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Microarray-based global differential expression profiling of P450 monooxygenases and regulatory proteins for signal transduction pathways in the white rot fungus Phanerochaete chrysosporium

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Abstract

Whole genome sequencing of the model white rot basidiomycete Phanerochaete chrysosporium has revealed the largest P450 contingent known to date in fungi, along with related phase I and phase II metabolic genes and signaling cascade genes. As a part of their functional characterization, genome-wide expression profiling under physiologically distinct conditions, nutrient-limited (ligninolytic) and nutrient-rich (non-ligninolytic), was investigated using a custom-designed 70-mer oligonucleotide microarray developed based on 190 target genes and 23 control genes. All 150 P450 genes were found to be expressible under the test conditions, with 27 genes showing differential expression based on a >twofold arbitrary cut-off limit. Of these, 23 P450 genes were upregulated (twofold to ninefold) in defined high-nitrogen cultures whereas four genes were upregulated (twofold to twentyfold) in defined low-nitrogen cultures. Furthermore, tandem P450 member genes in ten of the 16 P450 genomic clusters showed nonassortative regulation of expression reflecting their functional diversity. Full-length cDNAs for two of the high-nitrogen upregulated genes pc-hn1 (CYP5035A1) and pc-hn2 (CYP5036A1) and partial cDNA for a low-nitrogen upregulated gene pc-ln1 (CYP5037A1) were cloned and characterized. The study provided first molecular evidence for the presence of active components of the cAMP- and MAP kinase-signaling pathways in a white rot fungus; four of these components (cpka and ste-12 of cAMP pathway and two MAP kinases, mps1 and sps1) were significantly upregulated (fourfold to eightfold) under nutrient-limited conditions, implying their likely role in the regulation of gene expression involved in secondary metabolism and biodegradation processes under these conditions.

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References

  • Ahlgren R, Suske G, Waterman MR, Lund J (1999) Role of Sp1 in cAMP-dependent transcriptional regulation of the bovine CYP11A gene. J Biol Chem 274:19422–19428

    Article  PubMed  CAS  Google Scholar 

  • Boominathan K, Reddy CA (1992) cAMP-mediated differential regulation of lignin peroxidase and manganese-dependent peroxidase production in the white rot basidiomycete Phanerochaete chrysosporium. Proc Natl Acad Sci USA 89:5586–5590

    Article  PubMed  CAS  Google Scholar 

  • Borges-Walmsley MI, Walmsley AR (2000) cAMP signaling in pathogenic fungi: control of dimorphic switching and pathogenicity. Trends Microbiol 8:133–141

    Article  PubMed  CAS  Google Scholar 

  • Chou HH, Hsia AP, Mooney DL, Schnable PS (2004) PICKY: oligo microarray design for large genomes. Bioinformatics 20:2893–2902

    Article  PubMed  CAS  Google Scholar 

  • Dhawale SS (1993) Is an activator protein-2-like transcription factor involved in regulating gene expression during nitrogen limitation in fungi? Appl Environ Microbiol 62:593–600

    Google Scholar 

  • Doddapaneni H, Yadav JS (2004) Differential regulation and xenobiotic induction of tandem P450 monooxygenase genes pc-1 (CYP63A1) and pc-2 (CYP63A2) in the white rot fungus Phanerochaete chrysosporium. Appl Microbiol Biotechnol 65:559–565

    Article  PubMed  CAS  Google Scholar 

  • Doddapaneni H, Chakraborty RC, Yadav JS (2005a) Genome-wide structural and evolutionary analysis of the P450 monooxygenase genes (P450ome) in the white rot fungus Phanerochaete chrysosporium: evidence of gene duplications and extensive gene clustering. BMC Genomics 6:92

    Article  PubMed  Google Scholar 

  • Doddapaneni H, Subramanian V, Yadav JS (2005b) Physiological regulation, xenobiotic induction and heterologous expression of P450 monooxygenase gene pc-3, a new member of the CYP63 gene cluster in the white rot fungus Phanerochaete chrysosporium. Curr Microbiol 50:292–298

    Article  PubMed  CAS  Google Scholar 

  • D’Souza CA, Heitman J (2001) Conserved cAMP signaling cascades regulate fungal development and virulence. FEMS Microbiol Rev 25:349–364

    Article  PubMed  CAS  Google Scholar 

  • Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863–14868

    Article  PubMed  CAS  Google Scholar 

  • Gold MH, Alic M (1993) Molecular biology of the lignin-degrading basidiomycetes Phanerochaete chrysosporium. Microbiol Rev 57:605–622

    PubMed  CAS  Google Scholar 

  • Hammel KE, Kalyanaraman B, Kirk TK (1986) Oxidation of polycyclic aromatic hydrocarbons and dibenzo[p]-dioxins by Phanerochaete chrysosporium ligninase. J Biol Chem 261:16948–16952

    PubMed  CAS  Google Scholar 

  • Hibbett DS, Pine EM, Langer E, Langer G, Donoghue MJ (1997) Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. Proc Natl Acad Sci USA 22:12002–12006

    Article  Google Scholar 

  • Honkakoski P, Negishi M (2000) Regulation of cytochrome P450 (CYP) genes by nuclear receptors. Biochem J 347:321–337

    Article  PubMed  CAS  Google Scholar 

  • Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey W, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19:342–347

    Article  PubMed  CAS  Google Scholar 

  • Jauregui J, Valderrama B, Albores A, Vazquez-Duhalt R (2003) Microsomal Transformation of organophosphorus pesticides by white rot fungi. Appl Microbiol Biotechnol 14:397–406

    CAS  Google Scholar 

  • Kullman SW, Matsumura F (1996) Metabolic pathways utilized by Phanerochaete chrysosporium for degradation of the cyclodiene pesticide endosulfan. Appl Environ Microbiol 62:593–600

    PubMed  CAS  Google Scholar 

  • Martinez D, Larrondo LF, Putnam N, Gelpke MD, Huang K, Chapman J, Helfenbein KG, Ramaiya P, Detter JC, Larimer F, Coutinho PM, Henrissat B, Berka R, Cullen D, Rokhsar D (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol 22:695–700

    Article  PubMed  CAS  Google Scholar 

  • Reiner A, Yekutieli D, Benjamini Y (2003) Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19:368–375

    Article  PubMed  CAS  Google Scholar 

  • Sutherland JB, Selby AL, Freeman JP, Evans FE, Cerniglia CE (1991) Metabolism of phenanthrene by Phanerochaete chrysosporium. Appl Environ Microbiol 57:3310–3316

    PubMed  CAS  Google Scholar 

  • Tan Z, Huang M, Puga A, Xia Y (2004) A critical role for MAP kinases in the control of Ah receptor complex activity. Toxicol Sci 82:80–87

    Article  PubMed  CAS  Google Scholar 

  • Van den Brink HJM, Van Gorcom RFM, Van den Hondel CAMJJ, Punt PJ (1998) Cytochrome P450 enzyme systems in fungi. Fungal Genet Biol 23:1–17

    Article  PubMed  Google Scholar 

  • Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, Afshari C, Paules RS (2001) Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8:625–637

    Article  PubMed  CAS  Google Scholar 

  • Xu JR (2000) MAP kinases in fungal pathogens. Fungal Genet Biol 31:137–152

    Article  PubMed  CAS  Google Scholar 

  • Yadav JS, Doddapaneni H (2003) Genome-wide expression profiling and xenobiotic inducibility of P450 monooxygenase genes in the white rot fungus Phanerochaete chrysosporium. In: Anzenbacher P, Hudecek J (eds) Cytochromes P450 biochemistry, biophysics and drug metabolism. Monduzzi Editore, Bologna, pp 333–340

    Google Scholar 

  • Yadav JS, Reddy CA (1992) Non-involvement of lignin peroxidases and manganese peroxidases in 2,4,5-trichlorophenoxyacetic acid degradation by Phanerochaete chrysosporium. Biotechnol Lett 14:1089–1092

    Article  CAS  Google Scholar 

  • Yadav JS, Reddy CA (1993) Degradation of benzene, toluene, ethylbenzene, and xylenes (BTEX) by the lignin-degrading basidiomycete Phanerochaete chrysosporium. Appl Environ Microbiol 59:756–762

    PubMed  CAS  Google Scholar 

  • Yadav JS, Loper JC (2000) Cytochrome P450 oxidoreductase gene and its differentially terminated cDNAs from the white rot fungus Phanerochaete chrysosporium. Curr Genet 37:65–73

    Article  PubMed  CAS  Google Scholar 

  • Yadav JS, Lawrence D, Nuck B, Federle T, Reddy CA (2001) Biotransformation of linear alkylbenzene sulfonate (LAS) by Phanerochaete chrysosporium: oxidation of alkyl side-chain. Biodegradation 12:443–453

    Article  PubMed  CAS  Google Scholar 

  • Yadav JS, Soellner MB, Loper JC, Mishra PK (2003) Tandem cytochrome P450 monooxygenase genes and splice variants in the white rot fungus Phanerochaete chrysosporium: cloning, sequence analysis, and regulation of differential expression. Fungal Genet Biol 38:10–21

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

This work was supported by the grant R01ES10210 (JSY) from the NIH’s National institute of Environmental Health Sciences (NIEHS). The authors thank Mario Medvedovic of the Department of Environmental Health for helping with the microarray data analysis. We acknowledge the help of David Nelson from the International P450 Nomenclature Committee for assigning the CYP names to the cloned P450 genes along with the other related P450 genes that were included in this study.

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Correspondence to J. S. Yadav.

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Communicated by S.Hohmann

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Doddapaneni, H., Yadav, J.S. Microarray-based global differential expression profiling of P450 monooxygenases and regulatory proteins for signal transduction pathways in the white rot fungus Phanerochaete chrysosporium . Mol Genet Genomics 274, 454–466 (2005). https://doi.org/10.1007/s00438-005-0051-2

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  • DOI: https://doi.org/10.1007/s00438-005-0051-2

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