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

Abstract

ABSTRACT Wood-decaying fungi typically have characteristic substrate ranges that partly define their ecological niche.Fomitopsis pinicolais 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 ofF. pinicolafrom 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 pinicolaexpressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Still, 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 provideF. pinicolawith 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 suitesmore » of genes subject to RNA editing were much less affected by culture conditions. These results illustrate the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi. IMPORTANCEAll 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 polyporeFomitopsis pinicolaon 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 thatF. pinicolais 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. Our work provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.« less

Authors:
 [1];  [2];  [3];  [3];  [4];  [5];  [6];  [3];  [3];  [4];  [5];  [3];  [2];  [1];  [7]
  1. Clark Univ., Worcester, MA (United States)
  2. US Dept. of Agriculture (USDA), Madison, WI (United States). Forest Products Lab.
  3. Univ. of Minnesota, St. Paul, MN (United States)
  4. Univ. of Toronto, ON (Canada)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  7. Univ. of Tartu (Estonia)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1544269
Grant/Contract Number:  
IOS-1456777; IOS-1456548; IOS-1456958; DEB-1457721
Resource Type:
Accepted Manuscript
Journal Name:
Applied and Environmental Microbiology
Additional Journal Information:
Journal Volume: 84; Journal Issue: 16; Journal ID: ISSN 0099-2240
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Basidiomycetes; decay; lignocellulose; RNA editing; transcriptome

Citation Formats

Wu, Baojun, Gaskell, Jill, Held, Benjamin W., Toapanta, Cristina, Vuong, Thu, Ahrendt, Steven, Lipzen, Anna, Zhang, Jiwei, Schilling, Jonathan S., Master, Emma, Grigoriev, Igor V., Blanchette, Robert A., Cullen, Dan, Hibbett, David S., and Kivisaar, Maia. Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola. United States: N. p., 2018. Web. doi:10.1128/AEM.00991-18.
Wu, Baojun, Gaskell, Jill, Held, Benjamin W., Toapanta, Cristina, Vuong, Thu, Ahrendt, Steven, Lipzen, Anna, Zhang, Jiwei, Schilling, Jonathan S., Master, Emma, Grigoriev, Igor V., Blanchette, Robert A., Cullen, Dan, Hibbett, David S., & Kivisaar, Maia. Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola. United States. doi:10.1128/AEM.00991-18.
Wu, Baojun, Gaskell, Jill, Held, Benjamin W., Toapanta, Cristina, Vuong, Thu, Ahrendt, Steven, Lipzen, Anna, Zhang, Jiwei, Schilling, Jonathan S., Master, Emma, Grigoriev, Igor V., Blanchette, Robert A., Cullen, Dan, Hibbett, David S., and Kivisaar, Maia. Fri . "Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola". United States. doi:10.1128/AEM.00991-18. https://www.osti.gov/servlets/purl/1544269.
@article{osti_1544269,
title = {Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus Fomitopsis pinicola},
author = {Wu, Baojun and Gaskell, Jill and Held, Benjamin W. and Toapanta, Cristina and Vuong, Thu and Ahrendt, Steven and Lipzen, Anna and Zhang, Jiwei and Schilling, Jonathan S. and Master, Emma and Grigoriev, Igor V. and Blanchette, Robert A. and Cullen, Dan and Hibbett, David S. and Kivisaar, Maia},
abstractNote = {ABSTRACT Wood-decaying fungi typically have characteristic substrate ranges that partly define their ecological niche.Fomitopsis pinicolais 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 ofF. pinicolafrom 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 pinicolaexpressed similar sets of wood-degrading enzymes typical of brown rot fungi across all culture conditions and time points. Still, 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 provideF. pinicolawith 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 results illustrate the need for standardization of culture conditions in studies of gene expression in wood-decaying fungi. IMPORTANCEAll 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 polyporeFomitopsis pinicolaon 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 thatF. pinicolais 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. Our work provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.},
doi = {10.1128/AEM.00991-18},
journal = {Applied and Environmental Microbiology},
number = 16,
volume = 84,
place = {United States},
year = {2018},
month = {6}
}

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