Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola

Abstract

Wood-decaying fungi tend to have characteristic substrate ranges that partly define their ecological niche. Fomitopsis pinicola is a brown rot species of Polyporales that is reported on 82 species of softwoods and 42 species of hardwoods. We analyzed the gene expression levels and RNA editing profiles of F. pinicola from submerged cultures with ground wood powder (sampled at 5 days) or solid wood wafers (sampled at 10 and 30 days), using aspen, pine, and spruce substrates (aspen was used only in submerged cultures). Fomitopsis pinicola expressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Nevertheless, differential gene expression and RNA editing were observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression and RNA editing encode diverse enzymes with known or potential function in brown rot decay, including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases. There was no overlap between differentially expressed and differentially edited genes, suggesting that these may provide F. pinicola with independent mechanisms for responding to different conditions. Comparing transcriptomes from submerged cultures and wood wafers, we found that culture conditions had a greater impact on global expression profiles than substrate wood species. In contrast, the suites of genes subject to RNA editing were much less affected by culture conditions. These findings highlight the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi.IMPORTANCE All species of wood-decaying fungi occur on a characteristic range of substrates (host plants), which may be broad or narrow. Understanding the mechanisms that enable fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood species, aspen, pine, and spruce, under various culture conditions. We examined both gene expression (transcription levels) and RNA editing (posttranscriptional modification of RNA, which can potentially yield different proteins from the same gene). We found that F. pinicola is able to modify both gene expression and RNA editing profiles across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This work provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.

Keywords: RNA editing; basidiomycetes; decay; lignocellulose; transcriptome.

FIG 1

Heatmap showing hierarchical clustering of 11 genes with predicted functions in wood decay with 4-fold change (FDR < 0.05) in pairwise-substrate comparisons at day 5. The scale above the map shows log2-based signals under the central row. Protein identifiers (IDs) and their enzyme names are indicated on the right side of the heatmap. Transporters are labeled in blue, and wood-decay enzymes are labeled in red. The bottom column designations refer to replicate libraries.

FIG 2

GO enrichment of upregulated genes from each substrate after 5-day submerged incubation. Categories of GO terms are labeled on the right side of the heatmap. Substrates are labeled at the bottom. Dark blue shading indicates presence and light blue indicates absence. The number of genes in each GO term is labeled in dark blue.

FIG 3

RNA editing in F. pinicola after 5-day submerged culture. (A) Distribution of RNA editing types from aspen, pine, and spruce substrates. (B) Venn diagram showing distribution of RNA editing sites between substrates. (C) Comparison between DEGs and DREGs in substrate pairs. (D) Examples of DREGs encoding enzymes associated with wood decay.

FIG 4

Differential expression of F. pinicola on different wood wafers (pine and spruce) after 10-day and 30-day incubations. (A) Relative percentages of upregulated DEGs on different substrates and at different time points. (B) GO enrichment of upregulated genes from each condition in each pairwise comparison. Four pairwise comparisons are labeled on the right side of the heatmap. Dark blue shading indicates presence and light blue indicates absence. The number of genes in each GO term is labeled in dark blue. Distributions in relative proportions of wood decay CAZymes (GH, CE, and PL), redox enzymes potentially involved in Fenton chemistry (AA families, HTP, POD, CRO, OXO, GLP, and QRD), and cytochrome_P450s at different time points (C) and on different substrates (D). For each category, only the upregulated genes at one time point/substrate relative to the other time point/substrate were considered.

FIG 5

Annotations of DEGs on wood wafers having TM domains. (A) Distributions in relative proportions of TM proteins at different time points (left) and on different substrates (right). For each category, only the upregulated gene at one time point/on one substrate relative to the other time point/substrate was considered. (B to E) Details for stacked bars in the panel A. The font size in the word cloud is directly related to the word (protein) frequency in each panel. The colors of words are consistent with the conditions used in panel A.

FIG 6

RNA editing of F. pinicola on wood wafers after 10-day and 30-day incubations. (A) Venn diagrams showing distribution of RNA editing sites between conditions. (B) Comparison of DREGs under different combinations of time points and substrates. (C) Examples of DREGs encoding enzymes associated with wood decay. The sample showing RNA editing is indicated after the gene annotation.

FIG 7

Cross-culture method comparisons. (A) Neighbor-joining tree with branch lengths inferred using 1 − Spearman's rho for all pairs of gene expression profiles. (B) Neighbor-joining tree with branch lengths inferred using 1 − Spearman's rho for frequency of RNA editing profiles.