Nickel_root-effect of nicotianamine over-accumulation in standard condition and in response to nickel treatment
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE7940 | GEO | 2007/05/31
SECONDARY ACCESSION(S): PRJNA100111
REPOSITORIES: GEO
Similar Datasets
Project description:rs04-05_nickel - nickel_leaf - Nicotianamine is a known metal chelator (of Mn, Fe, Zn, Ni, Cu) suspected to be involved in metal delivery and/or circulation in planta. This project aim at understanding the effect of the modulation of the nicotianamine content on the transcriptome of Arabidopsis thaliana in control hydroponic condition and in response to nickel treatment both at the root and at the leaf level. - After germination, plants were grown hydroponically for 6 weeks in classical nutrient solution (Marques et al, New Phytol, 2004, vol 164, pp 289-95) and then treated for 48 hours with 50 uM NiSO4 or with no nickel added for control. Keywords: gene knock in (transgenic),organ comparison
2007-05-31 | GSE7938 | GEO
Project description:Effect of nicotianamine over-accumulation on the transcriptome of A. thaliana in standard condition and in response to nickel treatment<br> <br> After germination, plants were grown hydroponically for 6 weeks in classical nutrient solution (Marques et al, New Phytol, 2004, vol 164, pp 289-95) and then treated for 48 hours with 50 uM NiSO4 or with no nickel added for control.<br> <br> Biological question : Nicotianamine is a known metal chelator (of Mn, Fe, Zn, Ni, Cu) suspected to be involved in metal delivery and/or circulation in planta. This project aim at understanding the effect of the modulation of the nicotianamine content on the transcriptome of Arabidopsis thaliana in control hydroponic condition and in response to nickel treatment both at the root and at the leaf level.<br>
2006-06-01 | E-MEXP-373 | biostudies-arrayexpress
Project description:A novel ArsR-SmtB family transcriptional repressor, KmtR, has been characterised from mycobacteria. Mutants of M. tuberculosis lacking kmtR show elevated expression of Rv2025c encoding a deduced CDF-family metal-exporter. KmtR-dependent repression of the cdf and kmtR operator-promoters was alleviated by nickel and cobalt in minimal medium. Electrophoretic mobility shift assays (EMSA) and fluorescence anisotropy (FA) show binding of purified KmtR to nucleotide sequences containing a region of dyad symmetry from the cdf and kmtR operator-promoters. A relatively large deltar(obs) in FA implies formation of high order apo-KmtR(n)-DNA and multiple complexes were detected by EMSA. Incubation of KmtR with cobalt inhibits DNA-complex assembly and metal-protein binding was confirmed by competition against 4-(2-pyridylazo)-resorcinol. KmtR is the second, to NmtR, characterised ArsR-SmtB sensor of nickel and cobalt from M. tuberculosis suggesting special significance for these ions in this pathogen. KmtR-dependent expression is elevated in complete medium with no increase in response to metals, while NmtR retains a response to nickel and cobalt under these conditions. Mixing equimolar apo-KmtR and apo-NmtR with 0.8 equivalents of nickel or cobalt gave nickel- and cobalt-dependent difference emission spectra similar to nickel(0.8)-KmtR and cobalt(0.8)-KmtR, respectively. Thus, KmtR has tighter affinities for nickel and cobalt than NmtR consistent with basal levels of these metals being sensed by KmtR but not NmtR in complete medium. More than a thousand genes encoding ArsR-SmtB related proteins are listed in databases and a proportion can be predicted to detect metals through known allosteric sites. KmtR has none of the previously defined sites. Substitution of His(88), Glu(101), His(102), His(110) or His(111) with Gln generated KmtR-variants that repress the cdf and kmtR operator-promoters even in elevated nickel and cobalt, revealing a new sensory site. Importantly, ArsR-SmtB sequence groupings do not correspond with the different sensory-motifs revealing that only the latter should be used to predict metal-sensing. Data is also available from http://bugs.sgul.ac.uk/E-BUGS-49
2007-09-17 | E-BUGS-49 | biostudies-arrayexpress
Project description:The recent development of a custom cDNA microarray platform for one of thé standard organisms in aquatic toxicology, Daphnia magna, opened up new ways to mechanistic insights of toxicological responses. In this study, gene expression and (sub)organismal responses (Cellular Energy Allocation, growth) were assayed after short-term waterborne metal exposure. Microarray analysis of Ni-exposed daphnids revealed several affected functional gene classes, of which the largest ones were involved in different metabolic processes (mainly protein and chitin related processes), cuticula turnover, transport and signal transduction. Furthermore, genes involved in oxygen transport and heme metabolism (hemoglobin, δ-aminolevilunate synthase) were down-regulated. Applying a Partial Least Squares regression on nickel fingerprints and biochemical (sub)organismal parameters revealed a set of co-varying genes (hemoglobin, RNA terminal phosphate cyclase, a ribosomal protein and an “unknown” gene fragment). An inverse relationship was seen between the mRNA expression levels of different cuticula proteins and available energy reserves. In addition to the nickel exposure, daphnids were exposed to binary mixtures of nickel and cadmium or nickel and lead. Using multivariate analysis techniques, the mixture gene expression fingerprints (Ni2++Cd2+, Ni2++Pb2+) were compared to those of the single metal treatments (Ni2+, Cd2+, Pb2+). It was hypothesized that the molecular fingerprints of the mixtures would be additive combinations of the gene expression profiles of the individual compounds present in the mixture. However, our results clearly showed additionally affected pathways after mixture treatment (e.g. additional affected genes involved in carbohydrate catabolic processes and proteolysis), indicating interactive molecular responses which are not merely the additive sum of the individual metals. These findings, although indicative of the complex nature of mixture toxicity evaluation, underline the potential of a toxicogenomics approach in gaining more mechanistic information on the effects of single compounds and mixtures.
2009-02-27 | GSE13866 | GEO
Project description:The model Zn hyperaccumulators Arabidopsis halleri and Noccaea caerulescens share elevated nicotianamine synthase (NAS) expression relative to non-accumulators among a core of alterations in metal homeostasis gene expression. Suppression of AhNAS2 expression by RNAi resulted in strongly reduced root NA accumulation and a concomitant decrease in root-to-shoot-translocation of Zn but not of other micronutrients. Few secondary effects on the root transcriptome were detected by microarray analysis. Vegetatively propagated clones of A. halleri wildtype plants and a line with strong suppression of AhNAS2 were grown hydroponically for weeks in two different media (control Hoagland and 10 µM Zn2+ added). Roots were harvested and analyzed. Three plants were pooled for one sample. Three independent experiments were performed.
2011-12-31 | E-GEOD-31778 | biostudies-arrayexpress
Project description:Essential metals such as iron are required for healthy plant growth. Fe is an important cofactor and catalytic element in many biological processes. Fe and other metals can also be toxic when present in excess. Therefore plants have mechanisms of metal homeostasis which involve coordination of metal ion transporters for uptake, translocation and compartmentalisation. The NAS genes are supposed to play an important role in Fe homeostasis. They are coding for enzymes called nicotianaminesynthase (NAS), which synthesize nicotianamine (NA) by a one-step condensation reaction of three molecules S-adenosyl-methionine. NA acts as a chelator for Fe, Cu, Ni and Zn and might be involved in the transport and allocation of Fe throughout the plant. We generated quadruple T-DNA insertion mutant nas plants to investigate NA function as described in Klatte et al., 2009, Plant Physiol. The nas4x-1 plants show an interveinal leaf chlorosis when turning from vegetative to reproductive stage, which intensifies when growing under Fe deficiency conditions. nas4x-1 plants have strongly reduced NA contents and show an elevated Fe deficiency response in roots. By performing microarray experiments we want to reveal global changes on transcriptional level in roots and leaves of nas4x-1 mutant compared to wild type plants grown under Fe supply and Fe deficiency conditions, respectively. The loss of NAS genes has a strong impact on the regulation of other metal homeostasis genes and allows to draw conclusions about nicotianamine function in metal homeostasis of A.thaliana.
2010-09-25 | GSE24348 | GEO
Project description:Nickel is an essential component of many eukaryotic and prokaryotic metallo-enzymes. Due to its employment in many industrial applications, wastewaters from industrial plants often contain millimolar concentrations of Ni2+ that are toxic and life-threatening for many organism. Several lines of preliminary evidence suggest that members of the genus Sphingobium are able to grow in the presence of high concentrations of metal ions. We have isolated a novel Sphingobium strain (sp. ba1) able to grow in the presence of high concentrations (up to 20 mM) of NiCl2. Sequencing of its genome allowed the identification of several genes coding for proteins potentially involved in efflux-mediated resistance mechanisms. Here we use the RNA-seq approach to analyze the response of the Sphingobium sp. ba1 strain to high concentrations (10 mM) of Ni ions. Transcriptomic data show the differential expression of about one-hundred and twenty genes, most of which are up-regulated and encode proteins such as membrane proteins and components of metal efflux systems, enzymes involved in oxidative stress responses (catalases, peroxidases) and signal transduction systems.
2017-07-03 | E-MTAB-5828 | biostudies-arrayexpress
Project description:Nickel compounds, important carcinogens and prime inducers of contact allergy in humans, are potent activators of endothelial cells (ECs). To elucidate the signaling pathways mediating the cellular responses to nickel we performed Affymetrix gene profiling of human primary ECs. Keywords: stress response
2006-12-31 | GSE4852 | GEO
Project description:Many heavy metals, including nickel (Ni), cadmium (Cd), and chromium (Cr) are toxic industrial chemicals with an exposure risk in both occupational and environmental settings that may cause harmful outcomes. While these substances are known to produce adverse health effects leading to disease or health problems, the detailed mechanisms remain unclear. To elucidate the processes involved in the of toxicity of nickel, cadmium, and chromium at the molecular level and to perform a comparative analysis, H4-II-E-C3 rat liver-derived cell lines were treated with soluble salts of each metal using concentrations derived from viability assays, and gene expression patterns were determined with DNA microarrays. We identified both common and unique biological responses to exposure to the three metals. Nickel, cadmium, chromium all induced oxidative stress with both similar and unique genes and pathways responding to this stress. Although all three metals are known to be genotoxic, evidence for DNA damage in our study only exists in response to chromium. Nickel induced a hypoxic response as well as inducing genes involved in chromatin structure, perhaps by replacing iron in key proteins. Cadmium distinctly perturbed genes related to endoplasmic reticulum stress and invoked the unfolded protein response leading to apoptosis. With these studies, we have completed the first gene expression comparative analysis of nickel, cadmium, and chromium in H4-II-E-C3 cells.
2011-08-19 | GSE31503 | GEO
Project description:Analysis of anti-CD3/anti-CD28 stimulated T cells treated with or without nickel chloride. Nickel is the most important contact allergen in the general population of the industrialized world. Results provide insight into the biological effects of nickel on human CD3+ T cells.
2011-05-18 | GSE23387 | GEO