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Lignocellulose depolymerization occurs via an environmentally adapted metabolic cascades in the wood-rotting basidiomycete Phanerochaete chrysosporium.

ABSTRACT: Plant biomass can be utilized by a lignocellulose-degrading fungus, Phanerochaete chrysosporium, but the metabolic and regulatory mechanisms involved are not well understood. A polyomics-based analysis (metabolomics, proteomics, and transcriptomics) of P. chrysosporium has been carried out using statistically optimized conditions for lignocellulolytic reaction. Thirty-nine metabolites and 123 genes (14 encoded proteins) that consistently exhibited altered regulation patterns were identified. These factors were then integrated into a comprehensive map that fully depicts all signaling cascades involved in P. chrysosporium. Despite the diversity of these cascades, they showed complementary interconnection among themselves, ensuring the efficiency of passive biosystem and thereby yielding energy expenditure for the cells. Particularly, many factors related to intracellular regulatory networks showed compensating activity in homeostatic lignocellulolysis. In the main platform of proactive biosystem, although several deconstruction-related targets (e.g., glycoside hydrolase, ureidoglycolate hydrolase, transporters, and peroxidases) were systematically utilized, well-known supporters (e.g., cellobiose dehydrogenase and ferroxidase) were rarely generated.

SUBMITTER: Bak JS

PROVIDER: S-EPMC4335982 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Crystallization of selenomethionyl exo-beta-1,3-galactanase from the basidiomycete Phanerochaete chrysosporium.

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Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium.

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Project description:Activity-based protein profiling (ABPP) has emerged as a versatile biochemical method for studying enzyme activity under various physiological conditions, with applications so far mainly in biomedicine. Here, we show the potential of ABPP in the discovery of biocatalysts from the thermophilic and lignocellulose-degrading white rot fungus Phanerochaete chrysosporium. By employing a comparative ABPP-based functional screen, including a direct profiling of wood substrate-bound enzymes, we identify those lignocellulose-degrading carbohydrate esterase (CE1 and CE15) and glycoside hydrolase (GH3, GH5, GH16, GH17, GH18, GH25, GH30, GH74 and GH79) enzymes specifically active in presence of the substrate. As expression of fungal enzymes remains challenging, our ABPP-mediated approach represents a preselection procedure for focusing experimental efforts on the most promising biocatalysts. Furthermore, this approach may also allow the functional annotation of domains-of-unknown functions (DUFs). The ABPP-based biocatalyst screening described here may thus allow the identification of active enzymes in a process of interest and the elucidation of novel biocatalysts that share no sequence similarity to known counterparts.

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Influence of Populus genotype on gene expression by the wood decay fungus Phanerochaete chrysosporium.

Project description:We examined gene expression patterns in the lignin-degrading fungus Phanerochaete chrysosporium when it colonizes hybrid poplar (Populus alba × tremula) and syringyl (S)-rich transgenic derivatives. A combination of microarrays and liquid chromatography-tandem mass spectrometry (LC-MS/MS) allowed detection of a total of 9,959 transcripts and 793 proteins. Comparisons of P. chrysosporium transcript abundance in medium containing poplar or glucose as a sole carbon source showed 113 regulated genes, 11 of which were significantly higher (>2-fold, P < 0.05) in transgenic line 64 relative to the parental line. Possibly related to the very large amounts of syringyl (S) units in this transgenic tree (94 mol% S), several oxidoreductases were among the upregulated genes. Peptides corresponding to a total of 18 oxidoreductases were identified in medium consisting of biomass from line 64 or 82 (85 mol% S) but not in the parental clone (65 mol% S). These results demonstrate that P. chrysosporium gene expression patterns are substantially influenced by lignin composition.

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Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium.

Project description:Cellulose degradation by brown rot fungi, such as Postia placenta, is poorly understood relative to the phylogenetically related white rot basidiomycete, Phanerochaete chrysosporium. To elucidate the number, structure, and regulation of genes involved in lignocellulosic cell wall attack, secretome and transcriptome analyses were performed on both wood decay fungi cultured for 5 days in media containing ball-milled aspen or glucose as the sole carbon source. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), a total of 67 and 79 proteins were identified in the extracellular fluids of P. placenta and P. chrysosporium cultures, respectively. Viewed together with transcript profiles, P. chrysosporium employs an array of extracellular glycosyl hydrolases to simultaneously attack cellulose and hemicelluloses. In contrast, under these same conditions, P. placenta secretes an array of hemicellulases but few potential cellulases. The two species display distinct expression patterns for oxidoreductase-encoding genes. In P. placenta, these patterns are consistent with an extracellular Fenton system and include the upregulation of genes involved in iron acquisition, in the synthesis of low-molecular-weight quinones, and possibly in redox cycling reactions.

| S-EPMC2876446 | biostudies-literature

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