Skip to main content
SpringerLink
Log in

Gene expression analysis of Phanerochaete chrysosporium during the transition time from primary growth to secondary metabolism

  • Published:
The Journal of Microbiology Aims and scope Submit manuscript

Abstract

In order to identify the secondary metabolism-related genes of Phanerochaete chrysosporium growing under pure O2 and nitrogen-limited conditions, 2322 ESTs fragments originated from two suppression-subtractive libraries were analyzed using the cDNA microarray technique. Ten significantly upregulated and 22 significantly downregulated genes were identified in the 72 h cultured mycelia RNA samples (secondary metabolism). According to qPCR, 16 out of the 32 genes were expressed differently in secondary metabolism. Transcripts of secondary metabolism up-regulation genes exhibited homologies to aryl-alcohol dehydrogenase (SShl554), ABC transporter gene (SSH624), chitinase (SSH963), heat shock protein (SSH1193), catalase (SSH317), cytochrome P450 (SSH331), glucosamine-6-phosphate isomerase (SSH611), and alkyl hydroperoxide reductase (SSH362) genes. Ninety-three genes could be classified by Eukaryotic Orthologous Groups (KOG). Among the genes assigned a function, gene expression patterns were different in both secondary metabolism and primary metabolism. In the group of “Cellular Processes and Signaling,” most of the genes were from the primary metabolism library. On the other hand, genes from the secondary metabolism library were found mainly in the “Information Storage” and “Processing and Poorly Characterized” groups. Based on the KOG functional assignments, six genes belong to the ubiquitin system, and all of them were from primary metabolism phase. The presence of the H2O2-relevant genes suggested that parts of the genes expressed in 72 h might be involved in the ligninolytic process during secondary metabolism of P. chrysosporium.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Altschul, S.F., T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.

    Article  PubMed  CAS  Google Scholar 

  • Assmann, E.M., L.M. Ottoboni, A. Ferraz, J. Rodriguez, and M.P. De Mello. 2003. Iron-responsive genes of Phanerochaete chrysosporium isolated by differential display reverse transcription polymerase chain reaction. Environ. Microbiol. 5, 777–786.

    Article  PubMed  CAS  Google Scholar 

  • Bar-Lev, S.S. and T.K. Kirk. 1981. Effects of molecular oxygen on lignin degradation by Phanerochaete chrysosporium. Biochem. Biophys. Res. Commun. 99, 373–378.

    Article  PubMed  CAS  Google Scholar 

  • Boominathan, K., T.M. D’souza, P.S. Naidu, C. Dosoretz, and C.A. Reddy. 1993. Temporal expression of the major lignin peroxidase genes of Phanerochaete chrysosporium. Appl. Environ. Microbiol. 59, 3496–3950.

    Google Scholar 

  • Broda, P.P., R. Brooks, and P.F. Sims. 1996. lignocellulose degradation by Phanerochaete chrysosporium: gene families and gene expression for a complex process. Mol. Microbiol. 19, 923–932.

    Article  PubMed  CAS  Google Scholar 

  • Cullen, D. 1997. Recent advances on the molecular genetics of ligninolytic fungi. J. Biotechnol. 53, 273–289.

    Article  PubMed  CAS  Google Scholar 

  • Daniel, G., P. Binarova, J. Volc, and E. Kubatova. 1995. Cytochemical and immunocytochemical studies on sites of H2O2 production and catalase activity in hyphae of Phanerochaete chrysosporium grown in liquid culture and on wood. In E. Srebotnik and K. Messner (ed.), Proceedings of the Sixth International Conference at Vienna, Austria.

  • Diatchenko, L., Y.F. Lau, A.P. Campbell, A. Chenchik, F. Moqadam, B. Huang, and S. Lukyanov. 1996. Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93, 6025–6030.

    Article  PubMed  CAS  Google Scholar 

  • Dixon, A.K., P.J. Richardson, K. Lee, N.P. Carter, and T.C. Freeman. 1998. Expression profiling of single cells using 3 prime end amplification (TPEA) PCR. Nucleic Acids Res. 26, 4426–4431.

    Article  PubMed  CAS  Google Scholar 

  • Gold, M. and M. Alic. 1993. Molecular biology of the lignin-de-grading basidiomycete Phanerochaete chrysosporium. Microbiol. Rev. 57, 605–622.

    PubMed  CAS  Google Scholar 

  • Hershko, A., A. Ciechanover, and A. Varshavsky. 2000. The ubiquitin system. Nature 6, 1073–1081.

    Article  CAS  Google Scholar 

  • Iimura, Y. and S.K. Tat. 1997. Isolation of mRNAs induced by a hazardous chemical in white-rot fungus, Coriolus versicolor, by differential display. FEBS Lett. 412, 370–374.

    Article  PubMed  CAS  Google Scholar 

  • Jiang, Q., Y.H. Yan, G.K. Hu, and Y.Z. Zhang. 2005. Molecular cloning and characterization of a peroxiredoxin from Phanerochaete chrysosporium. Cell Mol. Biol. Lett. 210, 659–668.

    Google Scholar 

  • Kersten, P. and D. Cullen. 2007. Extracellular oxidative systems of the lignin-degrading basidiomycete Phanerochaete chrysosporium. Fungal Genet. Biol. 44, 77–87.

    Article  PubMed  CAS  Google Scholar 

  • Keyser, P., T.K. Kirk, and J.G. Zeikus. 1978. Ligninolytic enzyme system of Phanaerochaete chrysosporium synthesized in the absence of lignin in response to nitrogen starvation. J. Bacteriol. 135, 790–797.

    PubMed  CAS  Google Scholar 

  • Kuang, W.W., D.A. Thompson, R.V. Hoch, and R.J. Weigel. 1998. Differential screening and suppression subtractive hybridization identify genes differentially expressed in an estrogen receptor-positive breast carcinoma cell line. Nucleic Acids Res. 26, 1116–1123.

    Article  PubMed  CAS  Google Scholar 

  • Kwon, S.I. and A.J. Anderson. 2001. Catalase activities of Phanerochaete chrysosporium are not coordinately produced with ligninolytic metabolism: catalases from a white-rot fungus. Curr. Microbiol. 42, 8–11.

    Article  PubMed  CAS  Google Scholar 

  • Lamar, R.T., B. Schoenike, A.V. Wymelenberg, P. Stewart, D.M. Dietrich, and D. Cullen. 1995. Quantitation of fungal mRNAs in complex substrates by reverse transcription PCR and its application to Phanerochaete chrysosporium-colonized soil. Appl. Environ. Microbiol. 61, 2122–2126.

    PubMed  CAS  Google Scholar 

  • Martinez, D., L.F. Larrondo, N. Putnam, M.D. Gelpke, K. Huang, J. Chapman, and K.G. Helfenbein. 2004. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat. Biotechnol. 22, 695–700.

    Article  PubMed  CAS  Google Scholar 

  • Miura, D., H. Tanaka, and H. Wariishi. 2004. Metabolic differential display analysis of the white-rot basidiomycete Phanerochaete chrysosporium grown under air and 100% oxygen. FEMS Microbiol. Lett. 234, 111–116.

    Article  PubMed  CAS  Google Scholar 

  • Moradas-Ferreira, P., V. Costa, P. Piper, and W. Mager. 1996. The molecular defences against reactive oxygen species in yeast. Mol. Microbiol. 19, 651–658.

    Article  PubMed  CAS  Google Scholar 

  • Nover, L. 1991. Inducers of HSP synthesis: Heat shock and chemical stressors. In L. Nover (ed.), Heat Shock Response, p. 5–40. CRC Press, Boca Raton, FL, USA.

    Google Scholar 

  • Sarah, J.R., J.F. Victoria, M. Panagiota, and A.M. Brian. 2001. Thioredoxin peroxidase is required for the transcriptional response to oxidative stress in budding yeast. Mol. Biol. Cell. 11, 2631–2642.

    Google Scholar 

  • Singh, D. and S. Chen. 2008. The white-rot fungus Phanerochaete chrysosporium: conditions for the production of lignin-degrading enzymes. Appl. Microbiol. Biotechnol. 2008 Sep 20. [Epub ahead of print].

  • Smith, L., P. Underhill, C. Pritchard, Z. Tymowska-Lalanne, S. Abdul-Hussein. H. Hilton, and L. Winchester. 2003. Single primer amplification (SPA) of cDNA for microarray expression analysis. Nucleic Acids Res. 31, E9.

    Article  PubMed  Google Scholar 

  • Tose, M.M. and M.S. Fracisca. 2000. Role of reactive oxygen species in apoptosis: implications for cancer therapy. Int. J. Biochem. Cell Biol. 32, 157–170.

    Article  Google Scholar 

  • Tien, M. and T.K. Kirk. 1987. Lignin peroxidase of Phanerochaete chrysosporium. Methods Enzymol. 161, 238–249.

    Article  Google Scholar 

  • Ward, P.G. 1963. A micro-Kjeldahl procedure for field use. J. Med. Lab. Technol. 20, 191–195.

    PubMed  CAS  Google Scholar 

  • Wysong, D.R., L. Christin, A.M. Sugar, P. W. Robbins, and R.D. Diamond. 1998. Cloning and sequencing of a Candida albicans catalase gene and effects of disruption of this gene. Infect. Immun. 66, 1953–1961.

    PubMed  CAS  Google Scholar 

  • Yang, Y.H., S. Dudoitm, P. Luum, D.M. Linm, V. Pengm, J. Ngaim, and T. P. Speedm. 2002. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, 38–41.

    Article  Google Scholar 

  • Yang, G.P., D.T. Ross, W. W. Kuang, P.O. Brown, and R.J. Weigel. 1999. Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes. Nucleic Acids Res. 27, 1517–1523.

    Article  PubMed  CAS  Google Scholar 

  • Zhang, Y.Z., G.J. Zylstra, R.H. Olsen, and C.A. Reddy. 1986. Identification of cDNA clones for ligninase from Phanerochaete chrysosporium using synthetic oligonucleotide probes. Biochem. Biophys. Res. Comm. 137, 649–656.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. College of Life Science, Sichuan University, Chengdu, 610064, P. R. China

    Mingfeng Jiang, Xiao Li, Hong Feng & Yizheng Zhang

  2. College of Life Science & Technology, Southwest University for Nationalities, Chengdu, 610041, P. R. China

    Mingfeng Jiang

  3. National Engineering Research Center for Beijing Biochip Technology, Beijing, 100084, P. R. China

    Liang Zhang

Authors
  1. Mingfeng Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiao Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Liang Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hong Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yizheng Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yizheng Zhang.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Jiang, M., Li, X., Zhang, L. et al. Gene expression analysis of Phanerochaete chrysosporium during the transition time from primary growth to secondary metabolism. J Microbiol. 47, 308–318 (2009). https://doi.org/10.1007/s12275-008-0275-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-008-0275-z

Keywords

Search

Navigation