Oxygen-sensing in Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB59551 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10848537_1.fastq.gz | Fastqsanger.gz | |||
| ERR10848537_2.fastq.gz | Fastqsanger.gz | |||
| ERR10848538_1.fastq.gz | Fastqsanger.gz | |||
| ERR10848538_2.fastq.gz | Fastqsanger.gz | |||
| ERR10848539_1.fastq.gz | Fastqsanger.gz |
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Project description:Oxygen-sensing through ERFVII action and modulation in Arabidopsis thaliana
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Project description:Oxygen is a key signalling component of plant biology, and whilst an oxygen-sensing mechanism was previously described in Arabidopsis thaliana, key features of the associated PCO N-degron pathway and Group VII ETHYLENE RESPONSE FACTOR (ERFVII) transcription factor substrates remain unknown. We demonstrate that ERFVIIs show non-autonomous activation of root hypoxia tolerance, and are essential for root development and survival under oxygen limiting conditions in the soil. We determine the combined effects of ERFVIIs in controlling genome expression and define genetic and environmental components required for proteasome-dependent oxygen-regulated stability of ERFVIIs through the PCO N-degron pathway. Using a plant extract, unexpected amino-terminal cysteine sulphonic acid oxidation level of ERFVIIs was observed, suggesting a requirement for additional enzymatic activity within the pathway. Our results provide a holistic understanding of the properties, functions and readouts of this oxygen-sensing mechanism defined through its role in modulating ERFVII stability.
2023-07-03 | GSE224694 | GEO
Project description:Oxygen is a key signalling component of plant biology and, whilst an oxygen-sensing mechanism was previously described in Arabidopsis thaliana. However, key features of the associated PCO N-degron pathway and Group VII ETHYLENE RESPONSE FACTOR (ERFVII) transcription factor substrates remain unknown. We demonstrate that ERFVIIs show non-autonomous activation of root hypoxia tolerance, and are essential for root development and survival under oxygen limiting conditions in the soil. We determine the combined effects of ERFVIIs in controlling genome expression and define genetic and environmental components required for proteasome-dependent oxygen-regulated stability of ERFVIIs through the PCO N-degron pathway. Using a plant extract, unexpected amino-terminal cysteine oxidation to sulphonic acid oxidation level of ERFVIIs was defined, suggesting a requirement for additional enzymatic activity within the pathway. Our results provide a holistic understanding of the properties, functions and readouts of this oxygen-sensing mechanism defined through its role in modulating ERFVII stability.
2023-07-02 | PXD039288 | Pride
Project description:This series compares the effects that two pharmacologically distinct ligands at the mitochondrial peripheral-type benzodiazepine receptor (Bzrp) has on gene expression in early mouse embryos cultured under different oxygen levels. Mouse embryos averaging 16-18 somite pairs were explanted on 9 d.p.c. and grown in culture under optimal oxygenation (21% oxygen, hyperbaric with respect to arterial blood = 80-100 mmHg). Most embryos (>90%) develop normally in over a 24h culture period. When embryos receive suboptimal oxygenation for 2.0h (5% oxygen, similar to venous blood = 38-40 mmHg) a high percentage of them (>60%) go on to develop abnormally or else fail. These hypoxic embryos are remediated with 5 uM PK11195 to ~25% malformation rate. Cultured embryos were exposed to different oxygen levels (5% or 21%) in the presence of the Bzrp ligands PK11195 (Bzrp antagonist) versus Ro5-4864 (Bzrp agonist). The sampling time was guided by p53 protein induction with hypoxia, and remediation with PK11195, at 4.0h of culture and exposures. Thus all measurements were on RNA from the prosencephalon collected 2.0h after start of the test period on 9 d.p.c. Keywords = peripheral benzodiazepine receptor Keywords = oxygen sensing Keywords = Bzrp ligands Keywords = PK11195 Keywords = Ro5-4864 Keywords = embryo Keywords = p53 protein induction
2010-06-09 | E-GEOD-1079 | biostudies-arrayexpress
Project description:This series compares the effects that two pharmacologically distinct ligands at the mitochondrial peripheral-type benzodiazepine receptor (Bzrp) has on gene expression in early mouse embryos cultured under different oxygen levels. Mouse embryos averaging 16-18 somite pairs were explanted on 9 d.p.c. and grown in culture under optimal oxygenation (21% oxygen, hyperbaric with respect to arterial blood = 80-100 mmHg). Most embryos (>90%) develop normally in over a 24h culture period. When embryos receive suboptimal oxygenation for 2.0h (5% oxygen, similar to venous blood = 38-40 mmHg) a high percentage of them (>60%) go on to develop abnormally or else fail. These hypoxic embryos are remediated with 5 uM PK11195 to ~25% malformation rate. Cultured embryos were exposed to different oxygen levels (5% or 21%) in the presence of the Bzrp ligands PK11195 (Bzrp antagonist) versus Ro5-4864 (Bzrp agonist). The sampling time was guided by p53 protein induction with hypoxia, and remediation with PK11195, at 4.0h of culture and exposures. Thus all measurements were on RNA from the prosencephalon collected 2.0h after start of the test period on 9 d.p.c. Keywords = peripheral benzodiazepine receptor Keywords = oxygen sensing Keywords = Bzrp ligands Keywords = PK11195 Keywords = Ro5-4864 Keywords = embryo Keywords = p53 protein induction Keywords: ordered
2004-03-11 | GSE1079 | GEO
Project description:Expression profiling of A. thaliana, A. stelleri, R. islandica, and T. salsuginea under the low-oxygen treatment(0.1% O2/99.9% N2, various time points at 0, 1, 3, 8, 24, 72h) Comparative analysis of transcriptional responses to low-oxygen stress with Arabidopsis and its related species to gain comprehensive insights into low-oxygen responses of the species.
2019-05-15 | GSE129468 | GEO
Project description:We used the flu mutant of Arabidopsis to detail gene expression in response to singlet oxygen. The conditional flu mutant of Arabidopsis accumulates excess protochlorophyllide in the dark within chloroplast membranes that upon illumination acts as a photosensitizer and generates singlet oxygen. Immediately after the release of singlet oxygen mature flu plants stop growing, whereas seedlings bleach and die. Within the first 30 min after the release of singlet oxygen rapid changes in nuclear gene expression occur. Distinct sets of genes were activated that were different from those induced by other reactive oxygen species, superoxide or hydrogen peroxide. Experiment Overall Design: Arabidopsis thaliana rosette leaves were harvested after 30 min, 1h, and 2 h of reillumination following a 8h dark period for RNA extraction and hybridization on Affymetrix ATH1 microarrays. Plants were grown on soil for 3 weeks under continuous light at 90 mmol. m-2 . s-1. For each sample, the rosette leaves of five to six 3-week-old plants (before they start bolting) were collected for RNA extraction. Total RNAs from two separate biological experiments were pooled for the preparation of cDNA and the subsequent synthesis of biotin-labeled complementary RNA as recommended by Affymetrix.
2008-04-05 | E-GEOD-10876 | biostudies-arrayexpress
Project description:Arabidopsis thaliana (Col-0) seedlings were grown on vertically oriented agar plates and subjected to hypoxia (0.2% oxygen, 99.8% nitrogen) for 30 to 240 minutes.
2014-08-07 | GSE60133 | GEO
Project description:This study analyzes transcriptomic data of Arabidopsis thaliana Col-0 and overexpression lines of Hypoxia Response Attenuator (HRA1; At3g10040) with Col-0 background (OE-HRA1). Two independent transgenic lines of OE-HRA1 were considered as biological replicates (OE-HRA1#1 and OE-HRA1#2). Seven-day-old seedlings were treated either with or without hypoxia (low oxygen) stress for 2 hours. This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls from total mRNA populations. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform.
2014-07-30 | GSE50679 | GEO
Project description:We identified a small zinc finger protein, MBS, as a new mediator of singlet oxygen responses in Chlamydomonas and Arabidopsis. MBS is required for induction of singlet oxygen-dependent gene expression and, upon oxidative stress, accumulates in distinct granules in the cytosol of Arabidopsis cells. First, we recorded changes in light stress-regulated gene expression profiles after genetically perturbing MBS function by isolating mutants for the two MBS genes (MBS1 and MBS2) and by overexpression of MBS1 in Arabidopsis thaliana. Then, these light stress-related gene expression profiles were analyzed with respect to genes specifically responding to singlet oxygen and hydrogen peroxide/superoxide. The results indicated that MBS inactivation leads to an impaired response to singlet oxygen signaling under light stress.
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