Retracted and Republished from: "Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola "

• Published in: Applied and environmental microbiology Vol. 87; no. 16; p. e0032921
• Main Authors: Wu, Baojun, Gaskell, Jill, Held, Benjamin W, Toapanta, Cristina, Vuong, Thu V, Ahrendt, Steven, Lipzen, Anna, Zhang, Jiwei, Schilling, Jonathan S, Master, Emma, Grigoriev, Igor V, Blanchette, Robert A, Cullen, Dan, Hibbett, David S
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 27.07.2021
• Subjects: Alcohol oxidase; Benzoquinone; Brown rot; Cytochrome; Cytochromes; Decay; Decay fungi; Ecological niches; Ecology; Environmental Microbiology; Enzymes; Fomitopsis pinicola; Fungi; Gene expression; Glycosidases; Glycoside hydrolase; Hardwoods; Laccase; Reductases; RNA editing; Softwoods; Species; Standardization; Substrates; Transcriptomes; Wafers; Wood; basidiomycetes; decay; Polyporales; brown rot; transcriptome; lignocellulose
• ISSN: 0099-2240; 1098-5336; 1098-5336
• DOI: 10.1128/AEM.00329-21

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 gene expression levels 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 was observed across all pairwise comparisons of substrates and time points. Genes exhibiting differential expression 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. 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. 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 allow 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 found that is able to modify gene expression (transcription levels) across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This study provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.