Substrate-specific differential gene expression and RNA editing in the brown rot fungus Fomitopsis pinicola

Research output: Contribution to journalArticleScientificpeer-review

Details

Original languageEnglish
Article numbere00991-18
Number of pages19
JournalApplied and Environmental Microbiology
Volume84
Issue number16
Publication statusPublished - 1 Aug 2018
MoE publication typeA1 Journal article-refereed

Researchers

  • Baojun Wu
  • Jill Gaskell
  • Benjamin W. Held
  • Cristina Toapanta
  • Thu Vuong
  • Steven Ahrendt
  • Anna Lipzen
  • Jiwei Zhang
  • Jonathan S. Schilling
  • Emma Master

  • Igor V. Grigoriev
  • Robert A. Blanchette
  • Dan Cullen
  • David S. Hibbett

Research units

  • Clark University
  • United States Department of Agriculture
  • University of Minnesota
  • University of Toronto
  • United States Department of Energy
  • University of California at Berkeley

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.

    Research areas

  • Basidiomycetes, Decay, Lignocellulose, RNA editing, Transcriptome

ID: 28870274