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Comparative transcriptomic analysis of a wood decomposing fungus in various atmospheres

ABSTRACT: Comparative transcriptomic analysis of a wood decomposing fungus in various atmospheres

PROVIDER: PRJNA592526 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10559902_1.fastq.gz	Fastqsanger.gz
	SRR10559902_2.fastq.gz	Fastqsanger.gz
	SRR10559903_1.fastq.gz	Fastqsanger.gz
	SRR10559903_2.fastq.gz	Fastqsanger.gz
	SRR10559904_1.fastq.gz	Fastqsanger.gz

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Comparative transcriptomic analysis of a wood decomposing fungus in various atmospheres

Project description:AIM: By adopting comparative transcriptomic approach, we investigated the gene expression of wood decomposing Basidiomycota fungus Phlebia radiata. Our aim was to reveal how hypoxia and lignocellulose structure affect primary metabolism and the expression of wood decomposition related genes. RESULTS: Hypoxia was a major regulator for intracellular metabolism and extracellular enzymatic degradation of wood polysaccharides by the fungus. Our results manifest how oxygen depletion affects not only over 200 genes of fungal primary metabolism but also plays central role in regulation of secreted CAZyme (carbohydrate-active enzyme) encoding genes. Based on these findings, we present a hypoxia-response mechanism in wood-decaying fungi divergent from the regulation described for Ascomycota fermenting yeasts and animal-pathogenic species of Basidiomycota.

2020-02-01 | GSE141153 | GEO

Transcriptomic analysis of copper tolerance and wood decay in the brown rot fungus Fibroporia radiculosa

Project description:Many brown rot fungi are capable of rapidly degrading wood and are copper-tolerant. To better understand the genes that control these processes, we examined gene expression of Fibroporia radiculosa growing on wood treated with a copper-based preservative that combined copper carbonate with dimethyldidecylammonium carbonate. A global profiling strategy called RNA-Seq was used to quantify gene expression of the fungus at days 31 and 154. At day 31, the preservative was still protecting the wood, which showed no strength loss. At day 154, the effects of the preservative were gone, and the wood exhibited 52% strength loss. Statistical analysis identified 917 genes that were differentially expressed (FDR < 1E-4). Transcripts that showed higher expression levels at the early time point were controlling increased oxalate metabolism, laccase for hydroquinone-driven hydroxyl free radical production, pectin degradation, ATP production, xenobiotic detoxification, copper resistance, and stress response. Transcripts that showed higher expression levels at the late time point were involved in degradation of cellulose, hemicellulose, and pectin, hexose transport, oxalate catabolism, catabolism of laccase substrates, extracellular proton reduction, and remodeling of the fungal cell membrane and cell wall to enhance survival at low pH.

2012-11-26 | GSE35333 | GEO

Proteomic analysis of brown rot wood decay fungus Fomitopsis pinicola grown on wood substrate

Project description:The brown rot wood decay fungus, Fomitopsis pinicola strain FP-58527, was cultivated for five dayes in media containing ground Populus tremuloides, Pinus taeda or Picea glauca wood as sole carbon source. Extracellular proteomic component was extracted and analyzed by LC-MS/MS.

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The molecular response of the white-rot fungus Dichomitus squalens to wood and non-woody biomass as examined by transcriptome and exoproteome analyses

Project description:The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi (post-)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well-adapted to the prevailing substrate. White-rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study we evaluated how well the white-rot fungus Dichomitus squalens has adapted to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analysed after cultivation on two natural substrates, aspen and spruce wood, and two non-woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non-woody polysaccharides was nearly as good match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant polysaccharides not present in its natural habitat.

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Proteome of the wood decay fungus Fomitopsis pinicola is altered by substrate

Project description:The brown rot fungus, Fomitopsis pinicola strain FP-58527, was cultivated in media containing ground Populus tremuloides, Pinus taeda or Picea glauca wood as sole carbon source. Mass spectrometry analyses identified proteins likely involved in the degradation of lignocellulose. Patterns of enzymes detected varied with substrate.

2021-09-29 | PXD028833 | Pride

Proteome of the wood decay fungus Fomitopsis pinicola is altered by substrate

2022-06-08 | PXD033887 | Pride

Puerto Rican fungal communities associated with decomposing wood following Hurricane Maria

Project description:Puerto Rican fungal communities associated with decomposing wood following Hurricane Maria Targeted loci environmental

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Functional transcriptomics reveal distinct combat strategies between lineages of wood-degrading fungi with redundant wood decay mechanisms

Project description:Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth’s largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched β‐glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single‐species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) employed secondary metabolite (SM) synthesis in response to a competitor, as shown by the upregulation of several SM-synthesizing genes in the interaction. R. placenta (Antrodia clade) instead upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that an oxidative burst may be a response to competitors in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving abundant unknowns on the battlefield. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.

2020-05-22 | GSE151023 | GEO

Capturing early gene expression dynamics during wood decay by brown rot fungus Rhodonia placenta

Project description:Brown rot fungi dominate wood decomposition in coniferous forests, and their carbohydrate-selective mechanisms are of commercial interest. Brown rot was recently described as a two-step, sequential mechanism orchestrated by fungi using differentially expressed genes (DEGs) and consisting of oxidation via reactive oxygen species (ROS) followed by enzymatic saccharification. There have been indications, however, that the initial oxidation step, itself, might require induction. To capture this early gene regulation event, here we integrated fine-scale cryo-sectioning with whole transcriptome sequencing to dissect gene expression at the single hyphal cell scale (tens of μm). We improved spatial resolution 50x, relative to previous work, and we were able to capture the activity of the first 100 μm of hyphal front growth by Rhodonia placenta in aspen wood. By comparing the first 100-μm section with a 100-μm from a later decay stage, it was clear that the early decay period was dominated by delayed gene expression patterns as the fungus ramped up its mechanism. These delayed DEGs included many genes implicated in ROS pathways (lignocellulose oxidation, LOX) that were previously and incorrectly assumed to be constitutively expressed. However, this delayed pattern was not universal, with a handful of genes upregulated immediately at the hyphal front.

2022-03-01 | GSE193915 | GEO

Early response of the fungus Pycnoporus coccineus to softwood and hardwood feedstocks

Project description:White-rot basidiomycete fungi are potent degraders of plant biomass with the ability to mineralize all lignocellulose components. Recent comparative genomics studies showed that these fungi use a wide diversity of enzymes for wood degradation. Deeper functional analyses are however necessary to understand the enzymatic mechanisms leading to lignocellulose breakdown. The Polyporale fungus Pycnoporus coccineus CIRM-BRFM310 grows well on both coniferous and deciduous wood. In the present study we analyzed the early response of the fungus to softwood (pine) and hardwood (aspen) feedstocks.

2016-10-10 | GSE74234 | GEO

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