Postia placenta
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA19791 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR031255.fastq.gz | Fastqsanger.gz | |||
| SRR065671_1.fastq.gz | Fastqsanger.gz | |||
| SRR065671_2.fastq.gz | Fastqsanger.gz | |||
| SRR079366.fastq.gz | Fastqsanger.gz |
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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:Localizing gene regulation by RNA-seq reveals a staggered wood decay mechanism for the brown rot fungus Postia placenta
| PRJNA329543 | ENA
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: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:Transcriptome of the Wood-Degrading Fungus Postia placenta of spruce wood dust
| PRJNA79531 | ENA
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: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
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
Project description:Using whole genome microarrays based on the annotated genomes of Postia placenta, we monitored the changes in its transcriptomes relevant to cell wall degradation during growth on three chemically distinct Populus trichocarpa (poplar) wood substrates. The research goal is to identtify genes essential for cellulose depolymerization. From a data set of 12438 unique gene models, each NimbleGen (Madison, WI) array targeted 9959 genes and featured 10 unique 60mers per gene, all in triplicate. RNA and protein were obtained from P. placenta strain MAD-698-R (USDA Forest Mycology Center, Forest Products Laboratory, Madison WI) grown in malt extract agar for 10 days prior to inoculation with wood wafers. Three poplar wood substrates with distinct cell wall chemical properties were selected from several hundred 4-year old poplar (Populus trichocarpa) trees grown in a common garden field trial at the University of British Columbia (Canada). We selected three poplar genotypes based on cell wall chemical traits. Substrate A corresponds to a genotype with a higher than average lignin content and lower that average glucose content; Substrate B, a lower than average lignin content and higher that average glucose content; Substrate C lignin and glucose contents are near the population average. Poplar wood stems were cut into 0.5 mm wafers on a microtome, sterilized for 20 min at 121°C, dried at 50°C overnight, and cooled to room temperature. The specimens were then inoculated in Petri dishes with actively growing mycelia. Approximately 5 g of wood wafers were placed in each Petri dish (exact weights were recorded), sealed and incubated at 22°C and 70 ± 5% relative humidity for 10, 20 or 30 days. For RNA, the degraded wafers were removed from the Petri dishes, immediately snap-frozen in liquid nitrogen and stored at -80°C for later use. Total RNA was converted to Cy3 labelled cDNA, hybridized to microarrays and scanned as previously described by Vanden Wymelenberg et al 2010 (Appl Enviro Microbiol 76:3599-3610).The 24 arrays per fungal species were scanned and data extracted using NimbleScan v.2.4. The raw data was loaded into GeneSpring, where the intensities were converted to log2 and quantile normalized, and all probes per gene averaged. This data was then exported and further analyzed in R. For substrates “A” and “B”, three replicates were used for each wood substrate/fungus and incubation period combination. For substrate “C” only 2 biological replicates were employed.
2015-05-19 | E-GEOD-69004 | biostudies-arrayexpress
Project description:A copper-tolerant fungus that causes brown rot decay of wood
| PRJNA81067 | ENA