Transcriptional regulation by Pho23 modulates the frequency of autophagosome formation

Current Biology

Volumn 24, Issue 12, 2014, Pages 1314-1322

  Jin, Meiyan ^a   He, Ding ^a   Backues, Steven K ^a   Freeberg, Mallory A ^b   Liu, Xu ^a   Kim, John K ^b   Klionsky, Daniel J ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATG9 PROTEIN, S CEREVISIAE; AUTOPHAGY RELATED PROTEIN; MEMBRANE PROTEIN; NUCLEAR PROTEIN; PHO23 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN;

AUTOPHAGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHAGOSOME; PHYSIOLOGY; REAL TIME POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE; TRANSMISSION ELECTRON MICROSCOPY;

AUTOPHAGY; AUTOPHAGY-RELATED PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; MEMBRANE PROTEINS; MICROSCOPY, ELECTRON, TRANSMISSION; NUCLEAR PROTEINS; PHAGOSOMES; REAL-TIME POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84902652820     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2014.04.048     Document Type: Article

References (41)

1. M. Tsukada, and Y. Ohsumi Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae FEBS Lett. 333 1993 169 174
2. J. Huang, and D.J. Klionsky Autophagy and human disease Cell Cycle 6 2007 1837 1849
3. N. Mizushima, B. Levine, A.M. Cuervo, and D.J. Klionsky Autophagy fights disease through cellular self-digestion Nature 451 2008 1069 1075
4. T.L. Lenstra, J.J. Benschop, T. Kim, J.M. Schulze, N.A. Brabers, T. Margaritis, L.A. van de Pasch, S.A. van Heesch, M.O. Brok, and M.J. Groot Koerkamp et al. The specificity and topology of chromatin interaction pathways in yeast Mol. Cell 42 2011 536 549
5. Z. Xie, and D.J. Klionsky Autophagosome formation: core machinery and adaptations Nat. Cell Biol. 9 2007 1102 1109
6. T.M. Harding, K.A. Morano, S.V. Scott, and D.J. Klionsky Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway J. Cell Biol. 131 1995 591 602
7. D.J. Klionsky, J.M. Cregg, W.A. Dunn Jr., S.D. Emr, Y. Sakai, I.V. Sandoval, A. Sibirny, S. Subramani, M. Thumm, M. Veenhuis, and Y. Ohsumi A unified nomenclature for yeast autophagy-related genes Dev. Cell 5 2003 539 545
8. M. Thumm, R. Egner, B. Koch, M. Schlumpberger, M. Straub, M. Veenhuis, and D.H. Wolf Isolation of autophagocytosis mutants of Saccharomyces cerevisiae FEBS Lett. 349 1994 275 280
9. A.P. Gasch, P.T. Spellman, C.M. Kao, O. Carmel-Harel, M.B. Eisen, G. Storz, D. Botstein, and P.O. Brown Genomic expression programs in the response of yeast cells to environmental changes Mol. Biol. Cell 11 2000 4241 4257
10. D. Chen, S. Pang, X. Feng, W. Huang, R.G. Hawley, and B. Yan Genetic analysis of the ATG7 gene promoter in sporadic Parkinson's disease Neurosci. Lett. 534 2013 193 198
11. H. Liu, Z. He, T. von Rutte, S. Yousefi, R.E. Hunger, and H.U. Simon Down-regulation of autophagy-related protein 5 (ATG5) contributes to the pathogenesis of early-stage cutaneous melanoma Sci. Transl. Med. 5 2013 202ra123
12. Y.K. Jo, S.C. Kim, I.J. Park, S.J. Park, D.H. Jin, S.W. Hong, D.H. Cho, and J.C. Kim Increased expression of ATG10 in colorectal cancer is associated with lymphovascular invasion and lymph node metastasis PLoS ONE 7 2012 e52705
13. J. Wang, X.L. Pan, L.J. Ding, D.Y. Liu, Da-Peng Lei, and T. Jin Aberrant expression of Beclin-1 and LC3 correlates with poor prognosis of human hypopharyngeal squamous cell carcinoma PLoS ONE 8 2013 e69038
14. C.R. Bartholomew, T. Suzuki, Z. Du, S.K. Backues, M. Jin, M.A. Lynch-Day, M. Umekawa, A. Kamath, M. Zhao, and Z. Xie et al. Ume6 transcription factor is part of a signaling cascade that regulates autophagy Proc. Natl. Acad. Sci. USA 109 2012 11206 11210
15. Z. Xie, U. Nair, and D.J. Klionsky Atg8 controls phagophore expansion during autophagosome formation Mol. Biol. Cell 19 2008 3290 3298
16. T. Noda, J. Kim, W.-P. Huang, M. Baba, C. Tokunaga, Y. Ohsumi, and D.J. Klionsky 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
17. F. Reggiori, K.A. Tucker, P.E. Stromhaug, and D.J. Klionsky The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure Dev. Cell 6 2004 79 90
18. F. Reggiori, T. Shintani, U. Nair, and D.J. Klionsky Atg9 cycles between mitochondria and the pre-autophagosomal structure in yeasts Autophagy 1 2005 101 109
19. T. Kirisako, M. Baba, N. Ishihara, K. Miyazawa, M. Ohsumi, T. Yoshimori, T. Noda, and Y. Ohsumi Formation process of autophagosome is traced with Apg8/Aut7p in yeast J. Cell Biol. 147 1999 435 446
20. T. Shintani, and D.J. Klionsky Cargo proteins facilitate the formation of transport vesicles in the cytoplasm to vacuole targeting pathway J. Biol. Chem. 279 2004 29889 29894
21. T. Noda, and D.J. Klionsky The quantitative Pho8Delta60 assay of nonspecific autophagy Methods Enzymol. 451 2008 33 42
22. M.A. Lynch-Day, and D.J. Klionsky The Cvt pathway as a model for selective autophagy FEBS Lett. 584 2010 1359 1366
23. S.V. Scott, D.C. Nice 3rd, J.J. Nau, L.S. Weisman, Y. Kamada, I. Keizer-Gunnink, T. Funakoshi, M. Veenhuis, Y. Ohsumi, and D.J. Klionsky 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
24. J. Geng, M. Baba, U. Nair, and D.J. Klionsky Quantitative analysis of autophagy-related protein stoichiometry by fluorescence microscopy J. Cell Biol. 182 2008 129 140
25. R. Loewith, J.S. Smith, M. Meijer, T.J. Williams, N. Bachman, J.D. Boeke, and D. Young Pho23 is associated with the Rpd3 histone deacetylase and is required for its normal function in regulation of gene expression and silencing in Saccharomyces cerevisiae J. Biol. Chem. 276 2001 24068 24074
26. S.K. Kurdistani, D. Robyr, S. Tavazoie, and M. Grunstein Genome-wide binding map of the histone deacetylase Rpd3 in yeast Nat. Genet. 31 2002 248 254
27. S.S. Wang, B.O. Zhou, and J.Q. Zhou Histone H3 lysine 4 hypermethylation prevents aberrant nucleosome remodeling at the PHO5 promoter Mol. Cell. Biol. 31 2011 3171 3181
28. N. Avvakumov, and J. Côté The MYST family of histone acetyltransferases and their intimate links to cancer Oncogene 26 2007 5395 5407
29. W.-L. Yen, J.E. Legakis, U. Nair, and D.J. Klionsky Atg27 is required for autophagy-dependent cycling of Atg9 Mol. Biol. Cell 18 2007 581 593
30. M. Mari, J. Griffith, E. Rieter, L. Krishnappa, D.J. Klionsky, and F. Reggiori An Atg9-containing compartment that functions in the early steps of autophagosome biogenesis J. Cell Biol. 190 2010 1005 1022
31. H. Yamamoto, S. Kakuta, T.M. Watanabe, A. Kitamura, T. Sekito, C. Kondo-Kakuta, R. Ichikawa, M. Kinjo, and Y. Ohsumi Atg9 vesicles are an important membrane source during early steps of autophagosome formation J. Cell Biol. 198 2012 219 233
32. R. Loewith, M. Meijer, S.P. Lees-Miller, K. Riabowol, and D. Young Three yeast proteins related to the human candidate tumor suppressor p33(ING1) are associated with histone acetyltransferase activities Mol. Cell. Biol. 20 2000 3807 3816
33. C. Guérillon, D. Larrieu, and R. Pedeux ING1 and ING2: multifaceted tumor suppressor genes Cell. Mol. Life Sci. 70 2013 3753 3772
34. J. Tang, H. Yan, and S. Zhuang Histone deacetylases as targets for treatment of multiple diseases Clin. Sci. 124 2013 651 662
35. M.S. Longtine, A. McKenzie 3rd, D.J. Demarini, N.G. Shah, A. Wach, A. Brachat, P. Philippsen, and J.R. Pringle Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae Yeast 14 1998 953 961
36. B. Langmead, and S.L. Salzberg Fast gapped-read alignment with Bowtie 2 Nat. Methods 9 2012 357 359
37. T. Noda, A. Matsuura, Y. Wada, and Y. Ohsumi Novel system for monitoring autophagy in the yeast Saccharomyces cerevisiae Biochem. Biophys. Res. Commun. 210 1995 126 132
38. S.K. Backues, D. Chen, J. Ruan, Z. Xie, and D.J. Klionsky Estimating the size and number of autophagic bodies by electron microscopy Autophagy 10 2014 155 164
39. W.-P. Huang, S.V. Scott, J. Kim, and D.J. Klionsky The itinerary of a vesicle component, Aut7p/Cvt5p, terminates in the yeast vacuole via the autophagy/Cvt pathways J. Biol. Chem. 275 2000 5845 5851
40. H. Abeliovich, C. Zhang, W.A. Dunn Jr., K.M. Shokat, and D.J. Klionsky Chemical genetic analysis of Apg1 reveals a non-kinase role in the induction of autophagy Mol. Biol. Cell 14 2003 477 490
41. D.J. Klionsky, R. Cueva, and D.S. Yaver Aminopeptidase I of Saccharomyces cerevisiae is localized to the vacuole independent of the secretory pathway J. Cell Biol. 119 1992 287 299