Transcriptome and Secretome Analyses of the Wood Decay Fungus Wolfiporia cocos Support Alternative Mechanisms of Lignocellulose Conversion

Abstract

Certain wood decay basidiomycetes, collectively referred to as brown rot fungi, rapidly depolymerize cellulose while leaving behind the bulk of cell wall lignin as a modified residue. The mechanism(s) employed is unclear, but considerable evidence implicates the involvement of diffusible oxidants generated via Fenton-like chemistry. Toward a better understanding of this process, we have examined the transcriptome and secretome of Wolfiporia cocos when cultivated on media containing glucose, purified crystalline cellulose, aspen (Populus grandidentata), or lodgepole pine (Pinus contorta) as the sole carbon source. Compared to the results obtained with glucose, 30, 183, and 207 genes exhibited 4-fold increases in transcript levels in cellulose, aspen, and lodgepole pine, respectively. Mass spectrometry identified peptides corresponding to 64 glycoside hydrolase (GH) proteins, and of these, 17 corresponded to transcripts upregulated on one or both woody substrates. Most of these genes were broadly categorized as hemicellulases or chitinases. Consistent with an important role for hydroxyl radical in cellulose depolymerization, high transcript levels and upregulation were observed for genes involved in iron homeostasis, iron reduction, and extracellular peroxide generation. These patterns of regulation differ markedly from those of the closely related brown rot fungus Postia placenta and expand the number of enzymes potentially involved in the oxidative depolymerization of cellulose. IMPORTANCEThe decomposition of wood is an essential component of nutrient cycling in forest ecosystems. Few microbes have the capacity to efficiently degrade woody substrates, and the mechanism(s) is poorly understood. Toward a better understanding of these processes, we show that when grown on wood as a sole carbon source the brown rot fungus W. cocos expresses a unique repertoire of genes involved in oxidative and hydrolytic conversions of cell walls.

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

“…Numerous studies have demonstrated the impact of culture conditions on transcript and protein accumulation levels in wood decay fungi (29,(40)(41)(42), including comparisons of expression on defined media (e.g., glucose, maltose, or crystalline cellulose) versus wood as a carbon source (43)(44)(45)(46)(47). However, there have been relatively few side-by-side comparisons of gene expression on different wood species (43,(48)(49)(50)(51)(52)(53)(54)(55).…”

“…Several prior transcriptomic analyses concluded that wood decay fungi express similar sets of plant cell wall-degrading enzymes on both hardwood and softwood, although there may be disparities in the expression of individual genes on different substrates (43,49,50,52,55). For example, Vanden Wymelenberg et al (55) found that 47 genes in the model white rot fungus Phanerochaete chrysosporium were upregulated Ͼ2-fold on aspen versus pine, including 13 genes encoding GHs, while in P. placenta, 164 genes showed differential expression on the two substrates (roughly equal numbers upregulated on each substrate).…”

The foliar endophytePhialocephala scopiformisDAOMC 229536 secretes enzymes supporting growth on wood as sole carbon source

“…P. scopiformis DAOMC 229536 was obtained from the Canadian Collection of Fungal Cultures. Two-liter flasks containing 250 ml of basal salt media (22) were supplemented with 1.25 g of P. contorta wood ground in a Wiley-mill (30 mesh screen) as the sole carbon source. Cultures were inoculated with mycelium scraped from the surface of malt extract agar (2% w/w malt extract, 2% glucose w/w, 0.5% peptone, 1.5% agar) and placed on a rotary shaker (150 RPM).…”

Caldicellulosiruptor saccharolyticus transcriptomes reveal consequences of chemical pretreatment and genetic modification of lignocellulose

“…Conversely, a more detailed view of compounds that the microbe senses and responds to (‘bioavailability’) could come from analysis of its transcriptome from growth on plant biomass feedstocks. Studies observing gene expression of either lignocellulosic fungi (Gaskell et al ., , ; Couturier et al ., ) or lignocellulosic bacteria (Raman et al ., ; VanFossen et al ., ) grown on plant biomass feedstocks and sugars have so far focused on extracellular enzymes. Novel and useful insights into the plant biomass matrix in question could be obtained, based not only on the differential transcription of genes encoding glycoside hydrolases, but also including ATP‐binding cassette (ABC) sugar transporters and key metabolic pathway enzymes.…”