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Characterization of the promoter, downstream target genes and recognition DNA sequence of Mhy1, a key filamentation-promoting transcription factor in the dimorphic yeast Yarrowia lipolytica

Abstract

Msn2/Msn4-family zinc finger transcription factors play important roles in stress response in yeast. However, some members of this family show significant functional divergence in different species. Here, we report that in the dimorphic yeast Yarrowia lipolytica, the Msn2/Msn4-like protein Mhy1 is a key regulator of yeast-to-hypha dimorphic transition but not stress response. Both MHY1 deletion and overexpression affect filamentation. In contrast, YlMsn4, the other Msn2/Msn4-like protein, regulates tolerance to acid-induced stress. We show that MHY1 has an unusually long (about 3800 bp) promoter featuring an upstream located enhancer and a double stress response element (STRE) motif, the latter of which mediates Mhy1’s regulation on its own transcription. Transcriptome profiling conducted in wild-type strain, mhy1Δ mutant and MHY1-overexpressing mutant revealed about 100 genes that are highly differentially expressed (≥ 5-fold) in each of the 2 mutants compared to the wild-type strain. The largest group of genes downregulated in mhy1Δ mutant encodes cell wall proteins or enzymes involved in cell wall organization, suggesting that Mhy1 may regulate dimorphic transition by controlling these cell wall genes. We confirmed that the genes YALI0C23452, YALI0C15268 and YALI0B09955 are directly regulated by Mhy1. We also characterized the Mhy1 consensus binding site as 5′-WNAGGGG-3′ (W = A or T; N = A, T, G or C). These results provide new insight in the functions of Msn2/Msn4-family transcription factors in fungi and the mechanism by which Mhy1 regulates dimorphic transition.

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References

  1. Baggett JJ, D’Aquino KE, Wendland B (2003) The Sla2p talin domain plays a role in endocytosis in Saccharomyces cerevisiae. Genetics 165:1661–1674

  2. Bailey D, Feldmann PJF, Boney M, Gow N, Brown AJP (1996) The Candida albicans HYR1 gene, which is activated in response to hyphal development, belongs to a gene family encoding yeast cell wall proteins. J Bacteriol 178:5353–5360. https://doi.org/10.1128/jb.178.18.5353-5360.1996

  3. Berman J, Sudbery PE (2002) Candida albicans: a molecular revolution built on lessons from budding yeast. Nat Rev Genet 3:918–930. https://doi.org/10.1038/nrg948

  4. Cervantes-Chavez JA, Ruiz-Herrera J (2006) STE11 disruption reveals the central role of a MAPK pathway in dimorphism and mating in Yarrowia lipolytica. FEMS Yeast Res 6:801–815. https://doi.org/10.1111/j.1567-1364.2006.00084.x

  5. Cervantes-Chavez JA, Ruiz-Herrera J (2007) The regulatory subunit of protein kinase A promotes hyphal growth and plays an essential role in Yarrowia lipolytica. FEMS Yeast Res 7:929–940. https://doi.org/10.1111/j.1567-1364.2007.00265.x

  6. Cervantes-Chavez JA, Kronberg F, Passeron S, Ruiz-Herrera J (2009) Regulatory role of the PKA pathway in dimorphism and mating in Yarrowia lipolytica. Fungal Genet Biol 46:390–399. https://doi.org/10.1016/j.fgb.2009.02.005

  7. Csank C, Schroppel K, Leberer E, Harcus D, Mohamed O, Meloche S et al (1998) Roles of the Candida albicans mitogen-activated protein kinase homolog, Cek1p, in hyphal development and systemic candiasis. Infect Immun 66:2713–2721

  8. Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I et al (2004) Genome evolution in yeasts. Nature 430:35–44. https://doi.org/10.1038/nature02579

  9. Gimeno CJ, Ljungdahl PO, Styles CA, Fink GR (1992) Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS. Cell 68:1077–1090. https://doi.org/10.1016/0092-8674(92)90079-R

  10. Glazier VE, Krysan DJ (2018) Transcription factor network efficiency in the regulation of Candida albicans biofilms: it is a small world. Curr Genet 64:883–888. https://doi.org/10.1007/s00294-018-0804-1

  11. Görner W, Durchschlag E, Martinez-Pastor MT, Estruch F, Ammerer G et al (1998) Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. Genes Dev 12:586–597. https://doi.org/10.1101/gad.12.4.586

  12. Groenewald M, Boekhout T, Neuveglise C, Gaillardin C, Van Dijck PWM, Wyss M (2014) Yarrowia lipolytica: safety assessment of an oleaginous yeast with a great industrial potential. Crit Rev Microbiol 40:187–206. https://doi.org/10.3109/1040841X.2013.770386

  13. Hurtado CA, Rachubinski RA (1999) MHY1 encodes a C2H2-type zinc finger protein that promotes dimorphic transition in the yeast Yarrowia lipolytica. J Bacteriol 181:3051–3057

  14. Kadosh D (2013) Shaping up for battle: morphological control mechanisms in human fungal pathogens. PLoS Pathog 9:e1003795. https://doi.org/10.1371/journal.ppat.1003795

  15. Kahana-Edwin S, Stark M, Kassir Y (2013) Multiple MAPK cascades regulate the transcription of IME1, the master transcriptional activator of meiosis in Saccharomyces cerevisiae. PLoS One 8:e78920. https://doi.org/10.1371/journal.pone.0078920

  16. Lahiri DK, Ge Y-W (2000) Electrophoretic mobility shift assay for the detection of specific DNA protein complex in nuclear extracts from the cultured cells and frozen autopsy human brain tissue. Brain Res Protoc 5:257–265. https://doi.org/10.1016/S1385-299X(00)00021-0

  17. Lambrechts MG, Bauer FF, Marmur J, Pretorius IS (1996) Muc1, a mucin-like protein that is regulated by Mss10, is critical for pseudohyphal differentiation in yeast. Proc Natl Acad Sci USA 93:8419–8424. https://doi.org/10.1073/pnas.93.16.8419

  18. Leberer E, Harcus D, Dignard D, Johnson L, Ushinsky S, Thomas DY, Schroppel K (2001) Ras links cellular morphogenesis to virulence by regulation of the MAP kinase and cAMP signaling pathways in the pathogenic fungus Candida albicans. Mol Microbiol 42:673–687. https://doi.org/10.1046/j.1365-2958.2001.02672.x

  19. Lengeler KB, Davidson RC, D’souza C, Harashima T, Shen WC, Wang P, Pan X, Waugh M, Heitman J (2000) Signal transduction cascades regulating fungal development and virulence. Microbiol Mol Biol Rev 64:746–785. https://doi.org/10.1128/mmbr.64.4.746-785.2000

  20. Li M, Li Y-Q, Zhao X, Gao X-D (2014) Roles of the three Ras proteins in the regulation of dimorphic transition in the yeast Yarrowia lipolytica. FEMS Yeast Res 14:451–463. https://doi.org/10.1111/1567-1364.12129

  21. Liang S-H, Wu H, Wang R-R, Wang Q, Shu T, Gao X-D (2017) The TORC1-Sch9-Rim15 signaling pathway represses yeast-to-hypha transition in response to glycerol availability in the oleaginous yeast Yarrowia lipolytica. Mol Microbiol 104:553–567. https://doi.org/10.1111/mmi.13645

  22. Liu H-H, Ji X-J, Huang H (2015) Biotechnological applications of Yarrowia lipolytica: past, present and future. Biotechnol Adv 33:1522–1546. https://doi.org/10.1016/j.biotechadv.2015.07.010

  23. Lo WS, Dranginis AM (1996) FLO11, a yeast gene related to the STA4 gene, encodes a novel cell surface flocculin. J Bacteriol 178:7144–7151. https://doi.org/10.1128/jb.178.24.7144-7151.1996

  24. Lo WS, Dranginis AM (1998) The cell surface flocculin Flo11 is required for pseudohyphae formation and invasion by Saccharomyces cerevisiae. Mol Biol Cell 9:161–171. https://doi.org/10.1091/mbc.9.1.161

  25. Marchler G, Schuller C, Adam G, Ruis H (1993) A Sacharomyces cerevisiae UAS element controlled by protein kinase A activates transcription in response to a variety of stress conditions. EMBO J 12:1997–2003

  26. Martinez-Pastor MT, Marchler G, Schuller C, Marchler-Bauer A, Ruis H, Estruch F (1996) The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). EMBO J 15:2227–2235

  27. Morales-Vargas AT, Domínguez A, Ruiz-Herrera J (2012) Identification of dimorphism-involved genes of Yarrowia lipolytica by means of microarray analysis. Res Microbiol 163:378–387. https://doi.org/10.1016/j.resmic.2012.03.002

  28. Moran GP, Anderson MZ, Myers LC, Sullivan DJ (2019) Role of Mediator in virulence and antifungal drug resistance in pathogenic fungi. Curr Genet 65:621–630. https://doi.org/10.1007/s00294-019-00932-8

  29. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Method 5:621–628. https://doi.org/10.1038/nmeth.1226

  30. Mosch HU, Roberts RL, Fink GR (1996) Ras2 signals via the Cdc42/Ste20/mitogen-activated protein kinase module to induce filamentous growth in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 93:5352–5356. https://doi.org/10.1073/pnas.93.11.5352

  31. Nicholls S, Straffon M, Enjalbert B, Nantel A, Macaskill S, Whiteway M, Brown AJ (2004) Msn2- and Msn4-like transcription factors play no obvious roles in the stress responses of the fungal pathogen Candida albicans. Eukaryot Cell 3:1111–1123. https://doi.org/10.1128/EC.3.5.1111-1123.2004

  32. Perez-Campo FM, Dominguez A (2001) Factors affecting the morphogenetic switch in Yarrowia lipolytica. Curr Microbiol 43:429–433. https://doi.org/10.1007/s002840010333

  33. Ramon AM, Gil R, Burgal M, Sentandreu R, Valentin E (1996) A novel cell wall protein specific to the mycelial form of Yarrowia lipolytica. Yeast 12:1535–1548. https://doi.org/10.1002/(SICI)1097-0061(199612)12:15%3C1535:AID-YEA59%3E3.0.CO;2-D

  34. Ramsdale M, Selway L, Stead D, Walker J, Yin Z, Nicholls SM, Crowe J, Sheils EM, Brown AJ (2008) MNL1 regulates weak acid-induced stress responses of the fungal pathogen Candida albicans. Mol Biol Cell 19:4393–4403. https://doi.org/10.1091/mbc.e07-09-0946

  35. Robertson LS, Fink GR (1998) The three yeast A kinases have specific signaling functions in pseudohyphal growth. Proc Natl Acad Sci USA 95:13783–13787. https://doi.org/10.1073/pnas.95.23.13783

  36. Ruiz-Herrera J, Sentandreu R (2002) Different effectors of dimorphism in Yarrowia lipolytica. Arch Microbiol 178:477–483. https://doi.org/10.1007/s00203-002-0478-3

  37. Rupp S, Summers E, Lo HJ, Madhani H, Fink G (1999) MAP kinase and cAMP filamentation signaling pathways converge on the unusually large promoter of the yeast FLO11 gene. EMBO J 18:1257–1269. https://doi.org/10.1093/emboj/18.5.1257

  38. Schmitt AP, McEntee K (1996) Msn2p, a zinc finger DNA-binding protein, is the transcriptional activator of the multistress response in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 93:5777–5782. https://doi.org/10.1073/pnas.93.12.5777

  39. Su C, Yu J, Lu Y (2018) Hyphal development in Candida albicans from different cell states. Curr Genet 64:1239–1243. https://doi.org/10.1007/s00294-018-0845-5

  40. Trapenll C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111. https://doi.org/10.1093/bioinformatics/btp120

  41. Wang G, Li D, Miao Z, Zhang S, Liang W, Liu L (2018) Comparative transcriptome analysis reveals multiple functions for Mhy1p in lipid biosynthesis in the oleaginous yeast Yarrowia lipolytica. Biochim Biophys Acta Mol Cell Biol Lipids 1863:81–90. https://doi.org/10.1016/j.bbalip.2017.10.003

  42. Wendland B, Emr SD (1998) Pan1p, yeast eps15, functions as a multivalent adaptor that coordinates protein-protein interactions essential for endocytosis. J Cell Biol 141:71–84. https://doi.org/10.1083/jcb.141.1.71

  43. Xue W, Yin Y, Ismail F, Hu C, Zhou M, Cao X, Li S, Sun X (2019) Transcription factor CCG-8 plays a pivotal role in azole adaptive responses of Neurospora crassa by regulating intracellular azole accumulation. Curr Genet 65:735–745. https://doi.org/10.1007/s00294-018-0924-7

  44. Yun Y, Zhou X, Yang S, Wen Y, You H, Zheng Y, Norvienyeku J, Shim WB, Wang Z (2019) Fusarium oxysporum f. sp. lycopersici C2H2 transcription factor FolCzf1 is required for conidiation, fusaric acid production, and early host infection. Curr Genet 65:773–783. https://doi.org/10.1007/s00294-019-00931-9

  45. Zhao X-F, Li M, Li Y-Q, Chen X-D, Gao X-D (2013) The TEA/ATTS transcription factor YlTec1p represses the yeast-to-hypha transition in the dimorphic yeast Yarrowia lipolytica. FEMS Yeast Res 13:50–61. https://doi.org/10.1111/j.1567-1364.2012.12008.x

  46. Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA et al (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19:556–566. https://doi.org/10.1101/gr.090233.108

  47. Zordan RE, Galgoczy DJ, Johnson AD (2006) Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop. Proc Natl Acad Sci USA 103:12807–12812. https://doi.org/10.1073/pnas.0605138103

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Acknowledgements

We thank Drs. Claude Gaillardin, Jean-Marie Beckerich, Jean-Marc Nicaud, and Richard Rachubinski for kindly providing yeast strains and plasmids. This work was supported by the National Natural Science Foundation of China Grants 31570076 and 31870062 to X. G.

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Correspondence to Xiang-Dong Gao.

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Wu, H., Shu, T., Mao, Y. et al. Characterization of the promoter, downstream target genes and recognition DNA sequence of Mhy1, a key filamentation-promoting transcription factor in the dimorphic yeast Yarrowia lipolytica. Curr Genet 66, 245–261 (2020). https://doi.org/10.1007/s00294-019-01018-1

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Keywords

  • Hyphae
  • Morphogenesis
  • Dimorphic transition
  • Filamentous growth
  • Filamentation