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Gene family expansions and transcriptome signatures uncover adaptations to wood decay in basidiomycetes fungi from the order Polyporales

ABSTRACT: Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. The transcriptomic trends of selected Polyporales species from the core polyporoid and phlebioid clades during degradation of diverse lignocellulosic substrates led to the discovery of conserved gene sets regulated for plant cell wall degradation. Our results unveil some of the mechanisms underlying Polyporales diversification and pinpoint to yet overlooked proteins that could contribute to the ability of Polyporales to degrade recalcitrant plant cell wall polymers. This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Irpex lacteus Cubamyces sp. BRFM 1775 Trametes elegans Pilatotrama ljubarskyi

PROVIDER: GSE156901 | GEO | 2021/08/11

REPOSITORIES: GEO

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Gene family expansions and transcriptome signatures uncover adaptations to wood decay in basidiomycetes fungi from the order Polyporales [Irpex lacteus]

Project description:Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. The transcriptomic trends of selected Polyporales species from the core polyporoid and phlebioid clades during degradation of diverse lignocellulosic substrates led to the discovery of conserved gene sets regulated for plant cell wall degradation. Our results unveil some of the mechanisms underlying Polyporales diversification and pinpoint to yet overlooked proteins that could contribute to the ability of Polyporales to degrade recalcitrant plant cell wall polymers.

2021-08-11 | GSE156899 | GEO

Gene family expansions and transcriptome signatures uncover adaptations to wood decay in basidiomycetes fungi from the order Polyporales [Trametes ljubarskyi]

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Gene family expansions and transcriptome signatures uncover adaptations to wood decay in basidiomycetes fungi from the order Polyporales [Leiotrametes sp.]

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Gene family expansions and transcriptome signatures uncover adaptations to wood decay in basidiomycetes fungi from the order Polyporales [Trametes elegans]

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Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa (RNA-seq)

Project description:The ability to rationally engineer filamentous fungi could greatly facilitate biotechnological enzyme production for the degradation of plant cell wall polysaccharides in biorefinery applications. However, an incomplete and fragmented knowledge base of the biomolecular networks responsible for plant cell wall deconstruction by filamentous fungi impedes experimental efforts in this direction. To expand this knowledge base, we have reconstructed a detailed network of those reactions occurring in the filamentous fungus Neurospora crassa that are important for the degradation of plant cell wall polysaccharides into simple sugars. To build this network, we integrated information from five heterogeneous data types: functional genomics, transcriptomics, proteomics, genetics, and biochemical characterizations. We encapsulated the combined information into a feature matrix and weighed evidence to assign annotation confidence scores for each gene within the network. Comparative analyses of next-generation transcriptome sequencing profiles for N. crassa grown on different substrates corresponding to specific plant cell wall polysaccharides revealed environment-specific modules within the network. Subsequent analyses of next-generation ChIP and RNA sequencing data within the network context shed new light on how N. crassa regulates the plant cell wall degradation network (PCWDN). Specifically, our system-level analyses led to the hypothesis-driven experimental validation of the role transcription factor CLR-2 plays in degradation of the major hemicellulose mannan. In the future, we expect the network to serve as a scaffold for integration of diverse experimental data, leading to elucidation of regulatory design principles for plant cell wall deconstruction by filamentous fungi. In turn, this will guide efforts to rationally engineer novel, industrially relevant fungal hyper-secretion strains.

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Early response of three Pycnoporus species to various carbon sources [Pycnoporus cinnabarinus]

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. In the present study we analyzed the early response of the Polyporales fungi Pycnoporus coccineus CIRM-BRFM310, Pycnoporus cinnabarinus CIRM-BRFM137 and Pycnoporus sanguineus CIRM-BRFM 1264 to various carbon sources including lignocellulosic biomass.

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RNA-seq analysis of Bacteroides xylanisolvens XB1AT grown on pectin or xylan

Project description:Dietary fiber degradation is a key function of the human gut microbiota. The aim of this study was to increase our knowledge on the degradation of plant cell wall polysaccharide degradation by a prominent human gut bacterial species, Bacteroides xylanisolvens. The transcriptome analysis of B. xylanisolvens XB1AT revealed the existence of six and two genomic loci dedicated to the degradation of pectins and xylan, respectively. These loci or PUL ("Polysaccharide Utilization Loci") are known to encode enzyme systems in Bacteroides that are specific to a particular polysaccharide.

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Expression Data from Arabidopsis suspension T87 cells, protoplasts, and osmotic stress-treated cells

Project description:Primary cell wall (PCW) in plant mainly consists of three kinds of polysaccharides, cellulose, hemicellulose, and pectin. Although many genes encoding a variety of enzymes involved in synthesis, degradation, or modification of the PCW-related polysaccharides have been reported, regulation on expression of these PCW-related genes during PCW formation is still not fully understood. In this study, expression changes of PCW-related genes were analyzed during PCW regeneration in protoplasts. We used microarrays to reveal the global gene expression response against primary cell wall integrity stress during the primary cell wall regeneration in protoplasts.

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