Advertisement

Applied Biochemistry and Biotechnology

, Volume 162, Issue 7, pp 1961–1977 | Cite as

Gene Expression in Secondary Metabolism and Metabolic Switching Phase of Phanerochaete chrysosporium

  • Jin-Ming Wu
  • Yi-zheng ZhangEmail author
Article

Abstract

Ligninolytic enzymes are well-known to play the crucial roles in lignin biodegradation and have potential applications in industrial processes. The filamentous white-rot fungus, Phanerochaete chrysosporium, has been widely used as a model organism for studying these ligninolytic enzymes that are able to degrade the lignin during the secondary metabolism. To study the gene expression in secondary metabolism and metabolic switching phase of P. chrysosporium, we constructed a metabolic-switching phase suppression subtractive hybridization (SSH) cDNA library and a secondary metabolic phase SSH cDNA library to compare their mRNA expression profiles. We isolated the genes that are specially expressed and subsequently identified four genes that specially expressed during metabolic-switching phase while 22 genes in secondary metabolic phase. Accordingly, these specially expressed genes might play key roles in different metabolic stages, which would offer more new insights into the shift from nitrogen to lignin metabolism.

Keywords

Ligninolytic enzymes Phanerochaete chrysosporium Metabolic-switching phase Secondary metabolic phase cDNA library 

Notes

Acknowledgements

We thank Dr. Hong Feng, Chuan He, and Fan Bai for their critical reviews on this manuscript.

References

  1. 1.
    Adler, E. (1977). Lignin chemistry—past, present and future. Wood Science and Technology, 11, 169–218.CrossRefGoogle Scholar
  2. 2.
    Kiem, R., & Kögel-Knabner, I. (2003). Contribution of lignin and polysaccharides to the refractory carbon pool in C-depleted arable soils. Soil Biology and Biochemistry, 35(1), 101–118.CrossRefGoogle Scholar
  3. 3.
    Kersten, P., & Cullen, D. (2007). Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium. Fungal Genetics and Biology, 44(2), 77–87.CrossRefGoogle Scholar
  4. 4.
    Reddy, C. A., & D'Souza, T. M. (1994). Physiology and molecular biology of the lignin peroxidases of Phanerochaete chrysosporium. FEMS Microbiology Reviews, 13(2–3), 137–152.CrossRefGoogle Scholar
  5. 5.
    Buswell, J. A., Odier, E., & Kent, K. T. (1987). Lignin biodegradation. Critical Reviews in Biotechnology, 6, 1–60.CrossRefGoogle Scholar
  6. 6.
    Garg, S. K., & Modi, D. R. (1999). Decolorization of pulp-paper mill effluents by white-rot fungi. Critical Reviews in Biotechnology, 19(2), 85–112.CrossRefGoogle Scholar
  7. 7.
    Wesenberg, D., Kyriakides, I., & Agathos, S. N. (2003). White-rot fungi and their enzymes for the treatment of industrial dye effluents. Biotechnology Advances, 22(1–2), 161–187.CrossRefGoogle Scholar
  8. 8.
    Martinez, D., Larrondo, L. F., Putnam, N., Gelpke, M. D., Huang, K., Chapman, J., et al. (2004). Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature Biotechnology, 22(6), 695–700.CrossRefGoogle Scholar
  9. 9.
    Vanden Wymelenberg, A., Minges, P., Sabat, G., Martinez, D., Aerts, A., Salamov, A., et al. (2006). Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins. Fungal Genetics and Biology, 43(5), 343–356.CrossRefGoogle Scholar
  10. 10.
    Keyser, P., Kirk, T. K., & Zeikus, J. G. (1978). Ligninolytic enzyme system of Phanaerochaete chrysosporium synthesized in the absence of lignin in response to nitrogen starvation. Journal of Bacteriology, 135(3), 790–797.Google Scholar
  11. 11.
    Boominathan, K., D'Souza, T. M., Naidu, P. S., Dosoretz, C., & Reddy, C. A. (1993). Temporal expression of the major lignin peroxidase genes of Phanerochaete chrysosporium. Applied and Environmental Microbiology, 59(11), 3496–3950.Google Scholar
  12. 12.
    Gold, M., & Alic, M. (1993). Molecular biology of the lignindegrading basidiomycete Phanerochaete chrysosporium. Microbiology and Molecular Biology Reviews, 57(3), 605–622.Google Scholar
  13. 13.
    Matsuzaki, F., Shimizu, M., & Wariishi, H. (2008). Proteomic and metabolomic analyses of the white-rot fungus Phanerochaete chrysosporium exposed to exogenous benzoic acid. Journal of Proteome Research, 7(6), 2342–2350.CrossRefGoogle Scholar
  14. 14.
    Masahiko, M., Kureha, O., Mori, M., Kamitsuji, H., Suzuki, K., & Irie, T. (2007). Long serial analysis of gene expression for transcriptome profiling during the initiation of ligninolytic enzymes production in Phanerochaete chrysosporium. Applied Microbiology and Biotechnology, 75(3), 609–618.CrossRefGoogle Scholar
  15. 15.
    Semarjit, S., Kapich, A. N., Panisko, E. A., Magnuson, J. K., Cullen, D., & Hammel, K. E. (2008). Differential expression in Phanerochaete chrysosporium of membrane-associated proteins relevant to lignin degradation. Applied and Environmental Microbiology, 74(23), 7252–7257.CrossRefGoogle Scholar
  16. 16.
    Ozcan, S., Yildirim, V., Kaya, L., Albrecht, D., Becher, D., Hecker, M., et al. (2007). Phanerochaete chrysosporium soluble proteome as a prelude for the analysis of heavy metal stress response. Proteomics, 7(8), 1249–1260.CrossRefGoogle Scholar
  17. 17.
    Vanden Wymelenberg, A., Gaskell, J., Mozuch, M., Kersten, P., Sabat, G., Martinez, D., et al. (2009). Transcriptome and secretome analysis of phanerochaete chrysosporium reveal complex patterns of gene expression. Applied and Environmental Microbiology, 75(12), 4058–4068.CrossRefGoogle Scholar
  18. 18.
    Wymelenberg, A. V., Sabat, G., Martinez, D., Rajangam, A. S., Teeri, T. T., Gaskell, J., et al. (2005). The Phanerochaete chrysosporium secretome: database predictions and initial mass spectrometry peptide identifications in cellulose-grown medium. Journal of Biotechnology, 118(1), 17–34.CrossRefGoogle Scholar
  19. 19.
    Jiang, M., Li, X., Zhang, L., Feng, H., & Zhang, Y. (2009). Gene expression analysis of Phanerochaete chrysosporium during the transition time from primary growth to secondary metabolism. Journal of Microbiology, 47(3), 308–318.CrossRefGoogle Scholar
  20. 20.
    Zhang, Y. Z., Zylstra, G. J., Olsen, R. H., & Reddy, C. A. (1986). Identification of cDNA clones for ligninase from using synthetic oligonucleotide probes. Biochemical and Biophysical Research Communications, 137(2), 649–656.CrossRefGoogle Scholar
  21. 21.
    Tien, M., & Kirk, T. K. (1988). Lignin peroxidase of Phanerochaete chrysosporium. Methods in Enzymology, 161, 238–349.CrossRefGoogle Scholar
  22. 22.
    Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., & Hirakawa, M. (2009). KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Research. doi: 10.1093/nar/gkp896.Google Scholar
  23. 23.
    Cullen, D. (1997). Recent advances on the molecular genetics of ligninolytic fungi. Journal of Biotechnology, 53(2–3), 273–289.CrossRefGoogle Scholar
  24. 24.
    Diatchenko, L., Lau, Y. F., Campbell, A. P., Chenchik, A., Moqadam, F., Huang, B., et al. (1996). Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proceedings of the National Academy of Science, 93(12), 6025–6030.CrossRefGoogle Scholar
  25. 25.
    Diatchenko, L., Lukyanov, S., Lau, Y. F., & Siebert, P. D. (1999). Suppression subtractive hybridization: a versatile method for identifying differentially expressed genes. Methods in Enzymology, 303, 349–380.CrossRefGoogle Scholar
  26. 26.
    Finazzi Agrò, A., Federici, G., Giovagnoli, C., Cannella, C., & Cavallini, D. (1972). Effect of sulfur binding on rhodanese fluorescence. European Journal of Biochemistry, 28(1), 83–93.CrossRefGoogle Scholar
  27. 27.
    Westley, J. (1973). Rhodanese. Advances in Enzymology and Related Areas of Molecular Biology, 39, 327–368.Google Scholar
  28. 28.
    Dhirendra, L. N., Paul, M. H., & John, W. (2000). Rhodanese as a thioredoxin oxidase. The International Journal of Biochemistry & Cell Biology, 32(4), 465–473.CrossRefGoogle Scholar
  29. 29.
    Godon, C., Lagniel, G., Lee, J., Buhler, J. M., Kieffer, S., Perrot, M., et al. (1998). The H2O2 Stimulon in Saccharomyces cerevisiae. The Journal of Biological Chemistry, 273(35), 22480–22489.CrossRefGoogle Scholar
  30. 30.
    Nordberg, J., & Arnér, E. S. (2001). Reactive oxygen species, antioxidants, and the mammalian thioredoxin system. Free Radical Biology & Medicine, 31(11), 1287–1312.CrossRefGoogle Scholar
  31. 31.
    Scharf, C., Riethdorf, S., Ernst, H., Engelmann, S., Völker, U., & Hecker, M. (1998). Thioredoxin is an essential protein induced by multiple stresses in Bacillus subtilis. Journal of Bacteriology, 180(7), 1869–1877.Google Scholar
  32. 32.
    Shi, M. M., Iwamoto, T., & Forman, H. J. (1994). gamma-Glutamylcysteine synthetase and GSH increase in quinone-induced oxidative stress in BPAEC. American Journal of Physiology. Lung Cellular and Molecular Physiology, 67(4), L414–L421.Google Scholar
  33. 33.
    Grant, C. M., Perrone, G., & Dawes, I. W. (1998). Glutathione and catalase provide overlapping defenses for protection against hydrogen peroxide in the yeast Saccharomyces cerevisiae. Biochemical and Biophysical Research Communications, 253(3), 893–898.CrossRefGoogle Scholar
  34. 34.
    Grant, C. M., MacIver, F. H., & Dawes, I. W. (1997). Glutathione synthetase is dispensable for growth under both normal and oxidative stress conditions in the yeast Saccharomyces cerevisiae due to an accumulation of the dipeptide gamma-glutamylcysteine. Molecular Biology of the Cell, 8(9), 1699–1707.Google Scholar
  35. 35.
    Mehdi, K., & Penninckx, M. J. (1997). An important role for glutathione and {gamma}-glutamyltranspeptidase in the supply of growth requirements during nitrogen starvation of the yeast Saccharomyces cerevisiae. Microbiology, 143(6), 1885–1889.CrossRefGoogle Scholar
  36. 36.
    Lee, J., Godon, C., Lagniel, G., Spector, D., Garin, J., Labarre, J., et al. (1999). Yap1 and Skn7 control two specialized oxidative stress response regulons in yeast. The Journal of Biological Chemistry, 274(23), 16040–16046.CrossRefGoogle Scholar
  37. 37.
    Daniel, G., Volc, J., Filonova, L., Plihal, E., Kubatova, E., & Halada, P. (2007). Characteristics of Gloeophyllum trabeum alcohol oxidase, an extracellular source of H2O2 in brown rot decay of wood. Applied and Environmental Microbiology, 73, 6241–6253.CrossRefGoogle Scholar
  38. 38.
    Assmann, E. M., Ottoboni, L. M., Ferraz, A., Rodríguez, J., & De Mello, M. P. (2003). Iron-responsive genes of Phanerochaete chrysosporium isolated by differential display reverse transcription polymerase chain reaction. Environmental Microbiology, 5(9), 777–786.CrossRefGoogle Scholar
  39. 39.
    Miura, D., Tanaka, H., & Wariishi, H. (2004). Metabolic differential display analysis of the white-rot basidiomycete Phanerochaete chrysosporium grown under air and 100% oxygen. FEMS Microbiology Letters, 234(1), 111–116.CrossRefGoogle Scholar
  40. 40.
    Lucic, E., Fourrey, C., Kohler, A., Martin, F., Chalot, M., & Brun-Jacob, A. (2008). A gene repertoire for nitrogen transporters in Laccaria bicolor. The New Phytologist, 180(2), 343–364.CrossRefGoogle Scholar
  41. 41.
    Benjdia, M., Rikirsch, E., Müller, T., Morel, M., Corratgé, C., Zimmermann, S., et al. (2006). Peptide uptake in the ectomycorrhizal fungus Hebeloma cylindrosporum: characterization of two tripeptide transporters (HcPTR2A and B). The New Phytologist, 170(2), 401–410.CrossRefGoogle Scholar
  42. 42.
    Larrondo, L. F., Vicuña, R., & Cullen, D. (2005). Phanerochaete chysosporium genomics. Applied Mycology and Biotechnology, 5, 315–352.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.School of Life Sciences, Sichuan Key Laboratory of Molecular Biology and BiotechnologySichuan UniversityChengduPeople’s Republic of China

Personalised recommendations