Cytosolic calcium and nuclear calcium-regulated transcription networks in response to ABA and JA
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE109611 | GEO | 2018/01/25
REPOSITORIES: GEO
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Project description:The objective of this study is to identify early calcium up/down-regulated genes in response to rapid cytosolic Ca2+ transients in Arabidopsis thaliana. Keywords: stress response
2006-11-01 | GSE5517 | GEO
Project description:Effect of CaM overexpression on Arabidopsis transcriptome. Unlike animals, plants are immobile and cannot simply move away from unfavourable environments and thus have developed complex mechanisms to respond to and sense biotic and abiotic signals. These stimuli often lead to tightly controlled changes in cytoplasmic free calcium concentration [Ca2+]cyt termed "calcium signatures" which are thought to be, at least partly, responsible for the specificity of plant responses to the environment. However little is known about how exactly these calcium signatures are decoded into specific end-responses. Calmodulin (CaM) is the most well characterised Ca2+ binding protein and is the primary sensor of changing [Ca2+]. Upon binding Ca2+ CaM undergoes a conformational change allowing binding and activation of a wide variety of target proteins. In plants CaM exists in gene families encoding multiple isoforms. The expression of individual CaM genes can be differentially regulated and isoforms may be differentially localised. Furthermore specific isoforms can bind and activate different target proteins. These features of plant CaM allow the possibility of specificity during calcium signalling in response to specific stimuli. The effect of overexpression of four CaM protein isoforms on the Arabidopsis thaliana transcriptome will be investigated. Ten day old transgenic Arabidopsis seedlings (containing estradiol inducible CaM overexpression constructs) were induced for 9hrs in 5uM estradiol with appropriate water (0.025% DMSO) and empty vector controls.
2008-02-15 | E-NASC-65 | biostudies-arrayexpress
Project description:Calcium is an essential macronutrient and plant requires it in large amounts for normal growth and development. This ion participated in innumerable processes and affects nearly all aspects of plant growth and development such as signal transduction, metabolism of lipids, proteins, and carbohydrates, cell growth, cell wall and membrane stabilization. We used whole genome microarrays to determine the transcriptomic profile of rice seedlings exposed to short-term and long term Ca2+ deficiency followed by Ca2+ resupply. Calcium treated seedlings were used for for RNA extraction and hybridization on Agilent microarray platform. Three biological replicates of each sample were used for microarray analysis. We wanted to know the altered expression patterns of calcium-responsive genes majorly involved in metabolic processes, signal transdction pathways, transcriptional regulation, and transport of multiple molecules including Ca2+. Seeds of indica rice were surface sterilized and grown hydroponically in rice growing medium. Plants were grown in the rice growth room under the condition of 16 h light/8 h dark (28M-BM-0C) photoperiod with 70 % humidity. After 5 days of normal growth, some of the seedlings were transferred to nutrient solution lacking CaCl2 (-Ca2+). After 5 and 14 days, calcium (0.798 mM CaCl2) was resupplied to the plants grown in -Ca2+ medium for 6 h.
2014-01-17 | E-GEOD-50917 | biostudies-arrayexpress
Project description:Pattern recognition receptors (PRRs) at the plasma membrane promote plant immunity through the detection of conserved microbe-associated molecular patterns (MAMPs). In plants, the PRR for bacterial flagellin (flg22) is encoded by the receptor kinase FLS2. One of the earliest MAMP responses is the rapid and transient increase of cytosolic calcium (Ca2+) ions, which is required for many of the well-described downstream responses, e.g. generation of reactive oxygen species (ROS) and the transcriptional activation of defence-associated genes. Despite its relevance, the molecular components regulating the Ca2+ burst remain largely unknown. Here, we show that the plasma membrane P2B-type Ca2+ ATPase ACA8 forms a dynamic complex with the PRR FLS2. ACA8 and its closest homologue ACA10 are required for immunity against virulent bacteria. Mutant aca8 aca10 plants are reduced in the flg22-induced Ca2+ burst, show reduced ROS production and exhibit altered transcriptional reprogramming. In particular, flg22-induced gene expression is elevated downstream of signalling mitogen-activated protein (MAP) kinases, but reduced downstream of the calcium-dependent protein (CDP) kinase cascade. These results demonstrate that the fine regulation of Ca2+ fluxes in the cytosol is critical for the coordination of the downstream MAMP responses and provide for the first time a link between the FLS2 receptor complex and signalling kinases via the secondary messenger Ca2+. ACA8 also interacted with the BRI1 and CLV1 receptor kinases, which correlated with the developmental phenotypes of aca8 aca10 mutants suggesting a broader role for Ca2+ ATPases in receptor-mediated signalling. We used Affymetrix Arabidopsis Tiling 1.0R Array to compare global transcript levels in 7 days-old sterile grown seedlings. Steady-state mRNA levels in total RNA samples of 7 days old sterile seedlings
2012-04-24 | E-GEOD-31517 | biostudies-arrayexpress
Project description:The response of osteoprogenitors to calcium (Ca2+) is of primary interest for both normal bone homeostasis and the clinical field of bone regeneration. The latter makes use of calcium phosphate-based bone void fillers to heal bone defects, but it is currently not known how Ca2+ released from these ceramic materials influences cells in situ. Here, we have created an in vitro environment with high extracellular Ca2+ concentration and investigated the response of human bone marrow-derived mesenchymal stromal cells (hMSCs) to it. Ca2+ enhanced proliferation and morphological changes in hMSCs. Moreover, the expression of osteogenic genes is highly increased. A 3-fold up-regulation of BMP-2 is observed after only 6 h and pharmaceutical interference with a number of proteins involved in Ca2+ sensing showed that not the calcium sensing receptor, but rather type L voltage-gated calcium channels are involved in mediating the signaling pathway between extracellular Ca2+ and BMP-2 expression. MEK1/2 activity is essential for the effect of Ca2+ and using microarray analysis, we have identified c-Fos as an early Ca2+ response gene. We have demonstrated that hMSC osteogenesis can be induced via extracellular Ca2+, a simple and economic way of priming hMSCs for bone tissue engineering applications. For more information check: https://cbit.maastrichtuniversity.nl/
2018-10-06 | E-MTAB-7222 | biostudies-arrayexpress
Project description:We have examined the nuclear (nuc) and cytoplasmic (cyt) polyA+ transcriptomes of undifferentiated mouse embryonic stem cells (un) and cells differentiated to neural precursors (d5) using strand-specific RNA-Seq. The 46C mouse embryonic stem cell line was used for this study.
2012-08-01 | GSE38990 | GEO
Project description:Schizophrenia is a chronic disease characterized by the impairment of mental functions with a marked social dysfunction. A proteomic approach using iTRAQ labeling and selected reaction monitoring, applied to the characterization of mitochondria (MIT), crude nuclear fraction (NUC) and cytoplasm (CYT), can allow the observation of dynamic changes in cell compartments providing valuable insights concerning schizophrenia physiopathology. Mass spectrometry analyses of the orbitofrontal cortex from 12 schizophrenia patients and 8 healthy controls identified 655 protein groups in MIT fraction, 1500 in NUC and 1591 in CYT. We found 166 groups of proteins dysregulated among all enriched cellular fractions. Through the quantitative proteomic analysis, we detect as the main biological pathways those related to calcium and glutamate imbalance, cell signaling disruption of CREB activation, axon guidance and proteins involved in the activation of NF-kB signaling along with the increase of complement proteins C3. Based on our data analysis, we suggest the activation of NF-kB as a possible pathway that links the deregulation of glutamate, calcium, apoptosis and the activation of the immune system in schizophrenia patients
2019-10-07 | PXD015356 | Pride
Project description:Pattern recognition receptors (PRRs) at the plasma membrane promote plant immunity through the detection of conserved microbe-associated molecular patterns (MAMPs). In plants, the PRR for bacterial flagellin (flg22) is encoded by the receptor kinase FLS2. One of the earliest MAMP responses is the rapid and transient increase of cytosolic calcium (Ca2+) ions, which is required for many of the well-described downstream responses, e.g. generation of reactive oxygen species (ROS) and the transcriptional activation of defence-associated genes. Despite its relevance, the molecular components regulating the Ca2+ burst remain largely unknown. Here, we show that the plasma membrane P2B-type Ca2+ ATPase ACA8 forms a dynamic complex with the PRR FLS2. ACA8 and its closest homologue ACA10 are required for immunity against virulent bacteria. Mutant aca8 aca10 plants are reduced in the flg22-induced Ca2+ burst, show reduced ROS production and exhibit altered transcriptional reprogramming. In particular, flg22-induced gene expression is elevated downstream of signalling mitogen-activated protein (MAP) kinases, but reduced downstream of the calcium-dependent protein (CDP) kinase cascade. These results demonstrate that the fine regulation of Ca2+ fluxes in the cytosol is critical for the coordination of the downstream MAMP responses and provide for the first time a link between the FLS2 receptor complex and signalling kinases via the secondary messenger Ca2+. ACA8 also interacted with the BRI1 and CLV1 receptor kinases, which correlated with the developmental phenotypes of aca8 aca10 mutants suggesting a broader role for Ca2+ ATPases in receptor-mediated signalling. We used Affymetrix Arabidopsis Tiling 1.0R Array to compare global transcript levels in 7 days-old sterile grown seedlings.
2012-04-25 | GSE31517 | GEO
Project description:High-throughput small molecule screening revealed that high concentrations of cytoplasmic calcium ([Ca2+]c) were linked to dormancy of HSCs.To clarify molecular difference between [Ca2+]chigh and [Ca2+]clow cells, we performed RNA-Seq analysis using [Ca2+]chigh and [Ca2+]clow cells.
2019-12-20 | GSE138884 | GEO
Project description:PAO1 was cultured planktonically to stationary phase with 10 mM calcium and no added calcium. The transcriptional response to calcium addition was determined. Pseudomonas aeruginosa is an opportunistic human pathogen that causes severe, life threatening infections in patients with cystic fibrosis (CF), endocarditis, wounds, or with artificial implants. During CF pulmonary infections, P. aeruginosa often encounters environments where the levels of calcium (Ca2+) are elevated. Previously, we showed that P. aeruginosa responds to externally added Ca2+ through enhanced biofilm formation, increased production of several secreted virulence factors, and by developing a transient increase in the intracellular Ca2+ followed by its removal to the basal sub-micromolar level. However, the molecular mechanisms responsible for regulating Ca2+-induced virulence factor production and Ca2+ homeostasis are not known. Here, we characterized the genome-wide transcriptional response of P. aeruginosa strains PAO1 and FRD1 to elevated [Ca2+] in both planktonic cultures and in biofilms. Among the genes induced by CaCl2 in PAO1 was an operon containing the two-component regulator PA2656-PA2657 (here called carS and carR), while the closely related two-component regulators, phoPQ and pmrAB were repressed by CaCl2 addition. To identify the regulatory targets of CarSR, we constructed a deletion mutant of carR, and performed transcriptome analysis of the mutant strain at low and high [Ca2+]. Among the genes regulated by CarSR in response to CaCl2 are the predicted periplasmic OB-fold protein, PA0320 and the inner membrane-anchored five-bladed -propeller protein, PA0327. Mutations in both PA0320 and PA0327 affected Ca2+ homeostasis, reducing the ability of P. aeruginosa to export excess Ca2+. In addition, a mutation in PA0327 had a pleotrophic effect in a Ca2+-dependent manner, altering swarming motility, pyocyanin production, and tobramycin sensitivity. Overall, the results indicate that the two-component system CarSR is responsible for sensing high levels of external Ca2+, and responding through its regulatory targets that modulate Ca2+ homeostasis, surface-associated motility, and production of the virulence factor, pyocyanin.
2015-12-02 | GSE74444 | GEO