Gloeophyllum trabeum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA64625 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR058911_1.fastq.gz | Fastqsanger.gz | |||
| SRR058911_2.fastq.gz | Fastqsanger.gz | |||
| SRR12386326_1.fastq.gz | Fastqsanger.gz | |||
| SRR12386326_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 59 |
Similar Datasets
Project description:Brown rot fungi evolved the unique strategy to efficiently decay wood structures and selectively extract carbohydrates, and this involved the sophistical regulation of functional genes (Zhang et al., PNAS, 2016, 113: 10968-). However, the regulatory mechanisms of brown rot genes were not well known, impeding the implication and application of brown rot machinery in biomass conversions. In this work, we systematically studied the roles of environmental carbon signals (e.g., aspen, cellobiose, glucose and no-carbon) in regulating gene expression in model brown rot fungus Postia placenta by RNA-seq. We found the complex substrate aspen (Populus sp.), but not the commonly recognized disaccharide cellobiose, was the universal inducer for Carbohydrate Active Enzymes (CAZYs) expression. Even though, cellobiose clearly induced the expression of cellulase (GH5 and GH12, endoglucanase) and xylanase (GH10, endoxylanase) (cellobiose vs. no-carbon, fold change > 4), as we reported previously (Zhang and Schilling, FGB, 2017, 106: 1-). When response to easy to use carbons, P. placenta lost the CCR effect on the main-chain cleaving CAZYs expression, but kept this repressing effect on side-chain cleaving CAZYs and AAs, which indicated a clear adaption relative to that in saprotrophic ascomycete ancestors. This “loss of CCR effect” was independent of the glucose concentrations. To explore the distinctive brown rot regulatory machinery, the gene modules subjected to inducing or CCR effects were then used to predict the regulatory motifs and transcriptional factors to build the regulatory network in P. placenta. Together, these findings will facilitate us to understand the adaptions of regulatory elements in brown rot fungi, as well as the efficient brown rot strategy.
2018-09-11 | GSE119714 | GEO
Project description:Wood-degrading brown rot fungi are essential recyclers of plant biomass in forest ecosystems. Their efficient cellulolytic systems, which have potential biotechnological applications, apparently depend on a combination of two mechanisms: lignocellulose oxidation by reactive oxygen species (ROS) and polysaccharide hydrolysis by a limited set of glycoside hydrolases (GHs). Given that ROS are strongly oxidizing and non-selective, these two steps are likely segregated. A common hypothesis has been that brown rot fungi use a concentration gradient of chelated metal ions to confine ROS generation inside wood cell walls before enzymes can infiltrate. We examined an alternative: that lignocellulose-oxidation (LOX) components involved in ROS production are differentially expressed by brown rot fungi ahead of GH components. We used spatial mapping to resolve a temporal sequence in Postia placenta, sectioning thin wood wafers colonized directionally. Among sections, we measured gene expression by whole transcriptome sequencing (RNAseq) and assayed relevant enzyme activities. We found a marked pattern of LOX upregulation in a narrow (5-mm; 48-hr) zone at the hyphal front, which included many genes likely involved in ROS generation. Upregulation of GH5 endoglucanases and many other GHs clearly occurred later, behind the hyphal front, with notable exceptions of two likely expansins and a GH28 pectinase. Our results support a staggered mechanism for brown rot that is controlled by differential expression rather than microenvironmental gradients. This mechanism likely results in an oxidative pretreatment of lignocellulose, possibly facilitated by expansin- and pectinase-assisted cell wall swelling, before cellulases and hemicellulases are deployed for polysaccharide depolymerization. We sequenced mRNA from 9 Postia placenta samples taken from 3 wood sections of wafer design, with 3 bioreplicates for each wood section, to compare the gene expression during brown rot processes. Three wood sections of the wafer are representing early to late decay stages.
2016-07-18 | E-GEOD-84529 | biostudies-arrayexpress
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. In order to improve our understanding on the enzymatic mechanisms leading to lignocellulose breakdown, we analysed the early response of the white-rot fungus Pycnoporus coccineus CIRM-BRFM310 to various lignocellulosic substrates at two time points; Day 3 and Day 7.
2017-05-21 | GSE94878 | GEO
Project description:Wood-degrading brown rot fungi are essential recyclers of plant biomass in forest ecosystems. Their efficient cellulolytic systems, which have potential biotechnological applications, apparently depend on a combination of two mechanisms: lignocellulose oxidation by reactive oxygen species (ROS) and polysaccharide hydrolysis by a limited set of glycoside hydrolases (GHs). Given that ROS are strongly oxidizing and non-selective, these two steps are likely segregated. A common hypothesis has been that brown rot fungi use a concentration gradient of chelated metal ions to confine ROS generation inside wood cell walls before enzymes can infiltrate. We examined an alternative: that lignocellulose-oxidation (LOX) components involved in ROS production are differentially expressed by brown rot fungi ahead of GH components. We used spatial mapping to resolve a temporal sequence in Postia placenta, sectioning thin wood wafers colonized directionally. Among sections, we measured gene expression by whole transcriptome sequencing (RNAseq) and assayed relevant enzyme activities. We found a marked pattern of LOX upregulation in a narrow (5-mm; 48-hr) zone at the hyphal front, which included many genes likely involved in ROS generation. Upregulation of GH5 endoglucanases and many other GHs clearly occurred later, behind the hyphal front, with notable exceptions of two likely expansins and a GH28 pectinase. Our results support a staggered mechanism for brown rot that is controlled by differential expression rather than microenvironmental gradients. This mechanism likely results in an oxidative pretreatment of lignocellulose, possibly facilitated by expansin- and pectinase-assisted cell wall swelling, before cellulases and hemicellulases are deployed for polysaccharide depolymerization.
2016-07-18 | GSE84529 | GEO
Project description:Infections by the fungus Monilinia laxa, the main cause of brown rot in Europe, result in considerable losses of stone fruit. Herein, we present a comprehensive transcriptomic approach to unravel strategies deployed by nectarine fruit and M. laxa during their interaction. We used M. laxa-inoculated immature and mature fruit, which were resistant and susceptible to brown rot, respectively, to perform a dual RNA-seq analysis. In immature fruit, host responses, pathogen biomass, and pathogen transcriptional activity peaked at 14 – 24 hours post inoculation (hpi), at which point M. laxa appeared to switch its transcriptional response to either quiescence or death. Mature fruit experienced an exponential increase in host and pathogen activity beginning at 6 hpi. Functional analyses in both host and pathogen highlighted differences in stage-dependent strategies. For example, in immature fruit, M. laxa unsuccessfully employed carbohydrate-active enzymes (CAZymes) for penetration, which the fruit was able to combat with tightly regulated hormone responses and an oxidative burst that challenged the pathogen’s survival at later time points. In contrast, in mature fruit, M. laxa was more dependent on proteolytic effectors than CAZymes and was able to invest in filamentous growth early during the interaction. Hormone analyses of mature fruit infected with M. laxa indicated that, while jasmonic acid activity was likely useful for defense, high ethylene activity may have promoted susceptibility through induction of ripening processes. Lastly, we identified M. laxa genes that were highly induced in both quiescent and active infections and may serve as targets for control of brown rot.
2020-08-01 | GSE146293 | GEO
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.
| MSV000084351 | MassIVE
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
Project description:Brown rot fungi have great potential in biorefinery wood conversion systems, because they are the primary wood decomposers in coniferous forests and have an efficient lignocellulose degrading system. Their initial wood degradation mechanism is thought to consist of an oxidative radical-based system that acts sequentially with an enzymatic saccharification system, but the complete molecular mechanism of this system has not yet been elucidated. Some studies have shown that wood degradation mechanisms of brown rot fungi have diversity in their substrate selectivity. Gloeophyllum trabeum, one of the most studied brown rot species, has broad substrate selectivity and even can degrade some grasses. However, the basis for this broad substrate specificity is poorly understood. In this study, we performed RNA-seq analyses on G. trabeum grown on media containing glucose, cellulose, or Japanese cedar (Cryptomeria japonica) as the sole carbon source. Beyond the gene expression on glucose, 1129 genes were upregulated on cellulose and 1516 genes were upregulated on cedar. Carbohydrate Active enZyme (CAZyme) genes upregulated on cellulose and cedar media by G. trabeum included GH12, GH131, CE1, AA3_1, AA3_2, AA3_4 and AA9, which is a newly reported expression pattern for brown rot fungi. The upregulation of both terpene synthase and cytochrome P450 genes on cedar media suggests the potential importance of these genes in the production of secondary metabolites associated with the chelator-mediated Fenton reaction. These results provide new insights into the inherent wood degradation mechanism of G. trabeum and the diversity of brown rot mechanisms.
2020-08-05 | GSE155681 | GEO
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
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.
2022-06-08 | PXD033887 | Pride