Transcriptome changes in response to lead exposure
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Patrick Doumas
PROVIDER: E-GEOD-65334 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Experiments were achieved on Arabidopsis thaliana. Transcriptional profiling of roots and shoots from plants treated with lead were compared to plants treated in similar conditions without lead. Four weeks old A. thaliana seedlings were treated in hydroponic cultures with Pb during 3 days, by adding or not 40 M-BM-5M Pb(NO3)2. Two-condition experiment, lead treated vs. untreated. Biological replicates: 3
2015-01-28 | E-GEOD-65333 | biostudies-arrayexpress
Project description:Experiments were achieved on Hirschfeldia incana, a Brassicaceae collected from metalliferous mine spoils as a Pb accumulator plant. Transcriptional profiling of roots and shoots from plants treated with lead were compared to plants treated in similar conditions without lead. Four weeks old H. incana seedlings were treated in hydroponic cultures with Pb during 3 days, by adding or not 100 M-BM-5M Pb(NO3)2. Two-condition experiment, lead treated vs. untreated. Biological replicates: 3
2015-01-28 | E-GEOD-65332 | biostudies-arrayexpress
Project description:Two Near Isogenic soybean (Glycine max) lines were grown in hydroponic conditions with either 50uM ferric nitrate or 100uM ferric nitrate. After 10 days, half the plants were harvested (total root tissue). At 12 days after planting, iron was added to plants grown in low iron conditions bringing them up to sufficient iron growth conditions. Root tissue was harvested for the remaining plants at 14 days after planting. Gene expression analysis from root tissue of two Near Isogenic Lines (NILs), Clark (PI548553) and IsoClark (PI547430), grown in iron stress or iron stress recovered conditions. A total of 24 samples from four growth conditions, three biological replicates per treatment
2010-09-06 | E-GEOD-22227 | biostudies-arrayexpress
Project description:Hydrogen cyanide (HCN) is coproduced with ethylene in plant cells and primarily enzymatically detoxified by the mitochondrial ß-cyanoalanine synthase (CAS-C1). Permanent or transient depletion of CAS-C1 activity in Arabidopsis results in physiological alterations in the plant that suggest that the function of HCN is a gasotransmitter molecule. Label-free quantitative proteomic analysis of enriched mitochondrial samples isolated from the wild type and cas-c1 mutant revealed significant changes in protein content, identifying 451 proteins that are absent or less abundant in cas-c1 and 353 proteins that are only present or more abundant in the mutant background. Gene ontology classification of these proteins highlights proteomic changes that explains the root hairless phenotype and the altered immune response observed in the cas-c1 mutant. The mechanism of action of cyanide as a signaling molecule has been addressed using two proteomic approaches focused on identifying the S-cyanylation of cysteine as a posttranslational modification of proteins. Both the 2-imino-thiazolidine chemical method and the direct untargeted analysis of proteins using LC-MS/MS identified a set of 163 proteins susceptible to S-cyanylation that included sedoheptulose 1, 7-bisphosphatase (SBPase), the peptidyl-prolyl cis-trans isomerase (CYP20-3) and enolase 2 (ENO2). In vitro analysis of these proteins identified that this modification in the SBPase Cys74, CYP20-3 Cys259 and ENO2 Cys346 residues affected the enzymatic activity of the enzymes. GO classification and protein-protein interaction cluster analysis revealed the function of S-cyanylation in the regulation of primary metabolic pathways, such as glycolysis, and the Calvin and S-adenosylmethionine cycles.
2019-01-09 | PXD009929 | Pride
Project description:Living organisms have to cope with multiple and combined fluctuations in their environment. According to their sessile mode of life, plants are even more subjected to such fluctuations impacting their physiology and development. In particular, nutrient availability is known to tune plant development through modulating hormonal signaling, and conversely, hormonal signals are key to control nutrient related signaling pathways (Krouk et al., 2011a). However, very few is known about molecular mechanisms leading to plant adaptation to such combined signals. Here we deployed an unprecedented combinatorial treatment matrix to reveal plant adaptation in response to nitrate (NO3-), ammonium (NH4+), auxin (IAA), cytokinins (CK) and abscisic acid (ABA) and their exhaustive binary combinations. In order to study the effect of 5 signaling molecules we developed a matrix of treatment including NO3- (1mM or 0.5mM), NH4+ (1mM, or 0.5mM), indol-acetic-acid (IAA: 500 nM), Kinetin (CK: 500 nM), abscisic acid (ABA: 1µM). When present, the overall nitrogen treatment has been maintained to 1mM. As such, when NO3- and NH4+ are present in the same media their concentration was divided by 2. Proper mock controls include KCl, and DMSO. Plants are grown on NH4+-succinate for 12 to 14 days (first visible true leaves). Transferred 24 hours on a refreshed N-free media (reset the background that may be exhausted in several elements), and then transferred toward fresh media containing combinations of signals. Plant roots are harvested after 4 hours of treatment for gene expression analysis. Please note that the treatment details for each sample were provided in the sample 'characteristics' column in 'NO-NH-IA-CK-AB' format followed by the Presence/Absence code used for each hormone/nutrient.
2016-10-26 | E-GEOD-71737 | biostudies-arrayexpress
Project description:Hydrogen cyanide (HCN) is co-produced with ethylene in plant cell and enzymatically detoxified mainly by the mitochondrial ß-cyanoalanine synthase (CAS-C1). Permanent or transient depletion of CAS-C1 activity in Arabidopsis results in physiological alteration in the plant that point to the function of HCN as a gasotransmitter molecule. Label-free quantitative proteomic analysis of enriched mitochondrial samples isolated from wild type and cas-c1 mutant reveled significant changes in protein content, identifying 451 proteins that are absent or less abundant in cas-c1 and 353 proteins only present or more abundant in the mutant background. Gene onthology classification of these proteins highlights proteomic changes that explains the root hairless phenotype and the altered inmune response observed in cas-c1 mutant. The mechanism of action of cyanide as signaling molecule has been addressed by two proteomic approaches focused on identifying S-cyanylation of cysteine as a posttranslational modification of proteins. Both the 2-imino-thiazolidine chemical method and direct untargeted analysis of proteins by LC-MS/MS identified a set of 163 proteins susceptibles to be S-cyanylated that include sedoheptulose 1, 7 biphosphatase (SBPase), the peptidyl-prolyl cis-trans isomerase (CYP20-3) and enolase 2 (ENO2). In vitro analysis of these proteins identified this modification in SBPase Cys74, CYP20-3 Cys259 and ENO2 Cys346 residues that affected the enzymatic activity of the enzymes. GO classification and protein-protein interaction cluster analysis revealed the function of S-cyanylation in the regulation of primary metabolic pathways as glycolysis, and the Calvin and S-adenosylmethionine cicles.
2019-01-09 | PXD009812 | Pride
Project description:Photosynthesis is affected by water deficiency (WD) stress, and nitric oxide (NO) is a free radical that participates in the photosynthesis process. Previous studies have suggested that NO regulates the excitation energy distribution of photosynthesis under WD stress. Here, quantitative phosphoproteomic profiling was conducted using isobaric tags for relative and absolute quantitation. Differentially phosphorylated protein species (DEPs) were identified in leaves of NO or polyethylene glycol (PEG)-treated wheat seedlings (D) and in control seedlings, 2,257 unique phosphorylated peptides and 2,416 phosphorylation sites were identified from 1,396 unique phosphoproteins. Of these, 96 DEPs displayed significant changes (≥ 1.50-fold, p < 0.01). These DEPs are involved in photosynthesis and signal transduction, etc. Furthermore, phosphorylation of several DEPs were up-regulated by both D and NO treatments, but down-regulated only in NO treatment. These differences affected the chlorophyll A-B binding protein, chloroplast post-illumination chlorophyll fluorescence increase protein, and SNT7, implying that NO indirectly regulated the absorption and transport of light energy in photosynthesis in response to WD stress. The significant difference of chlorophyll (Chl) content, Chl a fluorescence transient, photosynthesis index, and trapping and transport of light energy further indicated that exogenous NO under D stress enhanced the primary reaction of photosynthesis compared to D treatment. A putative pathway is proposed to elucidate NO regulation of the primary reaction of photosynthesis under WD.
2019-11-14 | PXD010724 | Pride
Project description:Gene expression profile of response to auxin at 3 h after treatment in rice root tips: IR64 (loss-of-function of DRO1 type) vs Near-isogenic line homozygous for the Kinandang Patong allele of DRO1 in an IR64 genetic background (Dro1-NIL; gain-of-function of DRO1 type) We used two rice varieties, IR64 and near-isogenic line homozygous for the Kinandang Patong allele of DRO1 in an IR64 genetic background (Dro1-NIL). We performed comprehensive microarray analysis of rice root tips with auxin treatment (3h) and pre-treatment (0h) in IR64 and Dro1-NIL. Seedling root tips of IR64 and Dro1-NIL were treated with 10 M-BM-5M 2,4-D. n = 3 biological repeats (15 seedlings per repeat).
2013-05-07 | E-GEOD-46255 | biostudies-arrayexpress
Project description:To investigate possible genetic basis of alkali tolerance in rice, we generated an introgressed rice line (K83) with significantly enhanced tolerance to alkali stress than its recipient parental cultivar (Jijing88). By using microarray analysis, we examined global gene expression profiles in K83 and Jijing88, found more than 1,200 genes were constitutively differentially expressed in K83 compared with Jijing88, with 572 up- and 654 down-regulated. Upon alkali treatment, a total of 347 genes in K83 were found up- and 156 down-regulated in K83, compared with 591 and 187 respectively in Jijing88. Seven-day-old uniform-sized seedlings grown in hydroponic medium were transferred to fresh hydroponic medium alone or containing 50 mM alkali salts. Shoots were harvested 24 h after transfer and 10 shoots were pooled for microarray analysis.
2014-05-16 | E-GEOD-45724 | biostudies-arrayexpress
Project description:Background: Lysine crotonylation (Kcr), as a novel evolutionarily conserved type of PTM, is ubiquitous and essential in cell biology. However, its functions in tea plant, an important beverage crop, are largely unknown. Our study firstly attempted to describe Kcr proteins in tea leaves under NH4+ deficiency/resupply, and provided significant insights into exploring the physiological role of Kcr in plants for N utilization. Results: We performed the global analysis of crotonylome in tea plants under NH4+ deficiency/resupply using high-resolution LC-MS/MS coupled with highly sensitive immune-antibody. A total of 2288 kcr sites on 971 proteins were identified, of which contained in 15 types of Kcr motifs. Most of Kcr proteins were located in chloroplast and cytoplasm. 120 and 151 Kcr proteins were significantly changed at 3 hours and 3days of NH4+ resupply, respectively. Bioinformatics analysis showed that differentially expressed Kcr proteins participated in diverse biological processes such as photosynthesis, carbon fixation and amino acid metabolism, suggesting Kcr plays important roles in these processes. Interestingly, a large number of enzymes were crotonylated, and the activity and Kcr level of these enzymes changed significantly after NH4+ resupply, indicating a potential function of Kcr in the regulation of enzyme activities. Moreover, the protein-protein interaction analysis revealed that the diverse interactions of identified Kcr proteins mainly involved in photosynthesis, carbon fixation, amino acid metabolism and ribosome. Conclusions: The results suggested that lysine crotonylated proteins might play regulating roles in metabolic process in tea leaves under NH4+ deficiency/resupply. The critical regulatory roles mainly involved in diverse aspects of primary metabolic processes, especially in photosynthesis, carbon fixation and amino acid metabolism. The provided data may serve as important resources for exploring the physiological, biochemical, and genetic role of lysine crotonylation in tea plants.
2019-05-09 | PXD011610 | Pride