Gene expression analysis of rice seedling under potassium deprivation
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Oryza sativa Indica Group
PROVIDER: GSE44250 | GEO | 2013/09/14
SECONDARY ACCESSION(S): PRJNA189246
REPOSITORIES: GEO
Similar Datasets
Project description:Potassium is one of the essential macronutrients required for plant growth and development. It plays a major role in different physiological processes like cell elongation, stomatal movement, turgor regulation, osmotic adjustment, and signal transduction by acting as a major osmolyte and component of the ionic environment in the cytosol and subcellular organelles. We used whole genome microarrays to determine the transcriptomic profile of rice seedlings exposed to short-term K+ deficiency followed by K+ resupply. Potassium treated seedlings were used for RNA extraction and hybridization on Affymetrix rice Genechip by microarrays. Three biological replicates of each sample were used for microarray analysis. We wanted to know the altered expression patterns of potassium-responsive genes majorly involved in metabolic processes, stress responses, signaling pathways, transcriptional regulation, and transport of multiple molecules including K+. 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 (28°C) photoperiod with 70 % humidity. After 5 days of normal growth, one half of the rice seedlings were transferred to nutrient media with normal concentration of potassium (KP, 0.409 mM K2SO4) and other one half to medium without potassium (KM, 0 mM). After 5 days, potassium (0.409 mM K2SO4) was resupplied to the plants grown in KM medium for 6 h.
2013-09-14 | E-GEOD-44250 | biostudies-arrayexpress
Project description:Bacteria respond to osmotic stress by a substantial increase in the intracellular osmolality, adjusting their cell turgor for altered growth conditions. Using E. coli as a model organism we demonstrate here that bacterial responses to hyperosmotic stress specifically depend on the nature of osmoticum used. We show that increasing acute hyperosmotic NaCl stress above ~1.0 Os kg-1 causes a dose-dependent K+ leak from the cell, resulting in a substantial decrease in cytosolic K+ content and a concurrent accumulation of Na+ in the cell. At the same time, isotonic sucrose or mannitol treatment (non-ionic osmotica) results in a gradual increase of the net K+ uptake. Ion flux data is consistent with growth experiments showing that bacterial growth is impaired by NaCl at the concentration resulting in a switch from net K+ uptake to efflux. Microarray experiments reveal that about 40% of up-regulated genes shared no similarity in their responses to NaCl and sucrose treatment, further suggesting specificity of osmotic adjustment in E. coli to ionic- and non-ionic osmotica The observed differences are explained by the specificity of the stress-induced changes in the membrane potential of bacterial cells highlighting the importance of voltage-gated K+ transporters for bacterial adaptation to hyperosmotic stress.
2008-07-25 | GSE12190 | GEO
Project description:Bacteria respond to osmotic stress by a substantial increase in the intracellular osmolality, adjusting their cell turgor for altered growth conditions. Using E. coli as a model organism we demonstrate here that bacterial responses to hyperosmotic stress specifically depend on the nature of osmoticum used. We show that increasing acute hyperosmotic NaCl stress above ~1.0 Os kg-1 causes a dose-dependent K+ leak from the cell, resulting in a substantial decrease in cytosolic K+ content and a concurrent accumulation of Na+ in the cell. At the same time, isotonic sucrose or mannitol treatment (non-ionic osmotica) results in a gradual increase of the net K+ uptake. Ion flux data is consistent with growth experiments showing that bacterial growth is impaired by NaCl at the concentration resulting in a switch from net K+ uptake to efflux. Microarray experiments reveal that about 40% of up-regulated genes shared no similarity in their responses to NaCl and sucrose treatment, further suggesting specificity of osmotic adjustment in E. coli to ionic- and non-ionic osmotica The observed differences are explained by the specificity of the stress-induced changes in the membrane potential of bacterial cells highlighting the importance of voltage-gated K+ transporters for bacterial adaptation to hyperosmotic stress. Experiment Overall Design: Two biological replicates per treatment with microarray analysis using the Affymetrix GeneChip E. coli Genome array. Treatments used included: Experiment Overall Design: Control - E. coli Frag1, grown to early stationary growth phase in a mineral salts medium with 0.1% glucose at 25 C Experiment Overall Design: Sucrose hyperosmotic treatment - 1.25 M sucrose added to control culture Experiment Overall Design: for 10 min. Experiment Overall Design: NaCl hyperosmotic treatment - 1.37 M NaCl added to control culture Experiment Overall Design: For microarray data comparisons the sucrose and NaCl hyperosmotic treatment data was compared to the no treatment control data separately. The sucrose to control and NaCL to control comparison data tables are linked below.
2008-10-21 | E-GEOD-12190 | biostudies-arrayexpress
Project description:The purpose of this study was to identify genes that are differentially expressed under conditions of potassium limitation, to elucidate how Mycobacterium tuberculosis (Mtb) senses and responds to ionic changes, and the role of these responses in host colonization.
2019-01-26 | GSE120725 | GEO
Project description:Ion transport and osmotic adjustment in E. coli in response to ionic and non-ionic osmotica
| PRJNA113407 | ENA
Project description:In a context of climate change, deciphering signaling pathways leading to plant adaptation to drought, water availability, and salt tolerance is a crucial question. A common crossing point of these plant stresses is their impact on plant water potential, a composite physico-chemical variable reflecting the availability of water for the plant biological and biochemical processes such as growth or stomatal aperture. The water potential of plant cells is mainly driven by their turgor pressure and osmotic potential. Here we investigated the effect of a variety of osmotic treatments in the root of Arabidopsis plants grown in hydroponics. Measurement of the cortical cells turgor pressure with a cell pressure probe allowed to control the intensity of the treatments and, in particular, preserve the cortex from plasmolysis. Transcriptome analyses at early time point (15min) showed specific and quantitative transcriptomic responses for both osmotic and turgor pressures in the root. Our results highlight how water-related biophysical parameters can shape the transcriptome and provide putative candidates to explore further the early perception of water stress in plants.
2023-09-11 | GSE223207 | GEO
Project description:In this study, we showed for the first time that c-di-AMP is produced by C. difficile and controls the uptake of potassium, making it essential for growth. We found that c-di-AMP is involved in biofilm formation, cell wall homeostasis, osmotolerance as well as detergent and bile salt resistance in C. difficile. We identified BusR as a new regulator that binds c-di-AMP and represses the expression of the compatible solute transporter BusAA-AB. Interestingly, a busR mutant is highly resistant to a hyperosmotic or bile salt stress compared to the parental strain while a busAA mutant is more susceptible. A short exposure of C. difficile cells to bile salts resulted in a decrease of the c-di-AMP concentrations reinforcing the hypothesis that changes in membrane characteristics due to variations of the cellular turgor or membrane damages constitute a signal for the adjustment of the intracellular c-di-AMP concentration. In a colonization mouse model, a strain producing elevated c-di-AMP concentrations failed to persist in the gut in contrast to the parental strain. Thus, c-di-AMP is a signaling molecule with pleiotropic effects that controls osmolyte uptake to confer osmotolerance and bile salt resistance in C. difficile and that is important for colonization of the host.
2021-12-27 | GSE192529 | GEO
Project description:High NH4+ load is known to competitively inhibit bacterial methane oxidation. This is due to a competition between CH4 and NH4+/NH3 for the active site of particulate methane monooxygenase (pMMO), which converts CH4 to CH3OH. Here, we combined growth experiments with global proteomics to elucidate the capability of the methanotroph Methylocystis sp. strain SC2 in acclimatizing to increased NH4+ levels. Our experimental approach also involved amino acid profiling and measurement of NOx compounds. Relative to 1 mM NH4+, high (50 mM and 75 mM) NH4+ load under CH4 replete conditions significantly increased lag phase duration required for proteome adjustment. The proteomic and metabolic responses to increasing ionic and osmotic stress involved significant upregulation of stress-responsive proteins, K+ “salt in” strategy, synthesis of compatible solutes (glutamate and proline), and induction of the glutathione metabolism pathway. A significant increase in the apparent Km value for CH4 oxidation during the growth phase was indicative of increased pMMO-based oxidation of NH4+/NH3 to toxic hydroxylamine. The detoxifying activity of hydroxlyamine oxidoreductase (HAO) led to a significant accumulation of NO2- and, upon decreasing O2 tension, N2O. Putative free intermediate of HAO activity was NO, with NO reductase and hybrid cluster proteins (Hcps) being the candidate enzymes for the reduction of NO to N2O. In summary, strain SC2 has the capacity to precisely rebalance enzymes and osmolyte composition, but the need to simultaneously combat both ionic-osmotic stress and the toxic effects of hydroxylamine may be the reason why its acclimatization capacity is limited to 75 mM NH4+.
2022-09-19 | PXD032347 | Pride
Project description:Rice is one of the most important food crops in the world, and its growth, development, yield, and grain quality are susceptible to a deficiency of the macronutrient potassium (K+). The molecular mechanism for K+ deficiency tolerance remains poorly understood. In this study, K+ deficient conditions were employed to investigate the resulting changes in the transcriptome of rice seedling roots. Using ribonucleic acid sequencing (RNA-Seq) and analysis, a total of 805 differentially expressed genes were obtained, of which 536 genes were upregulated and 269 were downregulated. Gene functional classification showed that the expression of genes involved in nutrient transport, protein kinases, transcription processes, and plant hormones were particularly altered in the roots. Although these changes were significant, the expression of most genes remained constant even in K+-deficient conditions. Interestingly, when our RNA-Seq results were compared to public microarray data, we found that most of the genes that were differentially expressed in low K+ conditions also exhibited changes in expression in other environmental stress conditions.
| S-EPMC5514036 | biostudies-literature
Project description:The effects of high potassium and normal potassium treatments on protein expression in roots of flue-cured tobacco plant HKDN-5 at the seedling stage were analyzed by an unlabeled protein quantification technique. The results showed that 555 proteins were differentially expressed (245 proteins were down-regulated and 310 proteins were up-regulated) in high potassium treatment compared with normal potassium treatment. Differentially expressed proteins were involved in 96 metabolic pathways (42 metabolic pathways, 21 synthetic pathways as well as catabolic pathways, including fatty acid metabolism, phenylpropane biosynthesis, ketone body synthesis and degradation, and butyric acid metabolism. Root processing of high potassium concentrations leads to increases in the synthesis of peroxidase, superoxide dismutase and acyl-coenzyme-A synthetase. Additional proteomic differences observed in tobacco roots grown in high potassium include proteins involved with genetic information processing as well as environmental sensing. Examples include RNA helicase, ABC transporters and large subunit GTPases. These up-regulated differentially expressed proteins function mainly in protein translation, ribosome structure and protein synthesis. This indicates that under high potassium treatment, root protein synthetic processes are accelerated and substance metabolism pathways are enhanced; thus, providing the material and energetic basis for root growth.
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