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Chapter 87 : Proteomic Analysis of Extracellular Enzymes Produced by Wood-Degrading Fungi

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Abstract:

This chapter reviews methods for proteomic analyses of white-rot fungi, which can degrade both the carbohydrate and the lignin components of wood to CO. Microbial degradation of lignocellulosic material, due to the heterogeneity of the substrate, involves an ensemble of extracellular enzymes. Woody biomass has three major components: cellulose, hemicellulose, and lignin. Lignin is formed by free radical coupling of the phenylpropanoid units and thus can be linked by more than 12 types of linkages. Another group of wood-degrading Basidiomycetes, the brown-rot fungi, can also degrade fully lignified tissue but without substantial depletion of the lignin. Ascomycetes and Fungi Imperfecti cause the soft-rot type of wood decay which was categorized only within the past 30 years. The enzymes that utilize HO and molecular oxygen to oxidize organic and inorganic substrates are the peroxidases and the laccases, respectively. Phenol extraction proved to be very effective in extracting plant proteins from interfering substances to obtain good resolution in 2-D gels. Methods are available for processing of the complete extracellular protein mixture by protease digestion and separation and identification by liquid chromatography and tandem mass spectrometry (MS-MS). For heavily glycoslyated proteins, CapLC–nanoelectrospray ionization–MS-MS can be used instead to analyze in-gel tryptic digests.

Citation: Liu F, Koc H, Tien M. 2007. Proteomic Analysis of Extracellular Enzymes Produced by Wood-Degrading Fungi, p 1089-1096. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch87

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Figures

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FIGURE 1

2-D gels of extracellular proteins from different cultures of (A) Proteins from liquid culture of grown on glucose as a carbon source (F. Liu and M. Tien, unpublished data). (B and C) Proteins from liquid-solid culture of grown on cellulose as a carbon source (B) (Liu and Tien, unpublished) or on wood (C) (reprinted from [1] with permission of the publisher). (D) Proteins from grown on solid wood substrate, which was stained with Coomassie blue except for the inset, for which after visualization with Coomassie blue, the gel was destained and then visualized with silver stain (reprinted from [1] with permission of the publisher).

Citation: Liu F, Koc H, Tien M. 2007. Proteomic Analysis of Extracellular Enzymes Produced by Wood-Degrading Fungi, p 1089-1096. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch87
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References

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Tables

Generic image for table
TABLE 1

Results of a BLAST search of oxidative enzymes of

Citation: Liu F, Koc H, Tien M. 2007. Proteomic Analysis of Extracellular Enzymes Produced by Wood-Degrading Fungi, p 1089-1096. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch87
Generic image for table
TABLE 2

Results of a BLAST search of hydrolytic enzymes of

Citation: Liu F, Koc H, Tien M. 2007. Proteomic Analysis of Extracellular Enzymes Produced by Wood-Degrading Fungi, p 1089-1096. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch87
Generic image for table
TABLE 3

Peptide masses and predicted amino acid sequence of laminarinase

Citation: Liu F, Koc H, Tien M. 2007. Proteomic Analysis of Extracellular Enzymes Produced by Wood-Degrading Fungi, p 1089-1096. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch87
Generic image for table
TABLE 4

Results of a BLAST homology search of genes identified by Protein Prospector

Citation: Liu F, Koc H, Tien M. 2007. Proteomic Analysis of Extracellular Enzymes Produced by Wood-Degrading Fungi, p 1089-1096. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch87
Generic image for table
TABLE 5

Primers for PCR of genes

Citation: Liu F, Koc H, Tien M. 2007. Proteomic Analysis of Extracellular Enzymes Produced by Wood-Degrading Fungi, p 1089-1096. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch87

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