Transcriptomic analysis of pea plant responses to chitooligosaccharides’ treatment revealed stimulation of calcium-regulated reactions and mitogen-activated protein kinase cascade
Ontology highlight
ABSTRACT:
ORGANISM(S): Pisum sativum
PROVIDER: GSE218057 | GEO | 2023/02/23
REPOSITORIES: GEO
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Project description:Cellulose is the major polysaccharide in the primary and secondary cell wall. Its breakdown generates short-chain cellooligomers (COs) which induce Ca2+-dependent cell wall integrity (CWI) responses. Recently, a mutant (cork1) which did not respond to COs was identified. To find out the early phosphorylation events following CO perception, roots of the segregated wild-type and homozygous mutants (F2 generation from cork1-2 X AeqWT) were treated with 10 µM cellotriose or water for 0, 5 and 15 minutes. Phosphoproteome analyses identified early targets involved in signaling, the endoplasmatic recticulum/Golgi secretory pathway, cell wall repair and immune responses. The result identified protein targets of the novel CO-CORK1 pathway and shine light on the role of COs in CWI maintenance.
2022-09-23 | PXD033224 | Pride
Project description:Abstract: Chemogenomic fitness assays were combined with a transcriptome analysis to understand both the mode of action and the mechanisms of resistance to Chitosan oligosaccharides (COS). COS are deacetylated chitin compounds, with antimicrobial properties, that are presumed to act by disrupting the cell membrane. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity. The genes identified encode membrane proteins and members of the protein degradation/ proteosome pathway. The transcriptomes of wild-type and five suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress) and furthermore, treatment with environmental stressors does not provide resistance to COS. Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the RAS signal transduction pathway. Down-regulated transcripts included those encoding protein folding components, and respiratory chain proteins. Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane trafficking, provides protection against COS-induced cell membrane permeability and damage. We found that the ARL1 COS-resistant over-expression strain was as sensitive to amphotericin B, fluconazole and terbinafine as the wild-type (vector control). The gene targets of COS identified in this study suggest that COSM-bM-^@M-^Ys mechanism of action is different from other commonly studied fungicides, suggesting that COS may be an effective fungicide for drug-resistant fungal pathogens. We selected the 5 overexpressing strains based on the characteristics of the genes. ARL1, encoding a GTPase and is involved in membrane trafficking, was selected since it was observed in the HIP-HOP assay as a sensitive homozygous deletion strain and in the MSP assay as multicopy suppressor. The rest of selected overexpressing strains were BCK2 and MSG5, involved in cell integrity pathways, ERG24 in ergosterol synthesis, and RBA50 in transcription. BCK2 is a Ser-Thr rich protein with protein kinase C activity that acts in signal transduction. Overexpression of BCK2 can rescue defects in yeast cwh43M-NM-^T, which displays several cell wall defects [29]. BCK2 overexpression also can suppress a cell lysis defect of mpk1M-NM-^T and pck1M-NM-^T [30]. MSG5 is also involved in signal transduction. This gene encodes a protein phosphatase involved in cell cycle control through the dephosphorylation of MAPK and is indispensable for restricting the signaling by the cell integrity pathway in yeast [31]. The inhibition of MAPK signaling leads to inhibition of cell differentiation and cell division [32]. The functions of ARL1 and ERG24 and their potential roles in chitosan resistance will be described in more detail in the Discussion. To gain a further understanding on the mode of action and mechanisms of resistance to COS, we performed a transcriptome analysis of the above mentioned five overexpressing strains known to increase resistance to COS-5.44. Each overexpressing strain and the wild type (vector control) were treated with COS-5.44 and RNAs isolated from both treated and untreated cells. The RNAs were converted to labeled cDNA and hybridized to NimbleGen expression microarrays (see Methods). Three cDNA biological replicates either with or without a 60 minutes exposure to COS-5.44 for each of the five overexpressing strains as well as an untransformed wild type BY4743 cells (vector control; for a total of 36 samples) were hybridized to NimbleGen 4X72k microarrays (Roche NimbleGen, Inc. Design ID A6186-00-01, TI4932 60mer expr X4).
2012-12-22 | E-GEOD-32888 | biostudies-arrayexpress
Project description:Transcriptional profiling of Arabidopsis thaliana roots comparing inoculated roots with a bacterial strain Antarctic (Pseudomonas sp, Da-bac TI-8) vs untreated roots (control)
2013-03-28 | GSE45559 | GEO
Project description:Abstract: Chemogenomic fitness assays were combined with a transcriptome analysis to understand both the mode of action and the mechanisms of resistance to Chitosan oligosaccharides (COS). COS are deacetylated chitin compounds, with antimicrobial properties, that are presumed to act by disrupting the cell membrane. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity. The genes identified encode membrane proteins and members of the protein degradation/ proteosome pathway. The transcriptomes of wild-type and five suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress) and furthermore, treatment with environmental stressors does not provide resistance to COS. Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the RAS signal transduction pathway. Down-regulated transcripts included those encoding protein folding components, and respiratory chain proteins. Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane trafficking, provides protection against COS-induced cell membrane permeability and damage. We found that the ARL1 COS-resistant over-expression strain was as sensitive to amphotericin B, fluconazole and terbinafine as the wild-type (vector control). The gene targets of COS identified in this study suggest that COS’s mechanism of action is different from other commonly studied fungicides, suggesting that COS may be an effective fungicide for drug-resistant fungal pathogens. We selected the 5 overexpressing strains based on the characteristics of the genes. ARL1, encoding a GTPase and is involved in membrane trafficking, was selected since it was observed in the HIP-HOP assay as a sensitive homozygous deletion strain and in the MSP assay as multicopy suppressor. The rest of selected overexpressing strains were BCK2 and MSG5, involved in cell integrity pathways, ERG24 in ergosterol synthesis, and RBA50 in transcription. BCK2 is a Ser-Thr rich protein with protein kinase C activity that acts in signal transduction. Overexpression of BCK2 can rescue defects in yeast cwh43Δ, which displays several cell wall defects [29]. BCK2 overexpression also can suppress a cell lysis defect of mpk1Δ and pck1Δ [30]. MSG5 is also involved in signal transduction. This gene encodes a protein phosphatase involved in cell cycle control through the dephosphorylation of MAPK and is indispensable for restricting the signaling by the cell integrity pathway in yeast [31]. The inhibition of MAPK signaling leads to inhibition of cell differentiation and cell division [32]. The functions of ARL1 and ERG24 and their potential roles in chitosan resistance will be described in more detail in the Discussion. To gain a further understanding on the mode of action and mechanisms of resistance to COS, we performed a transcriptome analysis of the above mentioned five overexpressing strains known to increase resistance to COS-5.44. Each overexpressing strain and the wild type (vector control) were treated with COS-5.44 and RNAs isolated from both treated and untreated cells. The RNAs were converted to labeled cDNA and hybridized to NimbleGen expression microarrays (see Methods).
2012-12-22 | GSE32888 | GEO
Project description:We report the single-cell transcriptional profiling of sea urchin primary mesenchyme cells isolated from embryos treated with DMSO or with 5-lox activating protein (FLAP) inhibitor MK-886. We find that inhibition of LOX activity with MK-886 prior to PMC isolation induces shifts in gene expression within the PMC population. We further demonstrate that control PMCs cluster into four transcriptionally-defined subsets, and MK-886-treated PMCs cluster into five distinct subsets. These data highlight novel transcriptional paradigms in the diversification of PMCs, and the requirement of ectodermal LOX activity for proper PMC transcriptional diversification.
2022-06-01 | GSE164240 | GEO
Project description:The etiology of inflammatory bowel disease (IBD) is complex, with much room for a greater understanding and development of improved therapies. Therefore, establishing a reliable IBD model is crucial for future advancements. In this study, human induced pluripotent stem (iPS) cell-derived colon organoids (hiPSC-COs) were treated with a combination of TNF-α, IFN-γ, and IL-1β (3 cytokines: 3CK), known to elevate in the serum of IBD patients. Inflammatory responses in stromal cells and damage to intestinal epithelial cells were observed in the 3CK-treated hiPSC-COs. Comparison of molecular signatures of 3CK-treated hiPSC-COs with those of ulcerative colitis (UC) patient’s colon revealed that 3CK-treated hiPSC-COs resemble UC patient’s colon. Furthermore, the elevated production of inflammatory cytokines observed in 3CK-treated hiPSC-COs was attenuated by treatment with tofacitinib. Our UC model will be an essential tool to understand its pathologic mechanisms and identify effective therapeutic approaches.
2024-09-22 | GSE244981 | GEO
Project description:Transcriptional profiling of Arabidopsis thaliana roots comparing inoculated roots with a bacterial strain Antarctic (Pseudomonas sp, Da-bac TI-8) vs untreated roots (control) Two-condition experiment, inoculated roots vs. untreated roots (control). Biological replicates: 4 inoculated roots replicates vs. 4 untreated roots replicates (control)
2013-03-28 | E-GEOD-45559 | biostudies-arrayexpress
Project description:The present prospective study included a total number of 3 patients with a final diagnosis of chronic thromboembolic pulmonary hypertension (CTEPH), who were treated by pulmonary endarterectomy (PEA) at the Kerckhoff Heart and Thorax Center between 2016 and 2020. Biopsies of the myocardial interventricular septum from 3 patients were collected at baseline (BL) before PEA surgery (pre-septal-PEA) In this case, to account for technical and safety aspects, the specimens were taken from the myocardial interventricular septum. The aim of the Study was a comparative characterization of RNA-profiles of septum in CTEPH patients after PEA surgery (postPEA) compared to before PEA surgery (pre-septal-PEA).
2024-04-18 | GSE249694 | GEO
Project description:The secretion of metabolites by plant roots is a key determinant of microbial growth and colonisation. We have used Pisum sativum and its natural symbiont Rhizobium leguminosarum (it can form N2 fixing nodules on pea roots) to study the natural metabolites secreted by roots. To do this root secretion was harvested from pea plants grown under sterile conditions. This root exudate was then concentrated and used as a sole carbon and nitrogen source for growth of the bacteria in the laboratory. These bacteria were harvested in mid-exponential growth and RNA extracted for microarray analysis. As control cultures the bacteria were grown on 30 mM pyruvate as a carbon source and 10 mM ammonium chloride as a nitrogen source and RNA extracted. Two colour microarrays were performed using root exudate cultures versus pyruvate ammonia grown cultures. This was done in biological triplicate.
2016-05-25 | E-MTAB-4790 | biostudies-arrayexpress
Project description:Purpose: We recently identified a mutant (cork1) which did not respond to cellooligomers (COs). To find out the signaling events following CO perception, roots from the segregated wild-type and homozygous mutants (F2 generation from cork1-2 X AeqWT) were treated with 10 µM cellotriose and water. Total RNA from root tissue was extracted after 1 hour. The raw reads were mapped to TAIR10 reference genome with STAR (v. 2.7.10a). Readcounts were generated from the mapped bam files with featureCount (v. 2.0.1). DESeq2 (v. 1.34.0) was applied to calculate the fold change and statistics for each mapped gene.
2022-09-20 | GSE198092 | GEO