Transcription profiling of Arabidopsis wild type and PII deficient plants grown on different nitrogen sources
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Axon GenePix 4000A scanning hardware
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Olivier Pichon
PROVIDER: E-MEXP-446 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:PII signal transduction proteins are widely spread among all domains of life where they regulate a multitude of carbon and nitrogen metabolism related processes. Non-diazotrophic cyanobacteria can utilize a high variety of organic and inorganic nitrogen sources. In recent years, several physiological studies indicated an involvement of the cyanobacterial PII protein in regulation of ammonium, nitrate/nitrite and cyanate uptake. However, direct interaction of PII has not been demonstrated so far. In this study, we used biochemical, molecular genetic and physiological approaches to demonstrate that PII regulates all relevant nitrogen uptake systems in Synechocystis sp. strain PCC 6803: PII controls ammonium uptake by interacting with the Amt1 ammonium permease, probably similar to the known regulation of E. coli ammonium permease AmtB by the PII homologue GlnK. We could further clarify that PII mediates the ammonium- and dark-induced inhibition of nitrate uptake by interacting with the NrtC and NrtD subunits of the nitrate/nitrite transporter NrtABCD. We further identified the ABC-type urea transporter UrtABCDE as novel PII target. PII interacts with the UrtE subunit without involving the standard interaction surface of PII interactions. The deregulation of urea uptake in a PII deletion mutant causes ammonium excretion when urea is provided as nitrogen source. Furthermore, the urea hydrolyzing urease enzyme complex appears to be coupled to urea uptake. Overall, this study underlines the great importance of the PII signal transduction protein in the regulation of nitrogen utilization in cyanobacteria.
2019-07-10 | PXD013411 | Pride
Project description:We propose the hypothesis that loss of estrogen receptor function which leads to endocrine resistance in breast cancer, also results in de-differentiation from an epithelial to a mesenchymal phenotype that is responsible for increased aggressiveness and metastatic propensity. siRNA mediated silencing of the estrogen receptor in MCF7 breast cancer cells resulted in estrogen/tamoxifen resistant cells (pII) with altered morphology, increased motility with rearrangement and switch from an actin to a vimentin based cytoskeleton, and ability to invade simulated components of the extracellular matrix. Phenotypic profiling using an Affymetrix Human Genome U133 plus 2.0 GeneChip indicated fold changes ⥠3 in approximately 2500 identifiable unique sequences, with about 1270 of these being up-regulated in pII cells. Changes were associated with genes whose products are involved in cell motility, loss of cellular adhesion and interaction with the extracellular matrix. Selective analysis of the data also showed a shift from luminal to basal cell markers and increased expression of a wide spectrum of genes normally associated with mesenchymal characteristics, with consequent loss of epithelial specific markers. Over-expression of several peptide growth factors and their receptors are indicative of an increased contribution to the higher proliferative rates of pII cells as well as aiding their potential for metastatic activity. Signalling molecules that have been identified as key transcriptional drivers of epithelial to mesenchymal transition were also found to be elevated in pII cells. We suggest that these data support our hypothesis that induced loss of estrogen receptor in previously antiestrogen sensitive cells is a trigger for the concomitant loss of endocrine dependence and onset of a series of possibly parallel events that changes the cell from an epithelial to a mesenchymal type. Inhibition of this transition through targeting of specific mediators may be a useful supplementary strategy to circumvent the effects of loss of endocrine sensitivity. We used microarrays to detail the global programme of gene expression underlying Epithelial to mesenchymal transition and identified distinct classes of regulated genes during this process. MCF7 cell line was selected before and after (PII) silencing of Estrogen receptor for RNA extraction and hybridization on Affymetrix expression microarrays.
2011-05-01 | E-GEOD-27473 | biostudies-arrayexpress
Project description:Nitrogen limitation imposes a major transition in the life-style of non-diazotrophic cyanobacteria, which is regulated via a complex interplay of regulatory factors, involving, the nitrogen-specific transcription factor NtcA and the pervasive signal processor PII. Immediately upon nitrogen-limitation, newly fixed carbon is re-directed towards glycogen synthesis. How operation of the metabolic switch for distributing fixed carbon to either glycogen or cellular building blocks was poorly understood. Here we identify from Synechocystis sp. PCC 6803 a novel PII interactor, PirC, (Sll0944) that controls 3-phosphoglycerate mutase (PGAM), the enzyme that deviates newly fixed CO2 towards lower glycolysis. PirC acts as competitive inhibitor of PGAM and this interaction is tuned by PII/2-oxoglutarate. High oxoglutarate release PirC from PII-complex to inhibit PGAM. Accordingly, PirC deficient mutant, as compared to the wild-type, shows strongly reduced glycogen levels upon nitrogen deprivation whereas polyhydroxybutyrate granules are over-accumulated. Metabolome analysis revealed an imbalance in 3-phosphoglycerate to pyruvate levels in the PirC mutant, conforming that PirC controls the carbon flux in cyanobacteria via mutually exclusive interaction with either PII or PGAM.
2020-12-17 | PXD021415 | Pride
Project description:Lipid remodeling is crucial for plant responses to abiotic stress and metabolic disturbances. A key aspect of this process involves the modification of phosphatidylcholine (PC) acyl chains by lysophosphatidylcholine: acyl-CoA acyltransferases (LPCATs). To understand their role in lipid homeostasis, we studied the trigalactosyldiacylglycerol1 (tgd1) mutant, which exhibits significant increases in fatty acid synthesis and flux through PC due to disrupted inter-organelle lipid trafficking. We discovered that the elevated fatty acid synthesis in tgd1 is due to the posttranslational activation of plastidic acetyl-coenzyme A carboxylase (ACCase). Global transcriptomic profiling revealed 62 significantly upregulated genes in tgd1, with 27 (44%) involved in RNA and DNA modifications, suggesting a role for posttranscriptional mechanisms in adapting to lipid trafficking disruptions. Additionally, transcript levels of LPCATs and several genes regulating ACCase were moderately increased in tgd1. Genetic analysis showed that knocking out LPCAT1 and LPCAT2 was lethal in the tgd1 background. Furthermore, plants homozygous for lpcat2 and heterozygous for lpcat1 in the tgd1 background displayed reduced levels of PC and TAG, along with altered fatty acid compositions. Our findings provide mechanistic insights into fatty acid synthesis regulation and highlight the critical role of LPCATs in maintaining cellular lipid homeostasis when fatty acid production exceeds the cellular demand for membrane lipid synthesis.
2024-09-16 | PXD054661 | Pride
Project description:PII proteins are pivotal regulators of nitrogen metabolism in most prokaryotes, controlling the activities of many targets, including nitrogen assimilation enzymes, two component regulatory systems and ammonium transport proteins. Escherichia coli contains two PII-like proteins, PII (product of glnB) and GlnK, both of which are uridylylated under nitrogen limitation at a conserved Tyrosine-51 residue by GlnD (a uridylyl transferase). PII-uridylylation in E. coli controls glutamine synthetase (GS) adenylylation by GlnE and mediates the NtrB/C transcriptomic response. Mycobacteria contain only one PII protein (GlnK) which in environmental Actinomycetales is adenylylated by GlnD under nitrogen limitation. However in mycobacteria, neither the type of GlnK (PII) covalent modification nor its precise role under nitrogen limitation is known. In this study, we used LC-Tandem MS to analyse the modification state of mycobacterial GlnK (PII), and demonstrate that during nitrogen limitation GlnK from both non-pathogenic Mycobacterium smegmatis and pathogenic Mycobacterium tuberculosis is adenylylated at the Tyrosine-51 residue; we also show that GlnD is the adenylyl transferase enzyme responsible. Further analysis shows that in contrast to E. coli, GlnK (PII) adenylylation in M. tuberculosis does not regulate GS adenylylation, nor does it mediate the transcriptomic response to nitrogen limitation. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-135]
2013-05-10 | E-BUGS-135 | biostudies-arrayexpress
Project description:We used all five current human African trypanosomiasis drugs for genome-scale RNA interference (RNAi) target sequencing (RIT-seq) screens in Trypanosoma brucei, revealing the transporters, organelles, enzymes and metabolic pathways that function to facilitate anti-trypanosomal drug action. RIT-seq profiling links more than fifty additional genes to drug action. This data has been described in the following article [doi:10.1038/nature10771] and its further analysis can be freely submitted for publication. For information on the proper use of data shared by the Wellcome Trust Sanger Institute (including information on acknowledgement), please see http://www.sanger.ac.uk/datasharing/. Protocol - Assembly of the bloodstream-form T. brucei RNAi library and the RNAi target sequencing (RIT-seq) approach were reported previously (Alsford, S. et al. High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res 21, 915-924, 264 doi:gr.115089.110 [pii] 265 10.1101/gr.115089.110 (2011). Briefly, a tetracycline-inducible RNAi plasmid library, containing randomly sheared genomic fragments (mean ~600 bp) under the control of head-to-head T7 promoters, was targeted to a single genomic locus that had been validated for robust expression. For this study, the library was grown under inducing conditions with drug selection and genomic DNA was isolated from surviving populations. For chemical RIT-seq profiling, adapter-ligated sequencing libraries were prepared from each genomic DNA sample and used to amplify DNA fragments containing RNAi cassette-insert junctions in semi-specific PCR reactions; one primer was specific for the RNAi vector and the other for the Illumina adapter. Size-selected DNA was sequenced with 76 cycle paired-end runs on an Illumina GAII. Illumina sequencing reads containing a nine-base RNAi vector junction sequence were then mapped to the T. brucei reference genome. Where loss of function increases drug tolerance, RNAi-target sequence representation is increased relative to the otherwise susceptible population, revealing hot spots.
2011-11-29 | E-ERAD-30 | biostudies-arrayexpress
Project description:Acquisition and utilization of nitrogen is governed by the Nitrogen Stress Response regulatory cascade. GlnD is the primary nitrogen sensor in this system, and modifies the PII proteins to effect changes in the expression of target genes. We used microarrays to evaluate changes in gene expression due to nitrogen availability, mutation of the glnD gene, and deletion of both PII proteins.
2013-01-18 | GSE43570 | GEO
Project description:The PII family comprises a group of widely distributed signal transduction proteins ubiquitous present in prokaryotes and in the chloroplast of plants. The PII proteins sense the levels of key metabolites ATP, ADP and 2-oxoglutarate which affect the PII structure and the ability of PII to interact with a range of target proteins. Here we performed multiple PII ligand fishing assays to identify proteins that are likely to be part of the PII protein interaction network in plant-growth promoting nitrogen-fixing bacterium Azospirillum brasilense. Among the PII targets identified were enzymes related to nitrogen and fatty acid metabolism, signaling, co-enzyme synthesis, RNA catabolism and transcription. Direct binary PII-target complex was confirmed for xx protein complex using pull-down assays with recombinant proteins. Untargeted metabolome showed that PII is required to proper maintenance of Coenzyme A, panthotenate, PRPP and SAICAR levels. Two enzymes involved in c-di-GMP metabolism were among the identified PII targets. A PII minus strain showed reduced c-di-GMP levels and swimming behavior. These data support that PII acts as a major metabolic hub controlling key metabolic enzymes and c-di-GMP homeostasis accordingly to the prevailing nutritional status.
2020-10-23 | PXD018530 | Pride
Project description:Acquisition and utilization of nitrogen is governed by the Nitrogen Stress Response regulatory cascade. GlnD is the primary nitrogen sensor in this system, and modifies the PII proteins to effect changes in the expression of target genes. We used microarrays to evaluate changes in gene expression due to nitrogen availability, mutation of the glnD gene, and deletion of both PII proteins. Sinorhizobium meliloti cultures were grown at 30C to mid-log phase (0.5–0.6 OD600) for RNA extraction and hybridization on Affymetrix microarrays. Wild-type 1021, a strain containing a mutation in glnD, and a strain with both PII proteins deleted were grown in media containing either 0.05% ammonium chloride or 0.02% sodium glutamate as the nitrogen source.
2013-01-18 | E-GEOD-43570 | biostudies-arrayexpress
Project description:Cortical 1.4C18 and medullary 3.10 TEC lines (mTEC) were cultured in 10% fetal bovine serum-supplemented RPMI 1640 medium at 37 ?C in a 5% CO2 atmosphere. Confluent cultures of 3.10 mTEC cell line were cultured during 72 h in RPMI medium as above mentioned and total RNA was extracted using the mirVana kitM-. (Ambion, Austin, TX, USA).
2011-08-31 | E-MEXP-3214 | biostudies-arrayexpress