Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA97043 | ENA |
REPOSITORIES: ENA
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Project description:Many cyanobacteria can form nitrogen-fixing symbioses with a broad range of plant species. Unlike other plant-bacteria symbioses, little is understood about the immunological responses induced by plant cyanobionts (symbiotic cyanobacteria). Here, we used Arabidopsis thaliana suspension cell cultures as a model system to demonstrate that the model plant-symbiotic cyanobacteria, Nostoc punctiforme is capable of protecting against plant programmed cell death (PCD). We also profiled the early transcriptomic changes that were induced in response to conditioned medium (CM) from N. punctiforme cell cultures. Interestingly, the PCD reduction was preceded by the induction of genes associated with defence and immunity, the most striking of which were a number of WRKY-family transcription factors. Down-regulated included genes involved in the regulation of cell growth and differentiation. This work is the first to show that a cyanobacteria can regulate plant PCD and provides a useful transcriptome resource for studying early plant cell responses to symbiotic cyanobacteria.
2020-12-10 | GSE155980 | GEO
Project description:We have published results demonstrating that UV-C induces apoptotic-like changes in Arabidopsis (Danon and Gallois FEBS lett (1998) 437: 131-136). The Programmed Cell Death "phenotype" of nucleus shape, DNA laddering caspase-like activity is similar to what has been described in other plant PCD. This demonstrates that UV-C is an appropriate and controllable trigger to study PCD in plants. Using selected mutants and a set of chosen conditions we are aiming at identifying genes that are part of the PCD pathways in plants and filter out the general stress response. We are asking for a medium size experiment knowing that additional microarray analysis are likely to be required to refine the results obtained. We are currently awaiting the results of Affymetrix RNAs hybridisation of PCD-induced wild type that will define the appropriate single time point of the proposed analysis. The rationale is to vary treatments in order to distinguish changes in gene transcription arising from general cellular stress responses to the trigger used from those specific to PCD: 1. We will use wild-type Arabidopsis seedlings as a negative control to provide the basal gene expression pattern. 2. A dose of UV-C radiation of 1KJ/m2. We will irradiate wild type with this non PCD-inducing dose of UV-C radiation to identify sets of genes that respond to UV-induced damage but whose expression is not linked to cell death. 3. A dose of UV-C radiation of 50 KJ/m2. We will irradiate wild type with a PCD-inducing dose of UV-C radiation to identify sets of genes that respond to UV-induced damage and cell death. 4. We have shown that the cell death induced by UV is light dependant, the control, sub-inducing dose and inducing dose treatments will be repeated and the plants kept in the dark until RNA sampling. In those conditions there is no PCD.
2022-11-21 | E-NASC-27 | biostudies-arrayexpress
Project description:Despite the critical role of programmed cell death (PCD) in plant development and defence responses, its regulation is not fully understood. It has been proposed that mitochondria may control the early stages of plant PCD, but the details of this regulation are currently unknown. Here, we used Arabidopsis thaliana cell suspension culture, a model system that enables induction and precise monitoring of PCD rates, as well as chemical manipulation of this process to generate a quantitative profile of the alterations in mitochondrial and cytosolic proteomes associated with early stages of plant PCD induced by heat stress. The cells were subjected to PCD-inducing heat levels (10 min, 54oC), with/without the calcium channel inhibitor and PCD blocker LaCl3. The stress treatment was followed by separation of cytosolic and mitochondrial fractions and mass spectrometry-based proteome analysis. Heat stress induced rapid and extensive changes in protein abundance in both fractions and 113 mitochondrial proteins were detected in the cytosol upon PCD induction. Western blot analysis confirmed the release of mitochondrial heat shock protein 60 family members occurring in response to PCD-inducing, but not sublethal level of heat stress, that may indicate their cytosolic role as positive regulators of PCD in plants. In our system, LaCl3 appeared to act downstream of cell death initiation signal, as it did not affect the release of mitochondrial proteins, but instead partially inhibited changes occurring in the cytosolic fraction, including upregulation of proteins with hydrolytic activity. Collectively, these generated data provide new insights into the regulation of cell death and survival decisions in plant cells.
2023-07-01 | PXD040584 | Pride
Project description:Transcriptional profiling after inhibition of cellulose synthesis by thaxtomin A and isoxaben in Arabidopsis thaliana suspension cells Perturbations in the cellulose content of the plant cell wall lead to global modifications in cellular homeostasis, as seen in cellulose synthase mutants or after inhibiting cellulose synthesis. In particular, application of inhibitors of cellulose synthesis such as thaxtomin A (TA) and isoxaben (IXB) initiates a programmed cell death (PCD) in Arabidopsis thaliana suspension cells that is dependent on de novo gene transcription. To further understand how TA and IXB activate PCD, a whole genome microarray analysis was performed on mRNA isolated from Arabidopsis suspension cells exposed to TA and IXB. More than 75% of the genes upregulated by TA were also upregulated by IXB, including genes encoding cell wall-related and calcium-binding proteins, defence/stress-related transcription factors, signalling components and cell death-related proteins. Comparisons with published transcriptional analyses revealed an important subset of genes generally induced in response to various biotic and abiotic stress.
2009-08-27 | GSE17824 | GEO
Project description:Programmed cell death (PCD) is essential for several aspects of plant life. We previously identified the mips1 mutant of Arabidopsis thaliana, which is deficient for the enzyme catalyzing myo-inositol synthesis, that displays light-dependent formation of lesions on leaves due to Salicylic Acid (SA) over-accumulation. Rationale of this work was to identify novel regulators of plant PCD using a genetic approach. A screen for secondary mutations that abolish the mips1 PCD phenotype identified a mutation in the BIG gene, encoding a factor of unknown molecular function that was previously shown to play pleiotropic roles in plant development and defence. Physiological analyses showed that BIG is required for lesion formation in mips1 via SA-dependant signalling. big mutations partly rescued transcriptomic and metabolomics perturbations as stress-related phytohormones homeostasis. In addition, since loss of function of the ceramide synthase LOH2 was not able to abolish cell death induction in mips1, we show that PCD induction is not fully dependent of sphingolipid accumulation as previously suggested. Our results provide further insights into the role of the BIG protein in the control of MIPS1-dependent cell death and also into the impact of sphingolipid homeostasis in this pathway.
2020-07-13 | GSE143244 | GEO
Project description:Transcriptional profiling after inhibition of cellulose synthesis by thaxtomin A and isoxaben in Arabidopsis thaliana suspension cells; Perturbations in the cellulose content of the plant cell wall lead to global modifications in cellular homeostasis, as seen in cellulose synthase mutants or after inhibiting cellulose synthesis. In particular, application of inhibitors of cellulose synthesis such as thaxtomin A (TA) and isoxaben (IXB) initiates a programmed cell death (PCD) in Arabidopsis thaliana suspension cells that is dependent on de novo gene transcription. To further understand how TA and IXB activate PCD, a whole genome microarray analysis was performed on mRNA isolated from Arabidopsis suspension cells exposed to TA and IXB. More than 75% of the genes upregulated by TA were also upregulated by IXB, including genes encoding cell wall-related and calcium-binding proteins, defence/stress-related transcription factors, signalling components and cell death-related proteins. Comparisons with published transcriptional analyses revealed an important subset of genes generally induced in response to various biotic and abiotic stress. Experiment Overall Design: TA, IXB and methanol (control) were added to Arabidopsis thaliana suspension cells three days after sub-culture. Cells were harvested for RNA isolation and frozen in liquid nitrogen after 6 hours of contact with the inhibitors. Samples consisted of four replicates for each condition. A total of 12 Affymetrix GeneChips® were used in this study, which correspond to 12 RNA samples from the four biological replicates for each of the TA, IXB or methanol addition.
2009-09-15 | E-GEOD-17824 | biostudies-arrayexpress
Project description:In plants, effector-triggered immunity (ETI) is often associated with programmed cell death (PCD). Although the intracellular immune receptors involved in ETI have been studied extensively, how their activation leads to PCD and disease resistance is poorly understood. We found that the Arabidopsis nuclear envelope protein, CPR5 (constitutive expresser of PR genes 5), plays a crucial role in controlling cell fate in response to stress, as the cpr5 mutant exhibits spontaneous cell death and heightened immunity. A genetic screen revealed that the Cip/Kip CKIs (cyclin-dependent kinase inhibitors), SIM (siamese) and SMR1 (siamese-related 1), are essential for CPR5 signaling, as the sim smr1 double mutant fully suppressed the cpr5 phenotype. More significantly, PCD and ETI are compromised in sim smr1 even with the wild-type CPR5.
2012-12-31 | GSE40322 | GEO
Project description:In plants, effector-triggered immunity (ETI) is often associated with programmed cell death (PCD). Although the intracellular immune receptors involved in ETI have been studied extensively, how their activation leads to PCD and disease resistance is poorly understood. We found that the Arabidopsis nuclear envelope protein, CPR5 (constitutive expresser of PR genes 5), plays a crucial role in controlling cell fate in response to stress, as the cpr5 mutant exhibits spontaneous cell death and heightened immunity. A genetic screen revealed that the Cip/Kip CKIs (cyclin-dependent kinase inhibitors), SIM (siamese) and SMR1 (siamese-related 1), are essential for CPR5 signaling, as the sim smr1 double mutant fully suppressed the cpr5 phenotype. More significantly, PCD and ETI are compromised in sim smr1 even with the wild-type CPR5. 10-day-old wild type (Col-0), cpr5, sim smr1 and cpr5 sim smr1. 12 samples total. Replicates are derived from three independent biological experiments. We used microarrays to identify differentially expressed genes. We focused on those genes that were cpr5-altered (>2-fold) and SIM/SMR1-dependent.
2012-12-31 | E-GEOD-40322 | biostudies-arrayexpress
Project description:Programmed cell death is an event displayed by many different organisms along the evolutionary scale. In plants, it is necessary for development and for the hypersensitive response to stress or pathogenic infection. A common feature to programmed cell death among organisms is the mitochondria-to-cytosol translocation of cytochrome c. To understand the role of cytochrome c in the onset of plant programmed cell death, a proteomic approach based on affinity chromatography has been developed, using Arabidopsis cytochrome c as bait. Eleven putative, new cytochrome c partners have been identified. Nine of them bind the heme protein in plant protoplasts and in human cells, as a heterologous system, according to Bimolecular Fluorescence Complementation. The binding affinities and the kinetic rate constants of three cytochrome c - target complexes have been estimated by Surface Plasmon Resonance. Our data suggest that the role of cytochrome c as a programmed cell death-signaling messenger could be evolutionarily well-conserved. Data Processing & data analysis: Peptides were analyzed using a nanoliquid chromatography-MS/MS on an LTQ linear ion trap mass spectrometer (Thermo Electron San Jose, CA, USA). The mass spectrometer was operated in the data-dependent mode to automatically switch between full MS and MS/MS acquisition. The parameters for ion scanning were the following: Full-scan MS(400-1800 m/z) plus top seven peaks Zoom/MS/MS (isolation width 2 m/z), normalized collision energy 35%. The scanning was performed using a dynamic exclusion list (120s exclusion list size of 50). Peak lists from all MS/MS spectra were extracted from the Xcalibur RAW files using a freely available program DTAsupercharge v.1.19 (http://msquant.sourceforge.net/). MASCOT 2.1 was used to search the Uniprot_Arabidopsis protein database 100323 (90895 sequences). Database search parameters used were the following: trypsin as enzyme; peptide tolerance, 300ppm; fragment ion tolerance, 0.6 Da; missed cleavage sites,1; fixed modification, carbamidomethyl cysteine and variable modifications, methionine oxidation. In all protein identifications the probability scores were greater than the score fixed by MASCOT (30) as significant with a p-value <0.05.
2013-11-11 | PXD000280 | Pride
Project description:Aerenchyma is continuous gas space between shoot and roots that contributes to the internal aeration in plants. In response to excess water stress and the plant hormone ethylene, maize (Zea mays) forms aerenchyma in root cortical cells by programmed cell death (PCD). The aim of this study was to understand the molecular mechanism of ethylene-induced aerenchyma formation by identifying genes that are up- or down-regulated by ethylene treatment in the maize root cortical cells isolated by laser microdissection. Gene expression analysis in cortical cells of maize primary root
2015-04-01 | E-GEOD-60944 | biostudies-arrayexpress