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.
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.
Project description:To study the differentially expressed genes in lightly and darkly pigmented human skin melanocytes, we isolated melanocytes from light and dark skin samples and performed RNA-seq using Illumina platform.
Project description:To study the differentially expressed genes in lightly and darkly pigmented human skin melanocytes, we isolated melanocytes from light and dark skin samples and performed RNA-seq using Illumina platform.
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.
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.
Project description:Methanol extractions of GI dissections of laboratory-reared wood frogs that were selectively inoculated with the herptile gut fungus, Basidiobolus.
Project description:The fungus Polyporus brumalis is a wood decay fungus previously evidenced as efficient lignin degrader with high potential for plant biomass pre-treatment before conversion into bio-energy. Here we used an RNASeq approach that highlighted the active transcription of an unparalleled number of lignin active peroxidases and H2O2 generating enzymes during growth on wheat straw. These enzymes, together with metabolic processes related to detoxification appear as key determinants of the fungal adaption to lignin degradation.