Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 17, 2012
Publication Date: December 21, 2012
Citation: Tang, J.D., Perkins, A.D., Sonstegard, T.S., Schroeder, S.G., Nicholas, D.D., Diehl, S.V. 2012. Gene expression analysis of copper tolerance and wood decay in the brown rot fungus Fibroporia radiculosa. Applied and Environmental Microbiology. 79(5):1523-33. Interpretive Summary: Copper has been used as a wood preservative; however many brown rot fungi are capable of degrading wood over time in the presence of copper. We completed a survey of gene expression of the brown rot fungus to identify which gene networks were responsible for this cooper tolerance activity. This gene information improves our understanding of the functional networks that regulate wood decay and copper tolerance. This information will be used by us and others to investigate new molecular targets for rational wood preservative development, as well as engineer efficient microbes that can be used in processing biomass to biofuel.
Technical Abstract: Many brown rot fungi are capable of rapidly degrading wood and are copper-tolerant. To better understand the genes that control these processes, we examined gene expression of Fibroporia radiculosa growing on wood treated with a copper-based preservative that combined copper carbonate with dimethyldidecylammonia carbonate. A global profiling strategy called RNA-Seq was used to quantify gene expression of the fungus at days 31 and 154. At day 31, the preservative was still protecting the wood, which showed no strength loss. At day 154, the effects of the preservative were gone, and the wood exhibited 52% strength loss. Statistical analysis identified 917 genes that were differentially expressed (FDR < 1E-4). The functions of transcripts that showed higher expression levels at the early time point suggested that they were regulating oxalate metabolism to lower pH and precipitate copper, laccase for hydroquinonedriven hydroxyl free radical production, pectin degradation, ATP production, xenobiotic detoxification, copper resistance, and stress response. The functions of transcripts that showed higher expression levels at the late time point indicated that they were controlling degradation of cellulose, hemicellulose, and pectin, hexose transport, oxalate catabolism to raise pH, catabolism of laccase substrates, and remodeling of the fungal cell membrane and cell wall to enhance survival at low pH. A total of 104 differentially expressed genes were discussed in relation to their functional roles for wood decay and copper tolerance.