Proteomics for biodeterioration of wood (Pinus taeda L.): Challenging analysis by 2-D PAGE and MALDI-TOF/TOF/MS

International Biodeterioration and Biodegradation

Volumn 63, Issue 8, 2009, Pages 1036-1044

  Kang, Young Min ^a   Prewitt, M Lynn ^a   Diehl, Susan V ^a  

^a MISSISSIPPI STATE UNIVERSITY   (United States)

Author keywords

Biodeterioration; Gloeophyllum trabeum; MALDI TOF TOF MS; Proteomics; Two dimensional polyacrylamide gel electrophoresis

Indexed keywords

ALCOHOL OXIDASE; BIODETERIORATION; BROWN ROT FUNGI; BROWN-ROT DECAY; CURRENT LIMITATION; DIFFERENT MECHANISMS; FUNCTIONAL PROTEINS; GENOMIC SEQUENCE; GLOEOPHYLLUM TRABEUM; HYPOTHETICAL PROTEIN; LIPOXYGENASES; METABOLIC PROTEINS; NUTRIENT SOURCES; PINUS TAEDA; PROTEOMIC ANALYSIS; PROTEOMICS; PUBLIC DATABASE; PURE CULTURE; TWO-DIMENSIONAL POLYACRYLAMIDE GEL ELECTROPHORESIS; WOOD BIODETERIORATION; YELLOW PINE SAPWOOD;

BIODEGRADATION; ELECTROPHORESIS; GELS; GLUCOSE; MOLECULAR BIOLOGY; TWO DIMENSIONAL; WOOD;

PROTEINS;

BIOASSAY; BIODEGRADATION; DATABASE; DECIDUOUS TREE; ELECTROKINESIS; ENZYME ACTIVITY; FUNGUS; PROTEOMICS;

AMIDES; BIODEGRADATION; ELECTROPHORESIS; GLUCOSE; POLYACRYLICS; PROTEINS; WOOD;

FUNGI; GLOEOPHYLLUM TRABEUM; PINUS ECHINATA; PINUS TAEDA;

EID: 71849102912     PISSN: 09648305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ibiod.2009.07.008     Document Type: Article

References (32)

1. Abbas A., Koc H., Liu F., and Tien M. Fungal degradation of wood: initial proteomic analyses of extracellular proteins of Phanerochaete chrysosporium grown on oak substrate. Current Genetics 47 (2005) 49-56
2. Arora A., Sairam R.K., and Srivastava G.C. Oxidative stress and antioxidative system in plants. Current Science 82 (2002) 1227-1238
3. Bradford M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical Biochemistry 72 (1976) 248-254
4. Brash A. Lipoxygenases: occurrence, functions, catalysis, and acquisition of substrate. Journal of Biological Chemistry 274 (1999) 23679-23682
5. Bruce A., King B., and Highley T.L. Decay resistance of wood removed from poles biologically treated with Trichoderma. Holzforschung 45 (1991) 307-311
6. Cease K.R., Blanchette R.A., and Highley T.L. Interactions between Scytalidium species and brown- or white-rot basidiomycetes in birch wood decayed in the laboratory. Wood Science and Technology 23 (1989) 151-161
7. 2 in brown rot decay of wood. Applied and Environmental Microbiology 73 (2007) 6241-6253
8. Flournoy D., Kirk T., and Highley T. Wood decay by brown-rot fungi: changes in pore structure and cell wall volume. Holzforschung 45 (1991) 383-388
9. Fromm J., Rockel B., Lautner S., Windeisen E., and Wanner G. Lignin distribution in wood cell walls determined by TEM and backscattered SEM techniques. Nature Structural Biology 143 (2003) 77-84
10. Fryksdale B.G., Jedrzejewski P.T., Wong D.L., Gaertner A.L., and Miller B.S. Impact of deglycosylation methods on two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-time of flight-mass spectrometry for proteomic analysis. Electrophoresis 23 (2002) 2184-2193
11. Green F., and Highley T.L. Brown-rot wood decay-insights gained from a low-decay isolate of Postia placenta. Trends in Plant Pathology 1 (1997) 1-17
12. Gromov P.S., and Celis J.E. From genomics to proteomics. Molecular Biology 34 (2000) 508-520
13. Goodell B. Brown-rot fungal degradation of wood: our evolving view. Wood deterioration and preservation: advances in our changing world. In: Goodell B., Nicholas D., and Schultz T. (Eds). ACS Symposium Series 845 (2003), American Chemical Society, Washington, DC 97-118
14. Keller M., and Hettich R. Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level. Microbiology and Molecular Biology Reviews 73 1 (2009) 62-70
15. Kobayashi Y. HIROX developed next generation digital microscope. Semiconductor FPD World 25 (2006) 100-101
16. Martinez D., Larrondo L.F., Putnam N., Gelpke M.D.S., Huang K., Chapman J., Helfenbein K.G., Ramaiya P., Detter J.C., Larimer F., Coutinho P.M., Henrissat B., Berka R., Cullen D., and Rokhsar D. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature Biotechnology 22 (2004) 695-700
17. Martinez D., Challacombe J., Morgenstern I., Hibbett D., Schmoll M., Kubicek C.P., Ferreira P., Ruiz-Duenas F.J., Martinez A.T., Kersten P., Hammel K.E., Vanden Wymelenberg A., Gaskell J., Lindquist E., Sabat G., Splinter BonDurant S., Larrondo L.F., Canessa P., Vicuna R., Yadav J., Doddapaneni H., Subramanian V., Pisabarro A.G., Lavin J.L., Oguiza J.A., Master E., Henrissat B., Coutinho P.M., Harris P., Magnuson J.K., Baker S.E., Bruno K., Kenealy W., Hoegger P.J., Kües U., Ramaiya P., Lucas S., Salamov A., Shapiro H., Tu H., Chee C.L., Misra M., Xie G., Teter S., Yaver D., James T., Mokrejs M., Pospisek M., Grigoriev I.V., Brettin T., Rokhsar D., Berka R., and Cullen D. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proceedings of the National Academy of Sciences 106 6 (2009) 1954-1959
18. Matsuzaki F., Shimizu M., and Wariishi H. Proteomic and metabolomic analyses of the white-rot fungus Phanerochaete chrysosporium exposed to exogenous benzoic acid. Journal of Proteome Research 7 (2008) 2342-2350
19. Nilsson T., Daniel G., Kirk T.K., and Obst J.R. Chemistry and microscopy of wood decay by some higher ascomycetes. Holzforschung 43 (1989) 11-18
20. Oliw E.H. Plant and fungal lipoxygenases. Prostaglandins and Other Lipid Mediators 68-69 (2002) 313-323
21. Pappin D.J.C., Hojrup P., and Bleasby A.J. Rapid identification of proteins by peptide mass fingerprinting. Current Biology 3 (1993) 327-332
22. Pechanova O., Stone W.D., Monroe W., Nebeker T.E., Klepzig K.D., and Yuceer K.D.C. Global and comparative protein profiles of the pronotum of the southern pine beetle, Dendroctonus frontalis Zimmermann (Coleoptera: Scolytidea). Insect Molecular Biology 17 3 (2008) 261-277
23. Phillips C., and Bogyo M. Proteomics meets microbiology: technical advances in the global mapping of protein expression and function. Cellular Microbiology 7 (2005) 1061-1076
24. Pointing S., Parungao M.M., and Hyde K.D. Production of wood-decay enzymes, mass loss and lignin solubilization in wood by tropical Xylariaceae. Mycological Research 107 (2003) 231-235
25. Preston F. Wood preservation: trends of today will influence the industry tomorrow. Forest Products Journal 50 (2000) 12-19
26. Prabakaran P., An J., Gromiha M., Selvaraj S., Uedaira H., Kono H., and Sarai A. Thermodynamic database for protein-nucleic acid interactions (ProNIT). Bioinformatics 17 (2001) 1027-1034
27. Sato S., Liu F., Koc H., and Tien M. Expression analysis of extracellular proteins from Phanerochaete chrysosporium grown on different liquid and solid substrates. Microbiology 153 (2007) 3023-3033
28. Shary S., Kapich A.N., Panisko E.A., Magnuson J.K., Cullen D., and Hammel K.E. Differential expression in Phanerochaete chrysosporium of membrane-associated proteins relevant to lignin degradation. Applied and Environmental Microbiology 74 23 (2008) 7252-7257
29. Shimizu M., and Wariishi H. Development of a sample preparation method for fungal proteomics. FEMS Microbiology Letters 247 (2005) 17-22
30. Vanden Wymelenberg A., Sabat G., Martinez D., Rajangam S., Teeri T.T., Gaskell P., Kersten P.J., and Cullen D. The Phanerochaete chrysosporium secretome: database predictions and initial mass spectrometry peptide identification in cellulose-grown medium. Journal of Biotechnology 118 (2005) 17-34
31. Varela E., and Tien M. Effect of pH and oxalate on hydroquinone-derived hydroxyl radical formation during brown rot wood degradation. Applied and Environmental Microbiology 69 (2003) 6025-6031
32. Zhou X.W., Blackman M.J., Howell S.A., and Carruthers V.B. Proteomic analysis of cleavage events reveals a dynamic two-step mechanism for proteolysis of a key parasite adhesive complex. Molecular and Cellular Proteomics 3 (2004) 565-576