Paxillus involutus
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ABSTRACT:
PROVIDER: PRJNA149635 | ENA |
REPOSITORIES: ENA
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Project description:Illumina HiSeq technology was used to generate mRNA profiles from Paxillus involutus ectomycorrhizal roots compared to mycelium patches . Mycorrhizal roots were harvested after 4 weeks, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Paxillus involutus (http://genome.jgi-psf.org/Paxin1/Paxin1.home.html) using CLC Genomics Workbench 6.
2015-02-06 | GSE63924 | GEO
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)
2013-09-01 | GSE47838 | GEO
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: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). A 18-subarray study (data from 18 subarrays collected from two 12-plex microarrays (IDs 468335 and 468400) using total RNA recovered from three separate wild-type glass-bead cultures after amendments of various soil-derived substrates.
2012-02-01 | E-GEOD-34402 | 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)
2013-09-01 | GSE47839 | GEO
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Paxillus involutus ectomycorrhizal roots compared to mycelium patches . Mycorrhizal roots were harvested after 4 weeks, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Paxillus involutus (http://genome.jgi-psf.org/Paxin1/Paxin1.home.html) using CLC Genomics Workbench 6. mRNA profiles from Paxillus involutus ectomycorrhizal roots and mycelium patches were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Two biological replicates were sequenced for mycorrhizal and mycelium samples.
2015-02-06 | E-GEOD-63924 | 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: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:Variations in gene content and sequence that could be associated with symbiotic adaptations of the ectomycorrhizal fungus Paxillus involutus were investigated by analyses of strains showing various abilities to form mycorrhiza. Five strains of Paxillus involutus (ATCC 200175, Maj; Nau, Pi01SE, and Pi08BE) and one strain of Paxillus filamentosus (Pf01De) were analyzed by comparative genomic hybridizations using cDNA microarrays. Two batches of arrays were used containing 1,076 unique fungal reporters. DNA was prepared from each strain, and after fragmentation and labelling used for dual-label microarray hybridizations. The experimental design includes 16 arrays (CGH_01 -- CGH_16), of which 12 arrays represent dye-swapped and direct contrasts between the sample strains and the reference strain ATCC 200175. Two arrays represent dye-swapped self-self hybridizations of the reference strain ATCC 200175 (CGH_01 and CGH_02). The remaining two arrays represent dye-swapped and direct contrasts between the sample strains Maj and Nau (CGH_06 and CGH_07).
2006-01-01 | E-MEXP-437 | 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.
2014-04-01 | GSE54940 | GEO