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. 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 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). 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 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. 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 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 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.

RETRACTED ARTICLE: Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi

“…Total RNA of samples from submerged culture was purified as described previously [29,31]. Plate-based RNA sample prep was performed on a PerkinElmer Sciclone NGS robotic liquid handling system (PerkinElmer, Inc., Waltham, MA) using the Illumina TruSeq Stranded mRNA HT sample prep kit utilizing poly-A selection of mRNA following the protocol outlined by Illumina in their user guide (Illumina, Inc., San Diego, CA).…”

“…The latter study identified 8906 putative RNA editing sites, without significant bias among substitution types, but did not investigate conditionspecific RNA-editing events. We recently studied transcriptional regulation and RNA editing in the brown rot fungus Fomitopsis pinicola [29], showing that it is able to modify both transcription and RNA editing levels on different wood types in diverse genes encoding enzymes with known or potential function in wood decay (including laccase, benzoquinone reductase, aryl alcohol oxidase, cytochrome P450s, and various glycoside hydrolases).…”

Aspects Determining the Dominance of Fomitopsis pinicola in the Colonization of Deadwood and the Role of the Pathogenicity Factor Oxalate

“…The continuous accumulation of oxalate indicated that Foma 4 persisted in the invasion mode until Km 10 was finally overgrown ( Table 1). The production of laccase ascribed to certain F. pinicola accessions [15,60,86] could not be recorded.…”

“…In spite of a host range of 82 softwood and 42 hardwood spp. [15], the brown rot basidiomycete F. pinicola is not regarded as a serious pathogen in managed Eurasian forests due to its low and primarily hidden incidence in living trees. It is an important disease agent of wounded conifer spp.…”

“…In F. pinicola, several accessions bear genes encoding laccase and several H 2 O 2 generating carbohydrate oxidases similar to white rot fungi but at lower activity. Class II peroxidases, such as MnP, are lacking [15,60,61]. This could explain the marginal modification of lignin in the brown rot wood decay [62,63] whose biochemistry is still hypothetical [63].…”