Transcriptional analyses of the ectomycorrhizal (ECM) fungus Paxillus involutus during growth on various lignocellulose soil substrates
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ABSTRACT:
ORGANISM(S): Paxillus involutus
SUBMITTER: Tomas Johansson
PROVIDER: E-GEOD-34402 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Abstract: A large part of the nitrogen in forest soils is found in recalcitrant organic matter-protein complexes. Ectomycorrhizal fungi are thought to have a key role in the decomposition and mobilization of nitrogen from such complexes. The knowledge on the functional mechanisms of these processes, and how they are regulated by carbon from the host plant and the availability of more easily available forms of nitrogen sources are limited. We used spectroscopic analyses and transcriptome profiling to examine how the presence/absence of glucose and ammonium regulates the decomposition and mobilization of nitrogen from litter material by the ectomycorrhizal fungus Paxillus involutus. Amendments of glucose triggered the assimilation of nitrogen and the decomposition of the litter material. Concomitantly, the expression of genes encoding enzymes involved in oxidative (i.e. Fenton chemistry) degradation of polysaccharides and polyphenols, peptidases, nitrogen transporters and enzymes in pathways of the nitrogen and carbon metabolism were upregulated in concert. Addition of ammonium had minute effects on both the expression of transcripts and decomposition of litter material, and only when glucose was present. Based on the spectroscopic analyses, three major types of chemical modifications of the litter material were observed. Each of them was correlated with the expression of specific sets of genes encoding extracellular enzymes. Our data suggests that the expression of the decomposition and nitrogen assimilation machinery of ectomycorrhizal fungi can be firmly regulated by the host carbon supply, i.e. priming, and that the availability of inorganic nitrogen as such has limited effects on the saprotrophic activities. Rineau F, Shah F., Smits M.M., Persson P., Johansson T., Carleer R., Troein C., Tunlid A. (2013) Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus (submitted) A one-chip study (data from 12 subarrays collected from a 12-plex Nimblegen microarray (ID 467991) using total RNA recovered from three separate glass-bead cultures of Paxillus involutus (ATCC200175) after amendments of various soil-derived substrates. Transcriptome profiling to examine how the presence/absence of glucose and ammonium regulates the decomposition and mobilization of nitrogen from litter material by the ectomycorrhizal fungus Paxillus involutus.
2013-04-30 | E-GEOD-45303 | biostudies-arrayexpress
Project description:Abstract: Proteins contribute to a major part of the organic nitrogen in forest soils. This nitrogen is mobilized and becomes available to trees as a result of the depolymerizing activities of symbiotic ectomycorrhizal fungi. The mechanisms by which these fungi depolymerize proteins and assimilate the released nitrogen are poorly characterized. Biochemical analysis and transcriptome profiling were performed to examine the proteolytic machinery and the uptake system of the ectomycorrhizal basidiomycete Paxillus involutus during the assimilation of organic nitrogen from various protein sources and extracts of organic matter. All substrates induced secretion of peptidase activity with an acidic pH optimum, mostly contributed by aspartic peptidases. The peptidase activity was transiently repressed by ammonium. Transcriptional analysis revealed a large number of extracellular endo- and exopeptidases. The expression levels of these peptidases were regulated in parallel with transporters and enzymes involved in the assimilation and metabolism of the released peptides and amino acids. For the first time the molecular components of the protein degradation pathways of an ectomycorrhizal fungus are described. The data suggest that the transcripts encoding these components are regulated in response to the chemical properties and the availability of the protein substrates. Firoz Shah, Francois Rineau, Björn Canbäck, Tomas Johansson and Anders Tunlid (2013) The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus (submitted) A one-chip study (data from 9 subarrays collected from a 12-plex Nimblegen microarray (ID: 461228)) using total RNA recovered from glass-bead cultures of Paxillus involutus (ATCC200175) after amendments of 3 different substrates (3 replicates of each).
2013-09-01 | E-GEOD-47838 | biostudies-arrayexpress
Project description:Ectomycorrhizal fungi are dependent on host trees for carbon supply. In return ectomycorrhizal fungi supply trees with water and nutrients. It is known that when ectomycorrhizal fungi have exploited a nutrient rich patch in soil, the carbon allocation to mycelia in that patch is reduced, with the consequence of mycelia dying, but less is known of the dynamics of this senescence. We cultivated the ectomycorrhizal fungus Paxillus involutus in an axenic system. We collected growth and transcriptome data at different stages of carbon starvation during fungal growth. Carbon starvation induced a decrease in fungal biomass, which coincided with the release of NH4+ and the expression of genes connected with autophagy as well as protease and chitinase activity. Monoaromatic compounds, chitin and protease activity was detected in the liquid growth media during carbon starvation. The exudation of NH4+ and increase of monoaromatic compound during C starvation suggests senescence and autolysis of P. involutus. Together with the upregulation of genes involved in autophagy, chitinase and endopeptidase activity this points towards a controlled senescence including recycling of compounds originating from the fungi. Reduced C allocation to ectomycorrhizal mycelia in recently depleted nutrient patches in forest soils must be of ubiquitous nature. Understanding the mechanisms during exploitation of nutrients by ectomycorrhizal fungi is of great importance for understanding carbon and nutrient dynamics in forest soils. This is to our knowledge the first study describing the carbon starvation response in an ectomycorrhizal fungus. A one-chip study (data from 12 subarrays collected from a 12-plex Nimblegen microarray (ID 527890) using total RNA recovered from three separate glass-bead cultures of Paxillus involutus (ATCC200175) grown on Minimum Melin Norkrans medium (MMN) amended with ammonium (C/N ratio 3) and harvested at different times of carbon starvation.)
2014-04-01 | E-GEOD-54940 | biostudies-arrayexpress
Project description:Abstract: Proteins contribute to a major part of the organic nitrogen in forest soils. This nitrogen is mobilized and becomes available to trees as a result of the depolymerizing activities of symbiotic ectomycorrhizal fungi. The mechanisms by which these fungi depolymerize proteins and assimilate the released nitrogen are poorly characterized. Biochemical analysis and transcriptome profiling were performed to examine the proteolytic machinery and the uptake system of the ectomycorrhizal basidiomycete Paxillus involutus during the assimilation of organic nitrogen from various protein sources and extracts of organic matter. All substrates induced secretion of peptidase activity with an acidic pH optimum, mostly contributed by aspartic peptidases. The peptidase activity was transiently repressed by ammonium. Transcriptional analysis revealed a large number of extracellular endo- and exopeptidases. The expression levels of these peptidases were regulated in parallel with transporters and enzymes involved in the assimilation and metabolism of the released peptides and amino acids. For the first time the molecular components of the protein degradation pathways of an ectomycorrhizal fungus are described. The data suggest that the transcripts encoding these components are regulated in response to the chemical properties and the availability of the protein substrates. Firoz Shah, Francois Rineau, Björn Canbäck, Tomas Johansson and Anders Tunlid (2013) The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus (submitted) A one-chip study (data from 12 subarrays collected from 12-plex Nimblegen microarray (IDs: 527896) using total RNA recovered from glass-bead cultures of Paxillus involutus (ATCC200175) after amendments of nitrogen (+/-NH4) to substrate followed by incubation for different periods of time (3 replicates of each).
2013-09-01 | E-GEOD-47839 | biostudies-arrayexpress
Project description:Decomposition of soil organic matter in forest soils is thought to be controlled by the activity of saprotrophic fungi, while biotrophic fungi including ectomycorrhizal fungi act as vectors for input of plant carbon. The limited decomposing ability of ectomycorrhizal fungi is supported by recent findings showing that they have lost many of the genes that encode hydrolytic plant cell-wall degrading enzymes in their saprophytic ancestors. Nevertheless, here we demonstrate that ectomycorrhizal fungi representing at least four origins of symbiosis have retained significant capacity to degrade humus-rich litter amended with glucose. Spectroscopy showed that this decomposition involves an oxidative mechanism and that the extent of oxidation varies with the phylogeny and ecology of the species. RNA-Seq analyses revealed that the genome-wide set of expressed transcripts during litter decomposition has diverged over evolutionary time. Each species expressed a unique set of enzymes that are involved in oxidative lignocellulose degradation by saprotrophic fungi. A comparison of closely related species within the Boletales showed that ectomycorrhizal fungi oxidized litter material as efficiently as brown-rot saprotrophs. The ectomycorrhizal species within this clade exhibited more similar decomposing mechanisms than expected from the species phylogeny in concordance with adaptive evolution occurring as a result of similar selection pressures. Our data shows that ectomycorrhizal fungi are potential organic matter decomposers, yet not saprotrophs. We suggest that the primary function of this decomposing activity is to mobilize nutrients embedded in organic matter complexes and that the activity is driven by host carbon supply. Comparative transcriptomics of ectomycorrhizal (ECM) versus brown-rot (BR) fungi while degrading soil-organic matter
2015-09-24 | E-GEOD-64897 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-09-01 | E-GEOD-47840 | biostudies-arrayexpress
Project description:In this study, examinations were performed on how the ECM fungus Paxillus involutus degrade complex, plant and litter material by using elemental analyses, FTIR spectroscopy, pyrolysis-GC/MS, and synchronous fluorescence spectroscopy together with microarray analyses screening 12,214 gene models, derived from 454 sequenced cDNA libraries. Rineau, F., Roth, D., Shah, F., Smits, M., Johansson, T., Canbäck, B., Bjarke Olsen, P., Persson, P., Nedergaard Grell, M., Lange, L., & Tunlid, A. (201X) Expression levels tune enzymatic exploitation of plant litter material by ectomycorrhizal fungi (manuscript in preparation).
2012-02-01 | GSE34402 | GEO
Project description:Ctcf heterozygous knockout mice are susceptible to neoplasia in a broad range of tissues, including lymphoma, endometrial cancer, and non-small cell lung cancer. Retention of the wild type Ctcf allele in these tumors establishes CTCF as a haploinsufficient tumor suppressor gene. Both human tumors and normal murine tissues with CTCF disruption are characterized by genome-wide differences in DNA methylation relative to CTCF wild type tissues, indicating even modest disruption of CTCF broadly destabilizes DNA methylation in vivo. This cross species functional analysis identifies CTCF as a commonly mutated tumor suppressor gene and establishes a central role for DNA methylation stability in tumor suppression. RRBS sequencing of transgenic Ctcf heterozygous mice and wild-type litter mate whole lung tissue.
2014-07-30 | E-GEOD-48975 | biostudies-arrayexpress
Project description:As maize (Zea mays) plants undergo vegetative phase change from juvenile to adult, they both exhibit heteroblasty, an abrupt change in patterns of leaf morphogenesis, and gain the ability to produce flowers. Both processes are under the control of microRNA 156, whose levels decline at the end of the juvenile phase. Gain of ability to flower is conferred by expression of miR156 targets that encode Squamosa Promoter-Binding (SBP) transcription factors, which when derepressed in the adult phase induce the expression of MADS-box transcription factors that promote maturation and flowering. What gene expression differences underlie heteroblasty, as well as what regulates miR156 levels, remain open questions. Here, we compare gene expression in primordia that will develop into juvenile or adult leaves to identify genes that define these two developmental states and may influence vegetative phase change. In comparisons among successive leaves at the same developmental stage of plastochron 6, three-fourths of approximately 1,100 differentially expressed genes were more highly expressed in primordia of juvenile leaves. This juvenile set was enriched in photosynthetic genes, particularly those associated with cyclic electron flow at photosystem I, and in genes involved in oxidative stress and retrograde redox signaling. Pathogen- and herbivory-responsive pathways including jasmonic acid and salicylic acid were also up-regulated in juvenile primordia and indeed, exogenous application of jasmonic acid both delayed the appearance of adult traits and the decline of miR156 levels in maize seedlings. The successful amelioration of stress signals thus plays an important role in inducing vegetative phase change in maize. 12 untreated samples (8mm primordia of leaves 1-12) and 1 treated sample (leaf 5 primordium, 15mM JA treatment). 2 or more technical replicates per sample
2015-10-24 | E-GEOD-74295 | biostudies-arrayexpress
Project description:Transcript profiles of Laccaria bicolor S238N mycelium on various media were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Laccaria bicolor genome sequence version 1. One goal was to evaluate the effect of nutrient deprivation on the transcriptome of Laccaria bicolor. We performed 15 hybridizations (Roche-NimbleGen) with samples derived from Laccaria bicolor free-living mycelium grown on MMN medium, on MMN with a 10 times reduction in all major macro-elements, on MMN with a 10 times reduction in the quantity of glucose or onto agar medium supplemented with the same nutrients used to fertilize our mycorrhization experiments.
2012-03-01 | E-GEOD-35556 | biostudies-arrayexpress