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Hac1 function revealed by the protein expression profile of a OtHAC1 mutant of thermotolerant methylotrophic yeast Ogataea thermomethanolica

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Abstract

In yeast, the accumulation of unfolded proteins in the ER triggers the unfolded protein response (UPR) pathway, which is mediated by Hac1 transcription factor. Here, we characterized the function of a gene encoding Hac1 in the thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC656 (OtHAC1). OtHAC1 mRNA contains a non-canonical intron of 176 nt, which was demonstrated to be spliced by RT-PCR. To characterize the function of this gene, we compared the proteome of a Othac1 mutant with wild-type. A total of 463 proteins with differential abundance were detected. The functions of these proteins were annotated in oxidative stress, metabolic pathways, transcription, translation, and of particular interest in secretory pathway. While many intracellular proteins differentially expressed in the mutant were similar to proteins with altered expression in UPR-stressed Saccharomyces cerevisiae, two novel OtHAC1-dependent proteins (Iml1 and Npr2) were identified that are potentially involved in the regulation of autophagy. The data show that OtHAC1 is an important regulator of several different processes in O. thermomethanolica TBRC656.

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References

  1. Walter P, Ron D (2011) The unfolded protein response: from stress pathway to homeostatic regulation. Science 334(6059):1081–1086

    Article  CAS  PubMed  Google Scholar 

  2. Travers KJ, Patil CK, Wodicka L, Lockhart DJ, Weissman JS, Walter P (2000) Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell 101(3):249–258

    Article  CAS  PubMed  Google Scholar 

  3. Harnpicharnchai P, Promdonkoy P, Sae-Tang K, Roongsawang N, Tanapongpipat S (2014) Use of the glyceraldehyde-3-phosphate dehydrogenase promoter from a thermotolerant yeast, Pichia thermomethanolica, for heterologous gene expression, especially at elevated temperature. Ann Microbiol 64(3):1457–1462

    Article  CAS  Google Scholar 

  4. Promdonkoy P, Tirasophon W, Roongsawang N, Eurwilaichitr L, Tanapongpipat S (2014) Methanol-inducible promoter of thermotolerant methylotrophic yeast Ogataea thermomethanolica BCC16875 potential for production of heterologous protein at high temperatures. Curr Microbiol 69(2):143–148

    Article  CAS  PubMed  Google Scholar 

  5. Roongsawang N, Puseenam A, Kitikhun S, Sae-Tang K, Harnpicharnchai P, Ohashi T, Fujiyama K, Tirasophon W, Tanapongpipat S (2016) A novel potential signal peptide sequence and overexpression of ER-resident chaperones enhance heterologous protein secretion in thermotolerant methylotrophic yeast Ogataea thermomethanolica. Appl Biochem Biotechnol 178(4):710–724

    Article  CAS  PubMed  Google Scholar 

  6. Phithakrotchanakoon C, Puseenam A, Wongwisansri S, Eurwilaichitr L, Ingsriswang S, Tanapongpipat S, Roongsawang N (2018) CRISPR-Cas9 enabled targeted mutagenesis in the thermotolerant methylotrophic yeast Ogataea thermomethanolica. FEMS Microbiol Lett. https://doi.org/10.1093/femsle/fny105

    Article  PubMed  Google Scholar 

  7. Johansson C, Samskog J, Sundstrom L, Wadensten H, Bjorkesten L, Flensburg J (2006) Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data. Proteomics 6(16):4475–4485

    Article  CAS  PubMed  Google Scholar 

  8. Howe E, Holton K, Nair S, Schlauch D, Sinha R, Quackenbush J (2010) MeV: multiexperiment viewer. In: Ochs MF, Casagrande JT, Davuluri RV (eds) Biomedical informatics for cancer research. Springer, Boston, pp 267–277

    Chapter  Google Scholar 

  9. Wu J, Mao X, Cai T, Luo J, Wei L (2006) KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res 34(Web Server issue):W720–W724

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh LS (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32(Database issue):D115–D119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M (2016) STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res 44(D1):D380–D384

    Article  CAS  PubMed  Google Scholar 

  12. Ruegsegger U, Leber JH, Walter P (2001) Block of HAC1 mRNA translation by long-range base pairing is released by cytoplasmic splicing upon induction of the unfolded protein response. Cell 107(1):103–114

    Article  CAS  PubMed  Google Scholar 

  13. Guerfal M, Ryckaert S, Jacobs PP, Ameloot P, Van Craenenbroeck K, Derycke R, Callewaert N (2010) The HAC1 gene from Pichia pastoris: characterization and effect of its overexpression on the production of secreted, surface displayed and membrane proteins. Microb Cell Fact 9:49

    Article  PubMed  PubMed Central  Google Scholar 

  14. Ravin NV, Eldarov MA, Kadnikov VV, Beletsky AV, Schneider J, Mardanova ES, Smekalova EM, Zvereva MI, Dontsova OA, Mardanov AV, Skryabin KG (2013) Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. BMC Genom 14:837

    Article  Google Scholar 

  15. Ruan L, Zhou C, Jin E, Kucharavy A, Zhang Y, Wen Z, Florens L, Li R (2017) Cytosolic proteostasis through importing of misfolded proteins into mitochondria. Nature 543(7645):443–446

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Grant CM (2001) Role of the glutathione/glutaredoxin and thioredoxin systems in yeast growth and response to stress conditions. Mol Microbiol 39(3):533–541

    Article  CAS  PubMed  Google Scholar 

  17. Wood LK, Thiele DJ (2009) Transcriptional activation in yeast in response to copper deficiency involves copper-zinc superoxide dismutase. J Biol Chem 284(1):404–413

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Tsang CK, Liu Y, Thomas J, Zhang Y, Zheng XF (2014) Superoxide dismutase 1 acts as a nuclear transcription factor to regulate oxidative stress resistance. Nat Commun 5:3446

    Article  PubMed  Google Scholar 

  19. Wolfe KJ, Ren HY, Trepte P, Cyr DM (2013) The Hsp70/90 cochaperone, Sti1, suppresses proteotoxicity by regulating spatial quality control of amyloid-like proteins. Mol Biol Cell 24(23):3588–3602

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Kiktev DA, Patterson JC, Muller S, Bariar B, Pan T, Chernoff YO (2012) Regulation of chaperone effects on a yeast prion by cochaperone Sgt2. Mol Cell Biol 32(24):4960–4970

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Jones JM, Morrell JC, Gould SJ (2004) PEX19 is a predominantly cytosolic chaperone and import receptor for class 1 peroxisomal membrane proteins. J Cell Biol 164(1):57–67

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Cashikar AG, Duennwald M, Lindquist SL (2005) A chaperone pathway in protein disaggregation. Hsp26 alters the nature of protein aggregates to facilitate reactivation by Hsp104. J Biol Chem 280(25):23869–23875

    Article  CAS  PubMed  Google Scholar 

  23. Liu Y, Chang A, A (2008) Heat shock response relieves ER stress. EMBO J 27(7):1049–1059

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Lussier M, Sdicu AM, Bussereau F, Jacquet M, Bussey H (1997) The Ktr1p, Ktr3p, and Kre2p/Mnt1p mannosyltransferases participate in the elaboration of yeast O- and N-linked carbohydrate chains. J Biol Chem 272(24):15527–15531

    Article  CAS  PubMed  Google Scholar 

  25. Copic A, Dorrington M, Pagant S, Barry J, Lee MC, Singh I, Hartman JL th, & Miller EA (2009) Genomewide analysis reveals novel pathways affecting endoplasmic reticulum homeostasis, protein modification and quality control. Genetics 182(3):757–769

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Kitajima T, Chiba Y, Jigami Y (2006) Saccharomyces cerevisiae α-1,6-mannosyltransferase has a catalytic potential to transfer a second mannose molecule. FEBS J 273(22):5074–5085

    Article  CAS  PubMed  Google Scholar 

  27. Beeler TJ, Fu D, Rivera J, Monaghan E, Gable K, Dunn TM (1997) SUR1 (CSG1/BCL21), a gene necessary for growth of Saccharomyces cerevisiae in the presence of high Ca2+ concentrations at 37 °C, is required for mannosylation of inositolphosphorylceramide. Mol Gen Genet 255(6):570–579

    Article  CAS  PubMed  Google Scholar 

  28. Odani T, Shimma Y, Wang XH, Jigami Y (1997) Mannosylphosphate transfer to cell wall mannan is regulated by the transcriptional level of the MNN4 gene in Saccharomyces cerevisiae. FEBS Lett 420(2–3):186–190

    Article  CAS  PubMed  Google Scholar 

  29. de Medina-Redondo M, Arnaiz-Pita Y, Fontaine T, Del Rey F, Latge JP, Vazquez de Aldana CR (2008) The β-1,3-glucanosyltransferase gas4p is essential for ascospore wall maturation and spore viability in Schizosaccharomyces pombe. Mol Microbiol 68(5):1283–1299

    Article  PubMed  Google Scholar 

  30. Ragni E, Coluccio A, Rolli E, Rodriguez-Pena JM, Colasante G, Arroyo J, Neiman AM, Popolo L (2007) GAS2 and GAS4, a pair of developmentally regulated genes required for spore wall assembly in Saccharomyces cerevisiae. Eukaryot Cell 6(2):302–316

    Article  CAS  PubMed  Google Scholar 

  31. Scrimale T, Didone L, de Mesy Bentley KL, Krysan DJ (2009) The unfolded protein response is induced by the cell wall integrity mitogen-activated protein kinase signaling cascade and is required for cell wall integrity in Saccharomyces cerevisiae. Mol Biol Cell 20(1):164–175

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. TerBush DR, Maurice T, Roth D, Novick P (1996) The Exocyst is a multiprotein complex required for exocytosis in Saccharomyces cerevisiae. EMBO J 15(23):6483–6494

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Wolf J, Nicks M, Deitz S, van Tuinen E, Franzusoff A (1998) An N-end rule destabilization mutant reveals pre-Golgi requirements for Sec7p in yeast membrane traffic. Biochem Biophys Res Commun 243(1):191–198

    Article  CAS  PubMed  Google Scholar 

  34. Vollert CS, Uetz P (2004) The phox homology (PX) domain protein interaction network in yeast. Mol Cell Proteomics 3(11):1053–1064

    Article  CAS  PubMed  Google Scholar 

  35. Smaczynska-de RII, Allwood EG, Aghamohammadzadeh S, Hettema EH, Goldberg MW, Ayscough KR (2010) A role for the dynamin-like protein Vps1 during endocytosis in yeast. J Cell Sci 123(Pt 20):3496–3506

    Google Scholar 

  36. Curwin AJ, von Blume J, Malhotra V (2012) Cofilin-mediated sorting and export of specific cargo from the Golgi apparatus in yeast. Mol Biol Cell 23(12):2327–2338

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Nakatogawa H, Suzuki K, Kamada Y, Ohsumi Y (2009) Dynamics and diversity in autophagy mechanisms: lessons from yeast. Nat Rev Mol Cell Biol 10(7):458–467

    Article  CAS  PubMed  Google Scholar 

  38. He C, Klionsky DJ (2009) Regulation mechanisms and signaling pathways of autophagy. Annu Rev Genet 43:67–93

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Bartholomew CR, Suzuki T, Du Z, Backues SK, Jin M, Lynch-Day MA, Umekawa M, Kamath A, Zhao M, Xie Z, Inoki K, Klionsky DJ (2012) Ume6 transcription factor is part of a signaling cascade that regulates autophagy. Proc Natl Acad Sci USA 109(28):11206–11210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Jin M, Klionsky DJ (2014) Transcriptional regulation of ATG9 by the Pho23-Rpd3 complex modulates the frequency of autophagosome formation. Autophagy 10(9):1681–1682

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Chan TF, Bertram PG, Ai W, Zheng XF (2001) Regulation of APG14 expression by the GATA-type transcription factor Gln3p. J Biol Chem 276(9):6463–6467

    Article  CAS  PubMed  Google Scholar 

  42. Yorimitsu T, Nair U, Yang Z, Klionsky DJ (2006) Endoplasmic reticulum stress triggers autophagy. J Biol Chem 281(40):30299–30304

    Article  CAS  PubMed  Google Scholar 

  43. Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MP, Dargemont C (2011) A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics 10(6), M110.006478

    Article  Google Scholar 

  44. Loewith R, Hall MN (2011) Target of rapamycin (TOR) in nutrient signaling and growth control. Genetics 189(4):1177–1201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Algret R, Fernandez-Martinez J, Shi Y, Kim SJ, Pellarin R, Cimermancic P, Cochet E, Sali A, Chait BT, Rout MP, Dokudovskaya S (2014) Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway. Mol Cell Proteomics 13(11):2855–2870

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was supported by National Center for Genetic Engineering and Biotechnology [P-15-50638]. We are grateful to Dr. Philip J. Shaw for critically editing the manuscript. CP is thankful to the Postdoctoral Research Fellowship from National Center for Genetic Engineering and Biotechnology.

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Authors and Affiliations

  1. Biodiversity and Biotechnological Resource Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand

    Chitwadee Phithakrotchanakoon, Aekkachai Puseenam, Sutipa Tanapongpipat & Niran Roongsawang

  2. Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand

    Narumon Phaonakrop & Sittiruk Roytrakul

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  1. Chitwadee Phithakrotchanakoon
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  2. Aekkachai Puseenam
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  3. Narumon Phaonakrop
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Correspondence to Niran Roongsawang.

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Phithakrotchanakoon, C., Puseenam, A., Phaonakrop, N. et al. Hac1 function revealed by the protein expression profile of a OtHAC1 mutant of thermotolerant methylotrophic yeast Ogataea thermomethanolica. Mol Biol Rep 45, 1311–1319 (2018). https://doi.org/10.1007/s11033-018-4287-4

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  • DOI: https://doi.org/10.1007/s11033-018-4287-4

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