/annurev-genet-102808-114910
   PubMed Web of Science ®Google Scholar
• Mizushima N, Yoshimori T, Ohsumi Y. The role of Atg proteins in autophagosome formation. Annu Rev Cell Dev Biol 2011; 27:107-32; PMID:21801009; http://dx.doi.org/10.1146/annurev-cellbio-092910-154005
   PubMed Web of Science ®Google Scholar
• Schreiber A, Peter M. Substrate recognition in selective autophagy and the ubiquitin-proteasome system. Biochim Biophys Acta 2014; 1843:163-81; PMID:23545414; http://dx.doi.org/10.1016/j.bbamcr.2013.03.019
   PubMed Web of Science ®Google Scholar
• Weidberg H, Shvets E, Elazar Z. Biogenesis and cargo selectivity of autophagosomes. Annu Rev Biochem 2011; 80:125-56; PMID:21548784; http://dx.doi.org/10.1146/annurev-biochem-052709-094552
   PubMed Web of Science ®Google Scholar
• 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 2000; 151:263-76; PMID:11038174; http://dx.doi.org/10.1083/jcb.151.2.263
   PubMed Web of Science ®Google Scholar
• 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 2000; 408:488-92; PMID:11100732; http://dx.doi.org/10.1038/35044114
   PubMed Web of Science ®Google Scholar
• Hanada T, Noda NN, Satomi Y, Ichimura Y, Fujioka Y, Takao T, Inagaki F, Ohsumi Y. The Atg12-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy. J Biol Chem 2007; 282:37298-302; PMID:17986448; http://dx.doi.org/10.1074/jbc.C700195200
   PubMed Web of Science ®Google Scholar
• Kim J, Huang WP, Klionsky DJ. Membrane recruitment of Aut7p in the autophagy and cytoplasm to vacuole targeting pathways requires Aut1p, Aut2p, and the autophagy conjugation complex. J Cell Biol 2001; 152:51-64; PMID:11149920; http://dx.doi.org/10.1083/jcb.152.1.51
   PubMed Web of Science ®Google Scholar
• Sakoh-Nakatogawa M, Matoba K, Asai E, Kirisako H, Ishii J, Noda NN, Inagaki F, Nakatogawa H, Ohsumi Y. Atg12-Atg5 conjugate enhances E2 activity of Atg3 by rearranging its catalytic site. Nat Struct Mol Biol 2013; 20:433-9; PMID:23503366; http://dx.doi.org/10.1038/nsmb.2527
   PubMed Web of Science ®Google Scholar
• Nair U, Yen WL, Mari M, Cao Y, Xie Z, Baba M, Reggiori F, Klionsky DJ. A role for Atg8-PE deconjugation in autophagosome biogenesis. Autophagy 2012; 8:780-93; PMID:22622160; http://dx.doi.org/10.4161/auto.19385
   PubMed Web of Science ®Google Scholar
• Nakatogawa H, Ishii J, Asai E, Ohsumi Y. Atg4 recycles inappropriately lipidated Atg8 to promote autophagosome biogenesis. Autophagy 2012; 8:177-86; PMID:22240591; http://dx.doi.org/10.4161/auto.8.2.18373
   PubMed Web of Science ®Google Scholar
• Yu ZQ, Ni T, Hong B, Wang HY, Jiang FJ, Zou S, Chen Y, Zheng XL, Klionsky DJ, Liang Y, et al. Dual roles of Atg8-PE deconjugation by Atg4 in autophagy. Autophagy 2012; 8:883-92; PMID:22652539; http://dx.doi.org/10.4161/auto.19652
   PubMed Web of Science ®Google Scholar
• Filomeni G, Desideri E, Cardaci S, Rotilio G, Ciriolo MR. Under the ROS…thiol network is the principal suspect for autophagy commitment. Autophagy 2010; 6:999-1005; PMID:20639698; http://dx.doi.org/10.4161/auto.6.7.12754
   PubMed Web of Science ®Google Scholar
• Huang J, Lam GY, Brumell JH. Autophagy signaling through reactive oxygen species. Antioxid Redox Signal 2011; 14:2215-31; PMID:20874258; http://dx.doi.org/10.1089/ars.2010.3554
   PubMed Web of Science ®Google Scholar
• Pérez-Pérez ME, Lemaire SD, Crespo JL. Reactive oxygen species and autophagy in plants and algae. Plant Physiol 2012; 160:156-64; PMID:22744983; http://dx.doi.org/10.1104/pp.112.199992
   PubMed Web of Science ®Google Scholar
• Scherz-Shouval R, Elazar Z. Regulation of autophagy by ROS: physiology and pathology. Trends Biochem Sci 2011; 36:30-8; PMID:20728362; http://dx.doi.org/10.1016/j.tibs.2010.07.007
   PubMed Web of Science ®Google Scholar
• Navarro-Yepes J, Burns M, Anandhan A, Khalimonchuk O, del Razo LM, Quintanilla-Vega B, Pappa A, Panayiotidis MI, Franco R. Oxidative stress, redox signaling, and autophagy: cell death versus survival. Antioxid Redox Signal 2014; 21:66-85; PMID:24483238; http://dx.doi.org/10.1089/ars.2014.5837
   PubMed Web of Science ®Google Scholar
• Scherz-Shouval R, Shvets E, Fass E, Shorer H, Gil L, Elazar Z. Reactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4. EMBO J 2007; 26:1749-60; PMID:17347651; http://dx.doi.org/10.1038/sj.emboj.7601623
   PubMed Web of Science ®Google Scholar
• Pérez-Pérez ME, Florencio FJ, Crespo JL. Inhibition of target of rapamycin signaling and stress activate autophagy in Chlamydomonas reinhardtii. Plant Physiol 2010; 152:1874-88; PMID:20107021; http://dx.doi.org/10.1104/pp.109.152520
   PubMed Web of Science ®Google Scholar
• Xiong Y, Contento AL, Nguyen PQ, Bassham DC. Degradation of oxidized proteins by autophagy during oxidative stress in Arabidopsis. Plant Physiol 2007; 143:291-9; PMID:17098847; http://dx.doi.org/10.1104/pp.106.092106
   PubMed Web of Science ®Google Scholar
• Pérez-Pérez ME, Couso I, Crespo JL. Carotenoid deficiency triggers autophagy in the model green alga Chlamydomonas reinhardtii. Autophagy 2012; 8:376-88; PMID:22302003; http://dx.doi.org/10.4161/auto.18864
   PubMed Web of Science ®Google Scholar
• Woo J, Park E, Dinesh-Kumar SP. Differential processing of Arabidopsis ubiquitin-like Atg8 autophagy proteins by Atg4 cysteine proteases. Proc Natl Acad Sci U S A 2014; 111:863-8; PMID:24379391; http://dx.doi.org/10.1073/pnas.1318207111
   PubMed Web of Science ®Google Scholar
• Auchère F, Santos R, Planamente S, Lesuisse E, Camadro JM. Glutathione-dependent redox status of frataxin-deficient cells in a yeast model of Friedreich's ataxia. Hum Mol Genet 2008; 17:2790-802; PMID:18562474; http://dx.doi.org/10.1093/hmg/ddn178
   PubMedGoogle Scholar
• Noda T, Ohsumi Y. Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast. J Biol Chem 1998; 273:3963-6; PMID:9461583; http://dx.doi.org/10.1074/jbc.273.7.3963
   PubMed Web of Science ®Google Scholar
• Mehdi K, Penninckx MJ. An important role for glutathione and gamma-glutamyltranspeptidase in the supply of growth requirements during nitrogen starvation of the yeast Saccharomyces cerevisiae. Microbiology 1997; 143:1885-9; PMID:9202464; http://dx.doi.org/10.1099/00221287-143-6-1885
   PubMedGoogle Scholar
• Simpson RJ. Stabilization of proteins for storage. Cold Spring Harb Protoc 2010; 2010:top79; PMID:20439424; http://dx.doi.org/10.1101/pdb.top79
   PubMedGoogle Scholar
• Muller EG. Thioredoxin deficiency in yeast prolongs S phase and shortens the G1 interval of the cell cycle. J Biol Chem 1991; 266:9194-202; PMID:2026619
   PubMed Web of Science ®Google Scholar
• Toledano MB, Delaunay-Moisan A, Outten CE, Igbaria A. Functions and cellular compartmentation of the thioredoxin and glutathione pathways in yeast. Antioxid Redox Signal 2013; 18:1699-711; PMID:23198979; http://dx.doi.org/10.1089/ars.2012.5033
   PubMedGoogle Scholar
• Shintani T, Huang WP, Stromhaug PE, Klionsky DJ. Mechanism of cargo selection in the cytoplasm to vacuole targeting pathway. Dev Cell 2002; 3:825-37; PMID:12479808; http://dx.doi.org/10.1016/S1534-5807(02)00373-8
   PubMed Web of Science ®Google Scholar
• Lillig CH, Holmgren A. Thioredoxin and related molecules–from biology to health and disease. Antioxid Redox Signal 2007; 9:25-47; PMID:17115886; http://dx.doi.org/10.1089/ars.2007.9.25
   PubMed Web of Science ®Google Scholar
• Garrido EO, Grant CM. Role of thioredoxins in the response of Saccharomyces cerevisiae to oxidative stress induced by hydroperoxides. Mol Microbiol 2002; 43:993-1003; PMID:11929546; http://dx.doi.org/10.1046/j.1365-2958.2002.02795.x
   PubMed Web of Science ®Google Scholar
• Dengjel J, Høyer-Hansen M, Nielsen MO, Eisenberg T, Harder LM, Schandorff S, Farkas T, Kirkegaard T, Becker AC, Schroeder S, et al. Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens. Mol Cell Proteomics 2012; 11:014035; PMID:22311637; http://dx.doi.org/10.1074/mcp.M111.014035
   PubMedGoogle Scholar
• Lemaire SD, Quesada A, Merchan F, Corral JM, Igeno MI, Keryer E, Issakidis-Bourguet E, Hirasawa M, Knaff DB, Miginiac-Maslow M. NADP-malate dehydrogenase from unicellular green alga Chlamydomonas reinhardtii. A first step toward redox regulation? Plant Physiol 2005; 137:514-21; PMID:15579663; http://dx.doi.org/10.1104/pp.104.052670
   PubMedGoogle Scholar
• Michelet L, Zaffagnini M, Morisse S, Sparla F, Pérez-Pérez ME, Francia F, Danon A, Marchand CH, Fermani S, Trost P, et al. Redox regulation of the Calvin-Benson cycle: something old, something new. Front Plant Sci 2013; 4:470; PMID:24324475; http://dx.doi.org/10.3389/fpls.2013.00470
   PubMed Web of Science ®Google Scholar
• Satoo K, Noda NN, Kumeta H, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F. The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy. EMBO J 2009; 28:1341-50; PMID:19322194; http://dx.doi.org/10.1038/emboj.2009.80
   PubMed Web of Science ®Google Scholar
• Sugawara K, Suzuki NN, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F. Structural basis for the specificity and catalysis of human Atg4B responsible for mammalian autophagy. J Biol Chem 2005; 280:40058-65; PMID:16183633; http://dx.doi.org/10.1074/jbc.M509158200
   PubMed Web of Science ®Google Scholar
• Fermani S, Sparla F, Falini G, Martelli PL, Casadio R, Pupillo P, Ripamonti A, Trost P. Molecular mechanism of thioredoxin regulation in photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase. Proc Natl Acad Sci U S A 2007; 104:11109-14; PMID:17573533; http://dx.doi.org/10.1073/pnas.0611636104
   PubMedGoogle Scholar
• Johansson K, Ramaswamy S, Saarinen M, Lemaire-Chamley M, Issakidis-Bourguet E, Miginiac-Maslow M, Eklund H. Structural basis for light activation of a chloroplast enzyme: the structure of sorghum NADP-malate dehydrogenase in its oxidized form. Biochemistry 1999; 38:4319-26; PMID:10194350; http://dx.doi.org/10.1021/bi982876c
   PubMedGoogle Scholar
• Trost P, Fermani S, Marri L, Zaffagnini M, Falini G, Scagliarini S, Pupillo P, Sparla F. Thioredoxin-dependent regulation of photosynthetic glyceraldehyde-3-phosphate dehydrogenase: autonomous vs. CP12-dependent mechanisms. Photosynth Res 2006; 89:263-75; PMID:17031544; http://dx.doi.org/10.1007/s11120-006-9099-z
   PubMedGoogle 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
• Tietze F. Enzymic method for quantitative determination of nanogram amounts of total and oxidized glutathione: applications to mammalian blood and other tissues. Anal Biochem 1969; 27:502-22; PMID:4388022; http://dx.doi.org/10.1016/0003-2697(69)90064-5
   PubMed Web of Science ®Google Scholar
• Zaffagnini M, Michelet L, Massot V, Trost P, Lemaire SD. Biochemical characterization of glutaredoxins from Chlamydomonas reinhardtii reveals the unique properties of a chloroplastic CGFS-type glutaredoxin. J Biol Chem 2008; 283:8868-76; PMID:18216016; http://dx.doi.org/10.1074/jbc.M709567200
   PubMed Web of Science ®Google Scholar