Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus

Abstract

White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood decaying activity within the Basidiomycota genus Pycnoporus. We observed strong conservation in the genome structures and the repertoires of protein coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analyzed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2 producing enzymes with H2O2 consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 LPMO gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood decaying process.

Discovery of fungal oligosaccharide-oxidising flavo-enzymes with previously unknown substrates, redox-activity profiles and interplay with LPMOs

“…Enzymatic priming of LPMOs by the modular pyrroloquinolinequinone-dependent pyranose dehydrogenase 24 (CAZy family AA12 dehydrogenase domain appended to an AA8 cytochrome b haem domain) and FAD-dependant glucose-methanol-choline (GMC) superfamily of oxidoreductases (AA3), most notably the fungal cellobiose dehydrogenase (CDH) that also possesses a cytochrome b haem domain [25][26][27] , has been reported. The activity on cellooligosaccharides and the transcriptional co-regulation as well as the co-secretion with cellulose active AA9 LPMOs 28 , justified extensive studies on CDH as a model for direct electron transfer and priming of LPMOs 25,27,29 . Not all fungi possess the CDH/LPMO pair, suggesting the presence of additional redox partners and mechanisms for LPMO activation.…”

Desert truffle genomes reveal their reproductive modes and new insights into plant–fungal interaction and ectendomycorrhizal lifestyle

“…S1; S2), permitting our transcriptomic analyses. Condition-specific differentiallyexpressed genes (log2 fold-change > 2 or < -2, FDR <0.05) were identified using a custom R script, SHIN+GO (Miyauchi et al, 2016(Miyauchi et al, , 2017(Miyauchi et al, , 2018(Miyauchi et al, , 2020b. Symbiosis-induced and repressed genes were queried against the 13 genomes analysed using BLASTP and they were classified according to eukaryotic orthologous groups (KOG) and secretome categories (i.e., SSPs and secreted CAZymes) as described in Pellegrin et al (2015).…”

“…Raw read counts were normalized (with the function counts in DESeq2) and differential transcription levels of the Accepted Article contigs (Bonferroni adjusted p < 0.05) were calculated with DESeq2 (Love et al, 2014). Condition-specific differentially transcribed genes (log2 fold-change > 2 or < -2, FDR <0.05) were identified with SHIN+GO pipeline (Miyauchi et al, 2016(Miyauchi et al, , 2017(Miyauchi et al, , 2018(Miyauchi et al, , 2020b.…”

The fungal root endophyteSerendipita vermiferadisplays inter-kingdom synergistic beneficial effects with the microbiota inArabidopsis thalianaand barley

“…Then, using the node-wise transcription values, highly-regulated genes specific to each of the conditions were determined by fulfilling either of two criteria: 1) > 12.6 log2 reads (above 95th percentile of the entire transcribed genes); or 2) over ± 2 log2 transcriptional differences between testing conditions and a control. The process above was performed in a semi-automated manner using co-gene expression pipeline (SHIN+GO; (Miyauchi et al, 2020; Miyauchi et al, 2016; Miyauchi et al, 2017; Miyauchi et al, 2018). R was used for operating the pipeline (R Core Team, 2013).…”