Archives of Microbiology

, Volume 197, Issue 4, pp 575–588 | Cite as

Regulation of the expression of the whole genome of Ustilago maydis by a MAPK pathway

  • Domingo Martínez-Soto
  • José Ruiz-HerreraEmail author
Original Paper


The operation of mitogen-activated protein kinase (MAPK) signal transduction pathways is one of the most important mechanisms for the transfer of extracellular information into the cell. These pathways are highly conserved in eukaryotic organisms. In fungi, MAPK pathways are involved in the regulation of a number of cellular processes such as metabolism, homeostasis, pathogenesis and cell differentiation and morphogenesis. Considering the importance of pathways, in the present work we proceeded to identify all the genes that are regulated by the signal transduction pathway involved in mating, pathogenesis and morphogenesis of Ustilago maydis. Accordingly we made a comparison between the transcriptomes from a wild-type strain and an Ubc2 mutant affected in the interacting protein of this pathway by use of microarrays. By this methodology, we identified 939 genes regulated directly or indirectly by the MAPK pathway. Of them, 432 were positively, and 507 were negatively found regulated. By functional grouping, genes encoding cyclin-dependent kinases, transcription factors, proteins involved in signal transduction, in synthesis of wall and cell membrane, and involved in dimorphism were identified as differentially regulated. These data reveal the importance of these global studies, and the large (and unsuspected) number of functions of the fungus under the control of this MAPK, providing clues to the possible mechanisms involved.


Ustilago maydis MAPK signaling pathway Ubc2 gene Transcriptome Gene regulation 



This work was supported by Consejo Nacional de Ciencia y Tecnología (CONACYT), Mexico. Thanks are given to Dr. Scott Gold for permission to use his microarray design, and QFB Claudia Geraldine León-Ramirez, IBQ Fernando Emilio Pérez-García, Biol. Mayela Fernanda Salazar-Chávez and M.S. Guillermo Antonio Silva-Martínez for assistance in some analyses. DMS is a doctoral student supported by a fellowship from CONACYT (México). JRH is Emeritus National Professor, México.

Supplementary material

203_2015_1087_MOESM1_ESM.xlsx (68 kb)
Supplementary material 1 (XLSX 68 kb)
203_2015_1087_MOESM2_ESM.docx (20 kb)
Supplementary material 2 (DOCX 19 kb)
203_2015_1087_MOESM3_ESM.docx (22 kb)
Supplementary material 3 (DOCX 21 kb)


  1. Andrews DL, Egan JD, Mayorga ME et al (2000) The Ustilago maydis ubc4 and ubc5 genes encode members of a MAPK kinase cascade required for filamentous growth. Mol Plant Microbe Interact 13:781–786CrossRefPubMedGoogle Scholar
  2. Aréchiga-Carvajal ET, Ruiz-Herrera J (2005) The RIM101/PacC homologue from the basidiomycete Ustilago maydis is functional in multiple pH-sensitive phenomena. Eukaryot Cell 4:999–1008CrossRefPubMedCentralPubMedGoogle Scholar
  3. Balázs A, Pócsi I, Hamari Z et al (2010) AtfA bZIP-type transcription factor regulates oxidative and osmotic stress responses in Aspergillus nidulans. Mol Genet Genomics 283:289–303CrossRefPubMedGoogle Scholar
  4. Ballario P, Vittorioso P, Magrelli A et al (1996) White collar-1, a central regulator of blue light responses in Neurospora, is a zinc finger protein. EMBO J 15:1650–1657PubMedCentralPubMedGoogle Scholar
  5. Banuett F, Herskowitz I (1989) Different a alleles of Ustilago maydis are necessary for maintenance of filamentous growth but not for meiosis. Proc Natl Acad Sci USA 86:5878–5882CrossRefPubMedCentralPubMedGoogle Scholar
  6. Banuett F, Herskowitz I (1994) Morphological transitions in the life cycle of Ustilago maydis and their genetic control by the a and b loci. Exp Mycol 18:247–266CrossRefGoogle Scholar
  7. Bendtsen JD, Nielsen H, von Heijne G et al (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783–795CrossRefPubMedGoogle Scholar
  8. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300Google Scholar
  9. Bernstein HS, Coughlin SR (1997) Pombe Cdc5-related protein. A putative human transcription factor implicated in mitogen-activated signaling. J Biol Chem 272:5833–5837CrossRefPubMedGoogle Scholar
  10. Bölker M (2001) Ustilago maydis—a valuble model system for the study of fungal dimorphism and virulence. Microbiology 147:1395–1401PubMedGoogle Scholar
  11. Bölker M, Urban M, Kahmann R (1992) The a mating type locus of U. maydis specifies cell signaling components. Cell 68:441–450CrossRefPubMedGoogle Scholar
  12. Brefort T, Doehlemann G, Mendoza-Mendoza A et al (2009) Ustilago maydis as a pathogen. Annu Rev Phytopathol 47:423–445CrossRefPubMedGoogle Scholar
  13. Brown JL, North S, Bussey H (1993) SKN7, a yeast multicopy suppressor of a mutation affecting cell wall beta-glucan assembly, encodes a product with domains homologous to prokaryotic two-component regulators and to heat shock transcription factors. J Bacteriol 175:6908–6915PubMedCentralPubMedGoogle Scholar
  14. Cabrera-Ponce JL, León-Ramírez CG, Verver-Vargas A et al (2012) Metamorphosis of the basidiomycota Ustilago maydis: transformation of yeast-like cells into basidiocarps. Fungal Genet Biol 49:765–771CrossRefPubMedGoogle Scholar
  15. Carbó N, Pérez-Martín J (2010) Activation of the cell wall integrity pathway promotes escape from G2 in the fungus Ustilago maydis. PLoS Genet. doi: 10.1371/journal.pgen.1001009 PubMedCentralPubMedGoogle Scholar
  16. Cervantes-Chávez JA, Ortiz-Castellanos L, Tejada-Santorius M et al (2010) Functional analysis of the pH responsive pathway Pal/Rim in the phytopathogenic basidiomycete Ustilago maydis. Fungal Genet Biol 47:446–457CrossRefPubMedGoogle Scholar
  17. Chen RE, Thorner J (2007) Function and regulation in MAPK signaling pathways: lessons learned from the yeast Saccharomyces cerevisiae. Biochim Biophys Acta 1773:1311–1340CrossRefPubMedCentralPubMedGoogle Scholar
  18. Chiariello M, Bruni CB, Bucci C (1999) The small GTPases Rab5a, Rab5b and Rab5c are differentially phosphorylated in vitro. FEBS Lett 453:20–24CrossRefPubMedGoogle Scholar
  19. Clotet J, Posas F (2007) Control of cell cycle in response to osmostress: lessons from yeast. Methods Enzymol 428:63–76CrossRefPubMedGoogle Scholar
  20. Davis D et al (2000) Candida albicans RIM101 pH response pathway is required for host-pathogen interaction. Infect Immun 68:5953–5959CrossRefPubMedCentralPubMedGoogle Scholar
  21. Dubois E, Bercy J, Messenguy F (1987) Characterization of two genes, ARGRI and ARGRIII required for specific regulation of arginine metabolism in yeast. Mol Gen Genet 207:142–148CrossRefPubMedGoogle Scholar
  22. Dürrenberger F, Laidlaw RD, Kronstad JW (2001) The hgl1 gene is required for dimorphism and teliospore formation in the fungal pathogen Ustilago maydis. Mol Microbiol 41:337–348CrossRefPubMedGoogle Scholar
  23. Estruch F (1991) The yeast putative transcriptional repressor RGM1 is a proline-rich zinc finger protein. Nucleic Acids Res 19:4873–4877CrossRefPubMedCentralPubMedGoogle Scholar
  24. Fonseca-Garcia C, León-Ramírez CG, Ruiz-Herrera J (2012) The regulation of different metabolic pathways through the Pal/Rim pathway in Ustilago maydis. FEMS Yeast Res 12:547–556CrossRefPubMedGoogle Scholar
  25. Franco-Frías E, Ruiz-Herrera J, Aréchiga-Carvajal ET (2014) Transcriptomic analysis of the role of Rim101/PacC in the adaptation of Ustilago maydis to an alkaline environment. Microbiology 160:1985–1998CrossRefPubMedGoogle Scholar
  26. Gancedo JM (2001) Control of pseudohyphae formation in Saccharomyces cerevisiae. FEMS Microbiol Rev 25:107–123CrossRefPubMedGoogle Scholar
  27. Garrido E, Voss U, Müller P et al (2004) The induction of sexual development and virulence in the smut fungus Ustilago maydis depends on Crk1, a novel MAPK protein. Genes Dev 18:3117–3130CrossRefPubMedCentralPubMedGoogle Scholar
  28. Guo Y, Feng Y, Trevedi NS et al (2011) Medusa structure of the gene regulatory network: dominance of transcription factors in cancer subtype c1assification. Exp Biol Med (Maywood) 236:628–636CrossRefGoogle Scholar
  29. Gustin MC, Albertyn J, Alexander M et al (1998) MAP kinase pathways in the yeast Saccharomyces cerevisiae. Microbiol Mol Biol Rev 62:1264–1300PubMedCentralPubMedGoogle Scholar
  30. Heimel K, Scherer M, Vranes M et al (2010) The transcription factor Rbf1 is the master regulator for b-mating type controlled pathogenic development in Ustilago maydis. Plos Pathog. doi: 10.1371/journal.ppat.1001035 PubMedCentralPubMedGoogle Scholar
  31. Hewald S, Linne U, Scherer M et al (2006) Identification a gene cluster for biosynthesis of mannosylerythritol lipids in the basidiomycetous fungus Ustilago maydis. Appl Environ Microbiol 72:5469–5477CrossRefPubMedCentralPubMedGoogle Scholar
  32. Holliday R (1974) Ustilago maydis. In: King RC (ed) The handbook of genetics. Plenum Press, New York, pp 575–595Google Scholar
  33. Hua X, Yuan X, Wilhelmus KR (2010) A fungal pH-responsive signaling pathway regulating Aspergillus adaptation and invasion into the cornea. Investig Ophthalmol Vis Sci 51:1517–1523CrossRefGoogle Scholar
  34. Kämper J, Kahmann R, Bölker M et al (2006) Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444:97–101CrossRefPubMedGoogle Scholar
  35. Kitada K, Johnson AL, Johnston LH et al (1993) A multicopy suppressor gene of the Saccharomyces cerevisiae G1 cell cycle mutant gene dbf4 encodes a protein kinase and is identified as CDC5. Mol Cell Biol 13:4445–4457PubMedCentralPubMedGoogle Scholar
  36. Krems B, Charizanis C, Entian KD (1996) The response regulator-like protein Pos9/Skn7 of Saccharomyces cerevisiae is involved in oxidative stress resistance. Curr Genet 29:327–334CrossRefPubMedGoogle Scholar
  37. Lamb TM, Mitchell AP (2003) The transcription factor Rim101p governs ion tolerance and cell differentiation by direct repression of the regulatory genes NRG1 and SMP1 in Saccharomyces cerevisiae. Mol Cell Biol 23:677–686CrossRefPubMedCentralPubMedGoogle Scholar
  38. León-Ramirez CG, Sánchez-Arreguín JA, Ruiz-Herrera J (2014) Ustilago maydis, a delicacy of the aztec cuisine and a model for research. Nat Resour 5:256–267Google Scholar
  39. León-Ramírez CG, Cabrera-Ponce JL, Martínez-Espinoza AD et al (2004) Infection of alternative host plant species by Ustilago maydis. New Phytol 164:337–346CrossRefGoogle Scholar
  40. Letunic I, Doerks T, Bork P (2012) SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res 40:302–305CrossRefGoogle Scholar
  41. Martínez-Espinoza AD, León-Ramírez CG, Elizarraraz G et al (1997) Monomorphic nonpathogenic mutants of Ustilago maydis. Phytopathology 87:259–265CrossRefPubMedGoogle Scholar
  42. Martínez-Espinoza AD, Ruiz-Herrera J, León-Ramírez CG et al (2004) MAP kinase and cAMP signaling pathways modulate the pH-induced yeast-to-mycelium dimorphic transition in the corn smut fungus Ustilago maydis. Curr Microbiol 49:274–281CrossRefPubMedGoogle Scholar
  43. Martínez-Pastor MT, Marchler G, Schüller C et al (1996) The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p required for transcriptional induction through the stress response element (STRE). EMBO J 15:2227–2235PubMedCentralPubMedGoogle Scholar
  44. Martínez-Soto D, Ruiz-Herrera J (2013) Transcriptomic analysis of the dimorphic transition of Ustilago maydis induced in vitro by a change in pH. Fungal Genet Biol 58–59:116–125CrossRefPubMedGoogle Scholar
  45. Martínez-Soto D, Briones-Robledo AM, Estrada-Luna AA et al (2013) Transcriptomic analysis of Ustilago maydis infecting Arabidopsis reveals important aspects of the fungus pathogenic mechanisms. Plant Signal Behav. doi: 10.4161/psb.25059 PubMedCentralPubMedGoogle Scholar
  46. Mayorga ME, Gold SE (1999) A MAP kinase encoded by the ubc3 gene of Ustilago maydisis required for filamentous growth and full virulence. Mol Microbiol 34:485–497CrossRefPubMedGoogle Scholar
  47. Mayorga ME, Gold SE (2001) The Ubc2 gene of Ustilago maydis encodes a putative novel adaptor protein required for filamentous growth, pheromone response and virulence. Mol Microbiol 41:1365–1379CrossRefPubMedGoogle Scholar
  48. Méndez-Morán L, Reynaga-Peña CG, Springer PS et al (2005) Ustilago maydis infection of the nonnatural host Arabidopsis thaliana. Phytopathology 95:480–488CrossRefPubMedGoogle Scholar
  49. Mendoza-Mendoza A, Eskova A, Weise C et al (2009) Hap2 regulates the pheromone response transcription factor prf1 in Ustilago maydis. Mol Microbiol 72:683–698CrossRefPubMedGoogle Scholar
  50. Millar JB, Russell P (1992) The cdc25 M-phase inducer: an unconventional protein phosphatase. Cell 68:407–410CrossRefPubMedGoogle Scholar
  51. Minehart PL, Magasanik B (1991) Sequence and expression of GLN3, a positive nitrogen regulatory gene of Saccharomyces cerevisiae encoding a protein with a putative zinc finger DNA-binding domain. Mol Cell Biol 11:6216–6228PubMedCentralPubMedGoogle Scholar
  52. Müller P, Aichinger C, Feldbrügge M et al (1999) The MAP kinase kpp2 regulates mating and pathogenic development in Ustilago maydis. Mol Microbiol 34:1007–1017CrossRefPubMedGoogle Scholar
  53. Müller P, Weinzierl G, Brachmann A et al (2003) Mating and pathogenic development of the smut fungus Ustilago maydis are regulated by one mitogen-activated protein kinase cascade. Eukaryot Cell 2:1187–1199CrossRefPubMedCentralPubMedGoogle Scholar
  54. Palecek SP, Parikh AS, Kron SJ (2002) Sensing, signalling and integrating physical processes during Saccharomyces cerevisiae invasive and filamentous growth. Microbiology 148:893–907PubMedGoogle Scholar
  55. Pan X, Harashima T, Heitman J (2000) Signal transduction cascades regulating pseudohyphal differentiation of Saccharomyces cerevisiae. Curr Opin Microbiol 3:567–572CrossRefPubMedGoogle Scholar
  56. Peñalva MA, Arst HN Jr (2002) Regulation of gene expression by ambient pH in filamentous fungi and yeasts. Microbiol Mol Biol Rev 66:426–446CrossRefPubMedCentralPubMedGoogle Scholar
  57. Perez-Nadales E, Almeida-Nogueira MF, Baldin C et al (2014) Fungal model systems and elucidation of pathogenicity determinants. Fungal Genet Biol 7:42–67CrossRefGoogle Scholar
  58. Pijnappel WW, Schaft D, Roquev A et al (2001) The S. cerevisiae SET3 complex two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program. Genes Dev 15:2991–3004CrossRefPubMedCentralPubMedGoogle Scholar
  59. Punta M, Coggill PC, Eberhardt RY et al (2012) The Pfam protein families database. Nucleic Acids Res 40:290–301CrossRefGoogle Scholar
  60. Ramon AM, Porta A, Fonzi WA (1999) Effect of environmental pH on morphological development of Candida albicans is mediated via the PacC-related transcription factor encoded by PRR2. J Bacteriol 181:7524–7530PubMedCentralPubMedGoogle Scholar
  61. Raudaskoski M, Kothe E (2010) Basidiomycete mating type genes and pheromone signaling. Eucaryot Cell 9:847–859CrossRefGoogle Scholar
  62. Robertson AS, Allwood EG, Smith AP et al (2009) The WASP homologue Las17 activates novel actin-regulatory activity of Ysc84 to promote endocitosis in yeast. Mol Biol Cell 20:1618–1628CrossRefPubMedCentralPubMedGoogle Scholar
  63. Robledo-Briones AM, Ruiz-Herrera J (2013) Regulation of genes involved in cell wall synthesis and structure during Ustilago maydis dimorphism. FEMS Yeast Res 13:74–84CrossRefPubMedGoogle Scholar
  64. Ruepp A, Zollner A, Maier D et al (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res 32:5539–5545CrossRefPubMedCentralPubMedGoogle Scholar
  65. Ruiz-Herrera J, Campos-Góngora E (2012) An introduction to fungal dimorphism. In: Ruiz-Herrera J (ed) Dimorphic fungi: their importance as models for differentiation and fungal pathogenesis. Bentham e Books, eISBN:978-1-60805-364-3Google Scholar
  66. Ruiz-Herrera J, León-Ramírez CG, Guevara-Olvera L et al (1995) Yeast-mycelial dimorphism of haploid end diploid strains of Ustilago maydis. Microbiology 141:695–703CrossRefGoogle Scholar
  67. Ruiz-Herrera J, Reynaga-Peña CG, Aréchiga-Carvajal ET (2009) Ustilago maydis as a model for phytopathogenic fungal development. In: Khachatourians GG, Arora DK, Rajendran TP, Srivastava AK (eds) Agriculturally important microorganisms, vol I. Academic World International, Bhopal, pp 107–122Google Scholar
  68. Ruiz-Herrera J, Robledo-Briones M, Martínez-Soto D (2013) Experimental pathosystems as a tool for the identification of virulence factors in pathogenic fungi. In: Deshpande MV, Ruiz-Herrera J (eds) Biotechnology: beyond borders. CSIR-National Chemical Laboratory, Pune, pp 30–38Google Scholar
  69. Sandrock B, Böhmer C, Bölker M (2006) Dual function of the germinal centre kinase Don3 during mitosis and cytokinesis in Ustilago maydis. Mol Micobiol 62:655–666CrossRefGoogle Scholar
  70. Singer-Krüger B, Stenmark H, Düsterhöft A et al (1994) Role of three rab5-like GTPases, Ypt51p, Ypt52p, and Ytp53p, in the endocytic and vacuolar protein sorting pathways of yeast. J Cell Biol 125:283–298CrossRefPubMedGoogle Scholar
  71. Singh P, Chauhan N, Ghosh A et al (2004) SKN7 of Candida albicans: mutant construction and phenotype analysis. Infect Immun 72:2390–2394CrossRefPubMedCentralPubMedGoogle Scholar
  72. Soulard A, Lechler T, Spiridonov V et al (2002) Saccharomyces cerevisiae Bzz1p is implicated with type I myosins in actin patch polarization and is able to recruit actin-polymerizing machinery in vitro. Mol Cell Biol 22:7889–7906CrossRefPubMedCentralPubMedGoogle Scholar
  73. Valdés-Santiago L, Ruiz-Herrera J (2014) Stress and polyamine metabolism in fungi. Front Chem. doi: 10.3389/fchem.2013.00042 PubMedCentralPubMedGoogle Scholar
  74. Valdés-Santiago L, Cervantes-Chávez JA, León Ramírez CG et al (2012) Polyamine metabolism in fungi with emphasis on phytopathogenic species. J Amino Acids. doi: 10.1155/2012/837932 PubMedCentralPubMedGoogle Scholar
  75. Vollmeister E, Schipper K, Baumann S et al (2011) Fungal development of the plant pathogen Ustilago maydis. FEMS Microbiol Rev 36:59–77CrossRefPubMedGoogle Scholar
  76. Ward MP, Garrett S (1994) Suppression of a yeast cyclic AMP-dependent protein kinase defect by overexpression of SOK1, a yeast gene exhibiting sequence similarity to a developmentally regulated mouse gene. Mol Cell Biol 14:5619–5627CrossRefPubMedCentralPubMedGoogle Scholar
  77. Weig M, Haynes K, Rogers TR et al (2001) A GAS-like gene family in the pathogenic fungus Candida glabrata. Microbiology 147:2007–2019PubMedGoogle Scholar
  78. Wilkinson MG, Millar JB (2000) Control of eukaryotic cell cycle by MAP kinase signaling pathways. FASEB J 14:2147–2157CrossRefPubMedGoogle Scholar
  79. Wormley FL Jr, Heinrich G, Miller JL et al (2005) Identification and characterization of an SKN7 homolog in Cryptococcus neoformans. Infect Immun 73:5022–5030CrossRefPubMedCentralPubMedGoogle Scholar
  80. Wurgler-Murphy SM, Maeda T, Witten EA et al (1997) Regulation of the Saccharomyces cerevisiae HOG1 mitogen-activated protein kinase by PTP2 and PTP3 protein tyrosine phosphatases. Mol Cell Biol 17:1289–1297PubMedCentralPubMedGoogle Scholar
  81. Xu S, Falvey DA, Brandriss MC (1995) Roles of URE2 and GLN3 in the proline utilization pathway Saccharomyces cerevisiae. Mol Cell Biol 15:2321–2330PubMedCentralPubMedGoogle Scholar
  82. Zhang W, Liu HT (2002) MAPK signal pathways in the regulation of cell proliferation in mammalian cells. Cell Res 12:9–18CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Departamento de Ingeniería Genética, Unidad IrapuatoCentro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuatoMexico

Personalised recommendations