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

Proteins expressed by the brown-rot fungus Gloeophyllum trabeum were characterized from inoculated southern yellow pine sapwood undergoing decay, from pure cultures of the fungus and from uninoculated pinewood. Analysis was carried out by two-dimensional polyacrylamide gel electrophoresis and MALDI-TOF/TOF/MS. No proteins were detected from the clean uncontaminated wood. The inoculated wood undergoing active brown-rot decay produced 76 proteins, including the Fenton-chemistry related enzymes, alcohol oxidase, lipoxygenase, and catalase. One hundred and eleven proteins were detected from the pure culture and most were common metabolic proteins. A majority of proteins in both samples were identified as hypothetical proteins. A surprising result is that there was very little overlap between proteins found in both sets of samples, indicating a very different mechanism in action when the fungus is growing on a cellulose-based nutrient source (wood) versus glucose media. This study also highlights a current limitation of this approach, which is the limited protein and genomic sequence information annotated on the public databases. Of the 187 proteins characterized, only 36 were identified with confidence. To our knowledge, this is the first reported proteomic analysis of pinewood decayed by a brown-rot fungus and provides the initial characterization of proteins involved in this type of wood biodeterioration. Although significant limitations still exist in identifying the proteins, this limitation will diminish as functional proteins are identified and added to the databases.