Snf1 AMPK positively regulates ER-phagy via expression control of Atg39 autophagy receptor in yeast ER stress response

Autoři: Tomoaki Mizuno aff001;  Kei Muroi aff001;  Kenji Irie aff001
Působiště autorů: Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan aff001
Vyšlo v časopise: Snf1 AMPK positively regulates ER-phagy via expression control of Atg39 autophagy receptor in yeast ER stress response. PLoS Genet 16(9): e32767. doi:10.1371/journal.pgen.1009053
Kategorie: Research Article
doi: 10.1371/journal.pgen.1009053


Autophagy is a fundamental process responsible for degradation and recycling of intracellular contents. In the budding yeast, non-selective macroautophagy and microautophagy of the endoplasmic reticulum (ER) are caused by ER stress, the circumstance where aberrant proteins accumulate in the ER. The more recent study showed that protein aggregation in the ER initiates ER-selective macroautophagy, referred to as ER-phagy; however, the mechanisms by which ER stress induces ER-phagy have not been fully elucidated. Here, we show that the expression levels of ATG39, encoding an autophagy receptor specific for ER-phagy, are significantly increased under ER-stressed conditions. ATG39 upregulation in ER stress response is mediated by activation of its promoter, which is positively regulated by Snf1 AMP-activated protein kinase (AMPK) and negatively by Mig1 and Mig2 transcriptional repressors. In response to ER stress, Snf1 promotes nuclear export of Mig1 and Mig2. Our results suggest that during ER stress response, Snf1 mediates activation of the ATG39 promoter and consequently facilitates ER-phagy by negatively regulating Mig1 and Mig2.

Klíčová slova:

Autophagic cell death – Cellular stress responses – Endoplasmic reticulum – Endoplasmic reticulum stress response – Gene expression – Mutant strains – Phosphorylation – Saccharomyces cerevisiae


1. Mori K. Signalling pathways in the unfolded protein response: development from yeast to mammals. J Biochem. 2009;146: 743–750. doi: 10.1093/jb/mvp166 19861400

2. Walter P, Ron D. The unfolded protein response: from stress pathway to homeostatic regulation. Science. 2011;334: 1081–1086. doi: 10.1126/science.1209038 22116877

3. Schuck S, Prinz WA, Thorn KS, Voss C, Walter P. Membrane expansion alleviates endoplasmic reticulum stress independently of the unfolded protein response. J. Cell. Biol. 2009;187: 525–536. doi: 10.1083/jcb.200907074 19948500

4. Bonilla M, Cunningham KW. Mitogen-activated protein kinase stimulation of Ca2+ signaling is required for survival of endoplasmic reticulum stress in yeast. Mol. Biol. Cell. 2003;14: 4296–4305. doi: 10.1091/mbc.e03-02-0113 14517337

5. Chen Y, Feldman DE, Deng C, Brown JA, De Giacomo AF, Gaw AF, et al. Identification of mitogen-activated protein kinase signaling pathways that confer resistance to endoplasmic reticulum stress in Saccharomyces cerevisiae. Mol. Cancer. Res. 2005;3: 669–677. doi: 10.1158/1541-7786.MCR-05-0181 16380504

6. Babour A, Bicknell AA, Tourtellotte J, Niwa M. A surveillance pathway monitors the fitness of the endoplasmic reticulum to control its inheritance. Cell. 2010;142: 256–269. doi: 10.1016/j.cell.2010.06.006 20619447

7. Bicknell AA, Tourtellotte J, Niwa M. Late phase of the endoplasmic reticulum stress response pathway is regulated by Hog1 MAP kinase. J Biol Chem. 2010;285: 17545–17555. doi: 10.1074/jbc.M109.084681 20382742

8. Torres-Quiroz F, García-Marqués S, Coria R, Randez-Gil F, Prieto JA. The activity of yeast Hog1 MAPK is required during endoplasmic reticulum stress induced by tunicamycin exposure. J Biol Chem. 2010;285: 20088–20096. doi: 10.1074/jbc.M109.063578 20430884

9. Ferrer-Dalmau J, Randez-Gil F, Marquina M, Prieto JA, Casamayor A. Protein kinase Snf1 is involved in the proper regulation of the unfolded protein response in Saccharomyces cerevisiae. Biochem J. 2015;468: 33–47. doi: 10.1042/BJ20140734 25730376

10. Mizuno T, Masuda Y, Irie K. The Saccharomyces cerevisiae AMPK, Snf1, negatively regulates the Hog1 MAPK Pathway in ER stress response. PLoS Genet. 2015;11: e1005491. doi: 10.1371/journal.pgen.1005491 26394309

11. Kimura Y, Irie K, Mizuno T. Expression control of the AMPK regulatory subunit and its functional significance in yeast ER stress response. Sci Rep. 2017;7: 46713. doi: 10.1038/srep46713 28429799

12. Mizuno T, Nakamura M, Irie K. Induction of Ptp2 and Cmp2 protein phosphatases is crucial for the adaptive response to ER stress in Saccharomyces cerevisiae. Sci Rep. 2018;8: 13078. doi: 10.1038/s41598-018-31413-6 30166606

13. Yorimitsu T, Nair U, Yang Z, Klionsky DJ. Endoplasmic reticulum stress triggers autophagy. J. Biol. Chem. 2006;281: 30299–30304. doi: 10.1074/jbc.M607007200 16901900

14. Schuck S, Gallagher CM, Walter P. ER-phagy mediates selective degradation of endoplasmic reticulum independently of the core autophagy machinery. J. Cell. Sci. 2014;127, 4078–4088. doi: 10.1242/jcs.154716 25052096

15. Reggiori F, Klionsky DJ. Autophagic processes in yeast: mechanism, machinery and regulation. Genetics. 2013;194: 341–361. doi: 10.1534/genetics.112.149013 23733851

16. Ohsumi Y. Historical landmarks of autophagy research. Cell. Res. 2014;24: 9–23 doi: 10.1038/cr.2013.169 24366340

17. Okamoto K, Kondo-Okamoto N, Ohsumi Y. Mitochondria-anchored receptor Atg32 mediates degradation of mitochondria via selective autophagy. Dev Cell. 2009;17: 87–97. doi: 10.1016/j.devcel.2009.06.013 19619494

18. Kanki T, Wang K, Cao Y, Baba M, Klionsky DJ. Atg32 is a mitochondrial protein that confers selectivity during mitophagy. Dev Cell. 2009;17; 98–109. doi: 10.1016/j.devcel.2009.06.014 19619495

19. Motley AM, Nuttall JM, Hettema EH. Pex3-anchored Atg36 tags peroxisomes for degradation in Saccharomyces cerevisiae. EMBO. J. 2012;31; 2852–2868. doi: 10.1038/emboj.2012.151 22643220

20. Mochida K, Oikawa Y, Kimura Y, Kirisako H, Hirano H, Ohsumi Y, et al. Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus. Nature. 2015;522: 359–362. doi: 10.1038/nature14506 26040717

21. Schäfer JA, Schessner JP, Bircham PW, Tsuji T, Funaya C, Pajonk O, et al. ESCRT machinery mediates selective microautophagy of endoplasmic reticulum in yeast. EMBO J. 2020;39: e102586. doi: 10.15252/embj.2019102586 31802527

22. Cui Y, Parashar S, Zahoor M, Needham PG, Mari M, Zhu M, et al. COPII subunit acts with an autophagy receptor to target endoplasmic reticulum for degradation. Science. 2019;365: 53–60. doi: 10.1126/science.aau9263 31273116

23. Friedman JR, Voeltz GK. The ER in 3D: a multifunctional dynamic membrane network. Trends Cell Biol. 2011;21: 709–717. doi: 10.1016/j.tcb.2011.07.004 21900009

24. Hedbacker K, Carlson M. SNF1/AMPK pathways in yeast. Front Biosci. 2008;13: 2408–2420. doi: 10.2741/2854 17981722

25. Broach JR. Nutritional control of growth and development in yeast. Genetics. 2012;192: 73–105. doi: 10.1534/genetics.111.135731 22964838

26. Sutherland CM, Hawley SA, McCartney RR, Leech A, Stark MJ, Schmidt MC, et al. Elm1p is one of three upstream kinases for the Saccharomyces cerevisiae SNF1 complex. Curr Biol. 2003;13: 1299–1305. doi: 10.1016/s0960-9822(03)00459-7 12906789

27. Lutfiyya LL, Johnston M. Two zinc-finger-containing repressors are responsible for glucose repression of SUC2 expression. Mol Cell Biol. 1996;16: 4790–4797. doi: 10.1128/mcb.16.9.4790 8756637

28. Westholm JO, Nordberg N, Murén E, Ameur A, Komorowski J, Ronne H. Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3. BMC Genomics. 2008;9: doi: 10.1186/1471-2164-9-601 19087243

29. Lundin M, Nehlin JO, Ronne H. Importance of a flanking AT-rich region in target site recognition by the GC box-binding zinc finger protein MIG1. Mol Cell Biol. 1994;14: 1979–1985. doi: 10.1128/mcb.14.3.1979 8114729

30. Treitel MA, Kuchin S, Carlson M. Snf1 protein kinase regulates phosphorylation of the Mig1 repressor in Saccharomyces cerevisiae. Mol Cell Biol. 1998;18: 6273–6280. doi: 10.1128/mcb.18.11.6273 9774644

31. Serra-Cardona A, Petrezsélyová S, Canadell D, Ramos J, Ariño J. Coregulated expression of the Na+/phosphate Pho89 transporter and Ena1 Na+-ATPase allows their functional coupling under high-pH stress. Mol Cell Biol. 2014;34: 4420–4435. doi: 10.1128/MCB.01089-14 25266663

32. Welter E, Thumm M, Krick R. Quantification of nonselective bulk autophagy in S. cerevisiae using Pgk1-GFP. Autophagy. 2010;6: 794–797. doi: 10.4161/auto.6.6.12348 20523132

33. Travers KJ, Patil CK, Wodicka L, Lockhart DJ, Weissman JS, Walter P. Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell. 2000;101: 249–258. doi: 10.1016/s0092-8674(00)80835-1 10847680

34. Fumagalli F, Noack J, Bergmann TJ, Cebollero E, Pisoni GB, Fasana E, et al. Translocon component Sec62 acts in endoplasmic reticulum turnover during stress recovery. Nat Cell Biol. 2016;18: 1173–1184. doi: 10.1038/ncb3423 27749824

35. Rousseau A, Bertolotti A. An evolutionarily conserved pathway controls proteasome homeostasis. Nature. 2016;536: 184–189. doi: 10.1038/nature18943 27462806

36. Aihara M, Jin X, Kurihara Y, Yoshida Y, Matsushima Y, Oku M, et al. Tor and the Sin3-Rpd3 complex regulate expression of the mitophagy receptor protein Atg32 in yeast. J. Cell. Sci. 2014;127: 3184–3196. doi: 10.1242/jcs.153254 24838945

37. Aoki Y, Kanki T, Hirota Y, Kurihara Y, Saigusa T, Uchiumi T, et al. Phosphorylation of Serine 114 on Atg32 mediates mitophagy. Mol. Biol. Cell. 2011;22: 3206–3217. doi: 10.1091/mbc.E11-02-0145 21757540

38. Tanaka C, Tan LJ, Mochida K, Kirisako H, Koizumi M, Asai E, et al. Hrr25 triggers selective autophagy-related pathways by phosphorylating receptor proteins. J. Cell. Biol. 2014;207: 91–105. doi: 10.1083/jcb.201402128 25287303

39. Smith MD, Harley ME, Kemp AJ, Wills J, Lee M, Arends M, et al. CCPG1 is a non-canonical autophagy cargo receptor essential for ER-Phagy and pancreatic ER proteostasis. Dev Cell. 2018;44: 217–232. doi: 10.1016/j.devcel.2017.11.024 29290589

40. Bartholomew CR, Suzuki T, Du Z, Backues SK, Jin M, Lynch-Day MA, et al. Ume6 transcription factor is part of a signaling cascade that regulates autophagy. Proc. Natl. Acad. Sci. U. S. A. 2012;109: 11206–11210. doi: 10.1073/pnas.1200313109 22733735

41. Jin M, He D, Backues SK, Freeberg MA, Liu X, Kim JK, et al. Transcriptional regulation by Pho23 modulates the frequency of autophagosome formation. Curr. Biol. 2014;24: 1314–1322. doi: 10.1016/j.cub.2014.04.048 24881874

42. Bernard A, Jin M, González-Rodríguez P, Füllgrabe J, Delorme-Axford E, Backues SK, et al. Rph1/KDM4 mediates nutrient-limitation signaling that leads to the transcriptional induction of autophagy. Curr. Biol. 2015;25: 546–555. doi: 10.1016/j.cub.2014.12.049 25660547

43. Hu G, McQuiston T, Bernard A, Park YD, Qiu J, Vural A, et al. A conserved mechanism of TOR-dependent RCK-mediated mRNA degradation regulates autophagy. Nat. Cell. Biol. 2015;17: 930–942. doi: 10.1038/ncb3189 26098573

44. Sakamaki JI, Wilkinson S, Hahn M, Tasdemir N, O’Prey J, Clark W, et al. Bromodomain protein BRD4 Is a transcriptional repressor of autophagy and lysosomal function. Mol Cell. 2017;66: 517–532. doi: 10.1016/j.molcel.2017.04.027 28525743

45. DeVit MJ, Johnston M. The nuclear exportin Msn5 is required for nuclear export of the Mig1 glucose repressor of Saccharomyces cerevisiae. Curr Biol. 1999;9: 1231–1241. doi: 10.1016/s0960-9822(99)80503-x 10556086

46. Papamichos-Chronakis M, Gligoris T, Tzamarias D. The Snf1 kinase controls glucose repression in yeast by modulating interactions between the Mig1 repressor and the Cyc8-Tup1 co-repressor. EMBO Rep. 2004;5: 368–372. doi: 10.1038/sj.embor.7400120 15031717

47. Kaiser CA, Adams A, Gottschling DE. Methods in yeast genetics. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY; 1994.

48. Longtine MS, McKenzie A 3rd, Demarini DJ, Shah NG, Wach A, Brachat A, et al. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast. 1998;14: 953–961. doi: 10.1002/(SICI)1097-0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U 9717241

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2020 Číslo 9
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