Significant alteration of gene expression in wood decay fungi Postia placenta and Phanerochaete chrysosporium by plant species

Abstract

Identification of specific genes and enzymes involved in conversion of lignocellulosics from an expanding number of potential feedstocks is of growing interest to bioenergy process development. The basidiomycetous wood decay fungi Phanerochaete chrysosporium and Postia placenta are promising in this regard because they are able to utilize a wide range of simple and complex carbon compounds. However, systematic comparative studies with different woody substrates have not been reported. To address this issue, we examined gene expression of these fungi colonizing aspen (Populus grandidentata) and pine (Pinus strobus). Transcript levels of genes encoding extracellular glycoside hydrolases, thought to be important for hydrolytic cleavage of hemicelluloses and cellulose, showed little difference for P. placenta colonizing pine versus aspen as the sole carbon source. However, 164 genes exhibited significant differences in transcript accumulation for these substrates. Among these, 15 cytochrome P450s were upregulated in pine relative to aspen. Of 72 P. placenta extracellular proteins identified unambiguously by mass spectrometry, 52 were detected while colonizing both substrates and 10 were identified in pine but not aspen cultures. Most of the 178 P. chrysosporium glycoside hydrolase genes showed similar transcript levels on both substrates, but 13 accumulated >2-fold higher levels on aspen than on pine. Of 118 confidently identified proteins, 31 were identified in both substrates and 57 were identified in pine but not aspen cultures. Thus, P. placenta and P. chrysosporium gene expression patterns are influenced substantially by wood species. Such adaptations to the carbon source may also reflect fundamental differences in the mechanisms by which these fungi attack plant cell walls.

Fig. 1.

Distribution of P. placenta (Ppl) and P. chrysosporium (Pchr) proteins identified by LC-MS/MS in BMA and BMP culture filtrates after 5 days of growth. Upper Venn diagrams show the partitioning of glucose-, BMA-, and BMP-derived proteins. In the lower panels, the numbers of proteins identified within glycoside hydrolase families are illustrated.

Fig. 2.

Heat map showing hierarchical clustering of P. placenta genes with >4-fold (P < 0.05) transcript accumulation in BMP relative to BMA (first 19 genes) and in BMA relative to BMP (last 15 genes). The scale above the map shows log₂-based signals.

Fig. 3.

Transcript levels of P. placenta genes encoding cytochrome P450s and aryl alcohol dehydrogenase. Protein model numbers are shown in parentheses, with slashes separating allelic variants. The upper panel indicates amounts of cDNA determined by competitive RT-PCR, whereas the lower panel shows log₂ microarray signals. Black and gray bars represent results for triplicate BMA and BMP cultures, respectively. PCR primers are listed in Table S1 in the supplemental material.