1887

Abstract

Fungi have developed the ability to overcome extreme growth conditions and thrive in hostile environments. The model fungus tolerates, for example, ambient alkalinity up to pH 10 or molar concentrations of multiple cations. The ability to grow under alkaline pH or saline stress depends on the effective function of at least three regulatory pathways mediated by the zinc-finger transcription factor PacC, which mediates the ambient pH regulatory pathway, the calcineurin-dependent CrzA and the cation homeostasis responsive factor SltA. Using RNA sequencing, we determined the effect of external pH alkalinization or sodium stress on gene expression. The data show that each condition triggers transcriptional responses with a low degree of overlap. By sequencing the transcriptomes of the null mutant, the role of SltA in the above-mentioned homeostasis mechanisms was also studied. The results show that the transcriptional role of SltA is wider than initially expected and implies, for example, the positive control of the PacC-dependent ambient pH regulatory pathway. Overall, our data strongly suggest that the stress response pathways in fungi include some common but mostly exclusive constituents, and that there is a hierarchical relationship among the main regulators of stress response, with SltA controlling expression, at least in .

Funding
This study was supported by the:
  • Oier Etxebeste , Euskal Herriko Unibertsitatea , (Award GIU19/635 014)
  • Oier Etxebeste , Euskal Herriko Unibertsitatea , (Award PPGA19/08)
  • Not Applicable , Eusko Jaurlaritza , (Award Elkartek19/72)
  • Eduardo Antonio Espeso , Ministerio de Ciencia, Innovación y Universidades , (Award RTI2018-094263-B-100)
  • Eduardo Antonio Espeso , Ministerio de Economía, Industria y Competitividad, Gobierno de España , (Award BFU2015-66806-R)
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000415
2020-07-31
2020-08-06
Loading full text...

Full text loading...

/deliver/fulltext/mgen/10.1099/mgen.0.000415/mgen000415.html?itemId=/content/journal/mgen/10.1099/mgen.0.000415&mimeType=html&fmt=ahah

References

  1. Etxebeste O, Espeso EA. Aspergillus nidulans in the post-genomic era: a top-model filamentous fungus for the study of signaling and homeostasis mechanisms. Int Microbiol 2020; 23:5–22 [CrossRef][PubMed]
    [Google Scholar]
  2. Tilburn J, Sarkar S, Widdick DA, Espeso EA, Orejas M et al. The Aspergillus PacC zinc finger transcription factor mediates regulation of both acid- and alkaline-expressed genes by ambient pH. Embo J 1995; 14:779–790[PubMed]
    [Google Scholar]
  3. Arst HN, Peñalva MA. pH regulation in Aspergillus and parallels with higher eukaryotic regulatory systems. Trends Genet 2003; 19:224–231 [CrossRef][PubMed]
    [Google Scholar]
  4. Peñalva MA, Tilburn J, Bignell E, Arst HN. Ambient pH gene regulation in fungi: making connections. Trends Microbiol 2008; 16:291–300 [CrossRef][PubMed]
    [Google Scholar]
  5. Spielvogel A, Findon H, Arst HN, Araújo-Bazán L, Hernández-Ortíz P et al. Two zinc finger transcription factors, CrzA and SltA, are involved in cation homoeostasis and detoxification in Aspergillus nidulans. Biochem J 2008; 414:419-29 [CrossRef][PubMed]
    [Google Scholar]
  6. Orejas M, Espeso EA, Tilburn J, Sarkar S, Arst HN et al. Activation of the Aspergillus PacC transcription factor in response to alkaline ambient pH requires proteolysis of the carboxy-terminal moiety. Genes Dev 1995; 9:1622–1632 [CrossRef][PubMed]
    [Google Scholar]
  7. Espeso EA, Tilburn J, Sánchez-Pulido L, Brown CV, Valencia A et al. Specific DNA recognition by the Aspergillus nidulans three zinc finger transcription factor PacC. J Mol Biol 1997; 274:466–480 [CrossRef][PubMed]
    [Google Scholar]
  8. Espeso EA, Roncal T, Díez E, Rainbow L, Bignell E et al. On how a transcription factor can avoid its proteolytic activation in the absence of signal transduction. Embo J 2000; 19:719–728 [CrossRef][PubMed]
    [Google Scholar]
  9. Díez E, Álvaro J, Espeso EA, Rainbow L, Suárez T et al. Activation of the Aspergillus PacC zinc finger transcription factor requires two proteolytic steps. Embo J 2002; 21:1350–1359 [CrossRef][PubMed]
    [Google Scholar]
  10. Calcagno-Pizarelli AM, Negrete-Urtasun S, Denison SH, Rudnicka JD, Bussink H-J et al. Establishment of the ambient pH signaling complex in Aspergillus nidulans: PalI assists plasma membrane localization of PalH. Eukaryot Cell 2007; 6:2365 LP–2375 [CrossRef][PubMed]
    [Google Scholar]
  11. Herranz S, Rodríguez JM, Bussink H-J, Sánchez-Ferrero JC, Arst HN et al. Arrestin-Related proteins mediate pH signaling in fungi. Proc Natl Acad Sci U S A 2005; 102:12141 LP–12146 [CrossRef][PubMed]
    [Google Scholar]
  12. Galindo A, Calcagno-Pizarelli AM, Arst HN, Peñalva Miguel Ángel. An ordered pathway for the assembly of fungal ESCRT-containing ambient pH signalling complexes at the plasma membrane. J Cell Sci 2012; 125:1784–1795 [CrossRef][PubMed]
    [Google Scholar]
  13. Lucena-Agell D, Hervás-Aguilar A, Múnera-Huertas T, Pougovkina O, Rudnicka J et al. Mutational analysis of the Aspergillus ambient pH receptor PalH underscores its potential as a target for antifungal compounds. Mol Microbiol 2016; 101:982–1002 [CrossRef][PubMed]
    [Google Scholar]
  14. Peñalva MA, Lucena-Agell D, Arst HN. Liaison alcaline: PalS entice non-endosomal ESCRTs to the plasma membrane for pH signaling. Curr Opin Microbiol 2014; 22:49–59 [CrossRef][PubMed]
    [Google Scholar]
  15. Galindo A, Hervás-Aguilar A, Rodríguez-Galán O, Vincent O, Arst HN et al. Palc, one of two BRO1 domain proteins in the fungal pH signalling pathway, localizes to cortical structures and binds Vps32. Traffic 2007; 8:1346–1364 [CrossRef][PubMed]
    [Google Scholar]
  16. Vincent O, Rainbow L, Tilburn J, Arst HN, Peñalva MA. YPXL/I is a protein interaction motif recognized by Aspergillus PalA and its human homologue, AIP1/Alix. Mol Cell Biol 2003; 23:1647 LP–1655 [CrossRef][PubMed]
    [Google Scholar]
  17. Peñas MM, Hervás-Aguilar A, Múnera-Huertas T, Reoyo E, Peñalva MA et al. Further characterization of the signaling proteolysis step in the Aspergillus nidulans pH signal transduction pathway. Eukaryot Cell 2007; 6:960–970 [CrossRef][PubMed]
    [Google Scholar]
  18. Hervás-Aguilar A, Rodríguez JM, Tilburn J, Arst HN, Peñalva MA. Evidence for the direct involvement of the proteasome in the proteolytic processing of the Aspergillus nidulans zinc finger transcription factor PacC. J Biol Chem 2007; 282:34735–34747 [CrossRef][PubMed]
    [Google Scholar]
  19. Espeso EA, Peñalva MA. Three binding sites for the Aspergillus nidulans PacC zinc-finger transcription factor are necessary and sufficient for regulation by ambient pH of the isopenicillin N synthase gene promoter. J Biol Chem 1996; 271:28825–28830 [CrossRef][PubMed]
    [Google Scholar]
  20. Espeso EA, Arst HN. On the mechanism by which alkaline pH prevents expression of an acid-expressed gene. Mol Cell Biol 2000; 20:3355 LP–3363 [CrossRef][PubMed]
    [Google Scholar]
  21. Caddick MX, Brownlee AG, Arst HN. Regulation of gene expression by pH of the growth medium in Aspergillus nidulans. Mol Gen Genet 1986; 203:346–353 [CrossRef][PubMed]
    [Google Scholar]
  22. MacCabe AP, Orejas M, Pérez-González JA, Ramón D. Opposite patterns of expression of two Aspergillus nidulans xylanase genes with respect to ambient pH. J Bacteriol 1998; 180:1331 LP–1333[PubMed]
    [Google Scholar]
  23. Mellado L, Arst HN, Espeso EA. Proteolytic activation of both components of the cation stress-responsive Slt pathway in Aspergillus nidulans. Mol Biol Cell 2016; 27:2598–2612 [CrossRef][PubMed]
    [Google Scholar]
  24. Mellado L, Calcagno-Pizarelli AM, Lockington RA, Cortese MS, Kelly JM et al. A second component of the SltA-dependent cation tolerance pathway in Aspergillus nidulans. Fungal Genet Biol 2015; 82:116–128 [CrossRef][PubMed]
    [Google Scholar]
  25. Saloheimo A, Aro N, Ilmén M, Penttilä M. Isolation of the ace1 gene encoding a Cys(2)-His(2) transcription factor involved in regulation of activity of the cellulase promoter cbh1 of Trichoderma reesei. J Biol Chem 2000; 275:5817–5825 [CrossRef][PubMed]
    [Google Scholar]
  26. O’Neil JD, Bugno M, Stanley MS, Barham-Morris JB, Woodcock NA et al. Cloning of a novel gene encoding a C2H2 zinc finger protein that alleviates sensitivity to abiotic stresses in Aspergillus nidulans. Mycol Res 2002; 106:491–498
    [Google Scholar]
  27. Cove DJ. The induction and repression of nitrate reductase in the fungus Aspergillus nidulans. Biochim Biophys Acta - Enzymol Biol Oxid 1966; 113:51–56
    [Google Scholar]
  28. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10 [CrossRef]
    [Google Scholar]
  29. Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S et al. FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res 2012; 40:D675–D681 [CrossRef][PubMed]
    [Google Scholar]
  30. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C et al. Star: ultrafast universal RNA-seq aligner. Bioinformatics 2013; 29:15–21 [CrossRef][PubMed]
    [Google Scholar]
  31. Liao Y, Smyth GK, Shi W. featureCounts: an efficient General purpose program for assigning sequence reads to genomic features. Bioinformatics 2014; 30:923–930 [CrossRef][PubMed]
    [Google Scholar]
  32. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011; 12:323 [CrossRef][PubMed]
    [Google Scholar]
  33. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol 2014; 15:550 [CrossRef][PubMed]
    [Google Scholar]
  34. R Core Team R: A language and environment for statistical computing Austria: R Found Stat Comput Vienna; 2107
    [Google Scholar]
  35. Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res 2018; gky1100-gky1100.:
    [Google Scholar]
  36. Priebe S, Kreisel C, Horn F, Guthke R, Linde J. FungiFun2: a comprehensive online resource for systematic analysis of gene Lists from fungal species. Bioinformatics 2015; 31:445–446 [CrossRef][PubMed]
    [Google Scholar]
  37. SX G, Jung D, Yao R. ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 2019
    [Google Scholar]
  38. Babicki S, Arndt D, Marcu A, Liang Y, Grant JR et al. Heatmapper: web-enabled heat mapping for all. Nucleic Acids Res 2016; 44:W147–W153 [CrossRef][PubMed]
    [Google Scholar]
  39. Heberle H, Meirelles GV, da Silva FR, Telles GP, Minghim R. InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics 2015; 16:169 [CrossRef][PubMed]
    [Google Scholar]
  40. Hernández-Ortiz P, Espeso EA. Phospho-regulation and nucleocytoplasmic trafficking of CrzA in response to calcium and alkaline-pH stress in Aspergillus nidulans. Mol Microbiol 2013; 89:532–551 [CrossRef][PubMed]
    [Google Scholar]
  41. Han K-H, Prade RA. Osmotic stress-coupled maintenance of polar growth in Aspergillus nidulans. Mol Microbiol 2002; 43:1065–1078 [CrossRef][PubMed]
    [Google Scholar]
  42. Delgado-Virgen F, Guzman-de-Peña D. Mechanism of sterigmatocystin biosynthesis regulation by pH in Aspergillus nidulans. Braz J Microbiol 2009; 40:933–942 [CrossRef][PubMed]
    [Google Scholar]
  43. Bussink H-J, Bignell EM, Múnera-Huertas T, Lucena-Agell D, Scazzocchio C et al. Refining the pH response in Aspergillus nidulans: a modulatory triad involving PacX, a novel zinc binuclear cluster protein. Mol Microbiol 2015; 98:1051–1072 [CrossRef][PubMed]
    [Google Scholar]
  44. Felenbok B, Sequeval D, Mathieu M, Sibley S, Gwynne DI et al. The ethanol regulon in Aspergillus nidulans: characterization and sequence of the positive regulatory gene alcR. Gene 1988; 73:385–396 [CrossRef][PubMed]
    [Google Scholar]
  45. Ferreira C, van Voorst F, Martins A, Neves L, Oliveira R et al. A member of the sugar transporter family, Stl1p is the glycerol/H+ symporter in Saccharomyces cerevisiae. Mol Biol Cell 2005; 16:2068–2076 [CrossRef][PubMed]
    [Google Scholar]
  46. Lages F, Lucas C. Characterization of a glycerol/H+ symport in the halotolerant yeast Pichia sorbitophila. Yeast 1995; 11:111–119 [CrossRef][PubMed]
    [Google Scholar]
  47. Espeso EA, Tilburn J, Arst HN, Peñalva MA. pH regulation is a major determinant in expression of a fungal penicillin biosynthetic gene. Embo J 1993; 12:3947–3956[PubMed]
    [Google Scholar]
  48. Ahuja M, Chiang Y-M, Chang S-L, Praseuth MB, Entwistle R et al. Illuminating the diversity of aromatic polyketide synthases in Aspergillus nidulans. J Am Chem Soc 2012; 134:8212–8221 [CrossRef][PubMed]
    [Google Scholar]
  49. Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC et al. SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol 2010; 47:736–741 [CrossRef][PubMed]
    [Google Scholar]
  50. Oiartzabal-Arano E, Garzia A, Gorostidi A, Ugalde U, Espeso EA et al. Beyond asexual development: modifications in the gene expression profile caused by the absence of the Aspergillus nidulans transcription factor FlbB. Genetics 2015; 199:1127–1142 [CrossRef][PubMed]
    [Google Scholar]
  51. Gerke J, Braus GH. Manipulation of fungal development as source of novel secondary metabolites for biotechnology. Appl Microbiol Biotechnol 2014; 98:8443-55 [CrossRef][PubMed]
    [Google Scholar]
  52. Findon H, Calcagno-Pizarelli A-M, Martínez JL, Spielvogel A, Markina-Iñarrairaegui A et al. Analysis of a novel calcium auxotrophy in Aspergillus nidulans. Fungal Genet Biol 2010; 47:647–655 [CrossRef][PubMed]
    [Google Scholar]
  53. Shantappa S, Dhingra S, Hernández-Ortiz P, Espeso EA, Calvo AM. Role of the zinc finger transcription factor SltA in morphogenesis and sterigmatocystin biosynthesis in the fungus Aspergillus nidulans. PLoS One 2013; 8:e68492 [CrossRef][PubMed]
    [Google Scholar]
  54. Fernández-Martínez J, Brown CV, Díez E, Tilburn J, Arst HN et al. Overlap of nuclear localisation signal and specific DNA-binding residues within the zinc finger domain of PacC. J Mol Biol 2003; 334:667–684 [CrossRef][PubMed]
    [Google Scholar]
  55. Coker JA. Recent advances in understanding extremophiles [version 1; peer review: 2 approved]. F1000 Research 2019; 8:
    [Google Scholar]
  56. Gasch AP. Comparative genomics of the environmental stress response in ascomycete fungi. Yeast 2007; 24:961–976 [CrossRef][PubMed]
    [Google Scholar]
  57. Ianutsevich EA, Tereshina VM. Combinatorial impact of osmotic and heat shocks on the composition of membrane lipids and osmolytes in Aspergillus niger. Microbiology 2019; 165:554–562 [CrossRef][PubMed]
    [Google Scholar]
  58. Ni M, Yu J-H. A novel regulator couples sporogenesis and trehalose biogenesis in Aspergillus nidulans. PLoS One 2007; 2:e970 [CrossRef][PubMed]
    [Google Scholar]
  59. Kawasaki L, Sánchez O, Shiozaki K, Aguirre J. SakA MAP kinase is involved in stress signal transduction, sexual development and spore viability in Aspergillus nidulans. Mol Microbiol 2002; 45:1153–1163 [CrossRef][PubMed]
    [Google Scholar]
  60. Klein M, Swinnen S, Thevelein JM, Nevoigt E. Glycerol metabolism and transport in yeast and fungi: established knowledge and ambiguities. Environ Microbiol 2017; 19:878–893 [CrossRef][PubMed]
    [Google Scholar]
  61. Furukawa K, Hoshi Y, Maeda T, Nakajima T, Abe K. Aspergillus nidulans hog pathway is activated only by two-component signalling pathway in response to osmotic stress. Mol Microbiol 2005; 56:1246–1261 [CrossRef][PubMed]
    [Google Scholar]
  62. Miskei M, Karányi Z, Pócsi I. Annotation of stress-response proteins in the aspergilli. Fungal Genet Biol 2009; 46 Suppl 1:S105–S120 [CrossRef][PubMed]
    [Google Scholar]
  63. Harris SD, Turner G, Meyer V, Espeso EA, Specht T et al. Morphology and development in Aspergillus nidulans: a complex puzzle. Fungal Genet Biol 2009; 46 Suppl 1:S82–S92 [CrossRef][PubMed]
    [Google Scholar]
  64. Aranda A, del Olmo Ml Marcel lí, l delOM. Response to acetaldehyde stress in the yeast Saccharomyces cerevisiae involves a strain-dependent regulation of several ALD genes and is mediated by the general stress response pathway. Yeast 2003; 20:747–759 [CrossRef][PubMed]
    [Google Scholar]
  65. Inglis DO, Binkley J, Skrzypek MS, Arnaud MB, Cerqueira GC et al. Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae. BMC Microbiol 2013; 13:91 [CrossRef][PubMed]
    [Google Scholar]
  66. Etxebeste O, Otamendi A, Garzia A, Espeso EA, Cortese MS. Rewiring of transcriptional networks as a major event leading to the diversity of asexual multicellularity in fungi. Crit Rev Microbiol 2019; 45:548–563 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000415
Loading
/content/journal/mgen/10.1099/mgen.0.000415
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL

Supplementary material 2

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error